Starting phenix.real_space_refine on Fri Jun 13 05:13:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ulg_42358/06_2025/8ulg_42358.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ulg_42358/06_2025/8ulg_42358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ulg_42358/06_2025/8ulg_42358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ulg_42358/06_2025/8ulg_42358.map" model { file = "/net/cci-nas-00/data/ceres_data/8ulg_42358/06_2025/8ulg_42358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ulg_42358/06_2025/8ulg_42358.cif" } resolution = 3.2 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= -0.002 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 Mg 2 5.21 5 S 101 5.16 5 C 9343 2.51 5 N 2462 2.21 5 O 2723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14635 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6774 Classifications: {'peptide': 827} Link IDs: {'PTRANS': 31, 'TRANS': 795} Chain: "B" Number of atoms: 6697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 824, 6697 Classifications: {'peptide': 824} Link IDs: {'PTRANS': 32, 'TRANS': 791} Chain: "C" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 540 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 6, 'TRANS': 62} Chain breaks: 1 Chain: "D" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 542 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 6, 'TRANS': 62} Chain breaks: 1 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' MG': 1, ' ZN': 1, 'IBM': 1, 'PCG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' MG': 1, ' ZN': 1, 'IBM': 1, 'PCG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 8.46, per 1000 atoms: 0.58 Number of scatterers: 14635 At special positions: 0 Unit cell: (108.54, 123.28, 168.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 101 16.00 P 2 15.00 Mg 2 11.99 O 2723 8.00 N 2462 7.00 C 9343 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.72 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 903 " pdb="ZN ZN A 903 " - pdb=" NE2 HIS A 599 " pdb="ZN ZN A 903 " - pdb=" NE2 HIS A 563 " pdb=" ZN B 903 " pdb="ZN ZN B 903 " - pdb=" NE2 HIS B 597 " pdb="ZN ZN B 903 " - pdb=" NE2 HIS B 561 " 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3400 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 4 sheets defined 59.4% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 6 through 16 Processing helix chain 'A' and resid 16 through 28 Processing helix chain 'A' and resid 28 through 38 Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 73 through 90 removed outlier: 3.728A pdb=" N PHE A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 removed outlier: 4.026A pdb=" N GLU A 131 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 148 Processing helix chain 'A' and resid 164 through 170 Processing helix chain 'A' and resid 204 through 215 Processing helix chain 'A' and resid 215 through 249 removed outlier: 3.658A pdb=" N LEU A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 221 " --> pdb=" O PHE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.696A pdb=" N THR A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 362 through 365 Processing helix chain 'A' and resid 413 through 430 Processing helix chain 'A' and resid 431 through 459 removed outlier: 3.563A pdb=" N ASP A 452 " --> pdb=" O ASP A 448 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 454 " --> pdb=" O PHE A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 removed outlier: 3.519A pdb=" N GLN A 466 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 475 Processing helix chain 'A' and resid 483 through 495 Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.755A pdb=" N TYR A 501 " --> pdb=" O ASP A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 529 removed outlier: 3.578A pdb=" N LEU A 529 " --> pdb=" O MET A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 536 Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.665A pdb=" N TYR A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 577 removed outlier: 3.680A pdb=" N GLY A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 598 Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 616 through 622 Processing helix chain 'A' and resid 625 through 641 removed outlier: 3.670A pdb=" N ASP A 641 " --> pdb=" O THR A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 645 removed outlier: 3.567A pdb=" N ASN A 645 " --> pdb=" O GLU A 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 642 through 645' Processing helix chain 'A' and resid 651 through 669 removed outlier: 3.715A pdb=" N THR A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 676 Processing helix chain 'A' and resid 677 through 688 removed outlier: 3.812A pdb=" N PHE A 681 " --> pdb=" O LYS A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 691 No H-bonds generated for 'chain 'A' and resid 689 through 691' Processing helix chain 'A' and resid 693 through 702 removed outlier: 3.520A pdb=" N TRP A 697 " --> pdb=" O THR A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 721 Processing helix chain 'A' and resid 722 through 725 Processing helix chain 'A' and resid 727 through 753 removed outlier: 3.732A pdb=" N LYS A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A 736 " --> pdb=" O SER A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 780 Processing helix chain 'A' and resid 780 through 792 removed outlier: 4.117A pdb=" N VAL A 784 " --> pdb=" O VAL A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 826 removed outlier: 3.686A pdb=" N LEU A 799 " --> pdb=" O ILE A 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 14 Processing helix chain 'B' and