Starting phenix.real_space_refine on Thu Jul 2 14:31:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yo3_33980/07_2026/7yo3_33980.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yo3_33980/07_2026/7yo3_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_33980/07_2026/7yo3_33980.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yo3_33980/07_2026/7yo3_33980.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yo3_33980/07_2026/7yo3_33980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yo3_33980/07_2026/7yo3_33980.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7yo3_33980/07_2026/7yo3_33980.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yo3_33980/07_2026/7yo3_33980.cif" } 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-dev-6108/lib/python3.11/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: 1.42, per 1000 atoms: 0.16 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: 0.68 Conformation dependent library (CDL) restraints added in 212.7 milliseconds 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: 0.43 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: 1.31 Time building geometry restraints manager: 0.87 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: 1.870 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: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.680 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 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 are 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/Z covalent geometry : bond 0.00433 / 0.25 ( 9164) covalent geometry : angle 0.67229 / 0.40 (12455) SS BOND : bond 0.00981 / 0.51 ( 4) SS BOND : angle 1.13471 / 0.68 ( 8) hydrogen bonds : bond 0.14820 / 9.51 ( 380) hydrogen bonds : angle 5.77328 / 4.21 ( 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 : 0.321 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: 0.6057 (mm-30) REVERT: A 265 ASN cc_start: 0.6268 (m-40) cc_final: 0.5410 (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: 0.1015 time to fit residues: 27.1435 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 : 0.220 ------------------------------------------------------------------------------- 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... ** 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 = 0.4365 r_free = 0.4365 target = 0.220475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.187012 restraints weight = 11097.693| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 1.64 r_work: 0.3747 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9168 Z= 0.122 Angle : 0.559 6.754 12463 Z= 0.286 Chirality : 0.041 0.147 1436 Planarity : 0.005 0.062 1574 Dihedral : 3.881 16.457 1229 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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 are not related in a simple way. whole: 0.55 (0.26), residues: 1130 helix: 1.16 (0.24), residues: 481 sheet: -0.23 (0.58), residues: 99 loop : -0.15 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 72 TYR 0.021 0.002 TYR A1032 PHE 0.023 0.001 PHE A1000 TRP 0.016 0.001 TRP B 215 HIS 0.006 0.001 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 9164) covalent geometry : angle 0.55768 / 0.29 (12455) SS BOND : bond 0.00662 / 0.34 ( 4) SS BOND : angle 1.59952 / 0.64 ( 8) hydrogen bonds : bond 0.04238 / 2.73 ( 380) hydrogen bonds : angle 4.61464 / 3.36 ( 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 138 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.6990 (mmm) cc_final: 0.6701 (mmm) REVERT: A 244 SER cc_start: 0.8845 (OUTLIER) cc_final: 0.8621 (m) REVERT: A 265 ASN cc_start: 0.6741 (m-40) cc_final: 0.5634 (t0) REVERT: A 321 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7462 (tt0) REVERT: A 453 LYS cc_start: 0.6510 (mppt) cc_final: 0.6025 (ttmt) REVERT: A 886 THR cc_start: 0.7582 (m) cc_final: 0.7371 (p) REVERT: A 930 ASN cc_start: 0.7526 (OUTLIER) cc_final: 0.7027 (p0) REVERT: A 1007 TYR cc_start: 0.5353 (OUTLIER) cc_final: 0.4531 (m-80) REVERT: B 74 ARG cc_start: 0.4586 (mmt180) cc_final: 0.3789 (mmm160) REVERT: B 190 LEU cc_start: 0.3397 (mp) cc_final: 0.3070 (mt) outliers start: 15 outliers final: 7 residues processed: 134 average time/residue: 0.0890 time to fit residues: 16.5345 Evaluate side-chains 108 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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: 