Starting phenix.real_space_refine on Thu Jul 31 20:07:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ugb_42220/07_2025/8ugb_42220.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ugb_42220/07_2025/8ugb_42220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ugb_42220/07_2025/8ugb_42220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ugb_42220/07_2025/8ugb_42220.map" model { file = "/net/cci-nas-00/data/ceres_data/8ugb_42220/07_2025/8ugb_42220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ugb_42220/07_2025/8ugb_42220.cif" } resolution = 3.0 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= -0.000 sd= 0.030 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 98 5.16 5 C 8771 2.51 5 N 2308 2.21 5 O 2543 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13726 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6645 Classifications: {'peptide': 811} Link IDs: {'PTRANS': 31, 'TRANS': 779} Chain: "B" Number of atoms: 6596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6596 Classifications: {'peptide': 811} Link IDs: {'PTRANS': 32, 'TRANS': 778} Chain: "C" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 187 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 4, 'TRANS': 19} Chain: "D" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 176 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 4, 'TRANS': 18} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Unusual residues: {' MG': 1, ' ZN': 1, 'PCG': 1, 'ZUD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Unusual residues: {' MG': 1, ' ZN': 1, 'PCG': 1, 'ZUD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 8.58, per 1000 atoms: 0.63 Number of scatterers: 13726 At special positions: 0 Unit cell: (78.6, 120.52, 168.99, 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 98 16.00 P 2 15.00 Mg 2 11.99 O 2543 8.00 N 2308 7.00 C 8771 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.31 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 599 " pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" NE2 HIS B 597 " pdb="ZN ZN B 902 " - pdb=" NE2 HIS B 561 " 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3188 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 4 sheets defined 62.9% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 7 through 16 Processing helix chain 'A' and resid 16 through 28 removed outlier: 3.685A pdb=" N GLN A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 38 removed outlier: 3.728A pdb=" N VAL A 32 " --> pdb=" O TYR A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 66 Processing helix chain 'A' and resid 73 through 90 Processing helix chain 'A' and resid 120 through 125 removed outlier: 3.519A pdb=" N CYS A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 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 249 removed outlier: 3.987A pdb=" N ASN A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N PHE A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 266 Processing helix chain 'A' and resid 266 through 271 removed outlier: 4.372A pdb=" N ASN A 271 " --> pdb=" O ARG A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 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 Processing helix chain 'A' and resid 461 through 466 removed outlier: 3.733A pdb=" N GLN A 466 " --> pdb=" O ASN A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 475 Processing helix chain 'A' and resid 483 through 495 removed outlier: 3.517A pdb=" N GLY A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 514 through 529 Processing helix chain 'A' and resid 530 through 535 removed outlier: 3.981A pdb=" N LYS A 534 " --> pdb=" O LYS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 Processing helix chain 'A' and resid 560 through 577 Processing helix chain 'A' and resid 579 through 584 removed outlier: 3.560A pdb=" N ARG A 582 " --> pdb=" O LYS A 579 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR A 583 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 598 Processing helix chain 'A' and resid 607 through 615 Processing helix chain 'A' and resid 616 through 622 Processing helix chain 'A' and resid 626 through 641 removed outlier: 3.609A pdb=" N ASP A 641 " --> pdb=" O THR A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 650 removed outlier: 6.370A pdb=" N ILE A 646 " --> pdb=" O SER A 643 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N PHE A 647 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN A 648 " --> pdb=" O ASN A 645 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN A 649 " --> pdb=" O ILE A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 669 removed outlier: 3.575A pdb=" N THR A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 688 removed outlier: 3.573A pdb=" N LYS A 676 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N THR A 679 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N MET A 680 " --> pdb=" O LYS A 676 " (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 704 removed outlier: 3.901A pdb=" N LEU A 703 " --> pdb=" O GLN A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 721 Processing