Starting phenix.real_space_refine on Fri Apr 12 03:20:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8so9_40650/04_2024/8so9_40650.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8so9_40650/04_2024/8so9_40650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8so9_40650/04_2024/8so9_40650.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8so9_40650/04_2024/8so9_40650.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8so9_40650/04_2024/8so9_40650.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8so9_40650/04_2024/8so9_40650.pdb" } resolution = 3.03 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= 0.984 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: 5 Type Number sf(0) Gaussians S 61 5.16 5 C 7864 2.51 5 N 2096 2.21 5 O 2229 1.98 5 H 12386 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 24636 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 16409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 16409 Classifications: {'peptide': 1008} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 962} Chain breaks: 6 Chain: "B" Number of atoms: 8227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 8227 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 489} Chain breaks: 8 Time building chain proxies: 11.07, per 1000 atoms: 0.45 Number of scatterers: 24636 At special positions: 0 Unit cell: (96.12, 114.48, 155.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 61 16.00 O 2229 8.00 N 2096 7.00 C 7864 6.00 H 12386 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.19 Conformation dependent library (CDL) restraints added in 2.6 seconds 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 13 sheets defined 50.5% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 66 through 82 removed outlier: 3.709A pdb=" N GLU A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 91 removed outlier: 3.751A pdb=" N LEU A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 115 through 118 Processing helix chain 'A' and resid 119 through 129 removed outlier: 3.643A pdb=" N ARG A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 159 Processing helix chain 'A' and resid 171 through 180 Processing helix chain 'A' and resid 180 through 190 removed outlier: 3.624A pdb=" N ARG A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 199 Processing helix chain 'A' and resid 208 through 213 removed outlier: 3.709A pdb=" N LYS A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 255 through 260 removed outlier: 3.973A pdb=" N MET A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 289 Processing helix chain 'A' and resid 290 through 299 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 345 through 349 removed outlier: 3.650A pdb=" N VAL A 349 " --> pdb=" O HIS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 548 through 560 removed outlier: 3.640A pdb=" N LYS A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 578 Processing helix chain 'A' and resid 581 through 587 Proline residue: A 586 - end of helix Processing helix chain 'A' and resid 588 through 593 Processing helix chain 'A' and resid 600 through 612 removed outlier: 3.596A pdb=" N LEU A 610 " --> pdb=" O LYS A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 620 Processing helix chain 'A' and resid 623 through 628 Processing helix chain 'A' and resid 637 through 649 removed outlier: 3.541A pdb=" N ILE A 643 " --> pdb=" O ASN A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 666 Processing helix chain 'A' and resid 667 through 670 Processing helix chain 'A' and resid 675 through 686 Processing helix chain 'A' and resid 690 through 706 removed outlier: 3.974A pdb=" N PHE A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP A 697 " --> pdb=" O HIS A 693 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN A 705 " --> pdb=" O SER A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 722 Processing helix chain 'A' and resid 726 through 752 removed outlier: 3.553A pdb=" N PHE A 732 " --> pdb=" O MET A 728 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A 738 " --> pdb=" O GLN A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 775 removed outlier: 3.666A pdb=" N GLN A 775 " --> pdb=" O LEU A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 858 removed outlier: 3.669A pdb=" N GLU A 858 " --> pdb=" O ILE A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 894 Processing helix chain 'A' and resid 905 through 915 Processing helix chain 'A' and resid 917 through 943 Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 988 through 996 Processing helix chain 'A' and resid 1003 through 1022 Processing helix chain 'A' and resid 1023 through 1037 removed outlier: 3.705A pdb=" N SER A1032 " --> pdb=" O ILE A1028 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET A1033 " --> pdb=" O ILE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1055 removed outlier: 3.564A pdb=" N ILE A1048 " --> pdb=" O SER A1044 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR A1050 " --> pdb=" O GLU A1046 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ILE A1051 " --> pdb=" O ASP A1047 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG A1052 " --> pdb=" O ILE A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1079 removed outlier: 3.620A pdb=" N LYS A1078 " --> pdb=" O VAL A1074 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY A1079 " --> pdb=" O CYS A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1092 removed outlier: 3.726A pdb=" N ASN A1085 " --> pdb=" O THR A1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 21 Processing helix chain 'B' and resid 38 through 48 removed outlier: 4.737A pdb=" N TRP B 42 " --> pdb=" O CYS B 38 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 44 " --> pdb=" O