0.0010 chunk 12 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4346 r_free = 0.4346 target = 0.218546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.182450 restraints weight = 10872.786| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 1.72 r_work: 0.3656 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2817 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= 0.108 Angle : 0.493 6.544 12463 Z= 0.253 Chirality : 0.040 0.151 1436 Planarity : 0.004 0.058 1574 Dihedral : 3.633 15.207 1229 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.65 % Allowed : 11.93 % Favored : 86.42 % 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 are not related in a simple way. whole: 0.80 (0.27), residues: 1130 helix: 1.42 (0.25), residues: 482 sheet: -0.35 (0.53), residues: 114 loop : 0.02 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 99 TYR 0.010 0.001 TYR A1032 PHE 0.017 0.001 PHE A1000 TRP 0.015 0.001 TRP B 215 HIS 0.007 0.001 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 9164) covalent geometry : angle 0.49349 / 0.25 (12455) SS BOND : bond 0.00494 / 0.25 ( 4) SS BOND : angle 0.50853 / 0.26 ( 8) hydrogen bonds : bond 0.03954 / 2.54 ( 380) hydrogen bonds : angle 4.27321 / 3.09 ( 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 130 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.7139 (mmm) cc_final: 0.6883 (mmm) REVERT: A 453 LYS cc_start: 0.6436 (mppt) cc_final: 0.5948 (ttmt) REVERT: A 477 TRP cc_start: 0.6071 (t60) cc_final: 0.5760 (t60) REVERT: A 565 MET cc_start: 0.6692 (ttm) cc_final: 0.6434 (tpp) REVERT: A 698 LYS cc_start: 0.6307 (mptt) cc_final: 0.6082 (mmtp) REVERT: A 739 MET cc_start: 0.7003 (ttt) cc_final: 0.6610 (ttm) REVERT: A 886 THR cc_start: 0.7799 (m) cc_final: 0.7545 (p) REVERT: A 930 ASN cc_start: 0.7452 (OUTLIER) cc_final: 0.7217 (p0) REVERT: A 933 ILE cc_start: 0.7800 (mm) cc_final: 0.7400 (tt) REVERT: A 1007 TYR cc_start: 0.5304 (OUTLIER) cc_final: 0.4777 (m-80) REVERT: B 74 ARG cc_start: 0.4878 (mmt180) cc_final: 0.3669 (tpt90) outliers start: 16 outliers final: 10 residues processed: 127 average time/residue: 0.0903 time to fit residues: 16.1952 Evaluate side-chains 109 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain B residue 131 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 99 optimal weight: 0.4980 chunk 54 optimal weight: 7.9990 chunk 90 optimal weight: 0.0980 chunk 0 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 53 optimal weight: 0.0000 chunk 112 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 64 optimal weight: 0.0030 chunk 96 optimal weight: 0.4980 overall best weight: 0.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 ASN A 772 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.219780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.183392 restraints weight = 11034.665| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 1.68 r_work: 0.3690 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9168 Z= 0.089 Angle : 0.458 5.649 12463 Z= 0.234 Chirality : 0.038 0.140 1436 Planarity : 0.004 0.051 1574 Dihedral : 3.445 13.610 1229 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.95 % Allowed : 13.37 % Favored : 84.67 % 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 are not related in a simple way. whole: 0.96 (0.27), residues: 1130 helix: 1.58 (0.25), residues: 482 sheet: -0.34 (0.53), residues: 114 loop : 0.10 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 99 TYR 0.009 0.001 TYR A1032 PHE 0.015 0.001 PHE A1000 TRP 0.015 0.001 TRP B 215 HIS 0.007 0.001 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00186 / 0.09 ( 9164) covalent geometry : angle 0.45764 / 0.23 (12455) SS BOND : bond 0.00152 / 0.09 ( 4) SS BOND : angle 0.35644 / 0.20 ( 8) hydrogen bonds : bond 0.03396 / 2.19 ( 380) hydrogen bonds : angle 4.05740 / 2.93 ( 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 118 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.7074 (mmm) cc_final: 0.6836 (mmm) REVERT: A 453 LYS cc_start: 0.6344 (mppt) cc_final: 0.5920 (ttmt) REVERT: A 477 TRP cc_start: 0.6015 (t60) cc_final: 0.5722 (t60) REVERT: A 565 MET cc_start: 0.6681 (ttm) cc_final: 0.6453 (tpp) REVERT: A 698 LYS cc_start: 0.6328 (mptt) cc_final: 0.6079 (mmtt) REVERT: A 739 MET cc_start: 0.7059 (ttt) cc_final: 0.6658 (ttm) REVERT: A 886 THR cc_start: 0.7755 (m) cc_final: 