Starting phenix.real_space_refine on Fri Sep 11 03:31:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6mg8_9111/09_2026/6mg8_9111.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mg8_9111/09_2026/6mg8_9111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6mg8_9111/09_2026/6mg8_9111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mg8_9111/09_2026/6mg8_9111.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6mg8_9111/09_2026/6mg8_9111.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6mg8_9111/09_2026/6mg8_9111.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mg8_9111/09_2026/6mg8_9111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mg8_9111/09_2026/6mg8_9111.map" } resolution = 3.6 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= 0.003 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: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 4653 2.51 5 N 1165 2.21 5 O 1187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7034 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 6922 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 266} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 940} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 881 Unresolved non-hydrogen angles: 1088 Unresolved non-hydrogen dihedrals: 717 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'ARG:plan': 19, 'GLN:plan1': 8, 'TYR:plan': 3, 'ASN:plan1': 14, 'PHE:plan': 7, 'GLU:plan': 33, 'ASP:plan': 32, 'TRP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 483 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.39, per 1000 atoms: 0.20 Number of scatterers: 7034 At special positions: 0 Unit cell: (83.84, 110.04, 121.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 1187 8.00 N 1165 7.00 C 4653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 313 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 290 " distance=2.04 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 Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 267.4 milliseconds 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1846 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 5 sheets defined 60.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 59 through 84 removed outlier: 3.753A pdb=" N LEU A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TRP A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 82 " --> pdb=" O CYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 100 removed outlier: 3.903A pdb=" N PHE A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 99 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 104 Processing helix chain 'A' and resid 120 through 133 removed outlier: 3.694A pdb=" N THR A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 161 through 166 Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 184 through 188 removed outlier: 3.548A pdb=" N HIS A 187 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 246 through 256 removed outlier: 4.093A pdb=" N GLU A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 304 through 309 removed outlier: 3.740A pdb=" N VAL A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 309' Processing helix chain 'A' and resid 354 through 362 removed outlier: 3.642A pdb=" N GLU A 360 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 395 removed outlier: 3.813A pdb=" N ALA A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 422 removed outlier: 3.609A pdb=" N LEU A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 445 removed outlier: 3.674A pdb=" N GLY A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 478 removed outlier: 3.949A pdb=" N ALA A 464 " --> pdb=" O VAL A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 496 removed outlier: 3.605A pdb=" N LEU A 494 " --> pdb=" O PRO A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 514 removed outlier: 3.552A pdb=" N VAL A 501 " --> pdb=" O GLY A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 530 removed outlier: 4.097A pdb=" N CYS A 526 " --> pdb=" O ARG A 522 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 530 " --> pdb=" O CYS A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 546 removed outlier: 3.562A pdb=" N SER A 538 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 553 through 589 removed outlier: 4.338A pdb=" N PHE A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Proline residue: A 579 - end of helix removed outlier: 3.636A pdb=" N ASP A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 