Starting phenix.real_space_refine on Thu Jul 2 09:15:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rhr_24467/07_2026/7rhr_24467.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rhr_24467/07_2026/7rhr_24467.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7rhr_24467/07_2026/7rhr_24467.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rhr_24467/07_2026/7rhr_24467.cif" model { file = "/net/cci-nas-00/data/ceres_data/7rhr_24467/07_2026/7rhr_24467.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rhr_24467/07_2026/7rhr_24467.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rhr_24467/07_2026/7rhr_24467.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rhr_24467/07_2026/7rhr_24467.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.137 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 40 5.16 5 C 5121 2.51 5 N 1265 2.21 5 O 1394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7820 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7680 Classifications: {'peptide': 974} Link IDs: {'PTRANS': 41, 'TRANS': 932} Chain breaks: 1 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 chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 112 Unusual residues: {'CLR': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.79, per 1000 atoms: 0.23 Number of scatterers: 7820 At special positions: 0 Unit cell: (79.5, 81.62, 138.86, 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 40 16.00 O 1394 8.00 N 1265 7.00 C 5121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 193 " - pdb=" SG CYS A 216 " distance=2.04 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 317 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 294 " 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-ASN " NAG A1503 " - " ASN A 302 " " NAG A1504 " - " ASN A 339 " " NAG B 1 " - " ASN A 989 " Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 370.9 milliseconds 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1828 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 7 sheets defined 63.6% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 69 through 87 Processing helix chain 'A' and resid 89 through 106 removed outlier: 3.879A pdb=" N VAL A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE A 102 " --> pdb=" O ILE A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 124 through 137 removed outlier: 3.755A pdb=" N ARG A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 137 " --> pdb=" O THR A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.601A pdb=" N LEU A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.607A pdb=" N GLN A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 229 removed outlier: 5.935A pdb=" N TRP A 226 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLU A 227 " --> pdb=" O CYS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.988A pdb=" N GLY A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 276 Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 328 through 332 removed outlier: 3.668A pdb=" N ILE A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 328 through 332' Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 378 through 400 Processing helix chain 'A' and resid 413 through 423 removed outlier: 3.596A pdb=" N LEU A 417 " --> pdb=" O THR A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 448 Processing helix chain 'A' and resid 456 through 481 Processing helix chain 'A' and resid 492 through 518 removed outlier: 4.180A pdb=" N ASP A 503 " --> pdb=" O GLY A 499 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASP A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASN A 518 " --> pdb=" O GLU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 553 removed outlier: 5.490A pdb=" N ALA A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N SER A 537 " --> pdb=" O ARG A 533 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET A 551 " --> pdb=" O THR A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 581 Processing helix chain 'A' and resid 581 through 595 removed outlier: 3.507A pdb=" N ILE A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL A 595 " --> pdb=" O TYR A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.995A pdb=" N LYS A 728 " --> pdb=" O SER A 724 " (cutoff:3.500A) Proline residue: A 732 - end of helix removed outlier: 3.737A pdb=" N LEU A 735 " --> pdb=" O ALA A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 758 removed outlier: 4.295A pdb=" N VAL