ASN B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 52 Proline residue: B 52 - end of helix No H-bonds generated for 'chain 'B' and resid 49 through 52' Processing helix chain 'B' and resid 53 through 73 removed outlier: 4.094A pdb=" N ILE B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 77 through 90 removed outlier: 4.083A pdb=" N LEU B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 90 " --> pdb=" O TYR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 111 removed outlier: 4.132A pdb=" N ARG B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 115 Processing helix chain 'B' and resid 118 through 136 removed outlier: 4.085A pdb=" N GLU B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.728A pdb=" N LEU B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 184 Processing helix chain 'B' and resid 188 through 206 removed outlier: 3.587A pdb=" N THR B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 210 through 220 removed outlier: 4.066A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 242 Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.704A pdb=" N ALA B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 removed outlier: 3.628A pdb=" N LEU B 270 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 310 removed outlier: 3.501A pdb=" N GLU B 303 " --> pdb=" O ASP B 299 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B 306 " --> pdb=" O GLN B 302 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 543 removed outlier: 4.075A pdb=" N GLU B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 613 Processing helix chain 'B' and resid 613 through 620 Processing helix chain 'B' and resid 621 through 623 No H-bonds generated for 'chain 'B' and resid 621 through 623' Processing helix chain 'B' and resid 650 through 663 Processing helix chain 'B' and resid 696 through 702 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 61 removed outlier: 3.850A pdb=" N GLY A 133 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N GLN A 134 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLN A 101 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 229 through 236 removed outlier: 10.842A pdb=" N ILE A 303 " --> pdb=" O CYS A 219 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE A 221 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N LEU A 305 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL A 223 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU A 307 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N HIS A 225 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 353 removed outlier: 6.392A pdb=" N VAL A 352 " --> pdb=" O ALA A 528 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 407 through 419 removed outlier: 7.519A pdb=" N VAL A 408 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ASP A 369 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP A 410 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY A 367 " --> pdb=" O TRP A 410 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE A 361 " --> pdb=" O PHE A 416 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N SER A 517 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE A 368 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER A 515 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 398 Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 398 removed outlier: 6.595A pdb=" N LEU A 429 " --> pdb=" O ASN A 465 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN A 465 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU A 431 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR A 463 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE A 433 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 463 " --> pdb=" O TRP A 485 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 783 through 784 removed outlier: 5.349A pdb=" N LYS A 816 " --> pdb=" O GLY A 794 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU A 796 " --> pdb=" O GLU A 814 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N GLU A 814 " --> pdb=" O LEU A 796 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 802 " --> pdb=" O TRP A 812 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 783 through 784 removed outlier: 5.349A pdb=" N LYS A 816 " --> pdb=" O GLY A 794 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU A 796 " --> pdb=" O GLU A 814 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N GLU A 814 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 885 through 887 Processing sheet with id=AB1, first strand: chain 'B' and resid 288 through 292 removed outlier: 3.687A pdb=" N TYR B 291 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B 166 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B 161 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL B 518 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL B 163 " --> pdb=" O VAL B 518 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N PHE B 520 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU B 165 " --> pdb=" O PHE B 520 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N SER B 513 " --> pdb=" O LYS B 551 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N GLN B 553 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU B 515 " --> pdb=" O GLN B 553 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N PHE B 555 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B 517 " --> pdb=" O PHE B 555 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL B 557 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL B 519 " --> pdb=" O VAL B 557 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 665 through 666 Processing sheet with id=AB3, first strand: chain 'B' and resid 683 through 688 removed outlier: 3.742A pdb=" N LYS B 732 " --> pdb=" O ARG B 740 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 691 through 695 removed outlier: 3.605A pdb=" N ASN B 752 " --> pdb=" O ASN B 773 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1650 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: 10.16 Time building geometry restraints manager: 18.