0.7494 (p) REVERT: A 1000 PHE cc_start: 0.3763 (OUTLIER) cc_final: 0.1956 (p90) REVERT: A 1002 LYS cc_start: 0.6700 (tppt) cc_final: 0.6374 (tttm) REVERT: A 1007 TYR cc_start: 0.5247 (OUTLIER) cc_final: 0.4790 (m-80) REVERT: B 74 ARG cc_start: 0.4858 (mmt180) cc_final: 0.3766 (tpt90) outliers start: 19 outliers final: 12 residues processed: 113 average time/residue: 0.0911 time to fit residues: 14.5487 Evaluate side-chains 102 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 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 935 THR Chi-restraints excluded: chain A residue 949 LEU 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 131 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 71 optimal weight: 0.4980 chunk 61 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 907 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.210270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.173321 restraints weight = 10859.804| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.71 r_work: 0.3565 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9168 Z= 0.170 Angle : 0.580 7.757 12463 Z= 0.298 Chirality : 0.043 0.152 1436 Planarity : 0.005 0.049 1574 Dihedral : 4.022 17.916 1229 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.57 % Allowed : 14.71 % Favored : 82.72 % 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 are not related in a simple way. whole: 0.45 (0.26), residues: 1130 helix: 1.13 (0.24), residues: 487 sheet: -0.36 (0.53), residues: 105 loop : -0.25 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 974 TYR 0.019 0.002 TYR A 928 PHE 0.019 0.002 PHE A 511 TRP 0.016 0.002 TRP B 215 HIS 0.008 0.002 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 9164) covalent geometry : angle 0.58035 / 0.30 (12455) SS BOND : bond 0.00208 / 0.11 ( 4) SS BOND : angle 0.61903 / 0.35 ( 8) hydrogen bonds : bond 0.04922 / 3.19 ( 380) hydrogen bonds : angle 4.41428 / 3.19 ( 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 133 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.302 Fit side-chains REVERT: A 201 ARG cc_start: 0.7035 (ttm-80) cc_final: 0.6623 (ttm170) REVERT: A 453 LYS cc_start: 0.6652 (mppt) cc_final: 0.6087 (ttmt) REVERT: A 739 MET cc_start: 0.7175 (ttt) cc_final: 0.6809 (ttm) REVERT: A 778 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.7362 (mt) REVERT: A 886 THR cc_start: 0.8416 (m) cc_final: 0.8142 (m) REVERT: A 933 ILE cc_start: 0.8014 (mm) cc_final: 0.7670 (tt) REVERT: A 1000 PHE cc_start: 0.4293 (OUTLIER) cc_final: 0.2081 (p90) REVERT: A 1007 TYR cc_start: 0.5120 (OUTLIER) cc_final: 0.4755 (m-80) REVERT: A 1047 ASP cc_start: 0.6246 (OUTLIER) cc_final: 0.5521 (t0) REVERT: B 74 ARG cc_start: 0.5088 (mmt180) cc_final: 0.3833 (tpt90) REVERT: B 126 LEU cc_start: 0.6312 (OUTLIER) cc_final: 0.5629 (tt) REVERT: B 230 LEU cc_start: 0.6063 (pp) cc_final: 0.5832 (pp) outliers start: 25 outliers final: 16 residues processed: 126 average time/residue: 0.1000 time to fit residues: 17.5183 Evaluate side-chains 114 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 287 THR 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 498 CYS 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 794 ILE Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 949 LEU 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 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: 6.9990 chunk 99 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 106 optimal weight: 0.0070 overall best weight: 1.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.211165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.174186 restraints weight = 10873.692| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 1.75 r_work: 0.3567 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9168 Z= 0.116 Angle : 0.496 6.079 12463 Z= 0.255 Chirality : 0.040 0.141 1436 Planarity : 0.004 0.047 1574 Dihedral : 3.758 16.091 1229 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.37 % Allowed : 16.87 % Favored : 80.76 % 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 are not related in a simple way. whole: 0.58 (0.26), residues: 1130 helix: 1.30 (0.25), residues: 488 sheet: -0.37 (0.54), residues: 103 loop : -0.23 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1031 TYR 0.011 0.002 TYR A 928 PHE 0.017 0.001 PHE A 120 TRP 0.015 0.001 TRP A 767 HIS 0.008 0.001 