Starting phenix.real_space_refine on Sat Oct 11 10:10:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ugb_42220/10_2025/8ugb_42220.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ugb_42220/10_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_42220/10_2025/8ugb_42220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ugb_42220/10_2025/8ugb_42220.map" model { file = "/net/cci-nas-00/data/ceres_data/8ugb_42220/10_2025/8ugb_42220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ugb_42220/10_2025/8ugb_42220.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 3.21, per 1000 atoms: 0.23 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: 1.19 Conformation dependent library (CDL) restraints added in 596.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.51 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: 2.41 Time building geometry restraints manager: 1.51 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.240 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.090 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.015 0.001 ARG B 531 TYR 0.014 0.001 TYR A 316 PHE 0.013 0.001 PHE B 209 TRP 0.010 0.001 TRP A 380 HIS 0.008 0.001 HIS B 629 Details of bonding type rmsd covalent geometry : bond 0.00939 (14044) covalent geometry : angle 0.74177 (19002) hydrogen bonds : bond 0.21538 ( 764) hydrogen bonds : angle 6.75199 ( 2205) metal coordination : bond 0.00245 ( 4) 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 : 0.543 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: 0.6983 time to fit residues: 96.0271 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 : 0.451 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.0870 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.083423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.064038 restraints weight = 35781.532| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.85 r_work: 0.3056 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14049 Z= 0.151 Angle : 0.615 8.888 19002 Z= 0.318 Chirality : 0.043 0.196 2058 Planarity : 0.005 0.108 2443 Dihedral : 9.627 140.642 1964 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.36 % Favored : 94.34 % Rotamer: Outliers : 2.40 % Allowed : 17.75 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.21), residues: 1661 helix: 1.51 (0.17), residues: 939 sheet: 0.38 (0.43), residues: 140 loop : -0.22 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 10 TYR 0.014 0.001 TYR A 674 PHE 0.012 0.001 PHE D 30 TRP 0.005 0.001 TRP B 695 HIS 0.009 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00345 (14044) covalent geometry : angle 0.61549 (19002) hydrogen bonds : bond 0.05421 ( 764) hydrogen bonds : angle 4.88374 ( 2205) metal coordination : bond 0.00155 ( 4) Misc. bond : bond 0.00045 ( 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 137 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9516 (mt) cc_final: 0.9294 (mp) REVERT: A 183 MET cc_start: 0.8605 (mmm) cc_final: 0.8255 (mmm) REVERT: A 733 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8984 (mmtm) REVERT: D 29 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7541 (tmtt) outliers start: 36 outliers final: 12 residues processed: 130 average time/residue: 0.7598 time to fit residues: 106.6732 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 : 0.545 ------------------------------------------------------------------------------- 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 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 191 MET 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 13 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 159 optimal weight: 0.0670 chunk 104 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 overall best weight: 1.3322 ------------------------------------------------------------------------------- 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 B 322 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.082194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.062763 restraints weight = 35551.150| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.84 r_work: 0.3013 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14049 Z= 0.187 Angle : 0.596 7.980 19002 Z= 0.306 Chirality : 0.043 0.204 2058 Planarity : 0.005 0.112 2443 Dihedral : 8.903 132.427 1952 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.94 % Favored : 94.76 % Rotamer: Outliers : 2.60 % Allowed : 17.