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 12350 1.03 - 1.22: 36 1.22 - 1.42: 5142 1.42 - 1.61: 7286 1.61 - 1.81: 86 Bond restraints: 24900 Sorted by residual: bond pdb=" N THR B 7 " pdb=" CA THR B 7 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N LEU A 37 " pdb=" CA LEU A 37 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 bond pdb=" N THR B 7 " pdb=" H THR B 7 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" N LEU A 37 " pdb=" H LEU A 37 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.23e+00 bond pdb=" NE2 GLN A 766 " pdb="HE22 GLN A 766 " ideal model delta sigma weight residual 0.860 0.831 0.029 2.00e-02 2.50e+03 2.10e+00 ... (remaining 24895 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.83: 448 106.83 - 113.64: 30029 113.64 - 120.45: 8020 120.45 - 127.26: 6450 127.26 - 134.06: 164 Bond angle restraints: 45111 Sorted by residual: angle pdb=" N ILE A 387 " pdb=" CA ILE A 387 " pdb=" C ILE A 387 " ideal model delta sigma weight residual 109.80 104.56 5.24 1.33e+00 5.65e-01 1.55e+01 angle pdb=" N ALA B 532 " pdb=" CA ALA B 532 " pdb=" C ALA B 532 " ideal model delta sigma weight residual 111.36 107.15 4.21 1.09e+00 8.42e-01 1.49e+01 angle pdb=" N TYR B 533 " pdb=" CA TYR B 533 " pdb=" C TYR B 533 " ideal model delta sigma weight residual 111.33 107.29 4.04 1.21e+00 6.83e-01 1.12e+01 angle pdb=" N LEU B 692 " pdb=" CA LEU B 692 " pdb=" C LEU B 692 " ideal model delta sigma weight residual 107.20 112.34 -5.14 1.70e+00 3.46e-01 9.14e+00 angle pdb=" N ILE A1029 " pdb=" CA ILE A1029 " pdb=" C ILE A1029 " ideal model delta sigma weight residual 113.39 109.10 4.29 1.47e+00 4.63e-01 8.52e+00 ... (remaining 45106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 10941 17.95 - 35.90: 499 35.90 - 53.86: 164 53.86 - 71.81: 40 71.81 - 89.76: 8 Dihedral angle restraints: 11652 sinusoidal: 6379 harmonic: 5273 Sorted by residual: dihedral pdb=" CA PHE B 520 " pdb=" C PHE B 520 " pdb=" N GLY B 521 " pdb=" CA GLY B 521 " ideal model delta harmonic sigma weight residual 180.00 -152.29 -27.71 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" N LEU B 77 " pdb=" CA LEU B 77 " pdb=" CB LEU B 77 " pdb=" CG LEU B 77 " ideal model delta sinusoidal sigma weight residual -180.00 -120.18 -59.82 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ASN B 535 " pdb=" CA ASN B 535 " pdb=" CB ASN B 535 " pdb=" CG ASN B 535 " ideal model delta sinusoidal sigma weight residual -60.00 -119.82 59.82 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 11649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1395 0.035 - 0.070: 387 0.070 - 0.105: 109 0.105 - 0.140: 44 0.140 - 0.175: 4 Chirality restraints: 1939 Sorted by residual: chirality pdb=" CA ILE B 122 " pdb=" N ILE B 122 " pdb=" C ILE B 122 " pdb=" CB ILE B 122 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" CA ILE B 729 " pdb=" N ILE B 729 " pdb=" C ILE B 729 " pdb=" CB ILE B 729 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA VAL B 117 " pdb=" N VAL B 117 " pdb=" C VAL B 117 " pdb=" CB VAL B 117 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.52e-01 ... (remaining 1936 not shown) Planarity restraints: 3579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 766 " 0.055 2.00e-02 2.50e+03 7.06e-02 7.47e+01 pdb=" CD GLN A 766 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLN A 766 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 GLN A 766 " -0.113 2.00e-02 2.50e+03 pdb="HE21 GLN A 766 " -0.010 2.00e-02 2.50e+03 pdb="HE22 GLN A 766 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 130 " -0.021 2.00e-02 2.50e+03 4.24e-02 1.79e+01 pdb=" C ILE B 130 " 0.073 2.00e-02 2.50e+03 pdb=" O ILE B 130 " -0.027 2.00e-02 2.50e+03 pdb=" N ASP B 131 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 773 " -0.026 2.00e-02 2.50e+03 3.34e-02 1.67e+01 pdb=" CG ASN A 773 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 773 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 773 " 0.055 2.00e-02 2.50e+03 pdb="HD21 ASN A 773 " 0.003 2.00e-02 2.50e+03 pdb="HD22 ASN A 773 " -0.052 2.00e-02 2.50e+03 ... (remaining 3576 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 615 2.14 - 2.76: 47509 2.76 - 3.37: 65327 3.37 - 3.99: 84528 3.99 - 4.60: 135938 Nonbonded interactions: 333917 Sorted by model distance: nonbonded pdb=" OD1 ASN A 66 " pdb=" H GLN A 69 " model vdw 1.531 1.850 nonbonded pdb="HE22 GLN A 114 " pdb=" O CYS A 329 " model vdw 1.550 1.850 nonbonded pdb=" H THR B 222 " pdb=" OE2 GLU B 225 " model vdw 1.585 1.850 nonbonded pdb=" H SER B 691 " pdb=" OD1 ASP B 817 " model vdw 1.604 1.850 nonbonded pdb="HH22 ARG A 947 " pdb=" O ASP A 964 " model vdw 1.608 1.850 ... (remaining 333912 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.340 Extract box with map and model: 10.120 Check model and map are aligned: 0.370 Set scattering table: 0.240 Process input model: 77.330 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5886 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12514 Z= 0.251 Angle : 0.595 6.486 16955 Z= 0.335 Chirality : 0.039 0.175 1939 Planarity : 0.005 0.052 2141 Dihedral : 12.344 89.759 4648 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.63 % Favored : 94.16 % Rotamer: Outliers : 2.79 % Allowed : 6.98 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -1.77 (0.21), residues: 1491 helix: -0.54 (0.21), residues: 651 sheet: -1.34 (0.31), residues: 230 loop : -1.69 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 292 HIS 0.004 0.001 HIS A 693 PHE 0.021 0.001 PHE A 175 TYR 0.026 0.002 TYR B 533 ARG 0.003 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 249 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.7874 (m90) cc_final: 0.7548 (m170) REVERT: A 134 GLN cc_start: 0.7224 (mt0) cc_final: 0.6708 (mt0) REVERT: A 209 GLU cc_start: 0.8061 (tt0) cc_final: 0.7506 (tp30) REVERT: A 216 THR cc_start: 0.6959 (m) cc_final: 0.6739 (t) REVERT: A 317 GLU cc_start: 0.7829 (pt0) cc_final: 0.7611 (pt0) REVERT: A 320 LYS cc_start: 0.8219 (tttp) cc_final: 0.7991 (ttpt) REVERT: A 479 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6815 (mt-10) REVERT: A 497 PHE cc_start: 0.6306 (t80) cc_final: 0.5889 (t80) REVERT: A 511 GLU cc_start: 0.7525 (mt-10) cc_final: 0.6991 (tp30) REVERT: A 531 LYS cc_start: 0.6769 (tttt) cc_final: 0.6321 (ttpp) REVERT: A 646 GLN cc_start: 0.6253 (tt0) cc_final: 0.5805 (mt0) REVERT: A 781 GLN cc_start: 0.7942 (mt0) cc_final: 0.7152 (mm110) REVERT: A 804 MET cc_start: 0.7460 (mtp) cc_final: 0.7063 (mtp) REVERT: A 809 LYS cc_start: 0.7272 (mttt) cc_final: 0.6425 (mmtt) REVERT: A 883 LYS cc_start: 0.7656 (mttt) cc_final: 0.7003 (mmtm) REVERT: A 953 MET cc_start: 0.6797 (mtp) cc_final: 0.6592 (mtp) REVERT: A 982 ARG cc_start: 0.6948 (mtp180) cc_final: 0.6175 (mtt-85) REVERT: A 995 MET cc_start: 0.5107 (mtt) cc_final: 0.4897 (mtt) REVERT: A 1053 ASP cc_start: 0.6342 (m-30) cc_final: 0.6084 (m-30) REVERT: A 1066 LYS cc_start: 0.6151 (tttp) cc_final: 0.5719 (mmmt) REVERT: B 77 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7888 (tt) REVERT: B 83 LEU cc_start: 0.7477 (mt) cc_final: 0.7233 (tt) REVERT: B 216 ARG cc_start: 0.8021 (mtt180) cc_final: 0.7755 (ttm110) REVERT: B 217 ARG cc_start: 0.8021 (mtt180) cc_final: 0.7550 (mmm-85) REVERT: B 227 GLU cc_start: 0.7469 (tt0) cc_final: 0.7080 (tm-30) REVERT: B 271 ASP cc_start: 0.7172 (t0) cc_final: 0.6859 (t0) REVERT: B 279 ARG cc_start: 0.7127 (ttt180) cc_final: 0.6883 (ttm170) REVERT: B 537 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6678 (mmm160) REVERT: B 548 ARG cc_start: 0.8124 (ttt180) cc_final: 0.7768 (tpp-160) REVERT: B 728 ILE cc_start: 0.7038 (mt) cc_final: 0.6752 (mt) outliers start: 38 outliers final: 23 residues processed: 283 average time/residue: 0.7277 time to fit residues: 275.3929 Evaluate side-chains 198 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 173 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 724 CYS Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 537 ARG Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 744 MET Chi-restraints excluded: chain B residue 767 THR Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 873 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 HIS A 391 GLN A 705 GLN B 258 GLN B 309 GLN B 670 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5895 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12514 Z= 0.193 Angle : 0.521 4.927 16955 Z= 0.270 Chirality : 0.039 0.149 1939 Planarity : 0.004 0.048 2141 Dihedral : 6.224 59.719 1674 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.28 % Allowed : 9.70 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 1491 helix: 0.44 (0.20), residues: 680 sheet: -0.85 (0.32), residues: 237 loop : -1.45 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 812 HIS 0.004 0.001 HIS A 834 PHE 0.011 0.001 PHE A1031 TYR 0.010 0.001 TYR A 935 ARG 0.003 0.000 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 173 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.7913 (m90) cc_final: 0.7545 (m170) REVERT: A 112 LYS cc_start: 0.7511 (pttp) cc_final: 0.7294 (pttp) REVERT: A 209 GLU cc_start: 0.7929 (tt0) cc_final: 0.7471 (tp30) REVERT: A 320 LYS cc_start: 0.8193 (tttp) cc_final: 0.7960 (ttpt) REVERT: A 391 GLN cc_start: 0.7778 (mt0) cc_final: 0.7561 (mt0) REVERT: A 479 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6998 (mt-10) REVERT: A 497 PHE cc_start: 0.6145 (t80) cc_final: 0.5853 (t80) REVERT: A 511 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6991 (tp30) REVERT: A 531 LYS cc_start: 0.6916 (tttt) cc_final: 0.6451 (ttpp) REVERT: A 646 GLN cc_start: 0.6284 (tt0) cc_final: 0.5840 (mt0) REVERT: A 777 LEU cc_start: 0.5782 (mt) cc_final: 0.5570 (mt) REVERT: A 781 GLN cc_start: 0.7853 (mt0) cc_final: 0.7097 (mm110) REVERT: A 804 MET cc_start: 0.7364 (mtp) cc_final: 0.6815 (mtp) REVERT: A 809 LYS cc_start: 0.7182 (mttt) cc_final: 0.6225 (mmtt) REVERT: A 883 LYS cc_start: 0.7673 (mttt) cc_final: 0.6971 (mmtm) REVERT: A 982 ARG cc_start: 0.6921 (mtp180) cc_final: 0.6131 (mtt-85) REVERT: A 995 MET cc_start: 0.5115 (mtt) cc_final: 0.4873 (mtt) REVERT: A 1053 ASP cc_start: 0.6674 (m-30) cc_final: 0.6464 (m-30) REVERT: A 1066 LYS cc_start: 0.6160 (tttp) cc_final: 0.5728 (mmmt) REVERT: B 216 ARG cc_start: 0.8023 (mtt180) cc_final: 0.7767 (ttm110) REVERT: B 217 ARG cc_start: 0.7971 (mtt180) cc_final: 0.7556 (mmm-85) REVERT: B 227 GLU cc_start: 0.7482 (tt0) cc_final: 0.7098 (tm-30) REVERT: B 271 ASP cc_start: 0.7157 (t0) cc_final: 0.6847 (t0) REVERT: B 279 ARG cc_start: 0.7110 (ttt180) cc_final: 0.6860 (ttm170) REVERT: B 548 ARG cc_start: 0.8106 (ttt180) cc_final: 0.7723 (tpp-160) REVERT: B 674 THR cc_start: 0.6932 (OUTLIER) cc_final: 0.6664 (t) REVERT: B 830 CYS cc_start: 0.8019 (t) cc_final: 0.7665 (t) outliers start: 31 outliers final: 21 residues processed: 199 average time/residue: 0.6659 time to fit residues: 184.3323 Evaluate side-chains 183 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 724 CYS Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain B residue 22 HIS Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 744 MET Chi-restraints excluded: chain B residue 767 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 873 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 37 optimal weight: 0.0670 chunk 137 optimal weight: 0.2980 chunk 148 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 46 optimal weight: 0.0970 chunk 110 optimal weight: 1.