Starting phenix.real_space_refine on Sun Aug 24 08:30:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qeb_18350/08_2025/8qeb_18350_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qeb_18350/08_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_18350/08_2025/8qeb_18350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qeb_18350/08_2025/8qeb_18350.map" model { file = "/net/cci-nas-00/data/ceres_data/8qeb_18350/08_2025/8qeb_18350_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qeb_18350/08_2025/8qeb_18350_trim.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.039 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.42, per 1000 atoms: 0.19 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: 1.61 Conformation dependent library (CDL) restraints added in 644.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.66 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: 3.60 Time building geometry restraints manager: 2.27 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: 0.740 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: 0.110 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.670 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.160 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (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 ARG 0.009 0.000 ARG A 886 TYR 0.006 0.001 TYR A 711 PHE 0.017 0.001 PHE A 265 TRP 0.015 0.001 TRP A 148 HIS 0.005 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9198) covalent geometry : angle 0.48665 (12503) SS BOND : bond 0.00201 ( 14) SS BOND : angle 0.70327 ( 28) hydrogen bonds : bond 0.27352 ( 432) hydrogen bonds : angle 9.33595 ( 1242) link_BETA1-4 : bond 0.00508 ( 3) link_BETA1-4 : angle 3.11355 ( 9) link_NAG-ASN : bond 0.00328 ( 3) link_NAG-ASN : angle 0.56858 ( 9) *********************** 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 : 0.463 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: 0.2079 time to fit residues: 26.0871 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 : 0.460 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- 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 A 919 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.182009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.138457 restraints weight = 29725.598| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.06 r_work: 0.3253 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9218 Z= 0.180 Angle : 0.580 8.854 12549 Z= 0.311 Chirality : 0.040 0.182 1433 Planarity : 0.004 0.039 1558 Dihedral : 9.203 99.996 1512 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.62 % Allowed : 13.60 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.25), residues: 1092 helix: 0.15 (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 ARG 0.003 0.000 ARG A 539 TYR 0.016 0.001 TYR A 711 PHE 0.019 0.001 PHE A 505 TRP 0.010 0.001 TRP A 466 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 9198) covalent geometry : angle 0.57605 (12503) SS BOND : bond 0.00214 ( 14) SS BOND : angle 0.86199 ( 28) hydrogen bonds : bond 0.06448 ( 432) hydrogen bonds : angle 6.23537 ( 1242) link_BETA1-4 : bond 0.00362 ( 3) link_BETA1-4 : angle 2.26401 ( 9) link_NAG-ASN : bond 0.00216 ( 3) link_NAG-ASN : angle 0.84240 ( 9) *********************** 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 114 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.297 Fit side-chains REVERT: A 25 MET cc_start: 0.6867 (tmm) cc_final: 0.6238 (tmm) REVERT: A 47 PHE cc_start: 0.4998 (OUTLIER) cc_final: 0.4482 (p90) REVERT: A 92 GLN cc_start: 0.7583 (tt0) cc_final: 0.7053 (tt0) REVERT: A 522 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: A 570 LEU cc_start: 0.8256 (tp) cc_final: 0.8048 (tt) REVERT: A 589 ILE cc_start: 0.8090 (mm) cc_final: 0.7636 (mt) REVERT: A 805 MET cc_start: 0.9150 (mmt) cc_final: 0.8789 (mmm) outliers start: 16 outliers final: 10 residues processed: 109 average time/residue: 0.1701 time to fit residues: 27.0836 Evaluate side-chains 102 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 52 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.176865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.131741 restraints weight = 30087.489| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.93 r_work: 0.3301 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9218 Z= 0.248 