730 removed outlier: 3.726A pdb=" N PHE A 721 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA A 727 " --> pdb=" O GLU A 723 " (cutoff:3.500A) Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 732 through 755 removed outlier: 3.648A pdb=" N ILE A 740 " --> pdb=" O LYS A 736 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 784 removed outlier: 3.908A pdb=" N PHE A 776 " --> pdb=" O ARG A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 811 Processing helix chain 'A' and resid 830 through 851 removed outlier: 4.152A pdb=" N ASP A 836 " --> pdb=" O HIS A 832 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN A 839 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 874 Processing helix chain 'A' and resid 884 through 889 removed outlier: 4.125A pdb=" N THR A 889 " --> pdb=" O SER A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 910 Processing helix chain 'A' and resid 917 through 922 Processing helix chain 'A' and resid 969 through 989 removed outlier: 3.807A pdb=" N ILE A 983 " --> pdb=" O LYS A 979 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 989 " --> pdb=" O ASN A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1004 removed outlier: 3.698A pdb=" N TRP A1004 " --> pdb=" O PRO A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1034 removed outlier: 4.448A pdb=" N SER A1009 " --> pdb=" O GLU A1005 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ARG A1011 " --> pdb=" O TYR A1007 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N HIS A1012 " --> pdb=" O ILE A1008 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A1019 " --> pdb=" O LEU A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1061 removed outlier: 3.505A pdb=" N GLY A1061 " --> pdb=" O MET A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1093 removed outlier: 3.750A pdb=" N GLY A1077 " --> pdb=" O ILE A1073 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL A1080 " --> pdb=" O VAL A1076 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU A1081 " --> pdb=" O GLY A1077 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE A1082 " --> pdb=" O ILE A1078 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N HIS A1085 " --> pdb=" O GLU A1081 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL A1086 " --> pdb=" O PHE A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1109 removed outlier: 4.257A pdb=" N ALA A1101 " --> pdb=" O LYS A1097 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET A1102 " --> pdb=" O ASN A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1123 Processing helix chain 'A' and resid 1124 through 1129 Processing helix chain 'A' and resid 1131 through 1138 removed outlier: 3.618A pdb=" N VAL A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1155 Processing helix chain 'A' and resid 1155 through 1164 removed outlier: 3.864A pdb=" N VAL A1159 " --> pdb=" O VAL A1155 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 352 Processing sheet with id=AA2, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.630A pdb=" N VAL A 176 " --> pdb=" O TRP A 183 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A 178 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 181 " --> pdb=" O MET A 178 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 232 Processing sheet with id=AA4, first strand: chain 'A' and resid 333 through 334 Processing sheet with id=AA5, first strand: chain 'A' and resid 959 through 964 389 hydrogen bonds defined for protein. 1122 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: 1.22 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2223 1.34 - 1.46: 1789 1.46 - 1.58: 3161 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 7221 Sorted by residual: bond pdb=" C10 CLR A1401 " pdb=" C5 CLR A1401 " ideal model delta sigma weight residual 1.519 1.402 0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" C10 CLR A1403 " pdb=" C5 CLR A1403 " ideal model delta sigma weight residual 1.519 1.404 0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C10 CLR A1402 " pdb=" C5 CLR A1402 " ideal model delta sigma weight residual 1.519 1.405 0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" C10 CLR A1404 " pdb=" C5 CLR A1404 " ideal model delta sigma weight residual 1.519 1.405 0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C4 CLR A1401 " pdb=" C5 CLR A1401 " ideal model delta sigma weight residual 1.506 1.397 0.109 2.00e-02 2.50e+03 3.00e+01 ... (remaining 