A 741 " --> pdb=" O PRO A 737 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 742 " --> pdb=" O LYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 770 removed outlier: 3.552A pdb=" N ASP A 769 " --> pdb=" O ASP A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 788 removed outlier: 3.706A pdb=" N ASP A 779 " --> pdb=" O THR A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 815 removed outlier: 3.610A pdb=" N LEU A 809 " --> pdb=" O ALA A 805 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A 810 " --> pdb=" O GLN A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 855 removed outlier: 3.647A pdb=" N TYR A 837 " --> pdb=" O MET A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 879 removed outlier: 3.892A pdb=" N GLN A 879 " --> pdb=" O LYS A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.916A pdb=" N ASN A 890 " --> pdb=" O ILE A 887 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN A 891 " --> pdb=" O ASN A 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 887 through 891' Processing helix chain 'A' and resid 908 through 920 Processing helix chain 'A' and resid 920 through 927 Processing helix chain 'A' and resid 972 through 992 removed outlier: 3.586A pdb=" N SER A 992 " --> pdb=" O ASN A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1006 Processing helix chain 'A' and resid 1008 through 1011 removed outlier: 3.635A pdb=" N ILE A1011 " --> pdb=" O GLU A1008 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1008 through 1011' Processing helix chain 'A' and resid 1012 through 1037 removed outlier: 3.656A pdb=" N TRP A1016 " --> pdb=" O SER A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1064 Processing helix chain 'A' and resid 1068 through 1096 removed outlier: 3.950A pdb=" N VAL A1079 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY A1080 " --> pdb=" O ILE A1076 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU A1084 " --> pdb=" O GLY A1080 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N PHE A1085 " --> pdb=" O ILE A1081 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR A1086 " --> pdb=" O GLY A1082 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N HIS A1088 " --> pdb=" O GLU A1084 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL A1089 " --> pdb=" O PHE A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1112 Processing helix chain 'A' and resid 1112 through 1126 removed outlier: 3.537A pdb=" N VAL A1126 " --> pdb=" O THR A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1130 Processing helix chain 'A' and resid 1141 through 1159 Processing helix chain 'A' and resid 1159 through 1167 removed outlier: 3.619A pdb=" N PHE A1166 " --> pdb=" O VAL A1162 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 218 through 219 Processing sheet with id=AA2, first strand: chain 'A' and resid 218 through 219 removed outlier: 3.669A pdb=" N ASN A 144 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 182 Processing sheet with id=AA4, first strand: chain 'A' and resid 236 through 237 Processing sheet with id=AA5, first strand: chain 'A' and resid 317 through 318 Processing sheet with id=AA6, first strand: chain 'A' and resid 337 through 338 removed outlier: 6.972A pdb=" N VAL A 337 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 961 through 968 446 hydrogen bonds defined for protein. 1293 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: 1.20 Time building geometry restraints manager: 0.82 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: 2384 1.34 - 1.46: 1327 1.46 - 1.58: 4236 1.58 - 1.70: 1 1.70 - 1.82: 65 Bond restraints: 8013 Sorted by residual: bond pdb=" CA ASP A 223 " pdb=" C ASP A 223 " ideal model delta sigma weight residual 1.522 1.488 0.034 1.38e-02 5.25e+03 6.06e+00 bond pdb=" CB PRO A 732 " pdb=" CG PRO A 732 " ideal model delta sigma weight residual 1.492 1.614 -0.122 5.00e-02 4.00e+02 5.91e+00 bond pdb=" CA ASN A 144 " pdb=" CB ASN A 144 " ideal model delta sigma weight residual 1.526 1.543 -0.016 9.30e-03 1.16e+04 3.12e+00 bond pdb=" CB VAL A 159 " pdb=" CG2 VAL A 159 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.75e+00 bond pdb=" C10 CLR A1502 " pdb=" C9 CLR A1502 " ideal model delta sigma weight residual 1.551 1.520 0.031 2.00e-02 2.50e+03 2.44e+00 ... (remaining 8008 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 10417 1.80 - 3.59: 422 3.59 - 5.39: 64 5.39 - 7.18: 9 7.18 - 8.98: 4 Bond angle restraints: 10916 Sorted by