Starting phenix.real_space_refine on Mon May 19 11:29:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qeb_18350/05_2025/8qeb_18350_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qeb_18350/05_2025/8qeb_18350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qeb_18350/05_2025/8qeb_18350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qeb_18350/05_2025/8qeb_18350.map" model { file = "/net/cci-nas-00/data/ceres_data/8qeb_18350/05_2025/8qeb_18350_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qeb_18350/05_2025/8qeb_18350_trim.cif" } resolution = 3.3 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= 0.039 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 57 5.16 5 C 5863 2.51 5 N 1400 2.21 5 O 1651 1.98 5 H 8700 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17671 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 17485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 17485 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 47, 'TRANS': 1050} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 102 Unusual residues: {'ERG': 1, 'Y01': 2} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Time building chain proxies: 8.16, per 1000 atoms: 0.46 Number of scatterers: 17671 At special positions: 0 Unit cell: (84.11, 102.226, 161.75, 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 57 16.00 O 1651 8.00 N 1400 7.00 C 5863 6.00 H 8700 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 75 " distance=2.03 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 41 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 110 " distance=2.03 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 235 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 438 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 480 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 828 " distance=2.03 Simple disulfide: pdb=" SG CYS A 868 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A 869 " - pdb=" SG CYS A 891 " distance=2.03 Simple disulfide: pdb=" SG CYS A 879 " - pdb=" SG CYS A 888 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG B 1 " - " ASN A 940 " " NAG C 1 " - " ASN A 900 " " NAG D 1 " - " ASN A 401 " Time building additional restraints: 4.58 Conformation dependent library (CDL) restraints added in 1.2 seconds 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 6 sheets defined 61.2% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 66 through 69 Processing helix chain 'A' and resid 77 through 96 removed outlier: 3.759A pdb=" N ALA A 83 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 98 through 115 removed outlier: 3.823A pdb=" N PHE A 109 " --> pdb=" O PHE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 removed outlier: 3.739A pdb=" N PHE A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 117 through 121' Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 178 through 188 removed outlier: 3.613A pdb=" N LEU A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 195 removed outlier: 4.109A pdb=" N GLY A 194 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.639A pdb=" N GLU A 210 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS A 211 " --> pdb=" O ASN A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 211' Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 257 through 279 Processing helix chain 'A' and resid 318 through 337 removed outlier: 4.074A pdb=" N ALA A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 removed outlier: 3.876A pdb=" N THR A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 375 through 389 Processing helix chain 'A' and resid 408 through 423 removed outlier: 3.520A pdb=" N ASP A 417 " --> pdb=" O HIS A 413 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 438 removed outlier: 3.642A pdb=" N LEU A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 459 removed outlier: 4.686A pdb=" N PHE A 456 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 476 Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.567A pdb=" N LEU A 481 " --> pdb=" O VAL A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 494 removed outlier: 3.705A pdb=" N LEU A 493 " --> pdb=" O LYS A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 532 removed outlier: 3.725A pdb=" N ARG A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU A 523 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A 524 " --> pdb=" O ARG A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 552 removed outlier: 4.183A pdb=" N LEU A 548 " --> pdb=" O THR A 544 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 556 removed outlier: 7.449A pdb=" N ASN A 556 " --> pdb=" O ASN A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 556' Processing helix chain 'A' and resid 557 through 576 removed outlier: 3.581A pdb=" N TRP A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 608 removed outlier: 3.764A pdb=" N ILE A 599 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR A 607 " --> pdb=" O ALA A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 645 removed outlier: 3.602A pdb=" N ILE A 621 " --> pdb=" O ILE A 617 " (cutoff:3.500A) Proline residue: A 622 - end of helix removed outlier: 3.782A pdb=" N ILE A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN A 632 " --> pdb=" O ILE A 628 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 633 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU A 645 " --> pdb=" O ASP A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 682 removed outlier: 3.553A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Proline residue: A 665 - end of helix removed outlier: 3.688A pdb=" N ALA A 681 " --> pdb=" O CYS A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.675A pdb=" N THR A 697 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 701 " --> pdb=" O THR A 697 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN A 703 " --> pdb=" O SER A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 723 Processing helix chain 'A' and resid 742 through 747 removed outlier: 4.018A pdb=" N THR A 747 " --> pdb=" O LYS A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 766 removed outlier: 3.515A pdb=" N ILE A 752 " --> pdb=" O GLN A 748 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 765 " --> pdb=" O PHE A 761 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 766 " --> pdb=" O THR A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 770 Processing helix chain 'A' and resid 775 through 780 removed outlier: 3.893A pdb=" N ALA A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 780 " --> pdb=" O GLN A 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 775 through 780' Processing helix chain 'A' and resid 786 through 794 removed outlier: 3.924A pdb=" N ASP A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 819 Processing helix chain 'A' and resid 832 through 840 Processing helix chain 'A' and resid 852 through 861 Processing helix chain 'A' and resid 908 through 919 removed outlier: 4.259A pdb=" N ILE A 916 " --> pdb=" O GLU A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 976 removed outlier: 3.862A pdb=" N PHE A 976 " --> pdb=" O ILE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 995 removed outlier: 4.358A pdb=" N GLN A 993 " --> pdb=" O PHE A 990 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A 994 " --> pdb=" O PHE A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1021 removed outlier: 3.580A pdb=" N LEU A1002 " --> pdb=" O GLY A 998 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A1017 " --> pdb=" O PHE A1013 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A1018 " --> pdb=" O PHE A1014 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE A1019 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1047 removed outlier: 3.523A pdb=" N ILE A1037 " --> pdb=" O VAL A1033 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA A1045 " --> pdb=" O GLY A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1079 removed outlier: 3.568A pdb=" N ASN A1058 " --> pdb=" O VAL A1054 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A1063 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A1069 " --> pdb=" O LEU A1065 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS A1070 " --> pdb=" O GLY A1066 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS A1072 " --> pdb=" O GLU A1068 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE A1073 " --> pdb=" O PHE A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1100 Processing helix chain 'A' and resid 1100 through 1105 Processing helix chain 'A' and resid 1106 through 1119 removed outlier: 3.710A pdb=" N VAL A1117 " --> pdb=" O ILE A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1130 Processing helix chain 'A' and resid 1136 through 1147 removed outlier: 