7216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 9732 2.16 - 4.31: 173 4.31 - 6.47: 46 6.47 - 8.62: 5 8.62 - 10.78: 1 Bond angle restraints: 9957 Sorted by residual: angle pdb=" C HIS A 930 " pdb=" N ARG A 931 " pdb=" CA ARG A 931 " ideal model delta sigma weight residual 120.97 131.75 -10.78 2.84e+00 1.24e-01 1.44e+01 angle pdb=" C GLU A 108 " pdb=" N THR A 109 " pdb=" CA THR A 109 " ideal model delta sigma weight residual 121.54 126.56 -5.02 1.91e+00 2.74e-01 6.90e+00 angle pdb=" N GLY A 862 " pdb=" CA GLY A 862 " pdb=" C GLY A 862 " ideal model delta sigma weight residual 111.78 116.20 -4.42 1.69e+00 3.50e-01 6.83e+00 angle pdb=" C ASP A 895 " pdb=" N ALA A 896 " pdb=" CA ALA A 896 " ideal model delta sigma weight residual 122.15 115.01 7.14 2.83e+00 1.25e-01 6.37e+00 angle pdb=" N ASP A 895 " pdb=" CA ASP A 895 " pdb=" C ASP A 895 " ideal model delta sigma weight residual 110.80 116.17 -5.37 2.13e+00 2.20e-01 6.37e+00 ... (remaining 9952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 3742 16.65 - 33.29: 293 33.29 - 49.94: 63 49.94 - 66.58: 4 66.58 - 83.23: 5 Dihedral angle restraints: 4107 sinusoidal: 1239 harmonic: 2868 Sorted by residual: dihedral pdb=" CB CYS A 220 " pdb=" SG CYS A 220 " pdb=" SG CYS A 313 " pdb=" CB CYS A 313 " ideal model delta sinusoidal sigma weight residual 93.00 168.74 -75.74 1 1.00e+01 1.00e-02 7.24e+01 dihedral pdb=" CA VAL A 894 " pdb=" C VAL A 894 " pdb=" N ASP A 895 " pdb=" CA ASP A 895 " ideal model delta harmonic sigma weight residual -180.00 -158.90 -21.10 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA LYS A 191 " pdb=" C LYS A 191 " pdb=" N SER A 192 " pdb=" CA SER A 192 " ideal model delta harmonic sigma weight residual -180.00 -160.12 -19.88 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 4104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1168 0.106 - 0.211: 26 0.211 - 0.317: 6 0.317 - 0.423: 3 0.423 - 0.529: 7 Chirality restraints: 1210 Sorted by residual: chirality pdb=" C10 CLR A1401 " pdb=" C1 CLR A1401 " pdb=" C5 CLR A1401 " pdb=" C9 CLR A1401 " both_signs ideal model delta sigma weight residual False -2.85 -2.32 -0.53 2.00e-01 2.50e+01 6.99e+00 chirality pdb=" C10 CLR A1404 " pdb=" C1 CLR A1404 " pdb=" C5 CLR A1404 " pdb=" C9 CLR A1404 " both_signs ideal model delta sigma weight residual False -2.85 -2.39 -0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" C10 CLR A1402 " pdb=" C1 CLR A1402 " pdb=" C5 CLR A1402 " pdb=" C9 CLR A1402 " both_signs ideal model delta sigma weight residual False -2.85 -2.39 -0.46 2.00e-01 2.50e+01 5.20e+00 ... (remaining 1207 not shown) Planarity restraints: 1242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A1067 " 0.027 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A1068 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A1068 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1068 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 931 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO A 932 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 932 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 932 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 354 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO A 355 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " -0.019 5.00e-02 4.00e+02 ... (remaining 1239 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 148 2.71 - 3.25: 7542 3.25 - 3.80: 11010 3.80 - 4.35: 13506 4.35 - 4.90: 22463 Nonbonded interactions: 54669 Sorted by model distance: nonbonded pdb=" NH2 ARG A 280 " pdb=" O GLY A 315 " model vdw 2.157 3.120 nonbonded pdb=" O PRO A 856 " pdb=" OH TYR A 870 " model vdw 2.229 3.040 nonbonded pdb=" O TRP A1013 " pdb=" OG SER A1017 " model vdw 2.280 3.040 nonbonded pdb=" OG1 THR A 485 " pdb=" OE1 GLN A 562 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR A 806 " pdb=" NE ARG A 835 " model vdw 2.310 3.120 ... (remaining 54664 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.940 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 : 0.006 0.117 7224 Z= 0.299 Angle : 0.748 10.778 9963 Z= 0.362 Chirality : 0.061 0.529 1210 Planarity : 0.004 0.040 1242 Dihedral : 12.854 83.230 2252 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 are not related in a simple way. whole: -3.49 (0.23), residues: 981 helix: -1.83 (0.18), residues: 562 sheet: -4.46 (0.49), residues: 47 loop : -2.59 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 931 TYR 0.015 0.001 