resid 15 through 23 removed outlier: 3.529A pdb=" N ASP B 20 " --> pdb=" O PRO B 16 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN B 21 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 36 Processing helix chain 'B' and resid 46 through 69 removed outlier: 3.620A pdb=" N GLU B 68 " --> pdb=" O GLN B 64 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASN B 69 " --> pdb=" O ASP B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 88 Processing helix chain 'B' and resid 118 through 122 removed outlier: 3.588A pdb=" N CYS B 122 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 removed outlier: 4.025A pdb=" N GLU B 129 " --> pdb=" O PRO B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 153 through 157 Processing helix chain 'B' and resid 162 through 169 removed outlier: 3.770A pdb=" N GLU B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU B 167 " --> pdb=" O PHE B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 213 removed outlier: 3.669A pdb=" N LEU B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 247 removed outlier: 3.628A pdb=" N LEU B 218 " --> pdb=" O ASN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.686A pdb=" N VAL B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 Proline residue: B 291 - end of helix Processing helix chain 'B' and resid 339 through 342 removed outlier: 3.729A pdb=" N SER B 342 " --> pdb=" O ALA B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 339 through 342' Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 411 through 428 Processing helix chain 'B' and resid 428 through 457 removed outlier: 4.218A pdb=" N THR B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS B 455 " --> pdb=" O MET B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 464 removed outlier: 3.752A pdb=" N GLN B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 473 Processing helix chain 'B' and resid 476 through 480 Processing helix chain 'B' and resid 481 through 493 removed outlier: 3.743A pdb=" N GLU B 491 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 492 " --> pdb=" O ILE B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 528 removed outlier: 3.541A pdb=" N GLY B 528 " --> pdb=" O TYR B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 533 removed outlier: 3.822A pdb=" N LYS B 532 " --> pdb=" O GLY B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.630A pdb=" N TYR B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 575 removed outlier: 3.537A pdb=" N GLY B 562 " --> pdb=" O ASN B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 582 removed outlier: 3.765A pdb=" N TYR B 581 " --> pdb=" O LEU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 596 Processing helix chain 'B' and resid 605 through 612 Processing helix chain 'B' and resid 614 through 620 Processing helix chain 'B' and resid 623 through 639 removed outlier: 3.603A pdb=" N LEU B 630 " --> pdb=" O GLU B 626 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU B 639 " --> pdb=" O PHE B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 643 removed outlier: 3.603A pdb=" N ASN B 643 " --> pdb=" O GLU B 640 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 640 through 643' Processing helix chain 'B' and resid 649 through 667 removed outlier: 3.509A pdb=" N ILE B 665 " --> pdb=" O ASP B 661 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 675 Processing helix chain 'B' and resid 676 through 690 removed outlier: 3.804A pdb=" N GLN B 680 " --> pdb=" O ARG B 676 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN B 688 " --> pdb=" O ASP B 684 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU B 690 " --> pdb=" O SER B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 700 removed outlier: 3.577A pdb=" N TRP B 695 " --> pdb=" O ASP B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 719 Processing helix chain 'B' and resid 720 through 723 Processing helix chain 'B' and resid 731 through 750 removed outlier: 3.845A pdb=" N LEU B 735 " --> pdb=" O LYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 778 Processing helix chain 'B' and resid 778 through 790 removed outlier: 4.042A pdb=" N VAL B 782 " --> pdb=" O VAL B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 823 removed outlier: 3.808A pdb=" N PHE B 797 " --> pdb=" O ILE B 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 removed outlier: 3.593A pdb=" N TYR C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 115 removed outlier: 6.563A pdb=" N LEU A 96 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE A 113 " --> pdb=" O MET A 94 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N MET A 94 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 93 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 95 " --> pdb=" O MET A 193 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL A 189 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A 182 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ILE A 191 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER A 180 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N MET A 193 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 178 " --> pdb=" O MET A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 328 through 333 removed outlier: 3.593A pdb=" N VAL A 318 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS A 317 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N CYS A 272 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG A 406 " --> pdb=" O CYS A 272 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 274 " --> pdb=" O TYR A 404 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A 398 