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5895 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12514 Z= 0.187 Angle : 0.476 4.540 16955 Z= 0.244 Chirality : 0.039 0.147 1939 Planarity : 0.004 0.046 2141 Dihedral : 5.366 58.385 1660 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.84 % Allowed : 10.65 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -0.18 (0.22), residues: 1491 helix: 1.05 (0.21), residues: 681 sheet: -0.72 (0.33), residues: 237 loop : -1.22 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 812 HIS 0.004 0.001 HIS B 690 PHE 0.011 0.001 PHE A 961 TYR 0.016 0.001 TYR B 533 ARG 0.004 0.000 ARG B 543 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.7941 (m90) cc_final: 0.7626 (m170) REVERT: A 320 LYS cc_start: 0.8200 (tttp) cc_final: 0.7973 (ttpt) REVERT: A 329 CYS cc_start: 0.6716 (m) cc_final: 0.6313 (m) REVERT: A 479 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7074 (mt-10) REVERT: A 511 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6995 (tp30) REVERT: A 531 LYS cc_start: 0.6936 (tttt) cc_final: 0.6437 (ttpp) REVERT: A 549 ASN cc_start: 0.7211 (m-40) cc_final: 0.6768 (t0) REVERT: A 646 GLN cc_start: 0.6317 (tt0) cc_final: 0.5854 (mt0) REVERT: A 777 LEU cc_start: 0.5751 (mt) cc_final: 0.5536 (mt) REVERT: A 781 GLN cc_start: 0.7711 (mt0) cc_final: 0.6885 (mm110) REVERT: A 804 MET cc_start: 0.7100 (mtp) cc_final: 0.6668 (mtp) REVERT: A 809 LYS cc_start: 0.7176 (mttt) cc_final: 0.6284 (mmtt) REVERT: A 883 LYS cc_start: 0.7643 (mttt) cc_final: 0.6949 (mmtt) REVERT: A 982 ARG cc_start: 0.6913 (mtp180) cc_final: 0.6081 (mtt-85) REVERT: A 995 MET cc_start: 0.4973 (mtt) cc_final: 0.4704 (mtt) REVERT: A 1053 ASP cc_start: 0.6671 (m-30) cc_final: 0.6470 (m-30) REVERT: A 1057 VAL cc_start: 0.8657 (t) cc_final: 0.8397 (m) REVERT: A 1066 LYS cc_start: 0.6295 (tttp) cc_final: 0.5875 (mmmt) REVERT: B 216 ARG cc_start: 0.8043 (mtt180) cc_final: 0.7808 (ttm110) REVERT: B 217 ARG cc_start: 0.7965 (mtt180) cc_final: 0.7564 (mmm-85) REVERT: B 227 GLU cc_start: 0.7418 (tt0) cc_final: 0.6971 (tm-30) REVERT: B 269 VAL cc_start: 0.7639 (t) cc_final: 0.7213 (t) REVERT: B 270 LEU cc_start: 0.6788 (mp) cc_final: 0.6538 (mp) REVERT: B 271 ASP cc_start: 0.7087 (t0) cc_final: 0.6842 (t0) REVERT: B 279 ARG cc_start: 0.7139 (ttt180) cc_final: 0.6873 (ttm170) REVERT: B 548 ARG cc_start: 0.8050 (ttt180) cc_final: 0.7590 (tpp-160) REVERT: B 674 THR cc_start: 0.6968 (OUTLIER) cc_final: 0.6693 (t) REVERT: B 678 PHE cc_start: 0.4988 (m-80) cc_final: 0.4720 (m-80) REVERT: B 830 CYS cc_start: 0.8025 (t) cc_final: 0.7662 (t) outliers start: 25 outliers final: 21 residues processed: 185 average time/residue: 0.6878 time to fit residues: 176.6228 Evaluate side-chains 175 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 153 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 HIS Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 967 HIS Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 767 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 873 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 15 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12514 Z= 0.262 Angle : 0.490 4.543 16955 Z= 0.253 Chirality : 0.040 0.153 1939 Planarity : 0.004 0.047 2141 Dihedral : 5.170 55.896 1653 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.98 % Allowed : 10.80 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -0.08 (0.22), residues: 1491 helix: 1.13 (0.20), residues: 683 sheet: -0.68 (0.32), residues: 244 loop : -1.19 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 812 HIS 0.015 0.001 HIS A 141 PHE 0.012 0.001 PHE A 961 TYR 0.011 0.001 TYR B 533 ARG 0.003 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.7847 (m90) cc_final: 0.7537 (m170) REVERT: A 141 HIS cc_start: 0.7642 (OUTLIER) cc_final: 0.6283 (p-80) REVERT: A 320 LYS cc_start: 0.8176 (tttp) cc_final: 0.7945 (ttpt) REVERT: A 329 CYS cc_start: 0.6759 (m) cc_final: 0.6318 (m) REVERT: A 479 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7229 (mt-10) REVERT: A 511 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7011 (tp30) REVERT: A 524 CYS cc_start: 0.8116 (m) cc_final: 0.7804 (m) REVERT: A 531 LYS cc_start: 0.6961 (tttt) cc_final: 0.6547 (ttpp) REVERT: A 549 ASN cc_start: 0.7220 (m-40) cc_final: 0.6761 (t0) REVERT: A 646 GLN cc_start: 0.6372 (tt0) cc_final: 0.5830 (mt0) REVERT: A 777 LEU cc_start: 0.5677 (mt) cc_final: 0.5469 (mt) REVERT: A 781 GLN cc_start: 0.7719 (mt0) cc_final: 0.6862 (mm110) REVERT: A 804 MET cc_start: 0.7020 (mtp) cc_final: 0.6589 (mtp) REVERT: A 809 LYS cc_start: 0.7199 (mttt) cc_final: 0.6312 (mmtt) REVERT: A 883 LYS cc_start: 0.7653 (mttt) cc_final: 0.6947 (mmtt) REVERT: A 982 ARG cc_start: 0.6899 (mtp180) cc_final: 0.6055 (mtt-85) REVERT: A 995 MET cc_start: 0.5000 (mtt) cc_final: 0.4756 (mtt) REVERT: A 1057 VAL cc_start: 0.8591 (t) cc_final: 0.8333 (m) REVERT: A 1066 LYS cc_start: 0.6183 (tttp) cc_final: 0.5761 (mmmt) REVERT: B 216 ARG cc_start: 0.8054 (mtt180) cc_final: 0.7831 (ttm110) REVERT: B 227 GLU cc_start: 0.7443 (tt0) cc_final: 0.6990 (tm-30) REVERT: B 270 LEU cc_start: 0.6825 (mp) cc_final: 0.6622 (mp) REVERT: B 271 ASP cc_start: 0.7076 (t0) cc_final: 0.6826 (t0) REVERT: B 279 ARG cc_start: 0.7177 (ttt180) cc_final: 0.6903 (ttm170) REVERT: B 548 ARG cc_start: 0.8042 (ttt180) cc_final: 0.7572 (tpp-160) REVERT: B 674 THR cc_start: 0.6935 (OUTLIER) cc_final: 0.6670 (t) REVERT: B 678 PHE cc_start: 