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.21), residues: 1661 helix: 1.54 (0.17), residues: 940 sheet: 0.14 (0.43), residues: 142 loop : -0.32 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 531 TYR 0.019 0.002 TYR A 674 PHE 0.013 0.001 PHE B 789 TRP 0.008 0.001 TRP A 380 HIS 0.010 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00443 (14044) covalent geometry : angle 0.59607 (19002) hydrogen bonds : bond 0.04954 ( 764) hydrogen bonds : angle 4.61946 ( 2205) metal coordination : bond 0.00367 ( 4) Misc. bond : bond 0.00046 ( 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 142 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 103 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9523 (mt) cc_final: 0.9263 (mp) REVERT: A 183 MET cc_start: 0.8638 (mmm) cc_final: 0.8348 (mmm) REVERT: A 616 ASN cc_start: 0.9309 (OUTLIER) cc_final: 0.9059 (t0) REVERT: A 733 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8928 (mmtm) REVERT: B 531 ARG cc_start: 0.8695 (mmm160) cc_final: 0.8333 (tpp80) REVERT: D 29 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7509 (tmtt) outliers start: 39 outliers final: 17 residues processed: 135 average time/residue: 0.7109 time to fit residues: 104.4623 Evaluate side-chains 118 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 14 GLN Chi-restraints excluded: chain B residue 45 THR 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 548 SER 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 116 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 GLN ** B 256 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 = 0.3581 r_free = 0.3581 target = 0.082726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.063333 restraints weight = 35695.180| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.83 r_work: 0.3041 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14049 Z= 0.177 Angle : 0.580 7.726 19002 Z= 0.298 Chirality : 0.043 0.198 2058 Planarity : 0.005 0.113 2443 Dihedral : 8.559 125.508 1949 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.06 % Favored : 94.64 % Rotamer: Outliers : 2.60 % Allowed : 18.15 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.21), residues: 1661 helix: 1.58 (0.17), residues: 941 sheet: 0.06 (0.42), residues: 142 loop : -0.34 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 531 TYR 0.013 0.002 TYR B 783 PHE 0.012 0.001 PHE B 789 TRP 0.005 0.001 TRP A 561 HIS 0.010 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00418 (14044) covalent geometry : angle 0.57998 (19002) hydrogen bonds : bond 0.04587 ( 764) hydrogen bonds : angle 4.50679 ( 2205) metal coordination : bond 0.00343 ( 4) Misc. bond : bond 0.00052 ( 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 140 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 101 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9476 (mt) cc_final: 0.9209 (mp) REVERT: A 183 MET cc_start: 0.8655 (mmm) cc_final: 0.8396 (mmm) REVERT: A 616 ASN cc_start: 0.9298 (OUTLIER) cc_final: 0.9049 (t0) REVERT: A 733 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8760 (mmtm) REVERT: B 20 ASP cc_start: 0.8906 (OUTLIER) cc_final: 0.8409 (m-30) REVERT: B 148 MET cc_start: 0.8382 (ttp) cc_final: 0.7789 (tmm) REVERT: B 442 GLU cc_start: 0.9018 (tp30) cc_final: 0.8419 (tm-30) REVERT: D 29 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7591 (tmtt) outliers start: 39 outliers final: 16 residues processed: 132 average time/residue: 0.6804 time to fit residues: 98.0609 Evaluate side-chains 116 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER 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 85 SER 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 250 LEU 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 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 118 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 158 optimal weight: 0.4980 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 HIS ** B 256 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 = 0.3598 r_free = 0.3598 target = 0.083566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.064279 restraints weight = 35811.194| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.84 r_work: 0.3055 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14049 Z= 0.140 Angle : 0.566 8.576 19002 Z= 0.289 Chirality : 0.042 0.192 2058 Planarity : 0.005 0.112 2443 Dihedral : 8.286 115.907 1947 