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE A 390 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL A 400 " --> pdb=" O MET A 388 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N MET A 388 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR A 402 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 386 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR A 404 " --> pdb=" O ASN A 384 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASN A 384 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.686A pdb=" N ARG B 91 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 187 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 188 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE B 175 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 326 through 330 removed outlier: 3.988A pdb=" N LYS B 315 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N CYS B 270 " --> pdb=" O ARG B 404 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG B 404 " --> pdb=" O CYS B 270 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG B 272 " --> pdb=" O TYR B 402 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL B 396 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE B 388 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL B 398 " --> pdb=" O MET B 386 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET B 386 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR B 400 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 384 " --> pdb=" O THR B 400 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 383 " --> pdb=" O ILE B 357 " (cutoff:3.500A) 753 hydrogen bonds defined for protein. 2193 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.29 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2496 1.31 - 1.44: 3908 1.44 - 1.56: 8383 1.56 - 1.69: 5 1.69 - 1.81: 175 Bond restraints: 14967 Sorted by residual: bond pdb=" C2' PCG B 901 " pdb=" C3' PCG B 901 " ideal model delta sigma weight residual 1.514 1.191 0.323 2.00e-02 2.50e+03 2.61e+02 bond pdb=" C2' PCG A 901 " pdb=" C3' PCG A 901 " ideal model delta sigma weight residual 1.514 1.192 0.322 2.00e-02 2.50e+03 2.60e+02 bond pdb=" C3' PCG B 901 " pdb=" C4' PCG B 901 " ideal model delta sigma weight residual 1.519 1.812 -0.293 2.00e-02 2.50e+03 2.14e+02 bond pdb=" C3' PCG A 901 " pdb=" C4' PCG A 901 " ideal model delta sigma weight residual 1.519 1.810 -0.291 2.00e-02 2.50e+03 2.12e+02 bond pdb=" C1' PCG B 901 " pdb=" N9 PCG B 901 " ideal model delta sigma weight residual 1.448 1.220 0.228 2.00e-02 2.50e+03 1.30e+02 ... (remaining 14962 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 19937 2.19 - 4.39: 228 4.39 - 6.58: 41 6.58 - 8.77: 24 8.77 - 10.96: 9 Bond angle restraints: 20239 Sorted by residual: angle pdb=" CB LYS A 821 " pdb=" CG LYS A 821 " pdb=" CD LYS A 821 " ideal model delta sigma weight residual 111.30 119.66 -8.36 2.30e+00 1.89e-01 1.32e+01 angle pdb=" O3' PCG A 901 " pdb=" PA PCG A 901 " pdb=" O5' PCG A 901 " ideal model delta sigma weight residual 103.94 114.82 -10.88 3.00e+00 1.11e-01 1.32e+01 angle pdb=" C5' PCG B 901 " pdb=" O5' PCG B 901 " pdb=" PA PCG B 901 " ideal model delta sigma weight residual 121.82 111.38 10.44 3.00e+00 1.11e-01 1.21e+01 angle pdb=" N VAL D 66 " pdb=" CA VAL D 66 " pdb=" C VAL D 66 " ideal model delta sigma weight residual 112.29 109.23 3.06 9.40e-01 1.13e+00 1.06e+01 angle pdb=" C5 PCG A 901 " pdb=" C6 PCG A 901 " pdb=" N1 PCG A 901 " ideal model delta sigma weight residual 110.52 120.09 -9.57 3.00e+00 1.11e-01 1.02e+01 ... (remaining 20234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 7614 17.65 - 35.29: 1068 35.29 - 52.94: 282 52.94 - 70.58: 62 70.58 - 88.23: 37 Dihedral angle restraints: 9063 sinusoidal: 3817 harmonic: 5246 Sorted by residual: dihedral pdb=" CA TYR B 402 " pdb=" C TYR B 402 " pdb=" N ASN B 403 " pdb=" CA ASN B 403 " ideal model delta harmonic sigma weight residual 180.00 156.58 23.42 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA TYR A 404 " pdb=" C TYR A 404 " pdb=" N ASN A 405 " pdb=" CA ASN A 405 " ideal model delta harmonic sigma weight residual 180.00 159.21 20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA PHE A 62 " pdb=" C PHE A 62 " pdb=" N ASP A 63 " pdb=" CA ASP A 63 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 9060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2147 0.106 - 0.212: 41 0.212 - 0.319: 0 0.319 - 0.425: 4 0.425 - 0.531: 2 Chirality restraints: 2194 Sorted by residual: chirality pdb=" PA PCG B 901 " pdb=" O2A PCG B 901 " pdb=" O3' PCG B 901 " pdb=" O5' PCG B 901 " both_signs ideal model delta sigma weight residual True 2.70 3.23 -0.53 2.00e-01 2.50e+01 7.05e+00 chirality pdb=" PA PCG A 901 " pdb=" O2A PCG A 901 " pdb=" O3' PCG A 901 " pdb=" O5' PCG A 901 " both_signs ideal model delta sigma weight residual True 2.70 3.18 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" C3' PCG A 901 " pdb=" C2' PCG A 901 " pdb=" C4' PCG A 901 " pdb=" O3' PCG A 901 " both_signs ideal model delta sigma weight residual False -2.45 -2.03 -0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 2191 not shown) Planarity restraints: 2609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 444 " 0.010 2.00e-02 2.50e+03 2.12e-02 4.52e+00 pdb=" CD GLU A 444 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU A 444 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 444 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 614 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO B 615 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 615 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 615 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 