3.525A pdb=" N ALA A1142 " --> pdb=" O ILE A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1155 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 4.214A pdb=" N CYS A 41 " --> pdb=" O TYR A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 129 removed outlier: 6.689A pdb=" N GLU A 139 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL A 127 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL A 137 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LYS A 129 " --> pdb=" O ASP A 135 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASP A 135 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 199 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 251 through 252 removed outlier: 3.604A pdb=" N VAL A 252 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 255 " --> pdb=" O VAL A 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 393 through 395 Processing sheet with id=AA5, first strand: chain 'A' and resid 504 through 506 Processing sheet with id=AA6, first strand: chain 'A' and resid 937 through 939 removed outlier: 4.304A pdb=" N ASP A 980 " --> pdb=" O LYS A 808 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1242 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: 5.96 Time building geometry restraints manager: 5.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8690 1.03 - 1.23: 43 1.23 - 1.43: 3849 1.43 - 1.62: 5240 1.62 - 1.82: 76 Bond restraints: 17898 Sorted by residual: bond pdb=" N ALA A 21 " pdb=" CA ALA A 21 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" C6 ERG A1201 " pdb=" C7 ERG A1201 " ideal model delta sigma weight residual 1.452 1.419 0.033 2.00e-02 2.50e+03 2.77e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.46e+00 bond pdb=" N ALA A 21 " pdb=" H ALA A 21 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.39e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 ... (remaining 17893 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 30143 1.04 - 2.09: 2003 2.09 - 3.13: 87 3.13 - 4.18: 34 4.18 - 5.22: 10 Bond angle restraints: 32277 Sorted by residual: angle pdb=" N VAL A 335 " pdb=" CA VAL A 335 " pdb=" C VAL A 335 " ideal model delta sigma weight residual 112.96 109.12 3.84 1.00e+00 1.00e+00 1.47e+01 angle pdb=" CB ARG A 886 " pdb=" CG ARG A 886 " pdb=" CD ARG A 886 " ideal model delta sigma weight residual 111.30 116.52 -5.22 2.30e+00 1.89e-01 5.16e+00 angle pdb=" N PRO A 955 " pdb=" CA PRO A 955 " pdb=" C PRO A 955 " ideal model delta sigma weight residual 112.47 116.93 -4.46 2.06e+00 2.36e-01 4.70e+00 angle pdb=" CA VAL A 335 " pdb=" C VAL A 335 " pdb=" N GLU A 336 " ideal model delta sigma weight residual 118.65 116.67 1.98 1.07e+00 8.73e-01 3.42e+00 angle pdb=" C HIS A 954 " pdb=" CA HIS A 954 " pdb=" CB HIS A 954 " ideal model delta sigma weight residual 109.96 112.73 -2.77 1.50e+00 4.44e-01 3.41e+00 ... (remaining 32272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.57: 8127 23.57 - 47.14: 507 47.14 - 70.70: 111 70.70 - 94.27: 25 94.27 - 117.84: 6 Dihedral angle restraints: 8776 sinusoidal: 4793 harmonic: 3983 Sorted by residual: dihedral pdb=" CB CYS A 869 " pdb=" SG CYS A 869 " pdb=" SG CYS A 891 " pdb=" CB CYS A 891 " ideal model delta sinusoidal sigma weight residual 93.00 143.15 -50.15 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CB CYS A 822 " pdb=" SG CYS A 822 " pdb=" SG CYS A 828 " pdb=" CB CYS A 828 " ideal model delta sinusoidal sigma weight residual -86.00 -40.98 -45.02 1 1.00e+01 1.00e-02 2.81e+01 dihedral pdb=" CB CYS A 223 " pdb=" SG CYS A 223 " pdb=" SG CYS A 235 " pdb=" CB CYS A 235 " ideal model delta sinusoidal sigma weight residual 93.00 49.27 43.73 1 1.00e+01 1.00e-02 2.66e+01 ... (remaining 8773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1179 0.047 - 0.094: 203 0.094 - 0.141: 46 0.141 - 0.187: 3 0.187 - 0.234: 2 Chirality restraints: 1433 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 940 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 900 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA PRO A 955 " pdb=" N PRO A 955 " pdb=" C PRO A 955 " pdb=" CB PRO A 955 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.18e-01 ... (remaining 1430 not shown) Planarity restraints: 2609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 886 " 0.090 9.50e-02 1.11e+02 3.04e-02 1.25e+00 pdb=" NE ARG A 886 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 