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.76 % Favored : 94.94 % Rotamer: Outliers : 2.07 % Allowed : 18.61 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.21), residues: 1661 helix: 1.70 (0.17), residues: 936 sheet: 0.12 (0.42), residues: 142 loop : -0.32 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 531 TYR 0.012 0.001 TYR B 783 PHE 0.013 0.001 PHE D 30 TRP 0.008 0.001 TRP A 380 HIS 0.008 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00329 (14044) covalent geometry : angle 0.56564 (19002) hydrogen bonds : bond 0.04265 ( 764) hydrogen bonds : angle 4.37924 ( 2205) metal coordination : bond 0.00239 ( 4) Misc. bond : bond 0.00035 ( 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 132 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9458 (mt) cc_final: 0.9197 (mp) REVERT: A 183 MET cc_start: 0.8658 (mmm) cc_final: 0.8343 (mmm) REVERT: A 256 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8649 (pm20) REVERT: A 616 ASN cc_start: 0.9278 (OUTLIER) cc_final: 0.9018 (t0) REVERT: A 733 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8926 (mmtm) REVERT: A 761 MET cc_start: 0.8625 (mmt) cc_final: 0.6969 (mmt) REVERT: B 20 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8363 (m-30) REVERT: B 148 MET cc_start: 0.8397 (ttp) cc_final: 0.7816 (tmm) REVERT: B 386 MET cc_start: 0.9321 (mtm) cc_final: 0.8800 (mpp) REVERT: D 29 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7552 (tmtt) outliers start: 31 outliers final: 16 residues processed: 126 average time/residue: 0.7021 time to fit residues: 96.3844 Evaluate side-chains 120 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 85 SER 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 238 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 544 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 59 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 152 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 149 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 134 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.083829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.064652 restraints weight = 35496.501| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.81 r_work: 0.3080 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1714 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 : 0.567 8.976 19002 Z= 0.291 Chirality : 0.042 0.185 2058 Planarity : 0.004 0.112 2443 Dihedral : 8.035 104.734 1946 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.82 % Favored : 94.94 % Rotamer: Outliers : 2.00 % Allowed : 19.01 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.21), residues: 1661 helix: 1.74 (0.17), residues: 936 sheet: 0.23 (0.42), residues: 139 loop : -0.34 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 531 TYR 0.016 0.001 TYR A 674 PHE 0.012 0.001 PHE B 215 TRP 0.005 0.001 TRP A 697 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00306 (14044) covalent geometry : angle 0.56683 (19002) hydrogen bonds : bond 0.04062 ( 764) hydrogen bonds : angle 4.31625 ( 2205) metal coordination : bond 0.00185 ( 4) Misc. bond : bond 0.00041 ( 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 134 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9454 (mt) cc_final: 0.9201 (mp) REVERT: A 183 MET cc_start: 0.8729 (mmm) cc_final: 0.8443 (mmm) REVERT: A 256 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8638 (pm20) REVERT: A 616 ASN cc_start: 0.9270 (OUTLIER) cc_final: 0.9013 (t0) REVERT: A 733 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8990 (mmtm) REVERT: A 761 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.6907 (mmt) REVERT: B 148 MET cc_start: 0.8412 (ttp) cc_final: 0.7794 (tmm) REVERT: B 282 LYS cc_start: 0.8072 (mppt) cc_final: 0.7803 (mmmt) REVERT: B 386 MET cc_start: 0.9355 (mtm) cc_final: 0.8959 (mpp) REVERT: B 442 GLU cc_start: 0.9000 (tp30) cc_final: 0.8273 (tm-30) REVERT: B 588 PHE cc_start: 0.8838 (t80) cc_final: 0.8458 (t80) REVERT: D 29 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7440 (tmtt) outliers start: 30 outliers final: 18 residues processed: 127 average time/residue: 0.6937 time to fit residues: 95.9538 Evaluate side-chains 123 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 A residue 761 MET 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 191 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 250 LEU 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 614 