residual: angle pdb=" CA PRO A 732 " pdb=" N PRO A 732 " pdb=" CD PRO A 732 " ideal model delta sigma weight residual 112.00 103.07 8.93 1.40e+00 5.10e-01 4.07e+01 angle pdb=" N PHE A1004 " pdb=" CA PHE A1004 " pdb=" C PHE A1004 " ideal model delta sigma weight residual 114.75 107.40 7.35 1.26e+00 6.30e-01 3.41e+01 angle pdb=" N ASN A 907 " pdb=" CA ASN A 907 " pdb=" C ASN A 907 " ideal model delta sigma weight residual 114.04 108.06 5.98 1.24e+00 6.50e-01 2.32e+01 angle pdb=" C TYR A 237 " pdb=" N LEU A 238 " pdb=" CA LEU A 238 " ideal model delta sigma weight residual 120.49 114.92 5.57 1.42e+00 4.96e-01 1.54e+01 angle pdb=" CA ARG A 932 " pdb=" CB ARG A 932 " pdb=" CG ARG A 932 " ideal model delta sigma weight residual 114.10 107.41 6.69 2.00e+00 2.50e-01 1.12e+01 ... (remaining 10911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4375 17.76 - 35.52: 262 35.52 - 53.28: 26 53.28 - 71.04: 13 71.04 - 88.80: 7 Dihedral angle restraints: 4683 sinusoidal: 1845 harmonic: 2838 Sorted by residual: dihedral pdb=" CA ARG A 932 " pdb=" C ARG A 932 " pdb=" N PRO A 933 " pdb=" CA PRO A 933 " ideal model delta harmonic sigma weight residual -180.00 -103.48 -76.52 0 5.00e+00 4.00e-02 2.34e+02 dihedral pdb=" CA LYS A 828 " pdb=" C LYS A 828 " pdb=" N GLN A 829 " pdb=" CA GLN A 829 " ideal model delta harmonic sigma weight residual -180.00 -150.91 -29.09 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA ASN A 882 " pdb=" C ASN A 882 " pdb=" N SER A 883 " pdb=" CA SER A 883 " ideal model delta harmonic sigma weight residual -180.00 -157.54 -22.46 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 4680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 920 0.050 - 0.101: 296 0.101 - 0.151: 52 0.151 - 0.201: 6 0.201 - 0.252: 3 Chirality restraints: 1277 Sorted by residual: chirality pdb=" C13 CLR A1502 " pdb=" C12 CLR A1502 " pdb=" C14 CLR A1502 " pdb=" C17 CLR A1502 " both_signs ideal model delta sigma weight residual False -2.93 -2.68 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C13 CLR A1505 " pdb=" C12 CLR A1505 " pdb=" C14 CLR A1505 " pdb=" C17 CLR A1505 " both_signs ideal model delta sigma weight residual False -2.93 -2.72 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C13 CLR A1501 " pdb=" C12 CLR A1501 " pdb=" C14 CLR A1501 " pdb=" C17 CLR A1501 " both_signs ideal model delta sigma weight residual False -2.93 -2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1274 not shown) Planarity restraints: 1350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 932 " 0.067 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO A 933 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO A 933 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 933 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 731 " 0.039 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO A 732 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 732 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 732 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 912 " 0.014 2.00e-02 2.50e+03 1.26e-02 3.15e+00 pdb=" CG TYR A 912 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 912 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 912 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 912 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 912 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 912 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 912 " 0.000 2.00e-02 2.50e+03 ... (remaining 1347 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 113 2.69 - 3.24: 7635 3.24 - 3.79: 11802 3.79 - 4.35: 16297 4.35 - 4.90: 27294 Nonbonded interactions: 63141 Sorted by model distance: nonbonded pdb=" OH TYR A 442 " pdb=" OD1 ASP A1117 " model vdw 2.131 3.040 nonbonded pdb=" NE2 GLN A 150 " pdb=" OE1 GLN A 407 " model vdw 2.172 3.120 nonbonded pdb=" NH2 ARG A 134 " pdb=" OE2 GLU A 140 " model vdw 2.191 3.120 nonbonded pdb=" NH2 ARG A 431 " pdb=" O MET A1128 " model vdw 2.235 3.120 nonbonded pdb=" OG1 THR A 880 " pdb=" O ASP A 884 " model vdw 2.315 3.040 ... (remaining 63136 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.750 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:5.