Starting phenix.real_space_refine on Sat Aug 23 01:41:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yo3_33980/08_2025/7yo3_33980.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yo3_33980/08_2025/7yo3_33980.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yo3_33980/08_2025/7yo3_33980.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yo3_33980/08_2025/7yo3_33980.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yo3_33980/08_2025/7yo3_33980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yo3_33980/08_2025/7yo3_33980.map" } resolution = 3.1 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= 0.005 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Mg 1 5.21 5 S 57 5.16 5 C 5790 2.51 5 N 1510 2.21 5 O 1601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8961 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 882, 7034 Classifications: {'peptide': 882} Link IDs: {'PTRANS': 27, 'TRANS': 854} Chain breaks: 5 Chain: "B" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1924 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 239} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.30, per 1000 atoms: 0.26 Number of scatterers: 8961 At special positions: 0 Unit cell: (127.488, 122.508, 176.292, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 57 16.00 Mg 1 11.99 O 1601 8.00 N 1510 7.00 C 5790 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS B 57 " distance=2.02 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 231 " distance=2.01 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 253 " 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 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 335.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2150 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 7 sheets defined 49.0% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 21 through 49 removed outlier: 4.321A pdb=" N PHE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 106 Processing helix chain 'A' and resid 109 through 134 Processing helix chain 'A' and resid 148 through 171 Processing helix chain 'A' and resid 173 through 179 removed outlier: 3.537A pdb=" N LEU A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 188 Processing helix chain 'A' and resid 189 through 200 removed outlier: 3.755A pdb=" N VAL A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 215 removed outlier: 4.427A pdb=" N PHE A 208 " --> pdb=" O GLY A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 224 Processing helix chain 'A' and resid 229 through 259 Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 297 through 327 removed outlier: 4.071A pdb=" N LEU A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 432 through 451 Processing helix chain 'A' and resid 462 through 471 removed outlier: 3.763A pdb=" N LYS A 466 " --> pdb=" O GLN A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 500 Processing helix chain 'A' and resid 502 through 510 removed outlier: 3.537A pdb=" N MET A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 533 removed outlier: 3.771A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 530 " --> pdb=" O LYS A 526 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 531 " --> pdb=" O TYR A 527 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 555 removed outlier: 3.802A pdb=" N VAL A 553 " --> pdb=" O SER A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 562 Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 740 through 743 removed outlier: 4.096A pdb=" N ALA A 743 " --> pdb=" O PRO A 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 740 through 743' Processing helix chain 'A' and resid 759 through 766 removed outlier: 3.707A pdb=" N LEU A 763 " --> pdb=" O SER A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 792 removed outlier: 3.519A pdb=" N VAL A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 806 through 809 Processing helix chain 'A' and resid 817 through 830 Processing helix chain 'A' and resid 872 through 876 removed outlier: 4.005A pdb=" N ASN A 875 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 886 No H-bonds generated for 'chain 'A' and resid 884 through 886' Processing helix chain 'A' and resid 887 through 892 removed outlier: 3.958A pdb=" N LEU A 891 " --> pdb=" O ASN A 887 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP A 892 " --> pdb=" O VAL A 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 887 through 892' Processing helix chain 'A' and resid 902 through 905 Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 916 through 921 removed outlier: 3.840A pdb=" N ASP A 921 " --> pdb=" O SER