Angle : 0.595 7.700 12549 Z= 0.315 Chirality : 0.042 0.202 1433 Planarity : 0.004 0.042 1558 Dihedral : 8.244 84.186 1510 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.77 % Favored : 94.14 % Rotamer: Outliers : 2.54 % Allowed : 14.01 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.25), residues: 1092 helix: -0.08 (0.21), residues: 604 sheet: -1.48 (0.66), residues: 65 loop : -0.95 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 886 TYR 0.016 0.002 TYR A 857 PHE 0.015 0.002 PHE A 569 TRP 0.013 0.002 TRP A 148 HIS 0.007 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00577 ( 9198) covalent geometry : angle 0.59044 (12503) SS BOND : bond 0.00311 ( 14) SS BOND : angle 1.20240 ( 28) hydrogen bonds : bond 0.05935 ( 432) hydrogen bonds : angle 5.83174 ( 1242) link_BETA1-4 : bond 0.00335 ( 3) link_BETA1-4 : angle 1.92297 ( 9) link_NAG-ASN : bond 0.00338 ( 3) link_NAG-ASN : angle 1.17668 ( 9) *********************** 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 112 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.6855 (tmm) cc_final: 0.6461 (tmm) REVERT: A 47 PHE cc_start: 0.5093 (OUTLIER) cc_final: 0.4585 (p90) REVERT: A 92 GLN cc_start: 0.7578 (tt0) cc_final: 0.7027 (tt0) REVERT: A 522 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: A 589 ILE cc_start: 0.8153 (mm) cc_final: 0.7751 (mt) REVERT: A 778 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7547 (pp) outliers start: 25 outliers final: 17 residues processed: 108 average time/residue: 0.1800 time to fit residues: 27.8973 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 : 0.461 ------------------------------------------------------------------------------- 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 448 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 522 GLU 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 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 844 SER 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 72 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 11 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.176387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.132846 restraints weight = 29891.419| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.00 r_work: 0.3165 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9218 Z= 0.220 Angle : 0.577 7.164 12549 Z= 0.304 Chirality : 0.041 0.201 1433 Planarity : 0.004 0.041 1558 Dihedral : 7.671 66.380 1510 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.86 % Favored : 94.05 % Rotamer: Outliers : 2.94 % Allowed : 14.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.25), residues: 1092 helix: -0.13 (0.21), residues: 606 sheet: -1.76 (0.65), residues: 65 loop : -1.06 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 642 TYR 0.013 0.001 TYR A 711 PHE 0.023 0.002 PHE A 569 TRP 0.009 0.001 TRP A 415 HIS 0.006 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 9198) covalent geometry : angle 0.57191 (12503) SS BOND : bond 0.00278 ( 14) SS BOND : angle 1.16798 ( 28) hydrogen bonds : bond 0.05001 ( 432) hydrogen bonds : angle 5.52624 ( 1242) link_BETA1-4 : bond 0.00344 ( 3) link_BETA1-4 : angle 1.98346 ( 9) link_NAG-ASN : bond 0.00350 ( 3) link_NAG-ASN : angle 1.01912 ( 9) *********************** 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 118 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.5112 (OUTLIER) cc_final: 0.4629 (p90) REVERT: A 370 TRP cc_start: 0.8131 (OUTLIER) cc_final: 0.6068 (m-90) REVERT: A 589 ILE cc_start: 0.8049 (mm) cc_final: 0.7635 (mt) REVERT: A 778 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7332 (pp) outliers start: 29 outliers final: 21 residues processed: 114 average time/residue: 0.1657 time to fit residues: 28.1899 Evaluate side-chains 108 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 370 TRP Chi-restraints excluded: chain A residue 431 ASN 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.179288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.134430 restraints weight = 29459.463| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.00 r_work: 0.3305 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9218 Z= 0.180 Angle : 0.554 6.910 12549 Z= 0.289 Chirality : 0.040 0.193 1433 Planarity : 0.004 0.041 1558 Dihedral : 7.314 58.325 1510 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.14 % Favored : 93.77 % Rotamer: Outliers : 2.44 % Allowed : 15.43 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.25), residues: 1092 helix: -0.01 (0.21), residues: 606 sheet: -1.73 (0.65), residues: 65 loop : -1.03 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 642 TYR 0.013 0.001 TYR A 711 PHE 0.020 0.001 PHE A 569 TRP 0.011 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 9198) covalent geometry : angle 0.55001 (12503) SS BOND : bond 0.00208 ( 14) SS BOND : angle 0.94485 ( 28) hydrogen bonds : bond 0.04698 ( 432) hydrogen bonds : angle 5.36174 ( 1242) link_BETA1-4 : bond 0.00336 ( 3) link_BETA1-4 : angle 1.91718 ( 9) link_NAG-ASN : bond 0.00290 ( 3) link_NAG-ASN : angle 1.00331 ( 9) *********************** 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 109 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.5164 (OUTLIER) cc_final: 0.4616 (p90) REVERT: A 89 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7776 (mm-40) REVERT: A 589 ILE cc_start: 0.8227 (mm) cc_final: 0.7754 (mt) REVERT: A 778 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7474 (pp) outliers start: 24 outliers final: 18 residues processed: 105 average time/residue: 0.1868 time to fit residues: 28.6126 Evaluate side-chains 103 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 443 GLU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 517 SER 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 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 8 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.176807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.131786 restraints weight = 29789.812| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.97 r_work: 0.3257 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9218 Z= 0.229 Angle : 0.575 6.442 12549 Z= 0.304 Chirality : 0.041 0.201 1433 Planarity : 0.004 0.042 1558 Dihedral : 7.322 59.390 1510 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.32 % Favored : 93.59 % Rotamer: Outliers : 3.25 % Allowed : 15.23 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.25), residues: 1092 helix: -0.06 (0.21), residues: 605 sheet: -1.94 (0.63), residues: 66 loop : -1.08 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 642 TYR 0.014 0.001 TYR A 711 PHE 0.024 0.002 PHE A 569 TRP 0.015 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 9198) covalent geometry : angle 0.57056 (12503) SS BOND : bond 0.00239 ( 14) SS BOND : angle 1.10195 ( 28) hydrogen bonds : bond 0.04742 ( 432) hydrogen bonds : angle 5.34681 ( 1242) link_BETA1-4 : bond 0.00320 ( 3) link_BETA1-4 : angle 1.93591 ( 9) link_NAG-ASN : bond 0.00361 ( 3) link_NAG-ASN : angle 1.05896 ( 9) *********************** 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 119 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.5132 (OUTLIER) cc_final: 0.4606 (p90) REVERT: A 89 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7787 (mm-40) REVERT: A 589 ILE cc_start: 0.8251 (mm) cc_final: 0.7771 (mt) REVERT: A 778 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7514 (pp) REVERT: A 1002 LEU cc_start: 0.8718 (mp) cc_final: 0.8495 (mt) outliers start: 32 outliers final: 21 residues processed: 112 average time/residue: 0.1672 time to fit residues: 27.6487 Evaluate side-chains 110 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 431 ASN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.177275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.128716 restraints weight = 30142.247| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.95 r_work: 0.3222 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9218 Z= 0.181 Angle : 0.551 6.439 12549 Z= 0.290 Chirality : 0.040 0.195 1433 Planarity : 0.004 0.042 1558 Dihedral : 7.257 59.861 1510 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.50 % Favored : 93.41 % Rotamer: Outliers : 2.74 % Allowed : 15.84 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.25), residues: 1092 helix: 0.04 (0.21), residues: 606 sheet: -1.87 (0.64), residues: 65 loop : -1.05 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 642 TYR 0.014 0.001 TYR A 711 PHE 0.022 0.001 PHE A 569 TRP 0.013 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 9198) covalent geometry : angle 0.54527 (12503) SS BOND : bond 0.00233 ( 14) SS BOND : angle 1.28876 ( 28) hydrogen bonds : bond 0.04482 ( 432) hydrogen bonds : angle 5.23617 ( 1242) link_BETA1-4 : bond 0.00326 ( 3) link_BETA1-4 : angle 1.87567 ( 9) link_NAG-ASN : bond 0.00277 ( 3) link_NAG-ASN : angle 1.03780 ( 9) *********************** 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 117 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8309 (tt) REVERT: A 47 PHE cc_start: 0.5165 (OUTLIER) cc_final: 0.4562 (p90) REVERT: A 89 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7760 (mm-40) REVERT: A 589 ILE cc_start: 0.8137 (mm) cc_final: 0.7645 (mt) REVERT: A 778 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7324 (pp) REVERT: A 1002 LEU cc_start: 0.8697 (mp) cc_final: 0.8460 (mt) outliers start: 27 outliers final: 21 residues processed: 113 average time/residue: 0.1545 time to fit residues: 25.4683 Evaluate side-chains 112 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 348 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 431 ASN 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 16 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.178638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.136042 restraints weight = 29650.427| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.10 r_work: 0.3228 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9218 Z= 0.168 Angle : 0.536 5.932 12549 Z= 0.282 Chirality : 0.039 0.190 1433 Planarity : 0.004 0.041 1558 Dihedral : 7.103 60.169 1510 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.23 % Favored : 93.59 % Rotamer: Outliers : 2.64 % Allowed : 16.14 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.25), residues: 1092 helix: 0.11 (0.21), residues: 606 sheet: -1.82 (0.64), residues: 65 loop : -1.02 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 642 TYR 0.013 0.001 TYR A 711 PHE 0.023 0.001 PHE A 569 TRP 0.015 0.001 TRP A 148 HIS 0.006 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 9198) covalent geometry : angle 0.53115 (12503) SS BOND : bond 0.00237 ( 14) SS BOND : angle 1.10882 ( 28) hydrogen bonds : bond 0.04298 ( 432) hydrogen bonds : angle 5.13702 ( 1242) link_BETA1-4 : bond 0.00321 ( 3) link_BETA1-4 : angle 1.80434 ( 9) link_NAG-ASN : bond 0.00283 ( 3) link_NAG-ASN : angle 0.98657 ( 9) *********************** 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 113 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8316 (tt) REVERT: A 47 PHE cc_start: 0.5200 (OUTLIER) cc_final: 0.4598 (p90) REVERT: A 89 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7827 (mm-40) REVERT: A 589 ILE cc_start: 0.8265 (mm) cc_final: 0.7784 (mt) REVERT: A 778 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7543 (pp) outliers start: 26 outliers final: 19 residues processed: 109 average time/residue: 0.1798 time to fit residues: 29.0331 Evaluate side-chains 109 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 364 THR Chi-restraints excluded: chain A residue 431 ASN 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 86 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.178834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.131291 restraints weight = 29756.459| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.90 r_work: 0.3136 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9218 Z= 0.164 Angle : 0.531 5.733 12549 Z= 0.279 Chirality : 0.039 0.191 1433 Planarity : 0.004 0.041 1558 Dihedral : 6.964 60.335 1510 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.14 % Favored : 93.68 % Rotamer: Outliers : 2.54 % Allowed : 16.14 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.25), residues: 1092 helix: 0.15 (0.21), residues: 606 sheet: -1.91 (0.63), residues: 67 loop : -1.01 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 642 TYR 0.013 0.001 TYR A 711 PHE 0.022 0.001 PHE A 569 TRP 0.017 0.001 TRP A 148 HIS 0.007 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 9198) covalent geometry : angle 0.52677 (12503) SS BOND : bond 0.00191 ( 14) SS BOND : angle 1.00857 ( 28) hydrogen bonds : bond 0.04217 ( 432) hydrogen bonds : angle 5.08254 ( 1242) link_BETA1-4 : bond 0.00304 ( 3) link_BETA1-4 : angle 1.77406 ( 9) link_NAG-ASN : bond 0.00263 ( 3) link_NAG-ASN : angle 0.99482 ( 9) *********************** 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 114 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8304 (tt) REVERT: A 47 PHE cc_start: 0.5170 (OUTLIER) cc_final: 0.4580 (p90) REVERT: A 89 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7748 (mm-40) REVERT: A 140 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7010 (pp) REVERT: A 589 ILE cc_start: 0.7944 (mm) cc_final: 0.7449 (mt) REVERT: A 778 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7025 (pp) outliers start: 25 outliers final: 19 residues processed: 110 average time/residue: 0.1919 time to fit residues: 30.8361 Evaluate side-chains 110 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 348 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 431 ASN 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 44 optimal weight: 2.9990 chunk 93 optimal weight: 0.0020 chunk 24 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 57 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.178093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.130332 restraints weight = 29733.773| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.91 r_work: 0.3162 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 9218 Z= 0.148 Angle : 0.547 14.284 12549 Z= 0.288 Chirality : 0.039 0.183 1433 Planarity : 0.004 0.040 1558 Dihedral : 6.837 60.170 1509 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.95 % Favored : 93.77 % Rotamer: Outliers : 2.34 % Allowed : 16.24 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.25), residues: 1092 helix: 0.25 (0.22), residues: 606 sheet: -1.84 (0.63), residues: 67 loop : -1.01 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 642 TYR 0.013 0.001 TYR A 711 PHE 0.023 0.001 PHE A 569 TRP 0.016 0.001 TRP A 148 HIS 0.007 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9198) covalent geometry : angle 0.52878 (12503) SS BOND : bond 0.00538 ( 14) SS BOND : angle 2.81313 ( 28) hydrogen bonds : bond 0.04091 ( 432) hydrogen bonds : angle 5.00903 ( 1242) link_BETA1-4 : bond 0.00418 ( 3) link_BETA1-4 : angle 1.74186 ( 9) link_NAG-ASN : bond 0.00261 ( 3) link_NAG-ASN : angle 0.98276 ( 9) ********************** 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 113 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8340 (tt) REVERT: A 47 PHE cc_start: 0.5199 (OUTLIER) cc_final: 0.4610 (p90) REVERT: A 89 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7751 (mm-40) REVERT: A 140 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7025 (pp) REVERT: A 589 ILE cc_start: 0.7958 (mm) cc_final: 0.7464 (mt) REVERT: A 778 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7057 (pp) REVERT: A 1037 ILE cc_start: 0.8037 (pt) cc_final: 0.7825 (pt) outliers start: 23 outliers final: 16 residues processed: 110 average time/residue: 0.1714 time to fit residues: 27.4927 Evaluate side-chains 110 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 348 SER 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 670 SER Chi-restraints excluded: chain A residue 675 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 0.0060 chunk 98 optimal weight: 1.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- 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 = 0.179462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.138536 restraints weight = 29592.475| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.00 r_work: 0.3182 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9218 Z= 0.147 Angle : 0.521 5.375 12549 Z= 0.274 Chirality : 0.039 0.185 1433 Planarity : 0.004 0.040 1558 Dihedral : 6.699 60.023 1509 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.95 % Favored : 93.86 % Rotamer: Outliers : 2.44 % Allowed : 16.35 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.25), residues: 1092 helix: 0.27 (0.22), residues: 606 sheet: -1.79 (0.64), residues: 67 loop : -1.02 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 642 TYR 0.013 0.001 TYR A 711 PHE 0.023 0.001 PHE A 569 TRP 0.016 0.001 TRP A 148 HIS 0.007 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9198) covalent geometry : angle 0.51605 (12503) SS BOND : bond 0.00185 ( 14) SS BOND : angle 1.12764 ( 28) hydrogen bonds : bond 0.04061 ( 432) hydrogen bonds : angle 4.98672 ( 1242) link_BETA1-4 : bond 0.00286 ( 3) link_BETA1-4 : angle 1.72216 ( 9) link_NAG-ASN : bond 0.00252 ( 3) link_NAG-ASN : angle 0.98297 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4020.82 seconds wall clock time: 68 minutes 53.26 seconds (4133.26 seconds total)