helix chain 'A' and resid 722 through 726 Processing helix chain 'A' and resid 727 through 735 removed outlier: 3.683A pdb=" N LYS A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 754 Processing helix chain 'A' and resid 765 through 767 No H-bonds generated for 'chain 'A' and resid 765 through 767' Processing helix chain 'A' and resid 768 through 778 removed outlier: 3.745A pdb=" N LEU A 772 " --> pdb=" O GLU A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 792 removed outlier: 3.838A pdb=" N VAL A 784 " --> pdb=" O VAL A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 817 removed outlier: 3.730A pdb=" N LEU A 799 " --> pdb=" O ILE A 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 15 Processing helix chain 'B' and resid 15 through 25 Processing helix chain 'B' and resid 47 through 67 removed outlier: 3.761A pdb=" N GLN B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 84 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 125 through 129 removed outlier: 3.620A pdb=" N GLU B 129 " --> pdb=" O PRO B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 removed outlier: 3.737A pdb=" N GLY B 140 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS B 141 " --> pdb=" O GLY B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 169 Processing helix chain 'B' and resid 202 through 247 removed outlier: 3.715A pdb=" N LEU B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N PHE B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 Processing helix chain 'B' and resid 264 through 269 removed outlier: 3.994A pdb=" N ASN B 269 " --> pdb=" O ARG B 265 " (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 337 through 342 removed outlier: 4.138A pdb=" N SER B 342 " --> pdb=" O TRP B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 360 through 363 Processing helix chain 'B' and resid 411 through 428 Processing helix chain 'B' and resid 429 through 457 removed outlier: 3.563A pdb=" N HIS B 455 " --> pdb=" O MET B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 466 Processing helix chain 'B' and resid 468 through 473 removed outlier: 3.543A pdb=" N ARG B 472 " --> pdb=" O PRO B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 480 Processing helix chain 'B' and resid 481 through 493 Processing helix chain 'B' and resid 512 through 528 removed outlier: 3.538A pdb=" N GLY B 528 " --> pdb=" O TYR B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 536 through 551 Processing helix chain 'B' and resid 558 through 575 Processing helix chain 'B' and resid 577 through 582 removed outlier: 3.762A pdb=" N SER B 580 " --> pdb=" O LYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 596 Processing helix chain 'B' and resid 605 through 613 Processing helix chain 'B' and resid 614 through 620 Processing helix chain 'B' and resid 626 through 639 removed outlier: 3.671A pdb=" N GLU B 639 " --> pdb=" O PHE B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 643 removed outlier: 3.558A 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 666 Processing helix chain 'B' and resid 668 through 675 Processing helix chain 'B' and resid 675 through 688 removed outlier: 3.586A pdb=" N PHE B 679 " --> pdb=" O LYS B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 700 Processing helix chain 'B' and resid 702 through 719 removed outlier: 3.626A pdb=" N LYS B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B 715 " --> pdb=" O ALA B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 750 removed outlier: 3.640A pdb=" N LYS B 731 " --> pdb=" O GLU B 727 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 734 " --> pdb=" O SER B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 760 removed outlier: 3.587A pdb=" N ASP B 760 " --> pdb=" O PRO B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 765 No H-bonds generated for 'chain 'B' and resid 763 through 765' Processing helix chain 'B' and resid 766 through 778 Processing helix chain 'B' and resid 778 through 790 removed outlier: 4.035A pdb=" N VAL B 782 " --> pdb=" O VAL B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 817 removed outlier: 3.667A pdb=" N PHE B 797 " --> pdb=" O ILE B 793 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS B 817 " --> pdb=" O GLU B 813 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.610A pdb=" N LEU A 96 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N PHE A 113 " --> pdb=" O MET A 94 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N MET A 94 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL A 115 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASP A 92 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA A 91 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LYS A 197 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 93 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL A 189 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 190 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 328 through 333 removed outlier: 3.824A pdb=" N LYS A 317 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A 398 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 