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 9164) covalent geometry : angle 0.49644 / 0.26 (12455) SS BOND : bond 0.00129 / 0.08 ( 4) SS BOND : angle 0.48540 / 0.30 ( 8) hydrogen bonds : bond 0.04087 / 2.65 ( 380) hydrogen bonds : angle 4.21111 / 3.03 ( 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 124 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.340 Fit side-chains REVERT: A 201 ARG cc_start: 0.6970 (ttm-80) cc_final: 0.6436 (ttm170) REVERT: A 453 LYS cc_start: 0.6565 (mppt) cc_final: 0.6036 (ttmt) REVERT: A 778 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7346 (mt) REVERT: A 886 THR cc_start: 0.8487 (m) cc_final: 0.8229 (m) REVERT: A 930 ASN cc_start: 0.7644 (OUTLIER) cc_final: 0.7234 (p0) REVERT: A 933 ILE cc_start: 0.8034 (mm) cc_final: 0.7649 (tt) REVERT: A 1000 PHE cc_start: 0.4314 (OUTLIER) cc_final: 0.2142 (p90) REVERT: A 1002 LYS cc_start: 0.6610 (mttp) cc_final: 0.6137 (tptt) REVERT: A 1007 TYR cc_start: 0.5100 (OUTLIER) cc_final: 0.4764 (m-80) REVERT: A 1047 ASP cc_start: 0.6254 (OUTLIER) cc_final: 0.5630 (t0) REVERT: B 74 ARG cc_start: 0.5173 (mmt180) cc_final: 0.3779 (tpt90) REVERT: B 230 LEU cc_start: 0.5940 (pp) cc_final: 0.5700 (pp) outliers start: 23 outliers final: 12 residues processed: 118 average time/residue: 0.0952 time to fit residues: 15.8227 Evaluate side-chains 113 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 416 ILE Chi-restraints excluded: chain A residue 498 CYS 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 788 ASP Chi-restraints excluded: chain A residue 930 ASN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 949 LEU 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 126 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.211471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.174732 restraints weight = 10898.037| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 1.69 r_work: 0.3562 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9168 Z= 0.108 Angle : 0.482 5.989 12463 Z= 0.248 Chirality : 0.040 0.142 1436 Planarity : 0.004 0.046 1574 Dihedral : 3.627 15.524 1229 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.16 % Allowed : 17.70 % Favored : 80.14 % 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 are not related in a simple way. whole: 0.66 (0.26), residues: 1130 helix: 1.36 (0.25), residues: 488 sheet: -0.30 (0.54), residues: 103 loop : -0.20 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 103 TYR 0.010 0.001 TYR A 279 PHE 0.016 0.001 PHE A 120 TRP 0.011 0.001 TRP B 215 HIS 0.005 0.001 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 9164) covalent geometry : angle 0.48229 / 0.25 (12455) SS BOND : bond 0.00126 / 0.08 ( 4) SS BOND : angle 0.46440 / 0.29 ( 8) hydrogen bonds : bond 0.03831 / 2.48 ( 380) hydrogen bonds : angle 4.12650 / 2.97 ( 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 123 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.355 Fit side-chains REVERT: A 201 ARG cc_start: 0.6966 (ttm-80) cc_final: 0.6482 (ttm170) REVERT: A 265 ASN cc_start: 0.7250 (m-40) cc_final: 0.6992 (m-40) REVERT: A 453 LYS cc_start: 0.6588 (mppt) cc_final: 0.5998 (ttmt) REVERT: A 739 MET cc_start: 0.7111 (ttt) cc_final: 0.6813 (ttp) REVERT: A 886 THR cc_start: 0.8506 (m) cc_final: 0.8266 (m) REVERT: A 930 ASN cc_start: 0.7733 (OUTLIER) cc_final: 0.7297 (p0) REVERT: A 933 ILE cc_start: 0.7854 (mm) cc_final: 0.7608 (tt) REVERT: A 1000 PHE cc_start: 0.4294 (OUTLIER) cc_final: 0.2120 (p90) REVERT: A 1002 LYS cc_start: 0.6494 (mttp) cc_final: 0.5977 (tppt) REVERT: A 1007 TYR cc_start: 0.5151 (OUTLIER) cc_final: 0.4820 (m-80) REVERT: B 74 ARG cc_start: 0.5133 (mmt180) cc_final: 0.3939 (tpt90) outliers start: 21 outliers final: 14 residues processed: 118 average time/residue: 0.0955 time to fit residues: 15.6942 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 : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 196 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 498 CYS 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 782 THR Chi-restraints excluded: chain A residue 930 ASN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 949 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 61 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 40 optimal weight: 0.0980 chunk 44 optimal weight: 0.8980 chunk 95 