A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 930 removed outlier: 3.658A pdb=" N PHE A 929 " --> pdb=" O SER A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 941 removed outlier: 4.209A pdb=" N THR A 935 " --> pdb=" O ASP A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 956 Processing helix chain 'A' and resid 965 through 971 Processing helix chain 'A' and resid 985 through 989 removed outlier: 4.096A pdb=" N ASP A 989 " --> pdb=" O PRO A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1008 Processing helix chain 'B' and resid 159 through 164 removed outlier: 3.882A pdb=" N LEU B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 159 through 164' Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.683A pdb=" N ARG B 189 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 209 through 219 removed outlier: 3.825A pdb=" N TRP B 215 " --> pdb=" O PRO B 211 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 241 through 245 removed outlier: 3.708A pdb=" N PHE B 245 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 Processing helix chain 'B' and resid 259 through 297 removed outlier: 3.586A pdb=" N ALA B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY B 269 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Proline residue: B 270 - end of helix removed outlier: 3.507A pdb=" N LEU B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 402 removed outlier: 3.588A pdb=" N HIS A 379 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY A 349 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N LEU A 423 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU A 425 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N CYS A 348 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ILE A 484 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N THR A 458 " --> pdb=" O ILE A 484 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 537 through 540 Processing sheet with id=AA4, first strand: chain 'A' and resid 776 through 779 removed outlier: 6.282A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N PHE A 915 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR A 880 " --> pdb=" O PHE A 915 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 976 through 980 removed outlier: 3.978A pdb=" N PHE A1050 " --> pdb=" O GLY A1013 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLY A1013 " --> pdb=" O PHE A1050 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 48 through 50 removed outlier: 3.577A pdb=" N LEU B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU B 148 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.827A pdb=" N LEU B 86 " --> pdb=" O SER B 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 380 hydrogen bonds defined for protein. 1062 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: 1.55 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2449 1.33 - 1.45: 1605 1.45 - 1.57: 5030 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 9164 Sorted by residual: bond pdb=" N GLN A 831 " pdb=" CA GLN A 831 " ideal model delta sigma weight residual 1.455 1.500 -0.045 1.25e-02 6.40e+03 1.30e+01 bond pdb=" N GLN A 19 " pdb=" CA GLN A 19 " ideal model delta sigma weight residual 1.456 1.500 -0.043 1.21e-02 6.83e+03 1.28e+01 bond pdb=" N ARG A 20 " pdb=" CA ARG A 20 " ideal model delta sigma weight residual 1.454 1.498 -0.043 1.31e-02 5.83e+03 1.10e+01 bond pdb=" CA SER A 744 " pdb=" CB SER A 744 " ideal model delta sigma weight residual 1.530 1.477 0.053 1.68e-02 3.54e+03 9.97e+00 bond pdb=" N VAL B 229 " pdb=" CA VAL B 229 " ideal model delta sigma weight residual 1.459 1.496 -0.038 1.24e-02 6.50e+03 9.20e+00 ... (remaining 9159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 11954 1.51 - 3.03: 397 3.03 - 4.54: 79 4.54 - 6.06: 17 6.06 - 7.57: 8 Bond angle restraints: 12455 Sorted by residual: angle pdb=" N ILE A 416 " pdb=" CA ILE A 416 " pdb=" C ILE A 416 " ideal model delta sigma weight residual 113.07 105.99 7.08 1.36e+00 5.41e-01 2.71e+01 angle pdb=" C THR B 228 " pdb=" N VAL B 229 " pdb=" CA VAL B 229 " ideal model delta sigma weight residual 122.90 116.70 6.20 1.28e+00 6.10e-01 2.34e+01 angle pdb=" N ASN A 745 " pdb=" CA ASN A 745 " pdb=" C ASN A 745 " ideal model delta sigma weight residual 113.01 107.37 5.64 1.20e+00 6.94e-01 2.21e+01 angle pdb=" N THR A1006 " pdb=" CA THR A1006 " pdb=" C THR A1006 " ideal model delta sigma weight residual 111.36 116.18 -4.82 1.09e+00 8.42e-01 1.96e+01 angle pdb=" N CYS A1001 " pdb=" CA CYS A1001 " pdb=" C CYS A1001 " ideal model delta sigma weight residual 111.28 106.53 4.75 1.09e+00 8.42e-01 1.90e+01 ... (remaining 12450 