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 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 0.122 8020 Z= 0.267 Angle : 0.840 8.980 10934 Z= 0.480 Chirality : 0.050 0.252 1277 Planarity : 0.005 0.101 1347 Dihedral : 11.910 88.803 2846 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.05 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: -0.44 (0.27), residues: 970 helix: 0.41 (0.22), residues: 563 sheet: 0.63 (0.77), residues: 47 loop : -1.49 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 284 TYR 0.031 0.002 TYR A 912 PHE 0.029 0.003 PHE A 249 TRP 0.014 0.002 TRP A 268 HIS 0.006 0.001 HIS A 813 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.27 ( 8013) covalent geometry : angle 0.83843 / 0.48 (10916) SS BOND : bond 0.00287 / 0.15 ( 3) SS BOND : angle 1.15647 / 0.49 ( 6) hydrogen bonds : bond 0.16437 / 10.74 ( 444) hydrogen bonds : angle 5.74722 / 4.08 ( 1293) link_BETA1-4 : bond 0.01190 / 0.63 ( 1) link_BETA1-4 : angle 1.35373 / 0.66 ( 3) link_NAG-ASN : bond 0.00168 / 0.08 ( 3) link_NAG-ASN : angle 1.72887 / 0.81 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.198 Fit side-chains REVERT: A 107 ARG cc_start: 0.7263 (pmt170) cc_final: 0.6571 (mmt180) REVERT: A 395 GLN cc_start: 0.7629 (mt0) cc_final: 0.7238 (tt0) REVERT: A 738 LYS cc_start: 0.7101 (mttt) cc_final: 0.6386 (tmtt) REVERT: A 785 PHE cc_start: 0.7810 (m-10) cc_final: 0.7451 (t80) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.4667 time to fit residues: 57.7372 Evaluate side-chains 93 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN A 245 GLN A 846 GLN A1000 ASN A1009 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.164782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.126459 restraints weight = 8703.764| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.01 r_work: 0.3081 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8020 Z= 0.150 Angle : 0.621 6.314 10934 Z= 0.318 Chirality : 0.042 0.154 1277 Planarity : 0.005 0.091 1347 Dihedral : 5.722 72.276 1074 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.57 % Rotamer: Outliers : 1.57 % Allowed : 7.61 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 0.30 (0.27), residues: 970 helix: 0.97 (0.22), residues: 568 sheet: 1.00 (0.80), residues: 46 loop : -1.13 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1103 TYR 0.019 0.002 TYR A 912 PHE 0.021 0.002 PHE A 78 TRP 0.007 0.001 TRP A 246 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 8013) covalent geometry : angle 0.62002 / 0.32 (10916) SS BOND : bond 0.00276 / 0.14 ( 3) SS BOND : angle 0.94959 / 0.41 ( 6) hydrogen bonds : bond 0.05017 / 3.38 ( 444) hydrogen bonds : angle 4.24838 / 2.97 ( 1293) link_BETA1-4 : bond 0.00799 / 0.42 ( 1) link_BETA1-4 : angle 1.02793 / 0.50 ( 3) link_NAG-ASN : bond 0.00386 / 0.19 ( 3) link_NAG-ASN : angle 1.16698 / 0.56 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.188 Fit side-chains REVERT: A 107 ARG cc_start: 0.7336 (pmt170) cc_final: 0.6373 (mmt180) REVERT: A 395 GLN cc_start: 0.7930 (mt0) cc_final: 0.7434 (tt0) REVERT: A 738 LYS cc_start: 0.7291 (mttt) cc_final: 0.6419 (tmtt) REVERT: A 785 PHE cc_start: 0.8097 (m-10) cc_final: 0.7307 (t80) REVERT: A 851 HIS cc_start: 0.7302 (m170) cc_final: 0.6926 (t-90) outliers start: 13 outliers final: 8 residues processed: 113 average time/residue: 0.4174 time to fit residues: 50.1960 Evaluate side-chains 106 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 13 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 57 optimal weight: 0.0070 chunk 58 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN A 135 GLN A 846 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.166031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.127392 restraints weight = 8573.806| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.95 r_work: 0.3059 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8020 Z= 0.140 Angle : 0.580 6.203 10934 Z= 0.298 Chirality : 0.041 0.140 1277 Planarity : 0.005 0.088 1347 Dihedral : 5.438 69.613 1074 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.23 % Favored : 95.67 % Rotamer: Outliers : 2.42 % Allowed : 11.11 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 0.55 (0.27), residues: 970 helix: 1.19 (0.22), residues: 568 sheet: 1.05 (0.77), residues: 46 loop : -1.05 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1103 TYR 0.016 0.002 TYR A 990 PHE 0.015 0.002 PHE A 963 TRP 0.007 0.001 TRP A 327 HIS 0.003 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 8013) covalent geometry : angle 0.57890 / 0.30 (10916) SS BOND : bond 0.00208 / 0.11 ( 3) SS BOND : angle 0.79013 / 0.35 ( 6) hydrogen bonds : bond 0.04609 / 3.12 ( 444) hydrogen bonds : angle 4.03384 / 2.82 ( 