886 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 886 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 886 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 886 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 886 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 886 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 886 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 43 " -0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO A 44 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 44 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 44 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 39 " 0.016 5.00e-02 4.00e+02 2.48e-02 9.87e-01 pdb=" N PRO A 40 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 40 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 40 " 0.014 5.00e-02 4.00e+02 ... (remaining 2606 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 1516 2.22 - 2.82: 38461 2.82 - 3.41: 47331 3.41 - 4.01: 63495 4.01 - 4.60: 97283 Nonbonded interactions: 248086 Sorted by model distance: nonbonded pdb=" O LEU A 493 " pdb=" H VAL A 506 " model vdw 1.629 2.450 nonbonded pdb=" O GLY A 969 " pdb=" HG SER A 973 " model vdw 1.637 2.450 nonbonded pdb=" HG SER A 547 " pdb=" OH TYR A 785 " model vdw 1.643 2.450 nonbonded pdb=" OD1 ASP A 154 " pdb=" HZ1 LYS A 157 " model vdw 1.664 2.450 nonbonded pdb=" O ALA A 83 " pdb="HD22 ASN A 87 " model vdw 1.681 2.450 ... (remaining 248081 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.300 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 36.530 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 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 : 0.003 0.033 9218 Z= 0.144 Angle : 0.494 7.910 12549 Z= 0.247 Chirality : 0.038 0.234 1433 Planarity : 0.003 0.040 1558 Dihedral : 17.617 117.838 3575 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.41 % Allowed : 15.03 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.26), residues: 1092 helix: 0.35 (0.23), residues: 570 sheet: -0.87 (0.67), residues: 68 loop : -0.46 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 148 HIS 0.005 0.001 HIS A 954 PHE 0.017 0.001 PHE A 265 TYR 0.006 0.001 TYR A 711 ARG 0.009 0.000 ARG A 886 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 3) link_NAG-ASN : angle 0.56858 ( 9) link_BETA1-4 : bond 0.00508 ( 3) link_BETA1-4 : angle 3.11355 ( 9) hydrogen bonds : bond 0.27352 ( 432) hydrogen bonds : angle 9.33595 ( 1242) SS BOND : bond 0.00201 ( 14) SS BOND : angle 0.70327 ( 28) covalent geometry : bond 0.00323 ( 9198) covalent geometry : angle 0.48665 (12503) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 1.346 Fit side-chains REVERT: A 805 MET cc_start: 0.9368 (mmt) cc_final: 0.9019 (mmm) outliers start: 4 outliers final: 3 residues processed: 89 average time/residue: 0.4558 time to fit residues: 57.2446 Evaluate side-chains 89 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 723 ASN A 817 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.182183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.138838 restraints weight = 29695.639| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.05 r_work: 0.3235 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9218 Z= 0.180 Angle : 0.583 8.955 12549 Z= 0.311 Chirality : 0.040 0.184 1433 Planarity : 0.004 0.039 1558 Dihedral : 9.146 99.123 1512 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.73 % Allowed : 13.71 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.25), residues: 1092 helix: 0.14 (0.21), residues: 604 sheet: -1.11 (0.66), residues: 67 loop : -0.66 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 466 HIS 0.004 0.001 HIS A 954 PHE 0.021 0.001 PHE A 505 TYR 0.016 0.001 TYR A 711 ARG 0.003 0.000 ARG A 539 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 3) link_NAG-ASN : angle 0.85282 ( 9) link_BETA1-4 : bond 0.00443 ( 3) link_BETA1-4 : angle 2.21971 ( 9) hydrogen bonds : bond 0.06345 ( 432) hydrogen bonds : angle 6.21021 ( 1242) SS BOND : bond 0.00195 ( 14) SS BOND : angle 0.86321 ( 28) covalent geometry : bond 0.00396 ( 9198) covalent geometry : angle 0.57891 (12503) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 1.454 Fit side-chains REVERT: A 25 MET cc_start: 0.6882 (tmm) cc_final: 0.6303 (tmm) REVERT: A 47 PHE cc_start: 0.5014 (OUTLIER) cc_final: 0.4500 (p90) REVERT: A 92 GLN