TYR A 999 PHE 0.015 0.001 PHE A 502 TRP 0.009 0.001 TRP A 830 HIS 0.003 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.30 ( 7221) covalent geometry : angle 0.74684 / 0.36 ( 9957) SS BOND : bond 0.00357 / 0.18 ( 3) SS BOND : angle 1.75972 / 0.90 ( 6) hydrogen bonds : bond 0.16786 / 12.16 ( 389) hydrogen bonds : angle 6.29175 / 4.41 ( 1122) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 248 LEU cc_start: 0.9229 (mp) cc_final: 0.8790 (tt) REVERT: A 358 MET cc_start: 0.9062 (tpt) cc_final: 0.8782 (tpp) REVERT: A 489 LEU cc_start: 0.8479 (tp) cc_final: 0.8277 (tp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0452 time to fit residues: 8.2961 Evaluate side-chains 84 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 GLN A 163 GLN A 182 GLN A 228 GLN A 314 GLN A 506 HIS A 809 HIS A 875 GLN A 915 ASN A 926 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.113972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.091468 restraints weight = 14376.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.094115 restraints weight = 7177.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.095844 restraints weight = 4584.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.096948 restraints weight = 3427.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.097414 restraints weight = 2844.466| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7224 Z= 0.139 Angle : 0.609 8.189 9963 Z= 0.302 Chirality : 0.041 0.146 1210 Planarity : 0.004 0.041 1242 Dihedral : 5.182 50.571 1078 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.40 % Allowed : 16.11 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 are not related in a simple way. whole: -1.97 (0.26), residues: 981 helix: -0.55 (0.21), residues: 566 sheet: -3.88 (0.60), residues: 46 loop : -2.04 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 280 TYR 0.016 0.001 TYR A 870 PHE 0.019 0.002 PHE A 781 TRP 0.015 0.001 TRP A 849 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 7221) covalent geometry : angle 0.60805 / 0.30 ( 9957) SS BOND : bond 0.00370 / 0.19 ( 3) SS BOND : angle 1.77803 / 0.96 ( 6) hydrogen bonds : bond 0.03374 / 2.38 ( 389) hydrogen bonds : angle 4.40889 / 3.04 ( 1122) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.247 Fit side-chains REVERT: A 204 GLN cc_start: 0.7608 (tt0) cc_final: 0.7364 (tt0) REVERT: A 248 LEU cc_start: 0.9097 (mp) cc_final: 0.8706 (tt) REVERT: A 358 MET cc_start: 0.8965 (tpt) cc_final: 0.8678 (tpp) REVERT: A 489 LEU cc_start: 0.8502 (tp) cc_final: 0.8264 (tp) REVERT: A 819 MET cc_start: 0.8273 (ttm) cc_final: 0.7949 (ttp) REVERT: A 1002 LEU cc_start: 0.9055 (mt) cc_final: 0.8714 (mt) REVERT: A 1091 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8515 (pt) outliers start: 8 outliers final: 4 residues processed: 111 average time/residue: 0.0482 time to fit residues: 8.4310 Evaluate side-chains 94 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1091 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 56 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 91 optimal weight: 0.2980 chunk 89 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 ASN ** A1152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.111535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.091678 restraints weight = 14278.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.092278 restraints weight = 6987.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.093480 restraints weight = 5154.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.093832 restraints weight = 3700.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.093956 restraints weight = 3329.910| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7224 Z= 0.190 Angle : 0.653 10.451 9963 Z= 0.320 Chirality : 0.042 0.154 1210 Planarity : 0.004 0.042 1242 Dihedral : 5.282 49.854 1078 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.80 % Allowed : 17.86 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 are not related in a simple way. whole: -1.40 (0.27), residues: 981 helix: -0.02 (0.22), residues: 570 sheet: -3.93 (0.55), residues: 46 loop : -1.87 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 124 TYR 0.017 0.002 TYR A 438 PHE 0.016 0.002 PHE A 569 TRP 0.009 0.001 TRP A 830 HIS 0.005 0.001 HIS A 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 ( 7221) covalent geometry : angle 0.65177 / 0.32 ( 9957) SS BOND : bond 0.00609 / 0.31 ( 3) SS BOND : angle 1.80937 / 0.96 ( 