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4878 18.00 - 36.01: 484 36.01 - 54.01: 64 54.01 - 72.01: 9 72.01 - 90.01: 6 Dihedral angle restraints: 5441 sinusoidal: 2121 harmonic: 3320 Sorted by residual: dihedral pdb=" CA TYR A1015 " pdb=" C TYR A1015 " pdb=" N ARG A1016 " pdb=" CA ARG A1016 " ideal model delta harmonic sigma weight residual -180.00 -161.78 -18.22 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CB GLU A 819 " pdb=" CG GLU A 819 " pdb=" CD GLU A 819 " pdb=" OE1 GLU A 819 " ideal model delta sinusoidal sigma weight residual 0.00 90.01 -90.01 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU A 699 " pdb=" CG GLU A 699 " pdb=" CD GLU A 699 " pdb=" OE1 GLU A 699 " ideal model delta sinusoidal sigma weight residual 0.00 89.70 -89.70 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 5438 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1196 0.057 - 0.114: 204 0.114 - 0.171: 27 0.171 - 0.228: 4 0.228 - 0.284: 5 Chirality restraints: 1436 Sorted by residual: chirality pdb=" CA ARG A 972 " pdb=" N ARG A 972 " pdb=" C ARG A 972 " pdb=" CB ARG A 972 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA CYS B 231 " pdb=" N CYS B 231 " pdb=" C CYS B 231 " pdb=" CB CYS B 231 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA THR A1006 " pdb=" N THR A1006 " pdb=" C THR A1006 " pdb=" CB THR A1006 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 1433 not shown) Planarity restraints: 1574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 159 " 0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO B 160 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 160 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 160 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 830 " -0.019 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C MET A 830 " 0.063 2.00e-02 2.50e+03 pdb=" O MET A 830 " -0.024 2.00e-02 2.50e+03 pdb=" N GLN A 831 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 17 " -0.016 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C ARG A 17 " 0.058 2.00e-02 2.50e+03 pdb=" O ARG A 17 " -0.022 2.00e-02 2.50e+03 pdb=" N GLY A 18 " -0.020 2.00e-02 2.50e+03 ... (remaining 1571 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 849 2.75 - 3.28: 9038 3.28 - 3.82: 14619 3.82 - 4.36: 17431 4.36 - 4.90: 29446 Nonbonded interactions: 71383 Sorted by model distance: nonbonded pdb=" OG SER A 708 " pdb=" OE1 GLU A 709 " model vdw 2.207 3.040 nonbonded pdb=" OD1 ASN B 147 " pdb=" OG SER B 171 " model vdw 2.237 3.040 nonbonded pdb=" O VAL A 727 " pdb=" NH2 ARG A 765 " model vdw 2.249 3.120 nonbonded pdb=" NH2 ARG B 210 " pdb=" OD1 ASP B 247 " model vdw 2.271 3.120 nonbonded pdb=" O GLN A 402 " pdb=" NH2 ARG A 413 " model vdw 2.287 3.120 ... (remaining 71378 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.360 Find NCS groups from input model: 0.050 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5971 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9168 Z= 0.249 Angle : 0.673 7.570 12463 Z= 0.401 Chirality : 0.047 0.284 1436 Planarity : 0.005 0.091 1574 Dihedral : 13.947 90.012 3279 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.21 % Allowed : 0.82 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.26), residues: 1130 helix: 0.82 (0.24), residues: 468 sheet: -0.33 (0.58), residues: 97 loop : -0.26 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 20 TYR 0.023 0.002 TYR B 266 PHE 0.025 0.001 PHE A 511 TRP 0.014 0.001 TRP B 116 HIS 0.004 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 9164) covalent geometry : angle 0.67229 (12455) SS BOND : bond 0.00981 ( 4) SS BOND : angle 1.13471 ( 8) hydrogen bonds : bond 0.14820 ( 380) hydrogen bonds : angle 5.77328 ( 1062) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 199 time to evaluate : 0.205 Fit side-chains REVERT: A 94 MET cc_start: 0.6175 (mmm) cc_final: 0.5832 (mmm) REVERT: A 264 GLU cc_start: 0.6344 (mm-30) cc_final: 0.6053 (mm-30) REVERT: A 265 ASN cc_start: 0.6268 (m-40) cc_final: 0.5414 (t0) REVERT: A 453 LYS cc_start: 0.6595 (mppt) cc_final: 0.5992 (ttmt) REVERT: A 884 ASN cc_start: 0.7807 (t0) cc_final: 0.7408 (m-40) REVERT: A 886 THR cc_start: 0.7231 (m) cc_final: 0.7018 (p) outliers start: 2 outliers final: 0 residues processed: 201 average time/residue: 0.1062 time to fit residues: 28.5054 Evaluate side-chains 115 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 772 ASN A 831 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.220529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.187878 restraints weight = 11098.940| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 1.60 