390 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL A 400 " --> pdb=" O MET A 388 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N MET A 388 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR A 402 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A 386 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 131 through 133 removed outlier: 6.589A pdb=" N LEU B 94 " --> pdb=" O ARG B 109 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL B 187 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N GLN B 99 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 13.900A pdb=" N ASP B 185 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ASN B 182 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA B 188 " --> pdb=" O ILE B 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 326 through 330 removed outlier: 3.822A pdb=" N LYS B 315 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL B 396 " --> pdb=" O LEU B 278 " (cutoff:3.500A) 764 hydrogen bonds defined for protein. 2205 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: 4.54 Time building geometry restraints manager: 3.89 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: 2321 1.31 - 1.44: 3700 1.44 - 1.57: 7842 1.57 - 1.69: 17 1.69 - 1.82: 164 Bond restraints: 14044 Sorted by residual: bond pdb=" C21 ZUD A 904 " pdb=" N6 ZUD A 904 " ideal model delta sigma weight residual 1.448 1.179 0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" C21 ZUD B 904 " pdb=" N6 ZUD B 904 " ideal model delta sigma weight residual 1.448 1.180 0.268 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C17 ZUD A 904 " pdb=" C18 ZUD A 904 " ideal model delta sigma weight residual 1.532 1.268 0.264 2.00e-02 2.50e+03 1.75e+02 bond pdb=" C17 ZUD B 904 " pdb=" C18 ZUD B 904 " ideal model delta sigma weight residual 1.532 1.271 0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C20 ZUD B 904 " pdb=" N6 ZUD B 904 " ideal model delta sigma weight residual 1.462 1.238 0.224 2.00e-02 2.50e+03 1.26e+02 ... (remaining 14039 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 18721 2.56 - 5.13: 221 5.13 - 7.69: 36 7.69 - 10.26: 17 10.26 - 12.82: 7 Bond angle restraints: 19002 Sorted by residual: angle pdb=" CA PRO B 179 " pdb=" N PRO B 179 " pdb=" CD PRO B 179 " ideal model delta sigma weight residual 112.00 100.48 11.52 1.40e+00 5.10e-01 6.77e+01 angle pdb=" C HIS A 202 " pdb=" CA HIS A 202 " pdb=" CB HIS A 202 " ideal model delta sigma weight residual 115.79 108.02 7.77 1.19e+00 7.06e-01 4.27e+01 angle pdb=" N ASP A 199 " pdb=" CA ASP A 199 " pdb=" C ASP A 199 " ideal model delta sigma weight residual 114.62 108.63 5.99 1.14e+00 7.69e-01 2.76e+01 angle pdb=" CB MET A 381 " pdb=" CG MET A 381 " pdb=" SD MET A 381 " ideal model delta sigma weight residual 112.70 125.52 -12.82 3.00e+00 1.11e-01 1.83e+01 angle pdb=" C1' PCG A 901 " pdb=" O4' PCG A 901 " pdb=" C4' PCG A 901 " ideal model delta sigma weight residual 108.99 96.96 12.03 3.00e+00 1.11e-01 1.61e+01 ... (remaining 18997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.69: 8053 29.69 - 59.38: 469 59.38 - 89.07: 28 89.07 - 118.76: 9 118.76 - 148.45: 1 Dihedral angle restraints: 8560 sinusoidal: 3646 harmonic: 4914 Sorted by residual: dihedral pdb=" CA LEU B 467 " pdb=" C LEU B 467 " pdb=" N PRO B 468 " pdb=" CA PRO B 468 " ideal model delta harmonic sigma weight residual -180.00 -154.27 -25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA ASP B 600 " pdb=" C ASP B 600 " pdb=" N HIS B 601 " pdb=" CA HIS B 601 " ideal model delta harmonic sigma weight residual 180.00 155.19 24.81 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA ASP B 598 " pdb=" C ASP B 598 " pdb=" N ILE B 599 " pdb=" CA ILE B 599 " ideal model delta harmonic sigma weight residual -180.00 -156.73 -23.27 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 8557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1822 0.063 - 0.127: 220 0.127 - 0.190: 12 0.190 - 0.253: 3 0.253 - 0.317: 1 Chirality restraints: 2058 Sorted by residual: chirality pdb=" C4' PCG B 901 " pdb=" C3' PCG B 901 " pdb=" C5' PCG B 901 " pdb=" O4' PCG B 901 " both_signs ideal model delta sigma weight residual False -2.50 -2.82 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA PRO B 179 " pdb=" N PRO B 179 " pdb=" C PRO B 179 " pdb=" CB PRO B 179 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C4' PCG A 901 " pdb=" C3' PCG A 901 " pdb=" C5' PCG A 901 " pdb=" O4' PCG A 901 " both_signs ideal model delta sigma weight residual False -2.50 -2.73 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 2055 not shown) Planarity restraints: 2443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 467 " 0.073 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO B 468 " -0.191 5.00e-02 4.00e+02 pdb=" CA PRO B 468 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 468 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 38 " 0.073 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO A 39 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 178 " -0.057 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO B 179 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 179 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 179 " -0.044 5.00e-02 4.00e+02 ... (remaining 2440 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 79 2.47 - 3.08: 9415 3.08 - 3.68: 20840 3.68 - 4.29: 31177 4.29 - 4.90: 52701 Nonbonded interactions: 114212 Sorted by model distance: nonbonded pdb=" OD1 ASP A 600 " pdb="MG MG A 903 " model vdw 1.862 2.170 nonbonded pdb=" OD1 ASP A 720 " pdb="ZN ZN A 902 " model vdw 2.015 2.230 nonbonded pdb=" OD2 ASP A 600 " pdb="ZN ZN A 902 " model vdw 2.025 2.230 nonbonded pdb=" OH TYR B 551 " pdb=" O LEU B 595 " model vdw 2.114 3.040 nonbonded pdb=" OD2 ASP B 598 " pdb="ZN ZN B 902 " model vdw 2.152 2.230 ... (remaining 114207 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 12 through 34) selection = chain 'D' } 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 36.420 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 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 : 0.009 0.269 14049 Z= 0.451 Angle : 0.742 12.824 19002 Z= 0.352 Chirality : 0.043 0.317 2058 Planarity : 0.005 0.110 2443 Dihedral : 17.431 148.447 5372 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.12 % Favored : 94.58 % Rotamer: Outliers : 1.27 % Allowed : 19.95 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.21), residues: 1661 helix: 1.18 (0.17), residues: 913 sheet: 0.52 (0.43), residues: 142 loop : -0.40 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 380 HIS 0.008 0.001 HIS B 629 PHE 0.013 0.001 PHE B 209 TYR 0.014 0.001 TYR A 316 ARG 0.015 0.001 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.21538 ( 764) hydrogen bonds : angle 6.75199 ( 2205) metal coordination : bond 0.00245 ( 4) covalent geometry : bond 0.00939 (14044) covalent geometry : angle 0.74177 (19002) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9427 (mt) cc_final: 0.9176 (mp) REVERT: B 181 MET cc_start: 0.8745 (mmm) cc_final: 0.8508 (mmm) REVERT: B 282 LYS cc_start: 0.8299 (mppt) cc_final: 0.7956 (mmmt) REVERT: B 386 MET cc_start: 0.9465 (mtm) cc_final: 0.8884 (mpp) REVERT: B 442 GLU cc_start: 0.9016 (tp30) cc_final: 0.8449 (tm-30) REVERT: B 651 ARG cc_start: 0.8083 (tmm160) cc_final: 0.7848 (tmm-80) outliers start: 19 outliers final: 13 residues processed: 124 average time/residue: 1.4393 time to fit residues: 194.8222 Evaluate side-chains 110 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 544 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.1980 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 84 optimal weight: 20.0000 chunk 67 optimal weight: 0.0770 chunk 130 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 96 optimal weight: 0.4980 chunk 150 optimal weight: 0.7980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 466 GLN ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 HIS B 729 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.083135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.063952 restraints weight = 34898.155| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.80 r_work: 0.3034 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14049 Z= 0.139 Angle : 0.608 9.128 19002 Z= 0.313 Chirality : 0.042 0.191 2058 Planarity : 0.005 0.108 2443 Dihedral : 9.588 140.380 1964 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.30 % Favored : 94.40 % Rotamer: Outliers : 2.27 % Allowed : 17.75 % Favored : 79.99 % 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: 1.18 (0.21), residues: 1661 helix: 1.49 (0.17), residues: 945 sheet: 0.40 (0.43), residues: 140 loop : -0.20 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 695 HIS 0.010 0.001 HIS B 9 PHE 0.011 0.001 PHE D 30 TYR 0.015 0.001 TYR A 674 ARG 0.004 0.000 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.05425 ( 764) hydrogen bonds : angle 4.85172 ( 2205) metal coordination : bond 0.00085 ( 4) covalent geometry : bond 0.00308 (14044) covalent geometry : angle 0.60825 (19002) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9510 (mt) cc_final: 0.9295 (mp) REVERT: A 183 MET cc_start: 0.8604 (mmm) cc_final: 0.8261 (mmm) REVERT: A 500 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.9004 (ttpt) REVERT: A 733 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8955 (mmtm) REVERT: B 9 HIS cc_start: 0.8960 (t70) cc_final: 0.8741 (t-90) REVERT: B 651 ARG cc_start: 0.8106 (tmm160) cc_final: 0.7853 (tmm-80) REVERT: D 29 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7580 (tmtt) outliers start: 34 outliers final: 11 residues processed: 130 average time/residue: 1.4375 time to fit residues: 203.0622 Evaluate side-chains 112 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain D residue 29 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 47 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 GLN B 219 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.082383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.063011 restraints weight = 35718.044| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.80 r_work: 0.3008 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14049 