796 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO A 797 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 797 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 797 " 0.025 5.00e-02 4.00e+02 ... (remaining 2606 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 124 2.64 - 3.21: 13209 3.21 - 3.77: 22147 3.77 - 4.34: 29520 4.34 - 4.90: 50466 Nonbonded interactions: 115466 Sorted by model distance: nonbonded pdb=" OD2 ASP B 598 " pdb="ZN ZN B 903 " model vdw 2.079 2.230 nonbonded pdb=" O ILE A 556 " pdb=" ND2 ASN A 560 " model vdw 2.232 3.120 nonbonded pdb=" O PHE A 289 " pdb=" NZ LYS B 675 " model vdw 2.235 3.120 nonbonded pdb=" OD2 ASP A 92 " pdb=" OH TYR A 172 " model vdw 2.235 3.040 nonbonded pdb=" O CYS A 163 " pdb=" O1A PCG A 901 " model vdw 2.256 3.040 ... (remaining 115461 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 11 through 39 or resid 49 through 87)) selection = (chain 'D' and resid 11 through 87) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 37.300 Find NCS groups from input model: 0.310 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 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 : 0.008 0.323 14971 Z= 0.411 Angle : 0.644 10.964 20239 Z= 0.304 Chirality : 0.045 0.531 2194 Planarity : 0.004 0.051 2609 Dihedral : 18.345 88.230 5663 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.66 % Favored : 96.29 % Rotamer: Outliers : 0.06 % Allowed : 20.33 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.20), residues: 1777 helix: 2.00 (0.17), residues: 951 sheet: 0.37 (0.46), residues: 138 loop : -0.67 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 559 HIS 0.005 0.000 HIS A 599 PHE 0.022 0.001 PHE B 11 TYR 0.010 0.001 TYR B 223 ARG 0.009 0.000 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.17844 ( 753) hydrogen bonds : angle 5.53621 ( 2193) metal coordination : bond 0.00103 ( 4) covalent geometry : bond 0.00829 (14967) covalent geometry : angle 0.64406 (20239) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 MET cc_start: 0.8775 (mmm) cc_final: 0.8334 (mmm) REVERT: C 15 ARG cc_start: 0.9249 (tpp80) cc_final: 0.8693 (mmm-85) REVERT: C 83 GLN cc_start: 0.9131 (tm-30) cc_final: 0.8708 (tm-30) REVERT: D 12 SER cc_start: 0.9058 (t) cc_final: 0.8855 (p) REVERT: D 15 ARG cc_start: 0.8766 (mtt90) cc_final: 0.8491 (mtm110) REVERT: D 16 VAL cc_start: 0.9214 (t) cc_final: 0.8285 (t) REVERT: D 74 ASN cc_start: 0.8931 (t0) cc_final: 0.8397 (t0) REVERT: D 76 LEU cc_start: 0.9742 (tp) cc_final: 0.9513 (mt) REVERT: D 78 LEU cc_start: 0.9738 (tp) cc_final: 0.9177 (mt) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.2968 time to fit residues: 60.4062 Evaluate side-chains 115 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 83 optimal weight: 0.4980 chunk 102 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN A 425 GLN A 539 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN B 537 GLN B 628 HIS ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.041921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.030142 restraints weight = 84887.232| |-----------------------------------------------------------------------------| r_work (start): 0.2603 rms_B_bonded: 4.58 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14971 Z= 0.120 Angle : 0.535 8.575 20239 Z= 0.279 Chirality : 0.040 0.164 2194 Planarity : 0.004 0.052 2609 Dihedral : 5.358 43.473 1997 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.60 % Favored : 96.34 % Rotamer: Outliers : 1.69 % Allowed : 19.89 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.20), residues: 1777 helix: 2.11 (0.17), residues: 973 sheet: 0.42 (0.44), residues: 144 loop : -0.55 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 480 HIS 0.006 0.000 HIS A 599 PHE 0.012 0.001 PHE C 38 TYR 0.015 0.001 TYR B 273 ARG 0.004 0.000 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.04609 ( 753) hydrogen bonds : angle 4.21028 ( 2193) metal coordination : bond 0.00052 ( 4) covalent geometry : bond 0.00266 (14967) covalent geometry : angle 0.53538 (20239) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.8549 (mmm) cc_final: 0.7701 (mmm) REVERT: A 193 MET cc_start: 0.9184 (mtp) cc_final: 0.8028 (ttm) REVERT: A 440 MET cc_start: 0.9341 (OUTLIER) cc_final: 0.8715 (mmm) REVERT: A 661 MET cc_start: 0.9434 (mmm) cc_final: 0.9202 (mmm) REVERT: A 760 MET cc_start: 0.9288 (tmm) cc_final: 0.8842 (tmm) REVERT: A 761 MET cc_start: 0.9030 (mmt) cc_final: 0.8688 (mmt) REVERT: A 824 GLU cc_start: 0.9719 (OUTLIER) cc_final: 0.9497 (pt0) REVERT: B 72 MET cc_start: 0.9113 (tmm) cc_final: 0.8893 (tmm) REVERT: B 438 MET cc_start: 0.9033 (mmt) cc_final: 0.8605 (mmt) REVERT: B 759 MET cc_start: 0.8392 (tpp) cc_final: 0.7819 (mmt) REVERT: C 15 ARG cc_start: 0.9097 (tpp80) cc_final: 0.8643 (mmm-85) REVERT: C 83 GLN cc_start: 0.8911 (tm-30) cc_final: 0.8321 (tm-30) REVERT: D 12 SER cc_start: 0.8705 (t) cc_final: 0.8258 (p) REVERT: D 16 VAL cc_start: 0.7828 (t) cc_final: 0.7556 (t) REVERT: D 36 ARG cc_start: 0.9430 (mpp-170) cc_final: 0.8909 (mpp-170) REVERT: D 39 LYS cc_start: 0.8609 (mmmt) cc_final: 0.8244 (mmpt) REVERT: D 74 ASN cc_start: 0.8215 (t0) cc_final: 0.7656 (t0) outliers start: 27 outliers final: 8 residues processed: 142 average time/residue: 0.2803 time to fit residues: 59.9532 Evaluate side-chains 126 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 64 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 145 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 0.0870 chunk 172 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 40 optimal weight: 8.