r_work: 0.3775 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9168 Z= 0.127 Angle : 0.561 7.028 12463 Z= 0.288 Chirality : 0.041 0.145 1436 Planarity : 0.005 0.061 1574 Dihedral : 3.881 16.347 1229 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.54 % Allowed : 9.57 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.26), residues: 1130 helix: 1.16 (0.24), residues: 481 sheet: -0.24 (0.58), residues: 99 loop : -0.14 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 217 TYR 0.021 0.002 TYR A1032 PHE 0.022 0.001 PHE A1000 TRP 0.016 0.001 TRP B 215 HIS 0.005 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9164) covalent geometry : angle 0.56014 (12455) SS BOND : bond 0.01098 ( 4) SS BOND : angle 1.53844 ( 8) hydrogen bonds : bond 0.04256 ( 380) hydrogen bonds : angle 4.62093 ( 1062) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.6957 (mmm) cc_final: 0.6662 (mmm) REVERT: A 244 SER cc_start: 0.8845 (OUTLIER) cc_final: 0.8621 (m) REVERT: A 265 ASN cc_start: 0.6745 (m-40) cc_final: 0.5644 (t0) REVERT: A 321 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7389 (tt0) REVERT: A 453 LYS cc_start: 0.6518 (mppt) cc_final: 0.6037 (ttmt) REVERT: A 886 THR cc_start: 0.7546 (m) cc_final: 0.7338 (p) REVERT: A 930 ASN cc_start: 0.7557 (OUTLIER) cc_final: 0.7057 (p0) REVERT: A 1007 TYR cc_start: 0.5335 (OUTLIER) cc_final: 0.4511 (m-80) REVERT: B 74 ARG cc_start: 0.4744 (mmt180) cc_final: 0.3901 (mmm160) REVERT: B 190 LEU cc_start: 0.3348 (mp) cc_final: 0.3016 (mt) outliers start: 15 outliers final: 7 residues processed: 136 average time/residue: 0.0993 time to fit residues: 18.3167 Evaluate side-chains 109 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 930 ASN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 1007 TYR Chi-restraints excluded: chain B residue 121 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 93 optimal weight: 6.9990 chunk 12 optimal weight: 0.0670 chunk 85 optimal weight: 0.0870 chunk 8 optimal weight: 6.9990 chunk 107 optimal weight: 0.0020 chunk 108 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN A 440 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.221315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.186443 restraints weight = 10967.486| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 1.71 r_work: 0.3712 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9168 Z= 0.096 Angle : 0.477 6.625 12463 Z= 0.245 Chirality : 0.039 0.144 1436 Planarity : 0.004 0.053 1574 Dihedral : 3.607 14.731 1229 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.13 % Allowed : 11.63 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.27), residues: 1130 helix: 1.44 (0.25), residues: 482 sheet: -0.35 (0.53), residues: 114 loop : 0.06 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 99 TYR 0.012 0.001 TYR A1032 PHE 0.017 0.001 PHE A1000 TRP 0.015 0.001 TRP B 215 HIS 0.005 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 9164) covalent geometry : angle 0.47686 (12455) SS BOND : bond 0.00160 ( 4) SS BOND : angle 0.60311 ( 8) hydrogen bonds : bond 0.03744 ( 380) hydrogen bonds : angle 4.25246 ( 1062) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.7013 (mmm) cc_final: 0.6769 (mmm) REVERT: A 321 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7513 (tt0) REVERT: A 453 LYS cc_start: 0.6461 (mppt) cc_final: 0.6003 (ttmt) REVERT: A 477 TRP cc_start: 0.5940 (t60) cc_final: 0.5657 (t60) REVERT: A 698 LYS cc_start: 0.6178 (mptt) cc_final: 0.5937 (mmtp) REVERT: A 886 THR cc_start: 0.7552 (m) cc_final: 0.7311 (p) REVERT: A 933 ILE cc_start: 0.7789 (mm) cc_final: 0.7382 (tt) REVERT: A 1007 TYR cc_start: 0.5380 (OUTLIER) cc_final: 0.4644 (m-80) REVERT: B 74 ARG cc_start: 0.4755 (mmt180) cc_final: 0.3638 (tpt90) outliers start: 11 outliers final: 9 residues processed: 118 average time/residue: 0.1042 time to fit residues: 16.8545 Evaluate side-chains 106 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 1007 TYR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 216 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 99 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 772 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.212259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.175176 restraints weight = 10945.334| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 1.78 r_work: 0.3610 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9168 Z= 0.158 Angle : 0.553 7.311 12463 Z= 0.284 Chirality : 0.042 0.150 1436 Planarity : 0.004 0.058 1574 Dihedral : 3.846 15.960 1229 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.47 % Allowed : 13.79 