ASN Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain D residue 14 THR 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 162 optimal weight: 0.1980 chunk 75 optimal weight: 0.0020 chunk 139 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 127 optimal weight: 0.1980 chunk 32 optimal weight: 0.3980 chunk 73 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 322 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.084545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.065317 restraints weight = 35427.056| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.85 r_work: 0.3107 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14049 Z= 0.116 Angle : 0.565 10.296 19002 Z= 0.289 Chirality : 0.042 0.192 2058 Planarity : 0.004 0.111 2443 Dihedral : 7.863 99.159 1946 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.76 % Favored : 95.00 % Rotamer: Outliers : 2.07 % Allowed : 19.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.21), residues: 1661 helix: 1.79 (0.17), residues: 937 sheet: 0.26 (0.43), residues: 139 loop : -0.30 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 531 TYR 0.021 0.001 TYR A 674 PHE 0.011 0.001 PHE B 215 TRP 0.006 0.001 TRP A 380 HIS 0.021 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00265 (14044) covalent geometry : angle 0.56537 (19002) hydrogen bonds : bond 0.03861 ( 764) hydrogen bonds : angle 4.25627 ( 2205) metal coordination : bond 0.00103 ( 4) 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 138 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9255 (mt) cc_final: 0.8998 (mp) REVERT: A 183 MET cc_start: 0.8702 (mmm) cc_final: 0.8416 (mmm) REVERT: A 256 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8640 (pm20) REVERT: A 616 ASN cc_start: 0.9258 (OUTLIER) cc_final: 0.8983 (t0) REVERT: A 701 MET cc_start: 0.8797 (mmm) cc_final: 0.8393 (mmm) REVERT: A 733 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8989 (mmtm) REVERT: A 761 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.6787 (mmt) REVERT: B 148 MET cc_start: 0.8364 (ttp) cc_final: 0.7766 (tmm) REVERT: B 282 LYS cc_start: 0.8035 (mppt) cc_final: 0.7756 (mmmt) REVERT: B 386 MET cc_start: 0.9322 (mtm) cc_final: 0.8864 (mpp) REVERT: B 414 ASP cc_start: 0.8556 (m-30) cc_final: 0.8074 (m-30) REVERT: B 442 GLU cc_start: 0.8991 (tp30) cc_final: 0.8368 (tm-30) REVERT: B 588 PHE cc_start: 0.8764 (t80) cc_final: 0.8351 (t80) REVERT: D 29 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7375 (tmtt) REVERT: D 30 PHE cc_start: 0.8555 (m-10) cc_final: 0.7790 (m-10) outliers start: 31 outliers final: 16 residues processed: 133 average time/residue: 0.6474 time to fit residues: 94.1813 Evaluate side-chains 122 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 147 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 A residue 761 MET Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 45 THR 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 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 656 VAL Chi-restraints excluded: chain D residue 14 THR 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 150 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 155 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.084499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.065260 restraints weight = 35411.473| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.87 r_work: 0.3073 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1864 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= 0.136 Angle : 0.580 10.020 19002 Z= 0.295 Chirality : 0.042 0.190 2058 Planarity : 0.004 0.112 2443 Dihedral : 7.589 99.186 1944 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.12 % Favored : 94.64 % Rotamer: Outliers : 1.67 % Allowed : 19.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.21), residues: 1661 helix: 1.83 (0.17), residues: 935 sheet: 0.24 (0.43), residues: 139 loop : -0.33 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 531 TYR 0.014 0.001 TYR A 674 PHE 0.020 0.001 PHE D 30 TRP 0.005 0.001 TRP A 380 HIS 0.006 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00321 (14044) covalent geometry : angle 0.58006 (19002) hydrogen bonds : bond 0.03958 ( 764) hydrogen bonds : angle 4.27129 ( 2205) metal coordination : bond 0.00209 ( 4) Misc. bond : bond 0.00030 ( 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 127 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9453 (t80) cc_final: 0.9237 (t80) REVERT: A 26 LEU cc_start: 0.9250 (mt) cc_final: 0.8991 (mp) REVERT: A 183 MET cc_start: 0.8722 (mmm) cc_final: 0.8441 (mmm) REVERT: A 256 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8649 (pm20) REVERT: A 270 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8584 (mt) REVERT: A 616 ASN cc_start: 0.9176 (OUTLIER) cc_final: 0.8933 (t0) REVERT: A 701 MET cc_start: 0.8836 (mmm) cc_final: 0.8439 (mmm) REVERT: A 733 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8956 (mmtm) REVERT: A 761 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.6811 (mmt) REVERT: B 148 MET cc_start: 0.8429 (ttp) cc_final: 0.7787 (tmm) REVERT: B 282 LYS cc_start: 0.8164 (mppt) cc_final: 0.7927 (mmmt) REVERT: B 386 MET cc_start: 0.9381 (mtm) cc_final: 0.8811 (mpp) REVERT: B 414 ASP cc_start: 0.8556 (m-30) cc_final: 0.8105 (m-30) REVERT: B 442 GLU cc_start: 0.9008 (tp30) cc_final: 0.8247 (tm-30) REVERT: B 588 PHE cc_start: 0.8779 (t80) cc_final: 0.8349 (t80) REVERT: D 29 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7540 (tptp) REVERT: D 30 PHE cc_start: 0.8381 (m-10) cc_final: 0.8146 (m-80) outliers start: 25 outliers final: 18 residues processed: 124 average time/residue: 0.6889 time to fit residues: 93.0862 Evaluate side-chains 123 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 270 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 A residue 761 MET 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 292 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 656 VAL Chi-restraints excluded: chain D residue 14 THR 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 129 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 45 optimal weight: 0.0570 chunk 29 optimal weight: 0.7980 chunk 138 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 83 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.082634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.063740 restraints weight = 34647.015| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.80 r_work: 0.3018 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1950 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= 0.122 Angle : 0.573 11.169 19002 Z= 0.291 Chirality : 0.042 0.180 2058 Planarity : 0.004 0.112 2443 Dihedral : 7.366 100.418 1944 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.88 % Favored : 94.88 % Rotamer: Outliers : 1.67 % Allowed : 19.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.21), residues: 1661 helix: 1.84 (0.17), residues: 936 sheet: 0.23 (0.43), residues: 139 loop : -0.29 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 33 TYR 0.025 0.001 TYR A 674 PHE 0.014 0.001 PHE D 30 TRP 0.005 0.001 TRP A 697 HIS 0.006 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00284 (14044) covalent geometry : angle 0.57261 (19002) hydrogen bonds : bond 0.03798 ( 764) hydrogen bonds : angle 4.23122 ( 2205) metal coordination : bond 0.00152 ( 4) Misc. bond : bond 0.00026 ( 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 125 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9461 (t80) cc_final: 0.9250 (t80) REVERT: A 26 LEU cc_start: 0.9227 (mt) cc_final: 0.8969 (mp) REVERT: A 183 MET cc_start: 0.8749 (mmm) cc_final: 0.8460 (mmm) REVERT: A 256 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8611 (pm20) REVERT: A 270 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8369 (mt) REVERT: A 616 ASN cc_start: 0.9188 (OUTLIER) cc_final: 0.8956 (t0) REVERT: A 701 MET cc_start: 0.8810 (mmm) cc_final: 0.8395 (mmm) REVERT: A 733 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8998 (mmtm) REVERT: B 148 MET cc_start: 0.8411 (ttp) cc_final: 0.7777 (tmm) REVERT: B 282 LYS cc_start: 0.8246 (mppt) cc_final: 0.7923 (mmmt) REVERT: B 386 MET cc_start: 0.9363 (mtm) cc_final: 0.9107 (mtp) REVERT: B 414 ASP cc_start: 0.8551 (m-30) cc_final: 0.8133 (m-30) REVERT: B 442 GLU cc_start: 0.8982 (tp30) cc_final: 0.8232 (tm-30) REVERT: B 588 PHE cc_start: 0.8688 (t80) cc_final: 0.8275 (t80) REVERT: B 609 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8115 (mp10) REVERT: D 29 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7340 (tmtt) outliers start: 25 outliers final: 15 residues processed: 122 average time/residue: 0.7152 time to fit residues: 95.1737 Evaluate side-chains 119 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 270 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 159 HIS Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 