1293) link_BETA1-4 : bond 0.00746 / 0.39 ( 1) link_BETA1-4 : angle 1.11260 / 0.53 ( 3) link_NAG-ASN : bond 0.00318 / 0.16 ( 3) link_NAG-ASN : angle 1.13990 / 0.52 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.178 Fit side-chains REVERT: A 86 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7814 (tmtm) REVERT: A 107 ARG cc_start: 0.7501 (pmt170) cc_final: 0.6487 (mmt180) REVERT: A 110 ASN cc_start: 0.7257 (m110) cc_final: 0.6958 (p0) REVERT: A 191 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: A 253 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: A 395 GLN cc_start: 0.7880 (mt0) cc_final: 0.7382 (tt0) REVERT: A 738 LYS cc_start: 0.7332 (mttt) cc_final: 0.6471 (tmtt) REVERT: A 785 PHE cc_start: 0.8166 (m-10) cc_final: 0.7389 (t80) REVERT: A 851 HIS cc_start: 0.7370 (m170) cc_final: 0.6954 (t-90) outliers start: 20 outliers final: 6 residues processed: 113 average time/residue: 0.4005 time to fit residues: 48.4604 Evaluate side-chains 107 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 40 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN A 846 GLN A1101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.166539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.128153 restraints weight = 8680.371| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.93 r_work: 0.3163 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8020 Z= 0.132 Angle : 0.565 9.982 10934 Z= 0.288 Chirality : 0.041 0.183 1277 Planarity : 0.005 0.086 1347 Dihedral : 5.235 67.926 1074 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.12 % Favored : 95.77 % Rotamer: Outliers : 3.02 % Allowed : 12.68 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 0.79 (0.28), residues: 970 helix: 1.36 (0.22), residues: 570 sheet: 1.04 (0.79), residues: 46 loop : -0.89 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 284 TYR 0.016 0.002 TYR A 990 PHE 0.024 0.002 PHE A 78 TRP 0.007 0.001 TRP A 327 HIS 0.003 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 8013) covalent geometry : angle 0.56410 / 0.29 (10916) SS BOND : bond 0.00176 / 0.09 ( 3) SS BOND : angle 0.73324 / 0.33 ( 6) hydrogen bonds : bond 0.04302 / 2.90 ( 444) hydrogen bonds : angle 3.93405 / 2.74 ( 1293) link_BETA1-4 : bond 0.01086 / 0.57 ( 1) link_BETA1-4 : angle 1.14281 / 0.51 ( 3) link_NAG-ASN : bond 0.00295 / 0.15 ( 3) link_NAG-ASN : angle 1.13978 / 0.50 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.210 Fit side-chains REVERT: A 107 ARG cc_start: 0.7647 (pmt170) cc_final: 0.6696 (mmt-90) REVERT: A 235 MET cc_start: 0.8786 (tpp) cc_final: 0.8542 (mmm) REVERT: A 395 GLN cc_start: 0.7779 (mt0) cc_final: 0.7344 (tt0) REVERT: A 738 LYS cc_start: 0.7273 (mttt) cc_final: 0.6519 (tmtt) REVERT: A 785 PHE cc_start: 0.8066 (m-10) cc_final: 0.7452 (t80) REVERT: A 851 HIS cc_start: 0.7437 (m170) cc_final: 0.7064 (t-90) REVERT: A 905 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.8044 (tm-30) outliers start: 25 outliers final: 14 residues processed: 116 average time/residue: 0.3677 time to fit residues: 45.7152 Evaluate side-chains 117 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 905 GLN Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 47 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 54 optimal weight: 0.0980 chunk 70 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 ASN A 846 GLN A1101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.167104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.128861 restraints weight = 8597.474| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.92 r_work: 0.3049 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8020 Z= 0.119 Angle : 0.547 9.328 10934 Z= 0.279 Chirality : 0.040 0.156 1277 Planarity : 0.004 0.083 1347 Dihedral : 5.069 66.023 1074 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.92 % Favored : 95.98 % 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 : 2.44 % 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: 0.95 (0.28), residues: 970 helix: 1.47 (0.22), residues: 576 sheet: 1.02 (0.78), residues: 46 loop : -0.84 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1103 TYR 0.014 0.001 TYR A 990 PHE 0.014 0.001 PHE A 963 TRP 0.006 0.001 TRP A 327 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 8013) covalent geometry : angle 0.54557 / 0.28 (10916) SS BOND : bond 0.00130 / 0.07 ( 3) SS BOND : angle 0.60319 / 0.27 ( 6) hydrogen bonds : bond 0.04023 / 2.72 ( 444) hydrogen bonds : angle 3.86264 / 