0.5148 (m-80) cc_final: 0.4882 (m-80) REVERT: B 830 CYS cc_start: 0.8001 (t) cc_final: 0.7640 (t) outliers start: 27 outliers final: 25 residues processed: 183 average time/residue: 0.6516 time to fit residues: 165.3564 Evaluate side-chains 180 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 HIS Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 967 HIS Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 22 HIS Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 767 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 873 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS B 743 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5925 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 12514 Z= 0.411 Angle : 0.544 4.975 16955 Z= 0.285 Chirality : 0.042 0.155 1939 Planarity : 0.004 0.050 2141 Dihedral : 5.228 52.844 1652 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.50 % Allowed : 11.09 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -0.25 (0.21), residues: 1491 helix: 0.98 (0.20), residues: 683 sheet: -0.69 (0.33), residues: 242 loop : -1.29 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 812 HIS 0.014 0.001 HIS A 141 PHE 0.016 0.002 PHE A 961 TYR 0.014 0.002 TYR B 141 ARG 0.005 0.001 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 155 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.7760 (m90) cc_final: 0.7479 (m170) REVERT: A 329 CYS cc_start: 0.6826 (m) cc_final: 0.6359 (m) REVERT: A 479 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7177 (mt-10) REVERT: A 511 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7034 (tp30) REVERT: A 524 CYS cc_start: 0.8037 (m) cc_final: 0.7700 (m) REVERT: A 531 LYS cc_start: 0.6933 (tttt) cc_final: 0.6478 (ttpp) REVERT: A 549 ASN cc_start: 0.7390 (m-40) cc_final: 0.7098 (t0) REVERT: A 646 GLN cc_start: 0.6499 (tt0) cc_final: 0.5965 (mt0) REVERT: A 777 LEU cc_start: 0.5701 (mt) cc_final: 0.5494 (mt) REVERT: A 781 GLN cc_start: 0.7699 (mt0) cc_final: 0.6861 (mm110) REVERT: A 804 MET cc_start: 0.6950 (mtp) cc_final: 0.6512 (mtp) REVERT: A 809 LYS cc_start: 0.7258 (mttt) cc_final: 0.6410 (mmtt) REVERT: A 883 LYS cc_start: 0.7602 (mttt) cc_final: 0.6951 (mmtm) REVERT: A 982 ARG cc_start: 0.6862 (mtp180) cc_final: 0.6005 (mtt-85) REVERT: A 995 MET cc_start: 0.5032 (mtt) cc_final: 0.4806 (mtt) REVERT: A 1066 LYS cc_start: 0.6282 (tttp) cc_final: 0.5809 (mmmt) REVERT: B 216 ARG cc_start: 0.8044 (mtt180) cc_final: 0.7809 (ttm110) REVERT: B 217 ARG cc_start: 0.7900 (mtt180) cc_final: 0.7418 (mmm-85) REVERT: B 227 GLU cc_start: 0.7442 (tt0) cc_final: 0.6977 (tm-30) REVERT: B 271 ASP cc_start: 0.7127 (t0) cc_final: 0.6852 (t0) REVERT: B 279 ARG cc_start: 0.7172 (ttt180) cc_final: 0.6850 (ttm170) REVERT: B 548 ARG cc_start: 0.8052 (ttt180) cc_final: 0.7568 (tpp-160) REVERT: B 678 PHE cc_start: 0.5135 (m-80) cc_final: 0.4868 (m-80) outliers start: 34 outliers final: 28 residues processed: 181 average time/residue: 0.6266 time to fit residues: 159.6791 Evaluate side-chains 179 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 151 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 141 HIS Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 724 CYS Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 967 HIS Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 22 HIS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 767 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 873 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 146 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5905 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12514 Z= 0.198 Angle : 0.477 4.469 16955 Z= 0.246 Chirality : 0.039 0.149 1939 Planarity : 0.003 0.041 2141 Dihedral : 4.774 51.566 1647 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.84 % Allowed : 11.46 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.09 (0.22), residues: 1491 helix: 1.28 (0.20), residues: 683 sheet: -0.66 (0.32), residues: 242 loop : -1.06 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 812 HIS 0.030 0.001 HIS A 141 PHE 0.010 0.001 PHE A1068 TYR 0.010 0.001 TYR A 935 ARG 0.002 0.000 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 2.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.7813 (m90) cc_final: 0.7529 (m170) REVERT: A 329 CYS cc_start: 0.6818 (m) cc_final: 0.6425 (m) REVERT: A 479 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7206 (mt-10) REVERT: A 511 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7031 (tp30) REVERT: A 524 CYS cc_start: 0.8009 (m) cc_final: 0.7686 (m) REVERT: A 531 LYS cc_start: 0.6912 (tttt) cc_final: 0.6461 (ttpp) REVERT: A 549 ASN cc_start: 0.7223 (m-40) cc_final: 0.6925 (t0) REVERT: A 646 GLN cc_start: 0.6349 (tt0) cc_final: 0.5805 (mt0) REVERT: A 781 GLN cc_start: 0.7649 (mt0) cc_final: 0.6773 (mm110) REVERT: A 804 MET cc_start: 0.6930 (mtp) cc_final: 0.6543 (mtp) REVERT: A 809 LYS cc_start: 0.7182 (mttt) cc_final: 0.6284 (mmtt) REVERT: A 883 LYS cc_start: 0.7695 (mttt) cc_final: 0.7121 (mmtm) REVERT: A 982 ARG cc_start: 0.6871 (mtp180) cc_final: 0.6037 (mtt-85) REVERT: A 995 MET cc_start: 0.4970 (mtt) cc_final: 0.4726 (mtt) REVERT: A 1066 LYS cc_start: 0.6231 (tttp) cc_final: 0.5771 (mmmt) REVERT: B 216 ARG cc_start: 0.8038 (mtt180) cc_final: 0.7811 (ttm110) REVERT: B 217 ARG cc_start: 0.7891 (mtt180) cc_final: 0.7531 (mmm-85) REVERT: B 227 GLU cc_start: 0.7425 (tt0) cc_final: 0.6968 (tm-30) REVERT: B 271 ASP cc_start: 0.7103 (t0) cc_final: 0.6827 (t0) REVERT: B 279 ARG cc_start: 0.7140 (ttt180) cc_final: 0.6820 (ttm170) REVERT: B 548 ARG cc_start: 0.8036 (ttt180) cc_final: 0.7594 (tpp-160) REVERT: B 678 PHE cc_start: 0.5081 (m-80) cc_final: 0.4814 (m-80) REVERT: B 696 HIS cc_start: 0.3404 (OUTLIER) cc_final: 