292 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 139 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 53 optimal weight: 0.0270 chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 0.0370 overall best weight: 0.4916 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.082966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.064010 restraints weight = 34503.776| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.80 r_work: 0.3059 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2024 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= 0.121 Angle : 0.593 12.116 19002 Z= 0.296 Chirality : 0.042 0.182 2058 Planarity : 0.004 0.112 2443 Dihedral : 7.243 101.893 1944 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.06 % Favored : 94.70 % Rotamer: Outliers : 1.67 % Allowed : 19.95 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.21), residues: 1661 helix: 1.86 (0.17), residues: 936 sheet: 0.29 (0.43), residues: 139 loop : -0.28 (0.28), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 33 TYR 0.014 0.001 TYR A 674 PHE 0.012 0.001 PHE D 30 TRP 0.006 0.001 TRP A 697 HIS 0.010 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00284 (14044) covalent geometry : angle 0.59347 (19002) hydrogen bonds : bond 0.03755 ( 764) hydrogen bonds : angle 4.19747 ( 2205) metal coordination : bond 0.00152 ( 4) Misc. bond : bond 0.00025 ( 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 125 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9462 (t80) cc_final: 0.9254 (t80) REVERT: A 26 LEU cc_start: 0.9144 (mt) cc_final: 0.8905 (mp) REVERT: A 116 HIS cc_start: 0.7992 (OUTLIER) cc_final: 0.7631 (p-80) REVERT: A 183 MET cc_start: 0.8748 (mmm) cc_final: 0.8461 (mmm) REVERT: A 256 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8592 (pm20) REVERT: A 285 GLN cc_start: 0.8887 (tp40) cc_final: 0.8641 (pp30) REVERT: A 616 ASN cc_start: 0.9184 (OUTLIER) cc_final: 0.8964 (t0) REVERT: A 701 MET cc_start: 0.8796 (mmm) cc_final: 0.8432 (mmm) REVERT: A 733 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8951 (mmtm) REVERT: B 148 MET cc_start: 0.8408 (ttp) cc_final: 0.7855 (tmm) REVERT: B 282 LYS cc_start: 0.8297 (mppt) cc_final: 0.7954 (mmmt) REVERT: B 386 MET cc_start: 0.9365 (mtm) cc_final: 0.9127 (mtp) REVERT: B 414 ASP cc_start: 0.8533 (m-30) cc_final: 0.8150 (m-30) REVERT: B 442 GLU cc_start: 0.8998 (tp30) cc_final: 0.8248 (tm-30) REVERT: B 588 PHE cc_start: 0.8668 (t80) cc_final: 0.8265 (t80) REVERT: B 609 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8134 (mp10) REVERT: D 29 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7735 (tptp) outliers start: 25 outliers final: 16 residues processed: 121 average time/residue: 0.7110 time to fit residues: 93.7860 Evaluate side-chains 119 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 191 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 292 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 104 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 37 optimal weight: 0.0870 chunk 119 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 78 optimal weight: 0.4980 chunk 136 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3603 r_free = 0.3603 target = 0.083271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.064297 restraints weight = 34683.004| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.81 r_work: 0.3065 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2062 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 : 0.582 11.678 19002 Z= 0.293 Chirality : 0.041 0.180 2058 Planarity : 0.004 0.112 2443 Dihedral : 7.154 101.436 1944 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.94 % Favored : 94.82 % Rotamer: Outliers : 1.47 % Allowed : 20.15 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.21), residues: 1661 helix: 1.89 (0.17), residues: 935 sheet: 0.24 (0.43), residues: 139 loop : -0.30 (0.28), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 33 TYR 0.013 0.001 TYR A 275 PHE 0.012 0.001 PHE D 30 TRP 0.007 0.001 TRP A 697 HIS 0.009 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00282 (14044) covalent geometry : angle 0.58184 (19002) hydrogen bonds : bond 0.03706 ( 764) hydrogen bonds : angle 4.16608 ( 2205) metal coordination : bond 0.00140 ( 4) Misc. bond : bond 0.00026 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3641.03 seconds wall clock time: 63 minutes 12.11 seconds (3792.11 seconds total)