cc_start: 0.7564 (tt0) cc_final: 0.7054 (tt0) REVERT: A 522 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: A 570 LEU cc_start: 0.8253 (tp) cc_final: 0.8041 (tt) REVERT: A 589 ILE cc_start: 0.8042 (mm) cc_final: 0.7588 (mt) REVERT: A 805 MET cc_start: 0.9182 (mmt) cc_final: 0.8822 (mmm) outliers start: 17 outliers final: 10 residues processed: 113 average time/residue: 0.4141 time to fit residues: 67.9329 Evaluate side-chains 103 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 75 optimal weight: 0.0570 chunk 16 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 70 optimal weight: 0.0470 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.184204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.140117 restraints weight = 29532.667| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.04 r_work: 0.3318 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9218 Z= 0.116 Angle : 0.509 8.065 12549 Z= 0.263 Chirality : 0.038 0.175 1433 Planarity : 0.003 0.038 1558 Dihedral : 7.874 83.061 1510 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.73 % Allowed : 14.62 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.26), residues: 1092 helix: 0.30 (0.21), residues: 607 sheet: -1.15 (0.67), residues: 67 loop : -0.64 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 PHE 0.015 0.001 PHE A 569 TYR 0.012 0.001 TYR A 711 ARG 0.005 0.000 ARG A 886 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 3) link_NAG-ASN : angle 1.10582 ( 9) link_BETA1-4 : bond 0.00344 ( 3) link_BETA1-4 : angle 1.83495 ( 9) hydrogen bonds : bond 0.05353 ( 432) hydrogen bonds : angle 5.59850 ( 1242) SS BOND : bond 0.00205 ( 14) SS BOND : angle 0.96312 ( 28) covalent geometry : bond 0.00245 ( 9198) covalent geometry : angle 0.50450 (12503) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.6617 (tmm) cc_final: 0.6305 (tmm) REVERT: A 47 PHE cc_start: 0.5038 (OUTLIER) cc_final: 0.4529 (p90) REVERT: A 92 GLN cc_start: 0.7497 (tt0) cc_final: 0.6933 (tt0) REVERT: A 589 ILE cc_start: 0.8117 (mm) cc_final: 0.7722 (mt) outliers start: 17 outliers final: 13 residues processed: 109 average time/residue: 0.4174 time to fit residues: 66.2294 Evaluate side-chains 106 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 71 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.178290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.132614 restraints weight = 29841.244| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.00 r_work: 0.3265 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9218 Z= 0.200 Angle : 0.552 7.084 12549 Z= 0.290 Chirality : 0.040 0.193 1433 Planarity : 0.004 0.039 1558 Dihedral : 7.604 65.249 1510 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.22 % Favored : 94.69 % Rotamer: Outliers : 2.54 % Allowed : 14.31 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.25), residues: 1092 helix: 0.14 (0.21), residues: 606 sheet: -1.40 (0.66), residues: 65 loop : -0.87 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 466 HIS 0.005 0.001 HIS A 954 PHE 0.021 0.001 PHE A 569 TYR 0.017 0.001 TYR A 857 ARG 0.002 0.000 ARG A 642 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 3) link_NAG-ASN : angle 0.97864 ( 9) link_BETA1-4 : bond 0.00322 ( 3) link_BETA1-4 : angle 1.95456 ( 9) hydrogen bonds : bond 0.04916 ( 432) hydrogen bonds : angle 5.45470 ( 1242) SS BOND : bond 0.00255 ( 14) SS BOND : angle 1.02461 ( 28) covalent geometry : bond 0.00465 ( 9198) covalent geometry : angle 0.54797 (12503) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.5074 (OUTLIER) cc_final: 0.4580 (p90) REVERT: A 589 ILE cc_start: 0.8127 (mm) cc_final: 0.7719 (mt) REVERT: A 778 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7443 (pp) REVERT: A 805 MET cc_start: 0.9159 (mmt) cc_final: 0.8768 (mmm) outliers start: 25 outliers final: 16 residues processed: 112 average time/residue: 0.4065 time to fit residues: 67.0610 Evaluate side-chains 106 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.179304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.134583 restraints weight = 29927.387| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.98 r_work: 0.3320 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9218 Z= 0.171 Angle : 0.536 7.103 12549 Z= 0.279 Chirality : 0.039 0.186 1433 Planarity : 0.003 0.040 1558 Dihedral : 7.174 55.857 1510 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.13 % Favored : 94.78 % Rotamer: Outliers : 2.23 % Allowed : 14.92 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.25), residues: 1092 helix: 0.19 (0.21), residues: 607 sheet: -1.51 (0.66), residues: 65 loop : -0.87 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 PHE 0.020 0.001 PHE A 569 TYR 0.014 0.001 TYR A 711 ARG 0.002 0.000 ARG A 642 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 3) link_NAG-ASN : angle 0.95013 ( 9) link_BETA1-4 : bond 0.00290 ( 3) link_BETA1-4 : angle 1.87592 ( 9) hydrogen bonds : bond 0.04616 ( 432) hydrogen bonds : angle 5.28255 ( 1242) SS BOND : bond 0.00214 ( 14) SS BOND : angle 0.88967 ( 28) covalent geometry : bond 0.00400 ( 9198) covalent geometry : angle 0.53226 (12503) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 1.409 Fit side-chains revert: symmetry clash REVERT: A 47 PHE cc_start: 0.5102 (OUTLIER) cc_final: 0.4533 (p90) REVERT: A 89 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7907 (mm-40) REVERT: A 140 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7269 (pp) REVERT: A 570 LEU cc_start: 0.8271 (tt) cc_final: 0.8046 (tp) REVERT: A 589 ILE cc_start: 0.8124 (mm) cc_final: 0.7708 (mt) REVERT: A 778 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7478 (pp) REVERT: A 805 MET cc_start: 0.9137 (mmt) cc_final: 0.8739 (mmm) outliers start: 22 outliers final: 14 residues processed: 112 average time/residue: 0.3997 time to fit residues: 66.4627 Evaluate side-chains 105 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 922 SER Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 84 optimal weight: 0.0870 chunk 106 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 29 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.181117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.136516 restraints weight = 29649.086| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.01 r_work: 0.3326 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9218 Z= 0.149 Angle : 0.521 5.861 12549 Z= 0.272 Chirality : 0.038 0.182 1433 Planarity : 0.003 0.039 1558 Dihedral : 7.062 56.593 1510 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.77 % Favored : 94.05 % Rotamer: Outliers : 2.54 % Allowed : 15.23 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.25), residues: 1092 helix: 0.27 (0.21), residues: 606 sheet: -1.56 (0.66), residues: 65 loop : -0.79 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 PHE 0.020 0.001 PHE A 569 TYR 0.014 0.001 TYR A 711 ARG 0.002 0.000 ARG A 642 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 3) link_NAG-ASN : angle 0.89130 ( 9) link_BETA1-4 : bond 0.00339 ( 3) link_BETA1-4 : angle 1.84360 ( 9) hydrogen bonds : bond 0.04328 ( 432) hydrogen bonds : angle 5.13822 ( 1242) SS BOND : bond 0.00198 ( 14) SS BOND : angle 0.84284 ( 28) covalent geometry : bond 0.00347 ( 9198) covalent geometry : angle 0.51759 (12503) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 1.272 Fit side-chains REVERT: A 47 PHE cc_start: 0.5138 (OUTLIER) cc_final: 0.4582 (p90) REVERT: A 89 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7887 (mm-40) REVERT: A 140 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7254 (pp) REVERT: A 570 LEU cc_start: 0.8265 (tt) cc_final: 0.8039 (tp) REVERT: A 589 ILE cc_start: 0.8219 (mm) cc_final: 0.7733 (mt) REVERT: A 805 MET cc_start: 0.9140 (mmt) cc_final: 0.8738 (mmm) outliers start: 25 outliers final: 17 residues processed: 110 average time/residue: 0.3792 time to fit residues: 63.1877 Evaluate side-chains 106 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 53 optimal weight: 0.0870 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.181132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.136289 restraints weight = 29580.071| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.01 r_work: 0.3346 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9218 Z= 0.119 Angle : 0.496 5.404 12549 Z= 0.259 Chirality : 0.038 0.182 1433 Planarity : 0.003 0.039 1558 Dihedral : 6.956 57.917 1510 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.31 % Favored : 94.51 % Rotamer: Outliers : 2.44 % Allowed : 15.13 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.26), residues: 1092 helix: 0.45 (0.22), residues: 606 sheet: -1.55 (0.64), residues: 68 loop : -0.72 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 PHE 0.022 0.001 PHE A 569 TYR 0.014 0.001 