Z= 0.204 Angle : 0.604 8.019 19002 Z= 0.309 Chirality : 0.043 0.208 2058 Planarity : 0.005 0.112 2443 Dihedral : 8.989 133.314 1952 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.94 % Favored : 94.76 % Rotamer: Outliers : 2.54 % Allowed : 17.88 % Favored : 79.59 % 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: 1.14 (0.21), residues: 1661 helix: 1.54 (0.17), residues: 940 sheet: 0.16 (0.43), residues: 142 loop : -0.31 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 561 HIS 0.009 0.001 HIS B 322 PHE 0.014 0.001 PHE B 789 TYR 0.017 0.002 TYR A 674 ARG 0.008 0.000 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.05043 ( 764) hydrogen bonds : angle 4.64263 ( 2205) metal coordination : bond 0.00468 ( 4) covalent geometry : bond 0.00483 (14044) covalent geometry : angle 0.60363 (19002) Misc. bond : bond 0.00048 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 101 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9525 (mt) cc_final: 0.9262 (mp) REVERT: A 183 MET cc_start: 0.8643 (mmm) cc_final: 0.8366 (mmm) REVERT: A 616 ASN cc_start: 0.9315 (OUTLIER) cc_final: 0.9069 (t0) REVERT: A 733 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8933 (mmtm) REVERT: B 531 ARG cc_start: 0.8686 (mmm160) cc_final: 0.8336 (tpp80) REVERT: D 29 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7519 (tmtt) outliers start: 38 outliers final: 16 residues processed: 133 average time/residue: 1.4177 time to fit residues: 205.7920 Evaluate side-chains 118 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain D residue 29 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 162 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 86 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.083463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.064199 restraints weight = 35143.293| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.80 r_work: 0.3056 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14049 Z= 0.130 Angle : 0.562 7.384 19002 Z= 0.288 Chirality : 0.042 0.195 2058 Planarity : 0.004 0.111 2443 Dihedral : 8.535 124.128 1951 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.88 % Favored : 94.82 % Rotamer: Outliers : 2.40 % Allowed : 18.15 % Favored : 79.45 % 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: 1.31 (0.21), residues: 1661 helix: 1.72 (0.17), residues: 933 sheet: 0.16 (0.43), residues: 142 loop : -0.26 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 695 HIS 0.009 0.001 HIS B 322 PHE 0.011 0.001 PHE D 30 TYR 0.012 0.001 TYR B 273 ARG 0.006 0.000 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 764) hydrogen bonds : angle 4.40176 ( 2205) metal coordination : bond 0.00174 ( 4) covalent geometry : bond 0.00299 (14044) covalent geometry : angle 0.56248 (19002) Misc. bond : bond 0.00044 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 1.538 Fit side-chains revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9481 (mt) cc_final: 0.9221 (mp) REVERT: A 183 MET cc_start: 0.8627 (mmm) cc_final: 0.8374 (mmm) REVERT: A 616 ASN cc_start: 0.9290 (OUTLIER) cc_final: 0.9052 (t0) REVERT: A 733 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8993 (mmtm) REVERT: B 442 GLU cc_start: 0.9003 (tp30) cc_final: 0.8441 (tm-30) REVERT: B 640 GLU cc_start: 0.8418 (tp30) cc_final: 0.8105 (tp30) REVERT: D 29 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7589 (tmtt) outliers start: 36 outliers final: 11 residues processed: 138 average time/residue: 1.3477 time to fit residues: 203.0994 Evaluate side-chains 114 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain D residue 29 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 147 optimal weight: 0.0270 chunk 69 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 158 optimal weight: 0.6980 chunk 28 optimal weight: 0.0970 chunk 90 optimal weight: 0.8980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 322 HIS B 653 HIS ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.084477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.065349 restraints weight = 35454.322| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.83 r_work: 0.3101 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14049 Z= 0.117 Angle : 0.553 8.494 19002 Z= 0.283 Chirality : 0.042 0.185 2058 Planarity : 0.004 0.111 2443 Dihedral : 8.033 110.558 1944 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.94 % Favored : 94.76 % Rotamer: Outliers : 2.13 % Allowed : 18.41 % Favored : 79.45 % 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: 1.36 (0.21), residues: 1661 helix: 1.78 (0.17), residues: 935 sheet: 0.34 (0.43), residues: 139 loop : -0.33 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 697 HIS 0.005 0.001 HIS B 322 PHE 0.013 0.001 PHE B 215 TYR 0.017 0.001 TYR A 674 ARG 0.010 0.000 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.03991 ( 764) hydrogen bonds : angle 4.28542 ( 2205) metal coordination : bond 0.00108 ( 4) covalent geometry : bond 0.00268 (14044) covalent geometry : angle 0.55346 (19002) Misc. bond : bond 0.00037 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 1.716 Fit