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.212138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.176579 restraints weight = 10841.456| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.60 r_work: 0.3579 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9168 Z= 0.098 Angle : 0.478 6.000 12463 Z= 0.244 Chirality : 0.039 0.141 1436 Planarity : 0.004 0.045 1574 Dihedral : 3.529 15.115 1229 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.16 % Allowed : 17.49 % Favored : 80.35 % 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 are not related in a simple way. whole: 0.72 (0.26), residues: 1130 helix: 1.38 (0.25), residues: 491 sheet: -0.46 (0.51), residues: 112 loop : -0.07 (0.29), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 113 TYR 0.009 0.001 TYR A 279 PHE 0.015 0.001 PHE A 120 TRP 0.020 0.001 TRP A 767 HIS 0.004 0.001 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 ( 9164) covalent geometry : angle 0.47767 / 0.24 (12455) SS BOND : bond 0.00104 / 0.07 ( 4) SS BOND : angle 0.43134 / 0.27 ( 8) hydrogen bonds : bond 0.03651 / 2.36 ( 380) hydrogen bonds : angle 4.07008 / 2.92 ( 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 125 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.352 Fit side-chains REVERT: A 201 ARG cc_start: 0.7122 (ttm-80) cc_final: 0.6616 (ttm110) REVERT: A 265 ASN cc_start: 0.7309 (m-40) cc_final: 0.7032 (m-40) REVERT: A 453 LYS cc_start: 0.6692 (mppt) cc_final: 0.5997 (ttmt) REVERT: A 481 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7196 (t70) REVERT: A 565 MET cc_start: 0.7520 (ttm) cc_final: 0.6872 (tpp) REVERT: A 739 MET cc_start: 0.7427 (ttt) cc_final: 0.7086 (ttp) REVERT: A 778 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7668 (mt) REVERT: A 886 THR cc_start: 0.8544 (m) cc_final: 0.8335 (m) REVERT: A 930 ASN cc_start: 0.7723 (OUTLIER) cc_final: 0.7287 (p0) REVERT: A 933 ILE cc_start: 0.7957 (mm) cc_final: 0.7697 (tt) REVERT: A 1000 PHE cc_start: 0.4443 (OUTLIER) cc_final: 0.2305 (p90) REVERT: A 1002 LYS cc_start: 0.6588 (mttp) cc_final: 0.6049 (tppt) REVERT: A 1007 TYR cc_start: 0.5228 (OUTLIER) cc_final: 0.4938 (m-80) REVERT: B 61 SER cc_start: 0.6952 (p) cc_final: 0.6569 (m) REVERT: B 74 ARG cc_start: 0.5135 (mmt180) cc_final: 0.3880 (tpt90) outliers start: 21 outliers final: 12 residues processed: 119 average time/residue: 0.1039 time to fit residues: 17.4897 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 : 0.339 ------------------------------------------------------------------------------- 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 481 ASP Chi-restraints excluded: chain A residue 498 CYS 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 782 THR Chi-restraints excluded: chain A residue 930 ASN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1007 TYR Chi-restraints excluded: chain B residue 126 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 47 optimal weight: 6.9990 chunk 81 optimal weight: 0.4980 chunk 110 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.211905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.176255 restraints weight = 10808.781| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 1.64 r_work: 0.3598 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9168 Z= 0.099 Angle : 0.480 6.727 12463 Z= 0.244 Chirality : 0.039 0.143 1436 Planarity : 0.004 0.045 1574 Dihedral : 3.520 15.019 1229 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.16 % Allowed : 18.11 % Favored : 79.73 % 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 are not related in a simple way. whole: 0.77 (0.26), residues: 1130 helix: 1.45 (0.25), residues: 490 sheet: -0.45 (0.51), residues: 112 loop : -0.06 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 103 TYR 0.009 0.001 TYR A 928 PHE 0.015 0.001 PHE A 120 TRP 0.027 0.001 TRP A 93 HIS 0.005 0.001 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 9164) covalent geometry : angle 0.47935 / 0.24 (12455) SS BOND : bond 0.00102 / 0.07 ( 4) SS BOND : angle 0.88758 / 0.40 ( 8) hydrogen bonds : bond 0.03636 / 2.35 ( 380) hydrogen bonds : angle 4.03309 / 2.90 ( 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 117 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.340 Fit side-chains REVERT: A 201 ARG cc_start: 0.7051 (ttm-80) cc_final: 0.6553 (ttm110) REVERT: A 453 LYS cc_start: 0.6571 (mppt) cc_final: 0.6013 (ttmt) REVERT: A 481 