2.69 ( 1293) link_BETA1-4 : bond 0.00810 / 0.43 ( 1) link_BETA1-4 : angle 1.07352 / 0.49 ( 3) link_NAG-ASN : bond 0.00287 / 0.14 ( 3) link_NAG-ASN : angle 1.10997 / 0.49 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.187 Fit side-chains REVERT: A 235 MET cc_start: 0.8870 (tpp) cc_final: 0.8618 (mmm) REVERT: A 395 GLN cc_start: 0.7784 (mt0) cc_final: 0.7256 (tt0) REVERT: A 422 LYS cc_start: 0.7595 (ttpt) cc_final: 0.7028 (mtpp) REVERT: A 574 ASN cc_start: 0.8197 (t0) cc_final: 0.7858 (m-40) REVERT: A 738 LYS cc_start: 0.7339 (mttt) cc_final: 0.6400 (tmtt) REVERT: A 785 PHE cc_start: 0.8182 (m-10) cc_final: 0.7421 (t80) outliers start: 21 outliers final: 12 residues processed: 114 average time/residue: 0.4171 time to fit residues: 50.9967 Evaluate side-chains 114 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 11 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 ASN A 846 GLN A1088 HIS A1101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.161491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.122824 restraints weight = 8680.082| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.99 r_work: 0.3007 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8020 Z= 0.193 Angle : 0.616 9.998 10934 Z= 0.313 Chirality : 0.043 0.149 1277 Planarity : 0.005 0.094 1347 Dihedral : 5.245 69.558 1074 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.85 % Favored : 95.05 % Rotamer: Outliers : 2.78 % Allowed : 14.25 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 0.75 (0.27), residues: 970 helix: 1.27 (0.22), residues: 577 sheet: 1.14 (0.80), residues: 46 loop : -0.88 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 284 TYR 0.021 0.002 TYR A 990 PHE 0.023 0.002 PHE A 963 TRP 0.006 0.001 TRP A 327 HIS 0.004 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.19 ( 8013) covalent geometry : angle 0.61486 / 0.31 (10916) SS BOND : bond 0.00222 / 0.11 ( 3) SS BOND : angle 1.06730 / 0.50 ( 6) hydrogen bonds : bond 0.04872 / 3.30 ( 444) hydrogen bonds : angle 4.03566 / 2.81 ( 1293) link_BETA1-4 : bond 0.00951 / 0.50 ( 1) link_BETA1-4 : angle 1.28610 / 0.59 ( 3) link_NAG-ASN : bond 0.00250 / 0.12 ( 3) link_NAG-ASN : angle 1.36766 / 0.57 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.294 Fit side-chains REVERT: A 107 ARG cc_start: 0.7565 (pmt170) cc_final: 0.6512 (mpp-170) REVERT: A 235 MET cc_start: 0.8902 (tpp) cc_final: 0.8670 (mmm) REVERT: A 360 LYS cc_start: 0.7991 (tttm) cc_final: 0.7481 (ttpp) REVERT: A 395 GLN cc_start: 0.7929 (mt0) cc_final: 0.7414 (tt0) REVERT: A 574 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7916 (m-40) REVERT: A 738 LYS cc_start: 0.7370 (mttt) cc_final: 0.6476 (tmtt) REVERT: A 785 PHE cc_start: 0.8174 (m-10) cc_final: 0.7408 (t80) REVERT: A 905 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8111 (tm-30) outliers start: 23 outliers final: 13 residues processed: 115 average time/residue: 0.4022 time to fit residues: 49.6902 Evaluate side-chains 115 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 905 GLN Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 74 optimal weight: 0.3980 chunk 81 optimal weight: 0.0170 chunk 5 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN A 87 ASN A 846 GLN A1088 HIS A1101 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.165308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.126138 restraints weight = 8636.056| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.99 r_work: 0.3036 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8020 Z= 0.116 Angle : 0.545 11.089 10934 Z= 0.278 Chirality : 0.040 0.149 1277 Planarity : 0.004 0.082 1347 Dihedral : 5.009 66.047 1074 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.92 % Favored : 95.98 % Rotamer: Outliers : 2.17 % Allowed : 16.06 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 1.07 (0.28), residues: 970 helix: 1.58 (0.22), residues: 575 sheet: 0.84 (0.82), residues: 48 loop : -0.78 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1103 TYR 0.016 0.001 TYR A 990 PHE 0.013 0.001 PHE A 963 TRP 0.007 0.001 TRP A 327 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 8013) covalent geometry : angle 0.54436 / 0.28 (10916) SS BOND : bond 0.00139 / 0.07 ( 3) SS BOND : angle 0.54767 / 0.24 ( 6) hydrogen bonds : bond 0.03953 / 2.68 ( 444) hydrogen bonds : angle 3.87394 / 2.69 ( 1293) link_BETA1-4 : bond 0.00827 / 0.44 ( 1) link_BETA1-4 : angle 1.08972 / 0.51 ( 3) link_NAG-ASN : bond 0.00304 / 0.15 ( 3) link_NAG-ASN : angle 1.05032 / 0.46 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 235 MET cc_start: 0.8768 (tpp) cc_final: 0.8491 (mmm) REVERT: A 360 LYS cc_start: 0.7861 (tttm) cc_final: 0.7370 (ttpp) REVERT: A 395 GLN cc_start: 0.7656 (mt0) cc_final: 0.7202 (tt0) REVERT: A 422 LYS cc_start: 0.7638 (ttpt) cc_final: 0.7079 (mtpp) REVERT: A 574 ASN cc_start: 0.8085 (t0) cc_final: 0.7753 (m-40) REVERT: A 738 LYS cc_start: 0.7283 (mttt) cc_final: 0.6451 (tmtt) REVERT: A 785 PHE cc_start: 0.7998 (m-10) cc_final: 0.7329 (t80) REVERT: A 905 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.8106 (tm-30) REVERT: A 1122 THR cc_start: 0.8331 (t) cc_final: 0.8067 (p) outliers start: 18 outliers final: 13 residues processed: 116 average time/residue: 0.3865 time to fit residues: 48.1292 Evaluate side-chains 118 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 905 GLN Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 47 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN A1101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.165044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.126043 restraints weight = 8654.888| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.99 r_work: 0.3092 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8020 Z= 0.140 Angle : 0.565 10.747 10934 Z= 0.287 Chirality : 0.041 0.147 1277 Planarity : 0.005 0.087 1347 Dihedral : 5.008 66.674 1074 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.23 % Favored : 95.67 % Rotamer: Outliers : 2.66 % Allowed : 15.94 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 1.15 (0.28), residues: 970 helix: 1.65 (0.22), residues: 571 sheet: 1.20 (0.84), residues: 46 loop : -0.75 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 284 TYR 0.018 0.001 TYR A 990 PHE 0.026 0.002 PHE A 78 TRP 0.006 0.001 TRP A 327 HIS 0.003 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 8013) covalent geometry : angle 0.56424 / 0.29 (10916) SS BOND : bond 0.00162 / 0.08 ( 3) SS BOND : angle 0.73343 / 0.35 ( 6) hydrogen bonds : bond 0.04268 / 2.89 ( 444) hydrogen bonds : angle 3.91395 / 2.72 ( 1293) link_BETA1-4 : bond 0.00915 / 0.48 ( 1) link_BETA1-4 : angle 1.19980 / 0.53 ( 3) link_NAG-ASN : bond 0.00264 / 0.13 ( 3) link_NAG-ASN : angle 1.21946 / 0.51 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.295 Fit side-chains REVERT: A 235 MET cc_start: 0.8786 (tpp) cc_final: 0.8539 (mmm) REVERT: A 360 LYS cc_start: 0.7947 (tttm) cc_final: 0.7508 (ttpp) REVERT: A 395 GLN cc_start: 0.7765 (mt0) cc_final: 0.7354 (tt0) REVERT: A 422 LYS cc_start: 0.7743 (ttpt) cc_final: 0.7209 (mtpp) REVERT: A 574 ASN cc_start: 0.8096 (OUTLIER) cc_final: 0.7799 (m-40) REVERT: A 738 LYS cc_start: 0.7281 (mttt) cc_final: 0.6509 (tmtt) REVERT: A 785 PHE cc_start: 0.8037 (m-10) cc_final: 0.7448 (t80) REVERT: A 1122 THR cc_start: 0.8517 (t) cc_final: 0.8222 (p) outliers start: 22 outliers final: 14 residues processed: 115 average time/residue: 0.4103 time to fit residues: 50.7984 Evaluate side-chains 119 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 45 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 23 optimal weight: 0.0170 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN A1101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.164901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.126416 restraints weight = 8702.522| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.07 r_work: 0.3126 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8020 Z= 0.122 Angle : 0.550 11.012 10934 Z= 0.280 Chirality : 0.040 0.148 1277 Planarity : 0.004 0.083 1347 Dihedral : 4.913 65.590 1074 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.12 % Favored : 95.77 % Rotamer: Outliers : 2.05 % Allowed : 16.67 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 1.28 (0.28), residues: 970 helix: 1.78 (0.22), residues: 571 sheet: 0.89 (0.83), residues: 48 loop : -0.71 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 284 TYR 0.017 0.001 TYR A 990 PHE 0.027 0.001 PHE A 78 TRP 0.007 0.001 TRP A 327 HIS 0.002 0.001 HIS A1015 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 8013) covalent geometry : angle 0.54893 / 0.28 (10916) SS BOND : bond 0.00131 / 0.07 ( 3) SS BOND : angle 0.57612 / 0.26 ( 6) hydrogen bonds : bond 0.03965 / 2.69 ( 444) hydrogen bonds : angle 3.87122 / 2.69 ( 1293) link_BETA1-4 : bond 0.00826 / 0.43 ( 1) link_BETA1-4 : angle 1.11617 / 0.51 ( 3) link_NAG-ASN : bond 