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.26), residues: 1130 helix: 1.32 (0.24), residues: 480 sheet: -0.29 (0.55), residues: 105 loop : -0.14 (0.29), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 157 TYR 0.016 0.002 TYR A 928 PHE 0.019 0.002 PHE A1000 TRP 0.015 0.002 TRP A 767 HIS 0.007 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9164) covalent geometry : angle 0.55325 (12455) SS BOND : bond 0.00247 ( 4) SS BOND : angle 0.49816 ( 8) hydrogen bonds : bond 0.04569 ( 380) hydrogen bonds : angle 4.35131 ( 1062) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.227 Fit side-chains REVERT: A 93 TRP cc_start: 0.6232 (p-90) cc_final: 0.6015 (p-90) REVERT: A 453 LYS cc_start: 0.6644 (mppt) cc_final: 0.6013 (ttmt) REVERT: A 739 MET cc_start: 0.7123 (ttt) cc_final: 0.6739 (ttm) REVERT: A 886 THR cc_start: 0.8242 (m) cc_final: 0.8003 (m) REVERT: A 930 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.6954 (p0) REVERT: A 949 LEU cc_start: 0.8158 (tp) cc_final: 0.7912 (mt) REVERT: A 955 GLU cc_start: 0.5691 (mp0) cc_final: 0.5467 (mp0) REVERT: A 1000 PHE cc_start: 0.3953 (OUTLIER) cc_final: 0.1930 (p90) REVERT: A 1007 TYR cc_start: 0.5247 (OUTLIER) cc_final: 0.4729 (m-80) REVERT: B 74 ARG cc_start: 0.4937 (mmt180) cc_final: 0.3857 (tpt90) REVERT: B 230 LEU cc_start: 0.6077 (pp) cc_final: 0.5875 (pp) outliers start: 24 outliers final: 16 residues processed: 126 average time/residue: 0.0978 time to fit residues: 17.3403 Evaluate side-chains 115 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 930 ASN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1007 TYR Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 131 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 71 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 27 optimal weight: 0.0370 chunk 29 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.210167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.173827 restraints weight = 10869.680| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.72 r_work: 0.3542 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9168 Z= 0.147 Angle : 0.562 12.663 12463 Z= 0.284 Chirality : 0.042 0.145 1436 Planarity : 0.004 0.050 1574 Dihedral : 3.975 16.714 1229 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.06 % Allowed : 15.53 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.26), residues: 1130 helix: 1.15 (0.24), residues: 488 sheet: -0.41 (0.54), residues: 103 loop : -0.33 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 974 TYR 0.013 0.002 TYR A1015 PHE 0.021 0.002 PHE A 511 TRP 0.031 0.002 TRP A 93 HIS 0.010 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9164) covalent geometry : angle 0.56182 (12455) SS BOND : bond 0.00156 ( 4) SS BOND : angle 0.64801 ( 8) hydrogen bonds : bond 0.04437 ( 380) hydrogen bonds : angle 4.34187 ( 1062) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.304 Fit side-chains REVERT: A 201 ARG cc_start: 0.7025 (ttm-80) cc_final: 0.6513 (ttm170) REVERT: A 453 LYS cc_start: 0.6695 (mppt) cc_final: 0.6072 (ttmt) REVERT: A 778 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.7371 (mt) REVERT: A 886 THR cc_start: 0.8660 (m) cc_final: 0.8438 (m) REVERT: A 930 ASN cc_start: 0.7567 (OUTLIER) cc_final: 0.6959 (p0) REVERT: A 1000 PHE cc_start: 0.4342 (OUTLIER) cc_final: 0.2113 (p90) REVERT: A 1002 LYS cc_start: 0.6381 (mttp) cc_final: 0.6051 (tptt) REVERT: A 1007 TYR cc_start: 0.5130 (OUTLIER) cc_final: 0.4666 (m-80) REVERT: B 74 ARG cc_start: 0.5177 (mmt180) cc_final: 0.3890 (tpt90) outliers start: 20 outliers final: 13 residues processed: 122 average time/residue: 0.1008 time to fit residues: 16.9478 Evaluate side-chains 112 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 930 ASN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1007 TYR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 126 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 92 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 107 optimal weight: 0.0570 chunk 106 optimal weight: 9.