6) hydrogen bonds : bond 0.03410 / 2.41 ( 389) hydrogen bonds : angle 4.30631 / 2.98 ( 1122) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 358 MET cc_start: 0.9007 (tpt) cc_final: 0.8533 (tpp) REVERT: A 569 PHE cc_start: 0.8867 (m-80) cc_final: 0.8555 (m-10) REVERT: A 819 MET cc_start: 0.8354 (ttm) cc_final: 0.8028 (ttp) REVERT: A 1002 LEU cc_start: 0.9102 (mt) cc_final: 0.8725 (mt) REVERT: A 1056 MET cc_start: 0.9049 (mmm) cc_final: 0.8814 (mmm) REVERT: A 1091 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8602 (pt) outliers start: 16 outliers final: 11 residues processed: 112 average time/residue: 0.0461 time to fit residues: 8.3987 Evaluate side-chains 94 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1113 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 4 optimal weight: 0.0770 chunk 55 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 64 optimal weight: 0.3980 chunk 77 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 0.0980 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.116460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.096035 restraints weight = 14493.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.096159 restraints weight = 7200.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.098014 restraints weight = 5121.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.097889 restraints weight = 3765.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.098358 restraints weight = 3749.293| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7224 Z= 0.113 Angle : 0.597 9.325 9963 Z= 0.288 Chirality : 0.040 0.199 1210 Planarity : 0.003 0.041 1242 Dihedral : 4.945 53.036 1078 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.68 % Allowed : 18.04 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 are not related in a simple way. whole: -0.76 (0.27), residues: 981 helix: 0.48 (0.22), residues: 569 sheet: -3.62 (0.59), residues: 45 loop : -1.60 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 124 TYR 0.031 0.001 TYR A 999 PHE 0.023 0.001 PHE A 781 TRP 0.007 0.001 TRP A 830 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 7221) covalent geometry : angle 0.59593 / 0.29 ( 9957) SS BOND : bond 0.00572 / 0.29 ( 3) SS BOND : angle 1.35924 / 0.73 ( 6) hydrogen bonds : bond 0.02952 / 2.09 ( 389) hydrogen bonds : angle 4.06432 / 2.80 ( 1122) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 282 CYS cc_start: 0.5840 (p) cc_final: 0.5635 (p) REVERT: A 358 MET cc_start: 0.8908 (tpt) cc_final: 0.8476 (tpp) REVERT: A 556 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8424 (mm) REVERT: A 561 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8959 (mm) REVERT: A 569 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8631 (m-80) REVERT: A 806 TYR cc_start: 0.8040 (m-80) cc_final: 0.7775 (m-80) REVERT: A 1002 LEU cc_start: 0.9062 (mt) cc_final: 0.8703 (mt) REVERT: A 1056 MET cc_start: 0.8961 (mmm) cc_final: 0.8735 (mmm) REVERT: A 1091 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8543 (pt) outliers start: 21 outliers final: 10 residues processed: 110 average time/residue: 0.0493 time to fit residues: 8.7394 Evaluate side-chains 105 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1113 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 56 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 chunk 78 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.113737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.092834 restraints weight = 14276.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.093795 restraints weight = 7162.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.094723 restraints weight = 5362.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.095216 restraints weight = 4029.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.095289 restraints weight = 3766.141| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7224 Z= 0.153 Angle : 0.620 10.488 9963 Z= 0.300 Chirality : 0.041 0.200 1210 Planarity : 0.003 0.040 1242 Dihedral : 5.127 55.413 1078 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.85 % Allowed : 20.14 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 are not related in a simple way. whole: -0.52 (0.28), residues: 981 helix: 0.70 (0.22), residues: 567 sheet: -3.62 (0.58), residues: 45 loop : -1.51 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 124 TYR 0.028 0.001 TYR A 999 PHE 0.015 0.001 PHE A1090 TRP 0.010 0.001 TRP A 837 