side-chains revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9265 (mt) cc_final: 0.9010 (mp) REVERT: A 183 MET cc_start: 0.8638 (mmm) cc_final: 0.8292 (mmm) REVERT: A 256 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8617 (pm20) REVERT: A 320 ASP cc_start: 0.8345 (t0) cc_final: 0.8133 (t0) REVERT: A 616 ASN cc_start: 0.9271 (OUTLIER) cc_final: 0.9011 (t0) REVERT: A 733 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8991 (mmtm) REVERT: B 20 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8337 (m-30) REVERT: B 148 MET cc_start: 0.8342 (ttp) cc_final: 0.7723 (tmm) REVERT: B 588 PHE cc_start: 0.8777 (t80) cc_final: 0.8386 (t80) REVERT: D 29 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7438 (tmtt) outliers start: 32 outliers final: 14 residues processed: 127 average time/residue: 1.3494 time to fit residues: 188.1618 Evaluate side-chains 117 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain D residue 29 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 156 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 83 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.083030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.063823 restraints weight = 36198.875| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.83 r_work: 0.3026 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14049 Z= 0.190 Angle : 0.597 9.066 19002 Z= 0.303 Chirality : 0.043 0.208 2058 Planarity : 0.005 0.114 2443 Dihedral : 7.958 103.158 1944 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.88 % Favored : 94.88 % Rotamer: Outliers : 1.80 % Allowed : 19.55 % Favored : 78.65 % 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: 1.33 (0.21), residues: 1661 helix: 1.77 (0.17), residues: 935 sheet: 0.25 (0.43), residues: 139 loop : -0.35 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 697 HIS 0.019 0.001 HIS B 322 PHE 0.013 0.001 PHE B 215 TYR 0.014 0.002 TYR A 674 ARG 0.009 0.000 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 764) hydrogen bonds : angle 4.38392 ( 2205) metal coordination : bond 0.00409 ( 4) covalent geometry : bond 0.00452 (14044) covalent geometry : angle 0.59679 (19002) Misc. bond : bond 0.00039 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 1.523 Fit side-chains revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9274 (mt) cc_final: 0.9015 (mp) REVERT: A 183 MET cc_start: 0.8675 (mmm) cc_final: 0.8383 (mmm) REVERT: A 256 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8670 (pm20) REVERT: A 320 ASP cc_start: 0.8364 (t0) cc_final: 0.8162 (t0) REVERT: A 616 ASN cc_start: 0.9291 (OUTLIER) cc_final: 0.9040 (t0) REVERT: A 733 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8932 (mmtm) REVERT: B 20 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8363 (m-30) REVERT: B 148 MET cc_start: 0.8412 (ttp) cc_final: 0.7843 (tmm) REVERT: B 282 LYS cc_start: 0.8091 (mppt) cc_final: 0.7827 (mmmt) REVERT: B 442 GLU cc_start: 0.9015 (tp30) cc_final: 0.8293 (tm-30) REVERT: B 588 PHE cc_start: 0.8951 (t80) cc_final: 0.8584 (t80) REVERT: D 29 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7540 (tmtt) outliers start: 27 outliers final: 15 residues processed: 124 average time/residue: 1.4076 time to fit residues: 190.2694 Evaluate side-chains 117 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain D residue 29 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 20 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 133 optimal weight: 0.4980 chunk 117 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 153 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.083634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.064267 restraints weight = 35545.864| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.87 r_work: 0.3077 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14049 Z= 0.134 Angle : 0.568 8.623 19002 Z= 0.290 Chirality : 0.042 0.185 2058 Planarity : 0.004 0.113 2443 Dihedral : 7.767 102.755 1944 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.00 % Favored : 94.76 % Rotamer: Outliers : 2.13 % Allowed : 19.21 % Favored : 78.65 % 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: 1.37 (0.21), residues: 1661 helix: 1.79 (0.17), residues: 935 sheet: 0.28 (0.43), residues: 139 loop : -0.31 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 697 HIS 0.005 0.001 HIS B 322 PHE 0.011 0.001 PHE B 215 TYR 0.016 0.001 TYR A 674 ARG 0.006 0.000 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 764) hydrogen bonds : angle 4.29005 ( 2205) metal coordination : bond 0.00207 ( 4) covalent geometry : bond 0.00313 (14044) covalent geometry : angle 0.56753 (19002) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9486 (t80) cc_final: 0.9264 (t80) REVERT: A 26 LEU cc_start: 0.9259 (mt) cc_final: 0.9004 (mp) REVERT: A 183 MET cc_start: 0.8722 (mmm) cc_final: 0.8441 (mmm) REVERT: A 256 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8655 (pm20) REVERT: A 616 ASN cc_start: 0.9273 (OUTLIER) cc_final: 0.9015 (t0) REVERT: A 701 MET cc_start: 0.8811 (mmm) cc_final: 0.8410 (mmm) REVERT: A 733 