0.2892 (t-90) outliers start: 25 outliers final: 23 residues processed: 176 average time/residue: 0.6729 time to fit residues: 164.0960 Evaluate side-chains 176 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 967 HIS Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 22 HIS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 696 HIS Chi-restraints excluded: chain B residue 767 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 867 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 145 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5900 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12514 Z= 0.187 Angle : 0.462 4.471 16955 Z= 0.237 Chirality : 0.039 0.148 1939 Planarity : 0.003 0.041 2141 Dihedral : 4.604 51.197 1646 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.06 % Allowed : 11.68 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.22), residues: 1491 helix: 1.47 (0.20), residues: 683 sheet: -0.54 (0.32), residues: 233 loop : -0.97 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 812 HIS 0.008 0.001 HIS A 141 PHE 0.010 0.001 PHE A1068 TYR 0.010 0.001 TYR A 935 ARG 0.003 0.000 ARG B 780 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 151 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.7806 (m90) cc_final: 0.7533 (m170) REVERT: A 329 CYS cc_start: 0.6821 (m) cc_final: 0.6424 (m) REVERT: A 479 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7214 (mt-10) REVERT: A 511 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7033 (tp30) REVERT: A 524 CYS cc_start: 0.8055 (m) cc_final: 0.7735 (m) REVERT: A 531 LYS cc_start: 0.6909 (tttt) cc_final: 0.6391 (ttpp) REVERT: A 549 ASN cc_start: 0.7212 (m-40) cc_final: 0.6879 (t0) REVERT: A 646 GLN cc_start: 0.6305 (tt0) cc_final: 0.5753 (mt0) REVERT: A 781 GLN cc_start: 0.7544 (mt0) cc_final: 0.6666 (mm110) REVERT: A 804 MET cc_start: 0.6909 (mtp) cc_final: 0.6525 (mtp) REVERT: A 809 LYS cc_start: 0.7217 (mttt) cc_final: 0.6325 (mmtt) REVERT: A 883 LYS cc_start: 0.7717 (mttt) cc_final: 0.7148 (mmtm) REVERT: A 982 ARG cc_start: 0.6869 (mtp180) cc_final: 0.6039 (mtt-85) REVERT: A 995 MET cc_start: 0.4954 (mtt) cc_final: 0.4702 (mtt) REVERT: A 1066 LYS cc_start: 0.6356 (tttp) cc_final: 0.5911 (mmmt) REVERT: B 216 ARG cc_start: 0.8040 (mtt180) cc_final: 0.7824 (ttm110) REVERT: B 217 ARG cc_start: 0.7885 (mtt180) cc_final: 0.7536 (mmm-85) REVERT: B 227 GLU cc_start: 0.7420 (tt0) cc_final: 0.6963 (tm-30) REVERT: B 271 ASP cc_start: 0.7102 (t0) cc_final: 0.6835 (t0) REVERT: B 279 ARG cc_start: 0.7152 (ttt180) cc_final: 0.6844 (ttm170) REVERT: B 548 ARG cc_start: 0.8037 (ttt180) cc_final: 0.7603 (tpp-160) REVERT: B 696 HIS cc_start: 0.3413 (OUTLIER) cc_final: 0.2883 (t-90) outliers start: 28 outliers final: 26 residues processed: 174 average time/residue: 0.6428 time to fit residues: 155.5860 Evaluate side-chains 178 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 967 HIS Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 22 HIS Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 696 HIS Chi-restraints excluded: chain B residue 767 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 867 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5891 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12514 Z= 0.164 Angle : 0.455 4.683 16955 Z= 0.232 Chirality : 0.039 0.149 1939 Planarity : 0.003 0.036 2141 Dihedral : 4.442 50.493 1646 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.28 % Allowed : 11.76 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.59 (0.22), residues: 1491 helix: 1.73 (0.20), residues: 682 sheet: -0.41 (0.33), residues: 232 loop : -0.86 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 812 HIS 0.003 0.001 HIS A 708 PHE 0.010 0.001 PHE A1068 TYR 0.010 0.001 TYR A 935 ARG 0.002 0.000 ARG B 780 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.7804 (m90) cc_final: 0.7532 (m170) REVERT: A 329 CYS cc_start: 0.6815 (m) cc_final: 0.6422 (m) REVERT: A 511 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7034 (tp30) REVERT: A 524 CYS cc_start: 0.8044 (m) cc_final: 0.7719 (m) REVERT: A 531 LYS cc_start: 0.6886 (tttt) cc_final: 0.6387 (ttpp) REVERT: A 549 ASN cc_start: 0.6864 (m-40) cc_final: 0.6485 (t0) REVERT: A 646 GLN cc_start: 0.6196 (tt0) cc_final: 0.5697 (mt0) REVERT: A 781 GLN cc_start: 0.7540 (mt0) cc_final: 0.6661 (mm110) REVERT: A 804 MET cc_start: 0.6881 (mtp) cc_final: 0.6458 (mtp) REVERT: A 809 LYS cc_start: 0.7211 (mttt) cc_final: 0.6320 (mmtt) REVERT: A 883 LYS cc_start: 0.7717 (mttt) cc_final: 0.7149 (mmtm) REVERT: A 982 ARG cc_start: 0.6816 (mtp180) cc_final: 0.6022 (mtt-85) REVERT: A 995 MET cc_start: 0.4848 (mtt) cc_final: 0.4600 (mtt) REVERT: A 1066 LYS cc_start: 0.6327 (tttp) cc_final: 0.5897 (mmmt) REVERT: B 216 ARG cc_start: 0.7980 (mtt180) cc_final: 0.7741 (ttm110) REVERT: B 227 GLU cc_start: 0.7419 (tt0) cc_final: 0.6973 (tm-30) REVERT: B 271 ASP cc_start: 0.7078 (t0) cc_final: 0.6798 (t0) REVERT: B 279 ARG cc_start: 0.7142 (ttt180) cc_final: 0.6834 (ttm170) REVERT: B 548 ARG cc_start: 0.8053 (ttt180) cc_final: 0.7617 (tpp-160) REVERT: B 696 HIS cc_start: 0.3558 (OUTLIER) cc_final: 0.2974 (t-90) outliers start: 31 outliers final: 27 residues processed: 180 average time/residue: 0.6303 time to fit residues: 158.4326 Evaluate side-chains 176 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 967 HIS Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 22 HIS Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 696 HIS Chi-restraints excluded: chain B residue 767 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 867 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5912 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12514 Z= 0.315 Angle : 0.501 4.548 16955 Z= 0.259 