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 HIS A 258 GLN A 745 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.041433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.029657 restraints weight = 84495.596| |-----------------------------------------------------------------------------| r_work (start): 0.2591 rms_B_bonded: 4.56 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14971 Z= 0.130 Angle : 0.513 6.515 20239 Z= 0.266 Chirality : 0.039 0.160 2194 Planarity : 0.004 0.053 2609 Dihedral : 4.879 41.264 1997 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.60 % Favored : 96.34 % Rotamer: Outliers : 2.13 % Allowed : 19.76 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.21), residues: 1777 helix: 2.18 (0.17), residues: 976 sheet: 0.47 (0.43), residues: 144 loop : -0.48 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 559 HIS 0.007 0.001 HIS D 75 PHE 0.015 0.001 PHE A 62 TYR 0.013 0.001 TYR B 97 ARG 0.008 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.04344 ( 753) hydrogen bonds : angle 4.03205 ( 2193) metal coordination : bond 0.00099 ( 4) covalent geometry : bond 0.00297 (14967) covalent geometry : angle 0.51339 (20239) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8548 (tp) REVERT: A 136 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9047 (tt) REVERT: A 183 MET cc_start: 0.8608 (mmm) cc_final: 0.7524 (mmm) REVERT: A 760 MET cc_start: 0.9353 (tmm) cc_final: 0.8825 (tmm) REVERT: A 824 GLU cc_start: 0.9715 (OUTLIER) cc_final: 0.9445 (pt0) REVERT: B 72 MET cc_start: 0.9234 (tmm) cc_final: 0.8871 (tmm) REVERT: B 759 MET cc_start: 0.8512 (tpp) cc_final: 0.7763 (mmt) REVERT: C 15 ARG cc_start: 0.9051 (tpp80) cc_final: 0.8845 (mmm-85) REVERT: C 83 GLN cc_start: 0.8969 (tm-30) cc_final: 0.8319 (tm-30) REVERT: D 12 SER cc_start: 0.8750 (t) cc_final: 0.8541 (p) REVERT: D 15 ARG cc_start: 0.8794 (mtt90) cc_final: 0.8108 (mtp180) REVERT: D 36 ARG cc_start: 0.9428 (mpp-170) cc_final: 0.8892 (mpp-170) outliers start: 34 outliers final: 15 residues processed: 143 average time/residue: 0.2949 time to fit residues: 61.8641 Evaluate side-chains 130 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 694 SER Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 64 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 170 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 132 optimal weight: 0.0570 chunk 123 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.040659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.028785 restraints weight = 84249.265| |-----------------------------------------------------------------------------| r_work (start): 0.2559 rms_B_bonded: 4.55 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14971 Z= 0.175 Angle : 0.535 7.148 20239 Z= 0.278 Chirality : 0.040 0.184 2194 Planarity : 0.004 0.053 2609 Dihedral : 4.861 41.488 1997 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.88 % Allowed : 19.82 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.21), residues: 1777 helix: 2.31 (0.17), residues: 966 sheet: 0.47 (0.42), residues: 144 loop : -0.46 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 559 HIS 0.004 0.001 HIS A 599 PHE 0.016 0.001 PHE D 73 TYR 0.014 0.001 TYR B 97 ARG 0.006 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.04472 ( 753) hydrogen bonds : angle 4.01978 ( 2193) metal coordination : bond 0.00156 ( 4) covalent geometry : bond 0.00399 (14967) covalent geometry : angle 0.53547 (20239) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9031 (tt) REVERT: A 183 MET cc_start: 0.8677 (mmm) cc_final: 0.7835 (mmm) REVERT: A 760 MET cc_start: 0.9396 (tmm) cc_final: 0.8984 (tmm) REVERT: B 72 MET cc_start: 0.9362 (tmm) cc_final: 0.8922 (tmm) REVERT: B 181 MET cc_start: 0.9042 (mmm) cc_final: 0.8419 (mmm) REVERT: B 438 MET cc_start: 0.8996 (mmt) cc_final: 0.8754 (mmt) REVERT: B 660 MET cc_start: 0.9537 (mtm) cc_final: 0.9309 (mtp) REVERT: B 714 MET cc_start: 0.9343 (mmm) cc_final: 0.9097 (mmm) REVERT: B 759 MET cc_start: 0.8732 (tpp) cc_final: 0.7863 (mmt) REVERT: C 83 GLN cc_start: 0.9061 (tm-30) cc_final: 0.8460 (tm-30) REVERT: D 12 SER cc_start: 0.8856 (t) cc_final: 0.8438 (p) REVERT: D 15 ARG cc_start: 0.8795 (mtt90) cc_final: 0.8161 (mtp180) REVERT: D 36 ARG cc_start: 0.9450 (mpp-170) cc_final: 0.8883 (mpp-170) REVERT: D 73 PHE cc_start: 0.8178 (m-80) cc_final: 0.7901 (m-80) outliers start: 30 outliers final: 17 residues processed: 139 average time/residue: 0.3025 time to fit residues: 62.6840 Evaluate side-chains 130 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 480 TRP Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 694 SER Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 64 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 77 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 166 optimal weight: 0.0670 chunk 42 optimal weight: 0.6980 chunk 171 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.041501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.029709 restraints weight = 84763.950| |-----------------------------------------------------------------------------| r_work (start): 0.2603 rms_B_bonded: 4.56 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14971 Z= 0.103 Angle : 0.519 11.220 20239 Z= 0.264 Chirality : 0.040 0.195 2194 Planarity : 0.004 0.054 2609 Dihedral : 4.775 40.304 1997 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.44 % Allowed : 21.01 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.21), residues: 1777 helix: 2.31 (0.17), residues: 970 sheet: 0.59 (0.42), residues: 146 loop : -0.47 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 559 HIS 0.004 0.000 HIS A 599 PHE 0.020 0.001 PHE D 73 TYR 0.014 