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.208102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.172005 restraints weight = 10872.176| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.74 r_work: 0.3540 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9168 Z= 0.149 Angle : 0.551 8.129 12463 Z= 0.282 Chirality : 0.042 0.167 1436 Planarity : 0.004 0.047 1574 Dihedral : 4.022 16.732 1229 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.57 % Allowed : 16.46 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.26), residues: 1130 helix: 1.13 (0.24), residues: 488 sheet: -0.42 (0.53), residues: 103 loop : -0.33 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 938 TYR 0.014 0.002 TYR A 928 PHE 0.032 0.002 PHE A 692 TRP 0.027 0.002 TRP A 93 HIS 0.010 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9164) covalent geometry : angle 0.55107 (12455) SS BOND : bond 0.00213 ( 4) SS BOND : angle 0.59406 ( 8) hydrogen bonds : bond 0.04526 ( 380) hydrogen bonds : angle 4.34613 ( 1062) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.351 Fit side-chains REVERT: A 93 TRP cc_start: 0.6390 (p-90) cc_final: 0.6086 (p-90) REVERT: A 99 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7582 (m-30) REVERT: A 201 ARG cc_start: 0.7143 (ttm-80) cc_final: 0.6665 (ttm170) REVERT: A 453 LYS cc_start: 0.6750 (mppt) cc_final: 0.6137 (ttmm) REVERT: A 481 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7115 (t0) REVERT: A 778 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7490 (mt) REVERT: A 886 THR cc_start: 0.8715 (m) cc_final: 0.8495 (m) REVERT: A 930 ASN cc_start: 0.7622 (OUTLIER) cc_final: 0.6992 (p0) REVERT: A 933 ILE cc_start: 0.7966 (mm) cc_final: 0.7632 (tt) REVERT: A 955 GLU cc_start: 0.5353 (mp0) cc_final: 0.5131 (mp0) REVERT: A 1000 PHE cc_start: 0.4518 (OUTLIER) cc_final: 0.2600 (p90) REVERT: A 1002 LYS cc_start: 0.6489 (mttp) cc_final: 0.6101 (tptt) REVERT: A 1007 TYR cc_start: 0.5097 (OUTLIER) cc_final: 0.4683 (m-80) REVERT: B 62 LEU cc_start: 0.5890 (mt) cc_final: 0.5559 (mt) REVERT: B 74 ARG cc_start: 0.5263 (mmt180) cc_final: 0.4028 (tpt90) REVERT: B 126 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6310 (tt) REVERT: B 143 ARG cc_start: 0.4006 (mtt90) cc_final: 0.3648 (tpt170) outliers start: 25 outliers final: 14 residues processed: 129 average time/residue: 0.0832 time to fit residues: 15.1067 Evaluate side-chains 125 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 930 ASN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1007 TYR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 126 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 0.0770 chunk 84 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.209417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.173701 restraints weight = 10941.167| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.60 r_work: 0.3563 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9168 Z= 0.114 Angle : 0.505 7.021 12463 Z= 0.257 Chirality : 0.040 0.153 1436 Planarity : 0.004 0.046 1574 Dihedral : 3.824 15.401 1229 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.95 % Allowed : 18.62 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.26), residues: 1130 helix: 1.26 (0.25), residues: 490 sheet: -0.35 (0.53), residues: 103 loop : -0.29 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 113 TYR 0.010 0.001 TYR A 279 PHE 0.027 0.001 PHE A 692 TRP 0.023 0.001 TRP A 93 HIS 0.005 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9164) covalent geometry : angle 0.50498 (12455) SS BOND : bond 0.00182 ( 4) SS BOND : angle 0.48420 ( 8) hydrogen bonds : bond 0.04013 ( 380) hydrogen bonds : angle 4.20811 ( 1062) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.364 Fit side-chains REVERT: A 93 TRP cc_start: 0.6203 (p-90) cc_final: 0.5920 (p-90) REVERT: A 201 ARG cc_start: 0.7127 (ttm-80) cc_final: 0.6657 (ttm170) REVERT: A 453 LYS cc_start: 0.6705 (mppt) cc_final: 0.6085 (ttmt) REVERT: A 477 TRP cc_start: 0.6217 (t60) cc_final: 0.6017 (t60) REVERT: A 481 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7039 (t70) REVERT: A 565 MET cc_start: 0.7219 (ttm) cc_final: 0.6606 (tpp) REVERT: A 691 MET cc_start: 0.5355 (mmm) cc_final: 0.5079 (mmm) REVERT: A 778 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7438 (mt) REVERT: A 886 THR cc_start: 0.8686 (m) cc_final: 0.8448 (m) REVERT: A 930 ASN cc_start: 0.7519 (OUTLIER) cc_final: 0.6875 (p0) REVERT: A 933 ILE cc_start: 0.7801 (mm) cc_final: 0.7489 (tt) REVERT: A 955 GLU cc_start: 0.5350 (mp0) cc_final: 0.5045 (mp0) REVERT: A 1000 PHE cc_start: 0.4338 (OUTLIER) cc_final: 0.2170 (p90) REVERT: A 1002 LYS cc_start: 0.6488 (mttp) cc_final: 0.6076 (tptt) REVERT: A 1007 TYR cc_start: 0.5215 (OUTLIER) cc_final: 0.4796 (m-80) REVERT: B 74 ARG cc_start: 0.5213 (mmt180) cc_final: 0.4030 (tpt90) outliers start: 19 outliers final: 12 residues processed: 119 average time/residue: 0.0942 time to fit residues: 15.9317 Evaluate side-chains 115 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 930 ASN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1007 TYR Chi-restraints excluded: chain B residue 277 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 61 optimal weight: 