Chirality : 0.040 0.142 1939 Planarity : 0.004 0.041 2141 Dihedral : 4.572 49.935 1646 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.28 % Allowed : 11.90 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.38 (0.22), residues: 1491 helix: 1.53 (0.20), residues: 682 sheet: -0.40 (0.33), residues: 232 loop : -1.00 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 812 HIS 0.004 0.001 HIS A 225 PHE 0.014 0.002 PHE A 961 TYR 0.012 0.002 TYR B 141 ARG 0.003 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 147 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.7785 (m90) cc_final: 0.7511 (m170) REVERT: A 329 CYS cc_start: 0.6822 (m) cc_final: 0.6423 (m) REVERT: A 511 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7049 (tp30) REVERT: A 524 CYS cc_start: 0.7998 (m) cc_final: 0.7658 (m) REVERT: A 531 LYS cc_start: 0.6913 (tttt) cc_final: 0.6451 (ttpp) REVERT: A 549 ASN cc_start: 0.7195 (m-40) cc_final: 0.6851 (t0) REVERT: A 646 GLN cc_start: 0.6264 (tt0) cc_final: 0.5771 (mt0) REVERT: A 781 GLN cc_start: 0.7664 (mt0) cc_final: 0.6783 (mm110) REVERT: A 809 LYS cc_start: 0.7224 (mttt) cc_final: 0.6329 (mmtt) REVERT: A 883 LYS cc_start: 0.7658 (mttt) cc_final: 0.7155 (mmtm) REVERT: A 982 ARG cc_start: 0.6817 (mtp180) cc_final: 0.6039 (mtt-85) REVERT: A 1066 LYS cc_start: 0.6256 (tttp) cc_final: 0.5793 (mmmt) REVERT: B 216 ARG cc_start: 0.8017 (mtt180) cc_final: 0.7806 (ttm110) REVERT: B 217 ARG cc_start: 0.7890 (mtt180) cc_final: 0.7442 (mmm-85) REVERT: B 227 GLU cc_start: 0.7412 (tt0) cc_final: 0.6978 (tm-30) REVERT: B 271 ASP cc_start: 0.7116 (t0) cc_final: 0.6772 (t0) REVERT: B 279 ARG cc_start: 0.7150 (ttt180) cc_final: 0.6826 (ttm170) REVERT: B 548 ARG cc_start: 0.8059 (ttt180) cc_final: 0.7617 (tpp-160) REVERT: B 696 HIS cc_start: 0.3411 (OUTLIER) cc_final: 0.2776 (t-90) outliers start: 31 outliers final: 27 residues processed: 174 average time/residue: 0.6369 time to fit residues: 155.2131 Evaluate side-chains 174 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 967 HIS Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 22 HIS Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 696 HIS Chi-restraints excluded: chain B residue 767 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 867 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 150 optimal weight: 0.0040 chunk 138 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5899 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12514 Z= 0.207 Angle : 0.471 4.818 16955 Z= 0.240 Chirality : 0.039 0.148 1939 Planarity : 0.003 0.039 2141 Dihedral : 4.445 49.385 1646 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.06 % Allowed : 12.12 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.55 (0.22), residues: 1491 helix: 1.71 (0.20), residues: 682 sheet: -0.41 (0.32), residues: 235 loop : -0.92 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 812 HIS 0.004 0.001 HIS A 708 PHE 0.010 0.001 PHE A1068 TYR 0.011 0.001 TYR B 730 ARG 0.003 0.000 ARG B 780 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.7791 (m90) cc_final: 0.7516 (m170) REVERT: A 259 MET cc_start: 0.2743 (mmt) cc_final: 0.2472 (mmt) REVERT: A 329 CYS cc_start: 0.6788 (m) cc_final: 0.6446 (m) REVERT: A 511 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7039 (tp30) REVERT: A 524 CYS cc_start: 0.8026 (m) cc_final: 0.7696 (m) REVERT: A 531 LYS cc_start: 0.6873 (tttt) cc_final: 0.6366 (ttpp) REVERT: A 549 ASN cc_start: 0.6884 (m-40) cc_final: 0.6500 (t0) REVERT: A 646 GLN cc_start: 0.6334 (tt0) cc_final: 0.5844 (mt0) REVERT: A 781 GLN cc_start: 0.7546 (mt0) cc_final: 0.6667 (mm110) REVERT: A 809 LYS cc_start: 0.7197 (mttt) cc_final: 0.6293 (mmtt) REVERT: A 883 LYS cc_start: 0.7655 (mttt) cc_final: 0.7142 (mmtm) REVERT: A 982 ARG cc_start: 0.6838 (mtp180) cc_final: 0.6069 (mtt-85) REVERT: A 1066 LYS cc_start: 0.6350 (tttp) cc_final: 0.5915 (mmmt) REVERT: B 216 ARG cc_start: 0.8017 (mtt180) cc_final: 0.7805 (ttm110) REVERT: B 217 ARG cc_start: 0.7803 (mtt180) cc_final: 0.7449 (mmm-85) REVERT: B 227 GLU cc_start: 0.7420 (tt0) cc_final: 0.6973 (tm-30) REVERT: B 271 ASP cc_start: 0.7224 (t0) cc_final: 0.6839 (t0) REVERT: B 279 ARG cc_start: 0.7125 (ttt180) cc_final: 0.6824 (ttm170) REVERT: B 548 ARG cc_start: 0.8026 (ttt180) cc_final: 0.7607 (tpp-160) outliers start: 28 outliers final: 28 residues processed: 171 average time/residue: 0.6661 time to fit residues: 157.7956 Evaluate side-chains 172 residues out of total 1361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 144 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 967 HIS Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 22 HIS Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 767 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 867 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3944 r_free = 0.3944 target = 0.156131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.104957 restraints weight = 43794.522| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.52 r_work: 0.3134 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12514 Z= 0.181 Angle : 0.459 4.584 16955 Z= 0.234 Chirality : 0.039 0.149 1939 Planarity : 0.003 0.037 2141 Dihedral : 4.308 48.733 1646 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.84 % Allowed : 12.34 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.72 (0.22), residues: 1491 helix: 1.86 (0.20), residues: 682 sheet: -0.39 (0.32), residues: 244 loop : -0.82 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 812 HIS 0.003 0.001 HIS A 708 PHE 0.011 0.001 PHE A1068 TYR 0.011 0.001 TYR B 730 ARG 0.003 0.000 ARG B 780 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6017.10 seconds wall clock time: 107 minutes 58.05 seconds (6478.05 seconds total)