0.001 TYR B 273 ARG 0.004 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 753) hydrogen bonds : angle 3.83567 ( 2193) metal coordination : bond 0.00048 ( 4) covalent geometry : bond 0.00230 (14967) covalent geometry : angle 0.51871 (20239) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8436 (m-10) cc_final: 0.8202 (m-10) REVERT: A 27 ARG cc_start: 0.8757 (mmm-85) cc_final: 0.8526 (mmm-85) REVERT: A 136 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8888 (tt) REVERT: A 183 MET cc_start: 0.8807 (mmm) cc_final: 0.7998 (mmm) REVERT: A 760 MET cc_start: 0.9368 (tmm) cc_final: 0.8918 (tmm) REVERT: A 761 MET cc_start: 0.8983 (mmt) cc_final: 0.8434 (mmt) REVERT: A 821 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.9164 (tptp) REVERT: B 72 MET cc_start: 0.9340 (tmm) cc_final: 0.8955 (tmm) REVERT: B 92 CYS cc_start: 0.9308 (OUTLIER) cc_final: 0.8914 (m) REVERT: B 181 MET cc_start: 0.9110 (mmm) cc_final: 0.8892 (mmm) REVERT: B 759 MET cc_start: 0.8676 (tpp) cc_final: 0.7822 (mmt) REVERT: C 15 ARG cc_start: 0.9222 (mtt90) cc_final: 0.8961 (mtt90) REVERT: C 83 GLN cc_start: 0.9077 (tm-30) cc_final: 0.8540 (tm-30) REVERT: D 12 SER cc_start: 0.8702 (t) cc_final: 0.8347 (p) REVERT: D 15 ARG cc_start: 0.8777 (mtt90) cc_final: 0.8395 (mtp180) REVERT: D 36 ARG cc_start: 0.9453 (mpp-170) cc_final: 0.8939 (mpp-170) REVERT: D 77 GLU cc_start: 0.7198 (tt0) cc_final: 0.6834 (tt0) outliers start: 23 outliers final: 14 residues processed: 136 average time/residue: 0.2827 time to fit residues: 56.3519 Evaluate side-chains 128 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 480 TRP Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 694 SER Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 64 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 160 optimal weight: 4.9990 chunk 174 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 141 optimal weight: 0.0270 chunk 113 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 129 optimal weight: 0.1980 chunk 118 optimal weight: 0.0670 chunk 128 optimal weight: 10.0000 overall best weight: 1.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.041147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.029423 restraints weight = 85729.194| |-----------------------------------------------------------------------------| r_work (start): 0.2589 rms_B_bonded: 4.52 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14971 Z= 0.124 Angle : 0.521 8.965 20239 Z= 0.268 Chirality : 0.040 0.188 2194 Planarity : 0.004 0.053 2609 Dihedral : 4.745 41.004 1997 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.38 % Allowed : 21.39 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.21), residues: 1777 helix: 2.31 (0.17), residues: 975 sheet: 0.63 (0.43), residues: 146 loop : -0.47 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 559 HIS 0.004 0.000 HIS A 599 PHE 0.011 0.001 PHE A 62 TYR 0.013 0.001 TYR B 273 ARG 0.005 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 753) hydrogen bonds : angle 3.84263 ( 2193) metal coordination : bond 0.00083 ( 4) covalent geometry : bond 0.00287 (14967) covalent geometry : angle 0.52149 (20239) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.992 Fit side-chains revert: symmetry clash REVERT: A 136 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8892 (tt) REVERT: A 183 MET cc_start: 0.8783 (mmm) cc_final: 0.8041 (mmm) REVERT: A 760 MET cc_start: 0.9375 (tmm) cc_final: 0.8962 (tmm) REVERT: B 72 MET cc_start: 0.9362 (tmm) cc_final: 0.8966 (tmm) REVERT: B 92 CYS cc_start: 0.9321 (OUTLIER) cc_final: 0.8935 (m) REVERT: B 181 MET cc_start: 0.9077 (mmm) cc_final: 0.8354 (mmm) REVERT: B 759 MET cc_start: 0.8780 (tpp) cc_final: 0.7847 (mmt) REVERT: C 15 ARG cc_start: 0.9232 (mtt90) cc_final: 0.8980 (mtt90) REVERT: C 34 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8113 (tp-100) REVERT: C 36 ARG cc_start: 0.9334 (mtm-85) cc_final: 0.9033 (mpp-170) REVERT: C 83 GLN cc_start: 0.9108 (tm-30) cc_final: 0.8562 (tm-30) REVERT: D 12 SER cc_start: 0.8642 (t) cc_final: 0.8345 (p) REVERT: D 15 ARG cc_start: 0.8824 (mtt90) cc_final: 0.8359 (mtp180) REVERT: D 17 MET cc_start: 0.8758 (mmt) cc_final: 0.8554 (mmm) REVERT: D 36 ARG cc_start: 0.9466 (mpp-170) cc_final: 0.8945 (mpp-170) outliers start: 22 outliers final: 18 residues processed: 132 average time/residue: 0.3489 time to fit residues: 69.4673 Evaluate side-chains 130 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 480 TRP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 694 SER Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 74 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 119 optimal weight: 7.9990 chunk 148 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 141 optimal weight: 0.1980 chunk 39 optimal weight: 6.9990 chunk 109 optimal weight: 0.0050 chunk 134 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.042033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.030204 restraints weight = 84121.488| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 4.60 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14971 Z= 0.099 Angle : 0.521 9.998 20239 Z= 0.264 Chirality : 0.039 0.184 2194 Planarity : 0.004 0.054 2609 Dihedral : 4.666 40.666 1997 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.63 % Allowed : 21.51 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.21), residues: 1777 helix: 2.28 (0.17), residues: 978 sheet: 0.86 (0.44), residues: 144 loop : -0.52 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 559 HIS 0.004 0.000 HIS A 599 PHE 0.017 0.001 PHE A 12 TYR 0.014 0.001 TYR B 273 ARG 0.004 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 