2.9990 chunk 31 optimal weight: 0.0980 chunk 54 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 9 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.210038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.174391 restraints weight = 10873.705| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.61 r_work: 0.3566 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9168 Z= 0.097 Angle : 0.488 6.454 12463 Z= 0.246 Chirality : 0.039 0.150 1436 Planarity : 0.004 0.045 1574 Dihedral : 3.676 15.055 1229 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.06 % Allowed : 18.83 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.26), residues: 1130 helix: 1.37 (0.25), residues: 490 sheet: -0.23 (0.54), residues: 103 loop : -0.24 (0.29), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 938 TYR 0.010 0.001 TYR A 279 PHE 0.021 0.001 PHE A 692 TRP 0.022 0.001 TRP A 93 HIS 0.004 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 9164) covalent geometry : angle 0.48755 (12455) SS BOND : bond 0.00244 ( 4) SS BOND : angle 0.90418 ( 8) hydrogen bonds : bond 0.03751 ( 380) hydrogen bonds : angle 4.11576 ( 1062) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.357 Fit side-chains REVERT: A 93 TRP cc_start: 0.6177 (p-90) cc_final: 0.5917 (p-90) REVERT: A 201 ARG cc_start: 0.7115 (ttm-80) cc_final: 0.6644 (ttm170) REVERT: A 265 ASN cc_start: 0.7225 (m-40) cc_final: 0.6993 (m-40) REVERT: A 453 LYS cc_start: 0.6718 (mppt) cc_final: 0.6142 (ttmm) REVERT: A 481 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7048 (t70) REVERT: A 565 MET cc_start: 0.7274 (ttm) cc_final: 0.6703 (tpp) REVERT: A 778 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7609 (mt) REVERT: A 886 THR cc_start: 0.8650 (m) cc_final: 0.8420 (m) REVERT: A 930 ASN cc_start: 0.7469 (OUTLIER) cc_final: 0.6851 (p0) REVERT: A 933 ILE cc_start: 0.7807 (mm) cc_final: 0.7525 (tt) REVERT: A 955 GLU cc_start: 0.5320 (mp0) cc_final: 0.4909 (mp0) REVERT: A 1000 PHE cc_start: 0.4408 (OUTLIER) cc_final: 0.2260 (p90) REVERT: A 1002 LYS cc_start: 0.6382 (mttp) cc_final: 0.5982 (tptt) REVERT: A 1007 TYR cc_start: 0.5329 (OUTLIER) cc_final: 0.4864 (m-80) REVERT: A 1046 THR cc_start: 0.6196 (OUTLIER) cc_final: 0.5973 (t) REVERT: B 74 ARG cc_start: 0.5252 (mmt180) cc_final: 0.4054 (tpt90) outliers start: 20 outliers final: 9 residues processed: 117 average time/residue: 0.0958 time to fit residues: 16.0210 Evaluate side-chains 113 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 930 ASN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1007 TYR Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain B residue 277 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 47 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 85 optimal weight: 0.2980 chunk 92 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.207970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.172500 restraints weight = 10812.208| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 1.72 r_work: 0.3557 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9168 Z= 0.137 Angle : 0.533 6.445 12463 Z= 0.271 Chirality : 0.041 0.158 1436 Planarity : 0.004 0.045 1574 Dihedral : 3.891 16.244 1229 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.57 % Allowed : 19.34 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.26), residues: 1130 helix: 1.30 (0.25), residues: 484 sheet: -0.63 (0.50), residues: 113 loop : -0.19 (0.29), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 938 TYR 0.013 0.002 TYR A 928 PHE 0.018 0.002 PHE A 692 TRP 0.023 0.002 TRP A 767 HIS 0.005 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9164) covalent geometry : angle 0.53295 (12455) SS BOND : bond 0.00137 ( 4) SS BOND : angle 0.87603 ( 8) hydrogen bonds : bond 0.04326 ( 380) hydrogen bonds : angle 4.27022 ( 1062) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.349 Fit side-chains REVERT: A 99 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7595 (m-30) REVERT: A 201 ARG cc_start: 0.7137 (ttm-80) cc_final: 0.6512 (ttm170) REVERT: A 339 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.8180 (t) REVERT: A 453 LYS cc_start: 0.6729 (mppt) cc_final: 0.6141 (ttmm) REVERT: A 481 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.6985 (t70) REVERT: A 778 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7476 (mt) REVERT: A 886 THR cc_start: 0.8714 (m) cc_final: 0.8469 (m) REVERT: A 930 ASN cc_start: 0.7590 (OUTLIER) cc_final: 0.6993 (p0) REVERT: A 933 ILE cc_start: 0.7791 (mm) cc_final: 0.7510 (tt) REVERT: A 955 GLU cc_start: 0.5350 (OUTLIER) cc_final: 0.5082 (mp0) REVERT: A 1000 PHE cc_start: 0.4476 (OUTLIER) cc_final: 0.2326 (p90) REVERT: A 1002 LYS cc_start: 0.6467 (mttp) cc_final: 0.6085 (tptt) REVERT: A 1007 TYR cc_start: 0.5104 (OUTLIER) cc_final: 0.4719 (m-80) REVERT: B 74 ARG cc_start: 0.5395 (mmt180) cc_final: 0.4127 (tpt90) REVERT: B 295 ARG cc_start: 0.6180 (ttp80) cc_final: 0.5780 (ttp-110) outliers start: 25 outliers final: 15 residues processed: 127 average time/residue: 0.1047 time to fit residues: 18.3706 Evaluate side-chains 127 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 930 ASN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1007 TYR Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 277 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 97 optimal weight: 0.5980 chunk 67 optimal weight: 9.9990 chunk 31 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 chunk 24 optimal weight: 0.0980 chunk 86 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.211171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.176072 restraints weight = 10863.102| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 1.58 r_work: 0.3588 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9168 Z= 0.095 Angle : 0.491 8.960 12463 Z= 0.246 Chirality : 0.039 0.157 1436 Planarity : 0.004 0.045 1574 Dihedral : 3.657 14.829 1229 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.75 % Allowed : 20.16 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.27), residues: 1130 helix: 1.40 (0.25), residues: 492 sheet: -0.52 (0.51), residues: 113 loop : -0.13 (0.29), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 294 TYR 0.009 0.001 TYR A 279 PHE 0.020 0.001 PHE A 692 TRP 0.031 0.001 TRP A 93 HIS 0.002 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 9164) covalent geometry : angle 0.49102 (12455) SS BOND : bond 0.00121 ( 4) SS BOND : angle 0.76621 ( 8) hydrogen bonds : bond 0.03639 ( 380) hydrogen bonds : angle 4.10082 ( 1062) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.370 Fit side-chains REVERT: A 201 ARG cc_start: 0.7068 (ttm-80) cc_final: 0.6623 (ttm170) REVERT: A 265 ASN cc_start: 0.7220 (m-40) cc_final: 0.6979 (m-40) REVERT: A 481 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.6979 (t70) REVERT: A 778 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7607 (mt) REVERT: A 886 THR cc_start: 0.8654 (m) cc_final: 0.8416 (m) REVERT: A 930 ASN cc_start: 0.7453 (OUTLIER) cc_final: 0.6878 (p0) REVERT: A 933 ILE cc_start: 0.7746 (mm) cc_final: 0.7461 (tt) REVERT: A 955 GLU cc_start: 0.5402 (OUTLIER) cc_final: 0.5137 (mp0) REVERT: A 976 ARG cc_start: 0.5187 (tpp-160) cc_final: 0.4911 (tpp-160) REVERT: A 1000 PHE cc_start: 0.4451 (OUTLIER) cc_final: 0.2300 (p90) REVERT: A 1002 LYS cc_start: 0.6314 (mttp) cc_final: 0.5897 (tppt) REVERT: A 1007 TYR cc_start: 0.5346 (OUTLIER) cc_final: 0.4823 (m-80) REVERT: A 1053 MET cc_start: 0.4488 (ppp) cc_final: 0.4170 (ppp) REVERT: B 74 ARG cc_start: 0.5369 (mmt180) cc_final: 0.4158 (tpt90) REVERT: B 295 ARG cc_start: 0.6082 (ttp80) cc_final: 0.5637 (ttp-110) outliers start: 17 outliers final: 10 residues processed: 114 average time/residue: 0.0905 time to fit residues: 14.5645 Evaluate side-chains 116 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 930 ASN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1007 TYR Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 277 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 42 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 64 optimal weight: 0.0020 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.210536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.175350 restraints weight = 10728.398| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 1.59 r_work: 0.3588 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9168 Z= 0.099 Angle : 0.512 8.440 12463 Z= 0.256 Chirality : 0.040 0.156 1436 Planarity : 0.004 0.044 1574 Dihedral : 3.656 14.680 1229 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.95 % Allowed : 19.86 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.26), residues: 1130 helix: 1.46 (0.25), residues: 486 sheet: -0.54 (0.51), residues: 113 loop : -0.06 (0.29), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 294 TYR 0.010 0.001 TYR A 450 PHE 0.018 0.001 PHE A 692 TRP 0.029 0.001 TRP A 93 HIS 0.004 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 9164) covalent geometry : angle 0.51075 (12455) SS BOND : bond 0.00131 ( 4) SS BOND : angle 1.47279 ( 8) hydrogen bonds : bond 0.03680 ( 380) hydrogen bonds : angle 4.09562 ( 1062) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2485.14 seconds wall clock time: 43 minutes 10.28 seconds (2590.28 seconds total)