0.00291 / 0.15 ( 3) link_NAG-ASN : angle 1.10505 / 0.47 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.168 Fit side-chains REVERT: A 235 MET cc_start: 0.8885 (tpp) cc_final: 0.8630 (mmm) REVERT: A 360 LYS cc_start: 0.7966 (tttm) cc_final: 0.7480 (ttpp) REVERT: A 395 GLN cc_start: 0.7786 (mt0) cc_final: 0.7296 (tt0) REVERT: A 574 ASN cc_start: 0.8219 (t0) cc_final: 0.7898 (m-40) REVERT: A 738 LYS cc_start: 0.7376 (mttt) cc_final: 0.6445 (tmtt) REVERT: A 785 PHE cc_start: 0.8154 (m-10) cc_final: 0.7393 (t80) REVERT: A 1122 THR cc_start: 0.8480 (t) cc_final: 0.8161 (p) outliers start: 17 outliers final: 14 residues processed: 115 average time/residue: 0.3762 time to fit residues: 46.3652 Evaluate side-chains 119 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 3 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 63 optimal weight: 0.0020 chunk 67 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN A1101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.166226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.128768 restraints weight = 8650.289| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.93 r_work: 0.3098 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8020 Z= 0.123 Angle : 0.548 11.176 10934 Z= 0.279 Chirality : 0.040 0.145 1277 Planarity : 0.004 0.083 1347 Dihedral : 4.878 65.341 1074 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.43 % Favored : 95.46 % Rotamer: Outliers : 1.93 % Allowed : 16.79 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 1.30 (0.28), residues: 970 helix: 1.80 (0.22), residues: 572 sheet: 0.89 (0.83), residues: 48 loop : -0.72 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 284 TYR 0.016 0.001 TYR A 990 PHE 0.028 0.001 PHE A 78 TRP 0.006 0.001 TRP A 327 HIS 0.002 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 8013) covalent geometry : angle 0.54733 / 0.28 (10916) SS BOND : bond 0.00135 / 0.07 ( 3) SS BOND : angle 0.60127 / 0.28 ( 6) hydrogen bonds : bond 0.03988 / 2.71 ( 444) hydrogen bonds : angle 3.86516 / 2.69 ( 1293) link_BETA1-4 : bond 0.00819 / 0.43 ( 1) link_BETA1-4 : angle 1.14238 / 0.52 ( 3) link_NAG-ASN : bond 0.00262 / 0.13 ( 3) link_NAG-ASN : angle 1.15100 / 0.49 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.286 Fit side-chains REVERT: A 235 MET cc_start: 0.8869 (tpp) cc_final: 0.8627 (mmm) REVERT: A 360 LYS cc_start: 0.7954 (tttm) cc_final: 0.7480 (ttpp) REVERT: A 395 GLN cc_start: 0.7800 (mt0) cc_final: 0.7333 (tt0) REVERT: A 574 ASN cc_start: 0.8199 (t0) cc_final: 0.7893 (m-40) REVERT: A 738 LYS cc_start: 0.7351 (mttt) cc_final: 0.6460 (tmtt) REVERT: A 785 PHE cc_start: 0.8147 (m-10) cc_final: 0.7424 (t80) REVERT: A 1122 THR cc_start: 0.8509 (t) cc_final: 0.8207 (p) outliers start: 16 outliers final: 14 residues processed: 118 average time/residue: 0.4434 time to fit residues: 55.7207 Evaluate side-chains 119 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 54 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN A 87 ASN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN A1101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.166822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.128233 restraints weight = 8696.661| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.99 r_work: 0.3040 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8020 Z= 0.140 Angle : 0.571 11.271 10934 Z= 0.290 Chirality : 0.041 0.150 1277 Planarity : 0.005 0.086 1347 Dihedral : 4.916 66.279 1074 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.43 % Favored : 95.46 % Rotamer: Outliers : 2.17 % Allowed : 16.79 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 1.25 (0.28), residues: 970 helix: 1.77 (0.22), residues: 571 sheet: 0.90 (0.84), residues: 48 loop : -0.74 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 284 TYR 0.017 0.001 TYR A 990 PHE 0.028 0.002 PHE A 78 TRP 0.006 0.001 TRP A 327 HIS 0.003 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 8013) covalent geometry : angle 0.56997 / 0.29 (10916) SS BOND : bond 0.00173 / 0.09 ( 3) SS BOND : angle 0.73653 / 0.35 ( 6) hydrogen bonds : bond 0.04231 / 2.88 ( 444) hydrogen bonds : angle 3.91779 / 2.72 ( 1293) link_BETA1-4 : bond 0.00851 / 0.45 ( 1) link_BETA1-4 : angle 1.21209 / 0.54 ( 3) link_NAG-ASN : bond 0.00260 / 0.13 ( 3) link_NAG-ASN : angle 1.22087 / 0.50 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2095.86 seconds wall clock time: 36 minutes 23.44 seconds (2183.44 seconds total)