753) hydrogen bonds : angle 3.74463 ( 2193) metal coordination : bond 0.00044 ( 4) covalent geometry : bond 0.00223 (14967) covalent geometry : angle 0.52081 (20239) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8417 (m-10) cc_final: 0.8197 (m-10) REVERT: A 136 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8844 (tt) REVERT: A 183 MET cc_start: 0.8900 (mmm) cc_final: 0.8267 (mmm) REVERT: A 440 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.8752 (mmm) REVERT: A 760 MET cc_start: 0.9332 (tmm) cc_final: 0.8933 (tmm) REVERT: A 761 MET cc_start: 0.9003 (mmt) cc_final: 0.8547 (mmt) REVERT: B 72 MET cc_start: 0.9360 (tmm) cc_final: 0.8939 (tmm) REVERT: B 92 CYS cc_start: 0.9342 (OUTLIER) cc_final: 0.8925 (m) REVERT: B 96 MET cc_start: 0.8757 (tpp) cc_final: 0.8488 (mpp) REVERT: B 181 MET cc_start: 0.9152 (mmm) cc_final: 0.8924 (mmm) REVERT: B 759 MET cc_start: 0.8768 (tpp) cc_final: 0.7851 (mmt) REVERT: C 15 ARG cc_start: 0.9236 (mtt90) cc_final: 0.8992 (mtt90) REVERT: C 74 ASN cc_start: 0.9138 (p0) cc_final: 0.8748 (p0) REVERT: C 83 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8585 (tm-30) REVERT: D 12 SER cc_start: 0.8632 (t) cc_final: 0.8322 (p) REVERT: D 15 ARG cc_start: 0.8813 (mtt90) cc_final: 0.8454 (mtp180) REVERT: D 17 MET cc_start: 0.8753 (mmt) cc_final: 0.8538 (mmm) REVERT: D 36 ARG cc_start: 0.9456 (mpp-170) cc_final: 0.9030 (mpp-170) outliers start: 26 outliers final: 16 residues processed: 133 average time/residue: 0.4030 time to fit residues: 81.3675 Evaluate side-chains 129 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 480 TRP Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 694 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 64 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 76 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.040874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.029062 restraints weight = 85010.441| |-----------------------------------------------------------------------------| r_work (start): 0.2573 rms_B_bonded: 4.50 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14971 Z= 0.154 Angle : 0.544 10.988 20239 Z= 0.278 Chirality : 0.040 0.196 2194 Planarity : 0.004 0.052 2609 Dihedral : 4.791 42.035 1997 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.63 % Allowed : 21.33 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.21), residues: 1777 helix: 2.39 (0.17), residues: 967 sheet: 0.72 (0.43), residues: 146 loop : -0.45 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 70 HIS 0.004 0.001 HIS C 75 PHE 0.015 0.001 PHE A 12 TYR 0.012 0.001 TYR B 97 ARG 0.004 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 753) hydrogen bonds : angle 3.89459 ( 2193) metal coordination : bond 0.00125 ( 4) covalent geometry : bond 0.00353 (14967) covalent geometry : angle 0.54421 (20239) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8936 (tt) REVERT: A 183 MET cc_start: 0.8867 (mmm) cc_final: 0.8224 (mmm) REVERT: A 381 MET cc_start: 0.8575 (tpp) cc_final: 0.8185 (mmm) REVERT: A 440 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.9017 (mmp) REVERT: A 760 MET cc_start: 0.9379 (tmm) cc_final: 0.8941 (tmm) REVERT: A 761 MET cc_start: 0.9021 (mmt) cc_final: 0.8478 (mmt) REVERT: B 72 MET cc_start: 0.9410 (tmm) cc_final: 0.8977 (tmm) REVERT: B 181 MET cc_start: 0.9022 (mmm) cc_final: 0.8208 (mmm) REVERT: B 690 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7589 (tp30) REVERT: B 759 MET cc_start: 0.8869 (tpp) cc_final: 0.8099 (tpp) REVERT: C 15 ARG cc_start: 0.9246 (mtt90) cc_final: 0.9013 (mtt90) REVERT: C 83 GLN cc_start: 0.9137 (tm-30) cc_final: 0.8633 (tm-30) REVERT: D 12 SER cc_start: 0.8582 (t) cc_final: 0.8209 (p) REVERT: D 15 ARG cc_start: 0.8782 (mtt90) cc_final: 0.8405 (mtp180) REVERT: D 36 ARG cc_start: 0.9477 (mpp-170) cc_final: 0.9041 (mpp-170) REVERT: D 73 PHE cc_start: 0.8090 (m-80) cc_final: 0.7841 (m-80) outliers start: 26 outliers final: 22 residues processed: 130 average time/residue: 0.2899 time to fit residues: 56.0083 Evaluate side-chains 132 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 480 TRP Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 694 SER Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 76 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 161 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 132 optimal weight: 0.0050 chunk 144 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 78 optimal weight: 0.2980 chunk 92 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.041853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.030040 restraints weight = 83332.524| |-----------------------------------------------------------------------------| r_work (start): 0.2618 rms_B_bonded: 4.54 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14971 Z= 0.102 Angle : 0.537 11.835 20239 Z= 0.270 Chirality : 0.039 0.245 2194 Planarity : 0.004 0.054 2609 Dihedral : 4.693 41.544 1997 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.88 % Allowed : 21.20 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.21), residues: 1777 helix: 2.32 (0.17), residues: 978 sheet: 0.79 (0.44), residues: 144 loop : -0.49 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 559 HIS 0.004 0.000 HIS A 599 PHE 0.009 0.001 PHE A 62 TYR 0.013 0.001 TYR B 273 ARG 0.005 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 753) hydrogen bonds : angle 3.76070 ( 2193) metal coordination : bond 0.00066 ( 4) covalent geometry : bond 0.00234 (14967) covalent geometry : angle 0.53703 (20239) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8862 (tt) REVERT: A 183 MET cc_start: 0.8906 (mmm) cc_final: 