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 7221) covalent geometry : angle 0.61810 / 0.30 ( 9957) SS BOND : bond 0.00474 / 0.24 ( 3) SS BOND : angle 2.26176 / 1.22 ( 6) hydrogen bonds : bond 0.03053 / 2.15 ( 389) hydrogen bonds : angle 4.07506 / 2.81 ( 1122) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 561 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.9003 (mm) REVERT: A 906 TYR cc_start: 0.8594 (m-10) cc_final: 0.8315 (m-10) REVERT: A 1002 LEU cc_start: 0.9069 (mt) cc_final: 0.8695 (mt) REVERT: A 1091 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8588 (pt) outliers start: 22 outliers final: 15 residues processed: 115 average time/residue: 0.0447 time to fit residues: 8.3925 Evaluate side-chains 109 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1113 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 16 optimal weight: 0.0870 chunk 63 optimal weight: 0.3980 chunk 57 optimal weight: 0.2980 chunk 91 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.114303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.093246 restraints weight = 14339.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.094398 restraints weight = 7095.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.095541 restraints weight = 5244.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.095599 restraints weight = 3871.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.096436 restraints weight = 3692.773| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7224 Z= 0.137 Angle : 0.632 11.626 9963 Z= 0.303 Chirality : 0.041 0.186 1210 Planarity : 0.003 0.039 1242 Dihedral : 5.045 43.988 1078 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.20 % Allowed : 20.49 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 are not related in a simple way. whole: -0.29 (0.28), residues: 981 helix: 0.91 (0.22), residues: 564 sheet: -3.64 (0.57), residues: 45 loop : -1.43 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 124 TYR 0.026 0.001 TYR A 999 PHE 0.023 0.002 PHE A 781 TRP 0.009 0.001 TRP A 837 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 7221) covalent geometry : angle 0.62939 / 0.30 ( 9957) SS BOND : bond 0.00399 / 0.20 ( 3) SS BOND : angle 2.34703 / 1.22 ( 6) hydrogen bonds : bond 0.02975 / 2.11 ( 389) hydrogen bonds : angle 4.02328 / 2.78 ( 1122) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 556 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8562 (mm) REVERT: A 561 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.9023 (mm) REVERT: A 819 MET cc_start: 0.8205 (ttm) cc_final: 0.7881 (ttp) REVERT: A 906 TYR cc_start: 0.8593 (m-10) cc_final: 0.8303 (m-10) REVERT: A 1002 LEU cc_start: 0.9014 (mt) cc_final: 0.8641 (mt) REVERT: A 1019 SER cc_start: 0.9512 (t) cc_final: 0.9265 (m) REVERT: A 1056 MET cc_start: 0.8916 (mmm) cc_final: 0.8697 (mmm) REVERT: A 1091 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8613 (pt) outliers start: 24 outliers final: 16 residues processed: 117 average time/residue: 0.0445 time to fit residues: 8.5624 Evaluate side-chains 114 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1113 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 51 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 58 optimal weight: 0.0970 chunk 75 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.114608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.093301 restraints weight = 14399.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.093767 restraints weight = 7221.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.095155 restraints weight = 5486.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.095388 restraints weight = 4030.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.095410 restraints weight = 3752.500| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7224 Z= 0.139 Angle : 0.634 11.700 9963 Z= 0.302 Chirality : 0.041 0.183 1210 Planarity : 0.003 0.038 1242 Dihedral : 4.983 40.464 1078 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 5.08 % Allowed : 20.84 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 are not related in a simple way. whole: -0.16 (0.28), residues: 981 helix: 1.04 (0.23), residues: 564 sheet: -3.44 (0.60), residues: 45 loop : -1.43 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 124 TYR 0.024 0.001 TYR A 999 PHE 0.015 0.001 PHE A1131 TRP 0.010 0.001 TRP A 837 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 7221) covalent geometry : angle 