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.9002 (mmtm) REVERT: B 148 MET cc_start: 0.8367 (ttp) cc_final: 0.7809 (tmm) REVERT: B 282 LYS cc_start: 0.8180 (mppt) cc_final: 0.7846 (mmmt) REVERT: B 386 MET cc_start: 0.9388 (OUTLIER) cc_final: 0.9152 (mtp) REVERT: B 414 ASP cc_start: 0.8543 (m-30) cc_final: 0.8107 (m-30) REVERT: B 588 PHE cc_start: 0.8829 (t80) cc_final: 0.8425 (t80) REVERT: B 609 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7976 (mp10) REVERT: D 29 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7391 (tmtt) REVERT: D 30 PHE cc_start: 0.8571 (m-10) cc_final: 0.7956 (m-10) outliers start: 32 outliers final: 16 residues processed: 134 average time/residue: 1.3645 time to fit residues: 200.4164 Evaluate side-chains 126 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain D residue 29 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 141 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 148 optimal weight: 0.6980 chunk 88 optimal weight: 0.0050 chunk 104 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 12 optimal weight: 0.4980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.082507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.063558 restraints weight = 34655.746| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.81 r_work: 0.3013 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14049 Z= 0.120 Angle : 0.570 10.193 19002 Z= 0.290 Chirality : 0.042 0.182 2058 Planarity : 0.004 0.112 2443 Dihedral : 7.496 102.131 1944 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.94 % Favored : 94.82 % Rotamer: Outliers : 1.53 % Allowed : 19.68 % Favored : 78.79 % 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: 1.42 (0.21), residues: 1661 helix: 1.84 (0.17), residues: 936 sheet: 0.29 (0.43), residues: 139 loop : -0.31 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 697 HIS 0.006 0.001 HIS B 322 PHE 0.012 0.001 PHE B 215 TYR 0.014 0.001 TYR A 275 ARG 0.005 0.000 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 764) hydrogen bonds : angle 4.23068 ( 2205) metal coordination : bond 0.00146 ( 4) covalent geometry : bond 0.00276 (14044) covalent geometry : angle 0.57008 (19002) Misc. bond : bond 0.00031 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 1.545 Fit side-chains revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9455 (t80) cc_final: 0.9239 (t80) REVERT: A 26 LEU cc_start: 0.9254 (mt) cc_final: 0.9004 (mp) REVERT: A 116 HIS cc_start: 0.7924 (OUTLIER) cc_final: 0.7584 (p-80) REVERT: A 183 MET cc_start: 0.8782 (mmm) cc_final: 0.8500 (mmm) REVERT: A 256 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8607 (pm20) REVERT: A 616 ASN cc_start: 0.9191 (OUTLIER) cc_final: 0.8966 (t0) REVERT: A 701 MET cc_start: 0.8817 (mmm) cc_final: 0.8418 (mmm) REVERT: A 733 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8999 (mmtm) REVERT: B 148 MET cc_start: 0.8258 (ttp) cc_final: 0.7755 (tmm) REVERT: B 282 LYS cc_start: 0.8189 (mppt) cc_final: 0.7856 (mmmt) REVERT: B 414 ASP cc_start: 0.8525 (m-30) cc_final: 0.8086 (m-30) REVERT: B 442 GLU cc_start: 0.9009 (tp30) cc_final: 0.8385 (tm-30) REVERT: B 588 PHE cc_start: 0.8700 (t80) cc_final: 0.8287 (t80) REVERT: B 609 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8029 (mp10) REVERT: D 29 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7538 (tptp) REVERT: D 30 PHE cc_start: 0.8360 (m-10) cc_final: 0.8119 (m-80) outliers start: 23 outliers final: 15 residues processed: 128 average time/residue: 1.4356 time to fit residues: 201.0940 Evaluate side-chains 124 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain D residue 29 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 73 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 137 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.082249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.063270 restraints weight = 34677.185| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.81 r_work: 0.3007 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14049 Z= 0.131 Angle : 0.577 11.118 19002 Z= 0.293 Chirality : 0.042 0.188 2058 Planarity : 0.004 0.113 2443 Dihedral : 7.368 104.289 1944 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.94 % Favored : 94.82 % Rotamer: Outliers : 1.47 % Allowed : 19.95 % Favored : 78.59 % 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: 1.41 (0.21), residues: 1661 helix: 1.84 (0.17), residues: 936 sheet: 0.26 (0.43), residues: 139 loop : -0.32 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 697 HIS 0.008 0.001 HIS B 322 PHE 0.014 0.001 PHE D 30 TYR 0.025 0.001 TYR A 674 ARG 0.005 0.000 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 764) hydrogen bonds : angle 4.22805 ( 2205) metal coordination : bond 0.00202 ( 4) covalent geometry : bond 0.00308 (14044) covalent geometry : angle 0.57705 (19002) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 2.045 Fit side-chains revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9460 (t80) cc_final: 0.9244 (t80) REVERT: A 26 LEU cc_start: 0.9157 (mt) cc_final: 0.8918 (mp) REVERT: A 183 MET cc_start: 0.8772 (mmm) cc_final: 0.8483 (mmm) REVERT: A 256 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8612 (pm20) REVERT: A 616 ASN cc_start: 0.9192 (OUTLIER) cc_final: 0.8967 (t0) REVERT: A 701 MET cc_start: 0.8831 (mmm) cc_final: 0.8437 (mmm) REVERT: A 733 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8957 (mmtm) REVERT: B 148 MET cc_start: 0.8276 (ttp) cc_final: 0.7769 (tmm) REVERT: B 282 LYS cc_start: 0.8194 (mppt) cc_final: 0.7862 (mmmt) REVERT: B 414 ASP cc_start: 0.8535 (m-30) cc_final: 0.8125 (m-30) REVERT: B 588 PHE cc_start: 0.8723 (t80) cc_final: 0.8311 (t80) REVERT: B 609 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8057 (mp10) REVERT: B 651 ARG cc_start: 0.8059 (tmm160) cc_final: 0.7678 (tmm-80) REVERT: D 29 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7774 (tptp) outliers start: 22 outliers final: 15 residues processed: 124 average time/residue: 1.6893 time to fit residues: 230.2667 Evaluate side-chains 122 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain D residue 29 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 16 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 146 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 118 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.082383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.063447 restraints weight = 34655.990| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.80 r_work: 0.3011 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14049 Z= 0.132 Angle : 0.588 11.685 19002 Z= 0.297 Chirality : 0.042 0.186 2058 Planarity : 0.004 0.113 2443 Dihedral : 7.283 104.355 1944 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.06 % Favored : 94.70 % Rotamer: Outliers : 1.33 % Allowed : 20.15 % Favored : 78.52 % 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: 1.41 (0.21), residues: 1661 helix: 1.84 (0.17), residues: 935 sheet: 0.30 (0.43), residues: 137 loop : -0.32 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 697 HIS 0.008 0.001 HIS B 322 PHE 0.012 0.001 PHE D 30 TYR 0.015 0.001 TYR A 674 ARG 0.005 0.000 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.03852 ( 764) hydrogen bonds : angle 4.22047 ( 2205) metal coordination : bond 0.00203 ( 4) covalent geometry : bond 0.00312 (14044) covalent geometry : angle 0.58798 (19002) Misc. bond : bond 0.00028 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 1.942 Fit side-chains revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9459 (t80) cc_final: 0.9245 (t80) REVERT: A 26 LEU cc_start: 0.9146 (mt) cc_final: 0.8910 (mp) REVERT: A 116 HIS cc_start: 0.7941 (OUTLIER) cc_final: 0.7592 (p-80) REVERT: A 183 MET cc_start: 0.8771 (mmm) cc_final: 0.8480 (mmm) REVERT: A 256 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8612 (pm20) REVERT: A 616 ASN cc_start: 0.9187 (OUTLIER) cc_final: 0.8950 (t0) REVERT: A 701 MET cc_start: 0.8831 (mmm) cc_final: 0.8425 (mmm) REVERT: A 733 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8958 (mmtm) REVERT: B 148 MET cc_start: 0.8346 (ttp) cc_final: 0.7791 (tmm) REVERT: B 282 LYS cc_start: 0.8255 (mppt) cc_final: 0.7917 (mmmt) REVERT: B 414 ASP cc_start: 0.8527 (m-30) cc_final: 0.8131 (m-30) REVERT: B 442 GLU cc_start: 0.8981 (tp30) cc_final: 0.8230 (tm-30) REVERT: B 588 PHE cc_start: 0.8722 (t80) cc_final: 0.8311 (t80) REVERT: B 609 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8080 (mp10) REVERT: B 651 ARG cc_start: 0.8060 (tmm160) cc_final: 0.7659 (tmm-80) REVERT: D 29 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7649 (tptp) outliers start: 20 outliers final: 14 residues processed: 124 average time/residue: 1.9108 time to fit residues: 257.3439 Evaluate side-chains 122 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain D residue 29 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 158 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 160 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.081462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.062388 restraints weight = 34888.736| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.80 r_work: 0.2986 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14049 Z= 0.162 Angle : 0.605 12.522 19002 Z= 0.304 Chirality : 0.043 0.203 2058 Planarity : 0.004 0.114 2443 Dihedral : 7.295 103.285 1944 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.06 % Favored : 94.70 % Rotamer: Outliers : 1.20 % Allowed : 20.35 % Favored : 78.45 % 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: 1.37 (0.21), residues: 1661 helix: 1.81 (0.17), residues: 935 sheet: 0.25 (0.43), residues: 137 loop : -0.35 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 697 HIS 0.009 0.001 HIS B 322 PHE 0.014 0.001 PHE D 30 TYR 0.027 0.001 TYR A 674 ARG 0.005 0.000 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.04058 ( 764) hydrogen bonds : angle 4.27707 ( 2205) metal coordination : bond 0.00308 ( 4) covalent geometry : bond 0.00386 (14044) covalent geometry : angle 0.60489 (19002) Misc. bond : bond 0.00037 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7818.32 seconds wall clock time: 138 minutes 53.93 seconds (8333.93 seconds total)