0.8441 (mmm) REVERT: A 381 MET cc_start: 0.8702 (tpp) cc_final: 0.8382 (mmm) REVERT: A 440 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8911 (mmt) REVERT: A 592 MET cc_start: 0.8921 (mmm) cc_final: 0.8691 (mmm) REVERT: A 712 MET cc_start: 0.9130 (tpt) cc_final: 0.8741 (tpp) REVERT: A 760 MET cc_start: 0.9313 (tmm) cc_final: 0.8890 (tmm) REVERT: A 761 MET cc_start: 0.9015 (mmt) cc_final: 0.8486 (mmt) REVERT: B 72 MET cc_start: 0.9392 (tmm) cc_final: 0.8933 (tmm) REVERT: B 92 CYS cc_start: 0.9346 (OUTLIER) cc_final: 0.8936 (m) REVERT: B 96 MET cc_start: 0.8741 (tpp) cc_final: 0.8469 (mpp) REVERT: B 181 MET cc_start: 0.9084 (mmm) cc_final: 0.8217 (mmm) REVERT: B 690 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7546 (tp30) REVERT: B 759 MET cc_start: 0.8853 (tpp) cc_final: 0.7918 (mmt) REVERT: C 15 ARG cc_start: 0.9295 (mtt90) cc_final: 0.9050 (mtt90) REVERT: C 83 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8622 (tm-30) REVERT: D 12 SER cc_start: 0.8578 (t) cc_final: 0.8183 (p) REVERT: D 15 ARG cc_start: 0.8777 (mtt90) cc_final: 0.8510 (mtp180) REVERT: D 36 ARG cc_start: 0.9460 (mpp-170) cc_final: 0.9019 (mpp-170) REVERT: D 86 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9027 (tt) outliers start: 30 outliers final: 22 residues processed: 135 average time/residue: 0.2985 time to fit residues: 60.3511 Evaluate side-chains 139 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 480 TRP Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 694 SER Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 86 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 152 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 165 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 141 optimal weight: 0.0030 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.041979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.030244 restraints weight = 83733.487| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 4.54 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 14971 Z= 0.104 Angle : 0.546 9.694 20239 Z= 0.274 Chirality : 0.039 0.236 2194 Planarity : 0.004 0.053 2609 Dihedral : 4.669 41.356 1997 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.63 % Allowed : 21.39 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.21), residues: 1777 helix: 2.34 (0.17), residues: 978 sheet: 0.83 (0.43), residues: 144 loop : -0.46 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 70 HIS 0.003 0.000 HIS A 599 PHE 0.022 0.001 PHE D 73 TYR 0.013 0.001 TYR B 273 ARG 0.005 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 753) hydrogen bonds : angle 3.72847 ( 2193) metal coordination : bond 0.00052 ( 4) covalent geometry : bond 0.00242 (14967) covalent geometry : angle 0.54603 (20239) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8848 (tt) REVERT: A 183 MET cc_start: 0.8853 (mmm) cc_final: 0.8276 (mmm) REVERT: A 193 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8186 (ttm) REVERT: A 381 MET cc_start: 0.8786 (tpp) cc_final: 0.8462 (mmm) REVERT: A 760 MET cc_start: 0.9289 (tmm) cc_final: 0.8911 (tmm) REVERT: A 761 MET cc_start: 0.9012 (mmt) cc_final: 0.8486 (mmt) REVERT: B 72 MET cc_start: 0.9390 (tmm) cc_final: 0.8928 (tmm) REVERT: B 92 CYS cc_start: 0.9345 (OUTLIER) cc_final: 0.8936 (m) REVERT: B 96 MET cc_start: 0.8739 (tpp) cc_final: 0.8524 (mpp) REVERT: B 181 MET cc_start: 0.8971 (mmm) cc_final: 0.8127 (mmm) REVERT: B 690 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7520 (tp30) REVERT: B 759 MET cc_start: 0.8923 (tpp) cc_final: 0.8028 (mmt) REVERT: C 15 ARG cc_start: 0.9303 (mtt90) cc_final: 0.9052 (mtt90) REVERT: C 83 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8626 (tm-30) REVERT: D 12 SER cc_start: 0.8498 (t) cc_final: 0.8159 (p) REVERT: D 15 ARG cc_start: 0.8750 (mtt90) cc_final: 0.8513 (mtp180) REVERT: D 36 ARG cc_start: 0.9465 (mpp-170) cc_final: 0.9018 (mpp-170) REVERT: D 86 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.8998 (tt) outliers start: 26 outliers final: 18 residues processed: 131 average time/residue: 0.2884 time to fit residues: 56.8427 Evaluate side-chains 133 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 480 TRP Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 694 SER Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 86 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 90 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 145 optimal weight: 0.2980 chunk 117 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.042156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.030327 restraints weight = 83760.834| |-----------------------------------------------------------------------------| r_work (start): 0.2631 rms_B_bonded: 4.59 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14971 Z= 0.104 Angle : 0.544 9.738 20239 Z= 0.273 Chirality : 0.039 0.231 2194 Planarity : 0.004 0.053 2609 Dihedral : 4.671 42.548 1997 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.56 % Allowed : 21.26 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.21), residues: 1777 helix: 2.29 (0.17), residues: 986 sheet: 0.77 (0.43), residues: 143 loop : -0.47 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 559 HIS 0.004 0.000 HIS A 599 PHE 0.023 0.001 PHE D 73 TYR 0.014 0.001 TYR B 273 ARG 0.004 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 753) hydrogen bonds : angle 3.72300 ( 2193) metal coordination : bond 0.00068 ( 4) covalent geometry : bond 0.00245 (14967) covalent geometry : angle 0.54378 (20239) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5569.87 seconds wall clock time: 97 minutes 44.05 seconds (5864.05 seconds total)