0.63272 / 0.30 ( 9957) SS BOND : bond 0.00401 / 0.21 ( 3) SS BOND : angle 1.72892 / 0.92 ( 6) hydrogen bonds : bond 0.02971 / 2.11 ( 389) hydrogen bonds : angle 4.02928 / 2.81 ( 1122) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 556 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8431 (mm) REVERT: A 561 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9030 (mm) REVERT: A 806 TYR cc_start: 0.8147 (m-80) cc_final: 0.7929 (m-80) REVERT: A 819 MET cc_start: 0.8274 (ttm) cc_final: 0.7983 (ttp) REVERT: A 1002 LEU cc_start: 0.9004 (mt) cc_final: 0.8622 (mt) REVERT: A 1019 SER cc_start: 0.9504 (t) cc_final: 0.9255 (m) REVERT: A 1056 MET cc_start: 0.8883 (mmm) cc_final: 0.8664 (mmm) REVERT: A 1091 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8568 (pt) REVERT: A 1125 MET cc_start: 0.8263 (tpp) cc_final: 0.7878 (tpp) outliers start: 29 outliers final: 22 residues processed: 116 average time/residue: 0.0432 time to fit residues: 8.1970 Evaluate side-chains 121 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1113 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 64 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 71 optimal weight: 0.0670 chunk 89 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.113510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.093332 restraints weight = 14372.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.093305 restraints weight = 7032.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.094823 restraints weight = 5433.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.095274 restraints weight = 3825.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.095651 restraints weight = 3501.229| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7224 Z= 0.168 Angle : 0.660 11.428 9963 Z= 0.315 Chirality : 0.043 0.270 1210 Planarity : 0.003 0.038 1242 Dihedral : 5.028 39.984 1078 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.90 % Allowed : 21.89 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 are not related in a simple way. whole: -0.19 (0.28), residues: 981 helix: 0.99 (0.23), residues: 567 sheet: -3.31 (0.65), residues: 45 loop : -1.44 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 835 TYR 0.023 0.001 TYR A 999 PHE 0.019 0.002 PHE A 743 TRP 0.012 0.001 TRP A 837 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 7221) covalent geometry : angle 0.65873 / 0.31 ( 9957) SS BOND : bond 0.00410 / 0.21 ( 3) SS BOND : angle 1.68004 / 0.89 ( 6) hydrogen bonds : bond 0.03040 / 2.16 ( 389) hydrogen bonds : angle 4.07037 / 2.84 ( 1122) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.251 Fit side-chains REVERT: A 561 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.9029 (mm) REVERT: A 1002 LEU cc_start: 0.9062 (mt) cc_final: 0.8673 (mt) REVERT: A 1019 SER cc_start: 0.9502 (t) cc_final: 0.9267 (m) REVERT: A 1125 MET cc_start: 0.8217 (tpp) cc_final: 0.7839 (tpp) outliers start: 28 outliers final: 24 residues processed: 119 average time/residue: 0.0445 time to fit residues: 8.6656 Evaluate side-chains 117 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1113 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 28 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 49 optimal weight: 0.0030 chunk 23 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.113128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.092432 restraints weight = 14248.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.093586 restraints weight = 6875.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.094734 restraints weight = 5016.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.094889 restraints weight = 3742.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.095001 restraints weight = 3654.221| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7224 Z= 0.158 Angle : 0.660 11.971 9963 Z= 0.312 Chirality : 0.042 0.187 1210 Planarity : 0.003 0.038 1242 Dihedral : 4.974 41.830 1078 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 5.08 % Allowed : 21.89 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 are not related in a simple way. whole: -0.13 (0.28), residues: 981 helix: 1.04 (0.23), residues: 563 sheet: -3.20 (0.67), residues: 45 loop : -1.40 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 835 TYR 0.022 0.001 TYR A 999 PHE 0.015 0.001 PHE A1131 TRP 0.011 0.001 TRP A 837 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 7221) covalent geometry : angle 0.65877 / 