TYR A 711 ARG 0.002 0.000 ARG A 642 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 3) link_NAG-ASN : angle 0.89414 ( 9) link_BETA1-4 : bond 0.00281 ( 3) link_BETA1-4 : angle 1.74256 ( 9) hydrogen bonds : bond 0.04037 ( 432) hydrogen bonds : angle 4.97653 ( 1242) SS BOND : bond 0.00150 ( 14) SS BOND : angle 0.78558 ( 28) covalent geometry : bond 0.00273 ( 9198) covalent geometry : angle 0.49311 (12503) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 1.239 Fit side-chains REVERT: A 47 PHE cc_start: 0.5149 (OUTLIER) cc_final: 0.4529 (p90) REVERT: A 89 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7886 (mm-40) REVERT: A 140 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.6959 (pp) REVERT: A 265 PHE cc_start: 0.7419 (t80) cc_final: 0.7065 (t80) REVERT: A 589 ILE cc_start: 0.8212 (mm) cc_final: 0.7727 (mt) REVERT: A 778 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7444 (pp) outliers start: 24 outliers final: 15 residues processed: 111 average time/residue: 0.3584 time to fit residues: 59.9790 Evaluate side-chains 109 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 922 SER Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 81 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.178360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.133350 restraints weight = 29614.125| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.98 r_work: 0.3317 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9218 Z= 0.187 Angle : 0.533 5.508 12549 Z= 0.281 Chirality : 0.039 0.190 1433 Planarity : 0.004 0.040 1558 Dihedral : 7.130 58.595 1510 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.86 % Favored : 93.96 % Rotamer: Outliers : 2.23 % Allowed : 15.13 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.25), residues: 1092 helix: 0.36 (0.21), residues: 606 sheet: -1.70 (0.63), residues: 68 loop : -0.80 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 PHE 0.022 0.001 PHE A 569 TYR 0.015 0.001 TYR A 711 ARG 0.002 0.000 ARG A 642 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 3) link_NAG-ASN : angle 0.93670 ( 9) link_BETA1-4 : bond 0.00304 ( 3) link_BETA1-4 : angle 1.78020 ( 9) hydrogen bonds : bond 0.04253 ( 432) hydrogen bonds : angle 5.02464 ( 1242) SS BOND : bond 0.00216 ( 14) SS BOND : angle 0.95889 ( 28) covalent geometry : bond 0.00438 ( 9198) covalent geometry : angle 0.52967 (12503) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 1.327 Fit side-chains revert: symmetry clash REVERT: A 47 PHE cc_start: 0.5137 (OUTLIER) cc_final: 0.4524 (p90) REVERT: A 89 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7888 (mm-40) REVERT: A 140 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.6970 (pp) REVERT: A 223 CYS cc_start: 0.7011 (OUTLIER) cc_final: 0.6679 (t) REVERT: A 265 PHE cc_start: 0.7295 (t80) cc_final: 0.6976 (t80) REVERT: A 570 LEU cc_start: 0.8260 (tp) cc_final: 0.8042 (tt) REVERT: A 589 ILE cc_start: 0.8230 (mm) cc_final: 0.7757 (mt) REVERT: A 778 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7464 (pp) outliers start: 22 outliers final: 16 residues processed: 112 average time/residue: 0.4277 time to fit residues: 68.8760 Evaluate side-chains 113 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 922 SER Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 71 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 23 optimal weight: 0.3980 chunk 22 optimal weight: 0.0980 chunk 49 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4034 r_free = 0.4034 target = 0.183241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.138497 restraints weight = 29525.978| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.04 r_work: 0.3352 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9218 Z= 0.105 Angle : 0.488 5.289 12549 Z= 0.255 Chirality : 0.038 0.177 1433 Planarity : 0.003 0.038 1558 Dihedral : 6.837 57.988 1510 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.85 % Favored : 94.96 % Rotamer: Outliers : 1.73 % Allowed : 15.43 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.26), residues: 1092 helix: 0.57 (0.22), residues: 606 sheet: -1.46 (0.66), residues: 66 loop : -0.69 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 PHE 0.022 0.001 PHE A 569 TYR 0.014 0.001 TYR A 711 ARG 0.003 0.000 ARG A 886 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 3) link_NAG-ASN : angle 0.89281 ( 9) link_BETA1-4 : bond 0.00328 ( 3) link_BETA1-4 : angle 1.70495 ( 9) hydrogen bonds : bond 0.03853 ( 432) hydrogen bonds : angle 4.86423 ( 1242) SS BOND : bond 0.00147 ( 14) SS BOND : angle 0.74086 ( 28) covalent geometry : bond 0.00236 ( 9198) covalent geometry : angle 0.48526 (12503) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.5153 (OUTLIER) cc_final: 0.4545 (p90) REVERT: A 89 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7815 (mm-40) REVERT: A 265 PHE cc_start: 0.7286 (t80) cc_final: 0.7037 (t80) REVERT: A 589 ILE cc_start: 0.8085 (mm) cc_final: 0.7663 (mt) REVERT: A 805 MET cc_start: 0.9128 (mmt) cc_final: 0.8828 (mmt) outliers start: 17 outliers final: 12 residues processed: 109 average time/residue: 0.4090 time to fit residues: 64.4137 Evaluate side-chains 111 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 822 CYS Chi-restraints excluded: chain A residue 922 SER Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 74 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.179709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.135400 restraints weight = 29436.872| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.93 r_work: 0.3332 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9218 Z= 0.156 Angle : 0.514 5.223 12549 Z= 0.268 Chirality : 0.039 0.181 1433 Planarity : 0.003 0.041 1558 Dihedral : 6.949 57.858 1510 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.68 % Favored : 94.14 % Rotamer: Outliers : 1.93 % Allowed : 15.53 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.26), residues: 1092 helix: 0.49 (0.21), residues: 607 sheet: -1.57 (0.64), residues: 68 loop : -0.71 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 PHE 0.021 0.001 PHE A 569 TYR 0.015 0.001 TYR A 711 ARG 0.002 0.000 ARG A 642 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 3) link_NAG-ASN : angle 0.88649 ( 9) link_BETA1-4 : bond 0.00291 ( 3) link_BETA1-4 : angle 1.70076 ( 9) hydrogen bonds : bond 0.03984 ( 432) hydrogen bonds : angle 4.88555 ( 1242) SS BOND : bond 0.00177 ( 14) SS BOND : angle 0.88297 ( 28) covalent geometry : bond 0.00368 ( 9198) covalent geometry : angle 0.51075 (12503) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.6608 (tmm) cc_final: 0.6278 (tmm) REVERT: A 47 PHE cc_start: 0.5171 (OUTLIER) cc_final: 0.4558 (p90) REVERT: A 89 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7854 (mm-40) REVERT: A 265 PHE cc_start: 0.7225 (t80) cc_final: 0.6902 (t80) REVERT: A 570 LEU cc_start: 0.8260 (tp) cc_final: 0.8025 (tt) REVERT: A 589 ILE cc_start: 0.8215 (mm) cc_final: 0.7744 (mt) REVERT: A 778 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7455 (pp) REVERT: A 805 MET cc_start: 0.9138 (mmt) cc_final: 0.8731 (mmm) outliers start: 19 outliers final: 13 residues processed: 111 average time/residue: 0.4252 time to fit residues: 68.8943 Evaluate side-chains 111 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 922 SER Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 30 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 104 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.182844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.138676 restraints weight = 29356.475| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.97 r_work: 0.3327 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 9218 Z= 0.121 Angle : 0.524 13.561 12549 Z= 0.274 Chirality : 0.038 0.174 1433 Planarity : 0.003 0.039 1558 Dihedral : 6.793 57.602 1509 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.22 % Favored : 94.41 % Rotamer: Outliers : 1.83 % Allowed : 15.84 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.13 (0.26), residues: 1092 helix: 0.57 (0.22), residues: 607 sheet: -1.51 (0.64), residues: 68 loop : -0.68 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 PHE 0.021 0.001 PHE A 569 TYR 0.014 0.001 TYR A 711 ARG 0.002 0.000 ARG A 642 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 3) link_NAG-ASN : angle 0.90038 ( 9) link_BETA1-4 : bond 0.00334 ( 3) link_BETA1-4 : angle 1.67577 ( 9) hydrogen bonds : bond 0.03818 ( 432) hydrogen bonds : angle 4.81240 ( 1242) SS BOND : bond 0.00594 ( 14) SS BOND : angle 2.65957 ( 28) covalent geometry : bond 0.00278 ( 9198) covalent geometry : angle 0.50711 (12503) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8626.75 seconds wall clock time: 148 minutes 24.19 seconds (8904.19 seconds total)