0.31 ( 9957) SS BOND : bond 0.00408 / 0.21 ( 3) SS BOND : angle 1.52683 / 0.80 ( 6) hydrogen bonds : bond 0.02988 / 2.13 ( 389) hydrogen bonds : angle 4.09294 / 2.85 ( 1122) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 325 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7851 (pm20) REVERT: A 561 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9030 (mm) REVERT: A 819 MET cc_start: 0.8390 (ttm) cc_final: 0.8116 (ttp) REVERT: A 1002 LEU cc_start: 0.9057 (mt) cc_final: 0.8653 (mt) REVERT: A 1019 SER cc_start: 0.9502 (t) cc_final: 0.9261 (m) outliers start: 29 outliers final: 25 residues processed: 117 average time/residue: 0.0463 time to fit residues: 8.7802 Evaluate side-chains 119 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 65 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.113098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.092662 restraints weight = 14303.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.093677 restraints weight = 6640.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.094928 restraints weight = 4670.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.095257 restraints weight = 3594.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.095607 restraints weight = 3494.616| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7224 Z= 0.159 Angle : 0.676 12.437 9963 Z= 0.318 Chirality : 0.043 0.193 1210 Planarity : 0.003 0.038 1242 Dihedral : 4.952 42.854 1078 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.55 % Allowed : 22.59 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 are not related in a simple way. whole: -0.15 (0.28), residues: 981 helix: 1.01 (0.23), residues: 567 sheet: -3.17 (0.67), residues: 45 loop : -1.43 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 835 TYR 0.022 0.001 TYR A 999 PHE 0.016 0.002 PHE A1090 TRP 0.011 0.001 TRP A 837 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 7221) covalent geometry : angle 0.67518 / 0.32 ( 9957) SS BOND : bond 0.00390 / 0.20 ( 3) SS BOND : angle 1.48585 / 0.78 ( 6) hydrogen bonds : bond 0.03042 / 2.17 ( 389) hydrogen bonds : angle 4.09329 / 2.85 ( 1122) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 325 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7850 (pm20) REVERT: A 556 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8519 (mm) REVERT: A 819 MET cc_start: 0.8379 (ttm) cc_final: 0.8098 (ttp) REVERT: A 1002 LEU cc_start: 0.9065 (mt) cc_final: 0.8670 (mt) REVERT: A 1019 SER cc_start: 0.9501 (t) cc_final: 0.9262 (m) outliers start: 26 outliers final: 23 residues processed: 115 average time/residue: 0.0486 time to fit residues: 9.1194 Evaluate side-chains 115 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 71 optimal weight: 0.9990 chunk 70 optimal weight: 0.0770 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 0.2980 chunk 90 optimal weight: 0.8980 chunk 78 optimal weight: 0.3980 chunk 15 optimal weight: 0.0870 chunk 68 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.114619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.093766 restraints weight = 14283.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.094920 restraints weight = 6902.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.095917 restraints weight = 5034.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.096015 restraints weight = 3855.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.096951 restraints weight = 3692.932| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7224 Z= 0.129 Angle : 0.681 13.036 9963 Z= 0.314 Chirality : 0.043 0.210 1210 Planarity : 0.003 0.038 1242 Dihedral : 4.825 43.905 1078 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 4.55 % Allowed : 22.77 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 are not related in a simple way. whole: -0.09 (0.28), residues: 981 helix: 1.05 (0.23), residues: 566 sheet: -3.10 (0.68), residues: 45 loop : -1.39 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 557 TYR 0.022 0.001 TYR A 999 PHE 0.026 0.001 PHE A1090 TRP 0.008 0.001 TRP A 837 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 7221) covalent geometry : angle 0.67997 / 0.31 ( 9957) SS BOND : bond 0.00375 / 0.19 ( 3) SS BOND : angle 1.41085 / 0.74 ( 6) hydrogen bonds : bond 0.02962 / 2.12 ( 389) hydrogen bonds : angle 4.12829 / 2.89 ( 1122) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1105.33 seconds wall clock time: 19 minutes 41.51 seconds (1181.51 seconds total)