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.6944 (t70) REVERT: A 565 MET cc_start: 0.7334 (ttm) cc_final: 0.6691 (tpp) REVERT: A 739 MET cc_start: 0.7091 (ttt) cc_final: 0.6790 (ttp) REVERT: A 778 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7579 (mt) REVERT: A 886 THR cc_start: 0.8503 (m) cc_final: 0.8263 (m) REVERT: A 930 ASN cc_start: 0.7747 (OUTLIER) cc_final: 0.7317 (p0) REVERT: A 933 ILE cc_start: 0.7755 (mm) cc_final: 0.7539 (tt) REVERT: A 1000 PHE cc_start: 0.4211 (OUTLIER) cc_final: 0.2112 (p90) REVERT: A 1002 LYS cc_start: 0.6391 (mttp) cc_final: 0.6039 (tppt) REVERT: A 1007 TYR cc_start: 0.5141 (OUTLIER) cc_final: 0.4913 (m-80) REVERT: B 74 ARG cc_start: 0.5182 (mmt180) cc_final: 0.4066 (tpt90) outliers start: 21 outliers final: 12 residues processed: 110 average time/residue: 0.1027 time to fit residues: 15.8567 Evaluate side-chains 111 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 196 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 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 949 LEU Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1007 TYR Chi-restraints excluded: chain B residue 126 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 97 optimal weight: 0.0770 chunk 67 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 86 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.210780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.175379 restraints weight = 10814.019| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.59 r_work: 0.3606 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9168 Z= 0.108 Angle : 0.492 6.806 12463 Z= 0.251 Chirality : 0.040 0.147 1436 Planarity : 0.004 0.045 1574 Dihedral : 3.586 14.999 1229 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.95 % Allowed : 18.42 % Favored : 79.63 % 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 are not related in a simple way. whole: 0.78 (0.26), residues: 1130 helix: 1.46 (0.25), residues: 484 sheet: -0.52 (0.51), residues: 113 loop : -0.03 (0.29), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 103 TYR 0.012 0.001 TYR A 928 PHE 0.015 0.001 PHE A 120 TRP 0.025 0.001 TRP A 93 HIS 0.005 0.001 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 9164) covalent geometry : angle 0.49173 / 0.25 (12455) SS BOND : bond 0.00136 / 0.08 ( 4) SS BOND : angle 0.94413 / 0.43 ( 8) hydrogen bonds : bond 0.03848 / 2.50 ( 380) hydrogen bonds : angle 4.07952 / 2.93 ( 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 129 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.359 Fit side-chains REVERT: A 201 ARG cc_start: 0.7122 (ttm-80) cc_final: 0.6619 (ttm170) REVERT: A 481 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7088 (t0) REVERT: A 565 MET cc_start: 0.7299 (ttm) cc_final: 0.7083 (tpp) REVERT: A 778 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7578 (mt) REVERT: A 886 THR cc_start: 0.8619 (m) cc_final: 0.8362 (m) REVERT: A 930 ASN cc_start: 0.7701 (OUTLIER) cc_final: 0.7284 (p0) REVERT: A 1000 PHE cc_start: 0.4598 (OUTLIER) cc_final: 0.2399 (p90) REVERT: A 1002 LYS cc_start: 0.6411 (mttp) cc_final: 0.6080 (tppt) REVERT: A 1007 TYR cc_start: 0.5296 (OUTLIER) cc_final: 0.4988 (m-80) REVERT: B 74 ARG cc_start: 0.5182 (mmt180) cc_final: 0.4125 (tpt90) REVERT: B 126 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6466 (tt) outliers start: 19 outliers final: 10 residues processed: 122 average time/residue: 0.1015 time to fit residues: 17.1372 Evaluate side-chains 117 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 196 SER 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 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 949 LEU Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1007 TYR Chi-restraints excluded: chain B residue 126 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 42 optimal weight: 6.9990 chunk 53 optimal weight: 0.4980 chunk 86 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 64 optimal weight: 0.0570 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 HIS A 930 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.209684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.174128 restraints weight = 10676.488| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.67 r_work: 0.3580 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9168 Z= 0.123 Angle : 0.515 7.282 12463 Z= 0.263 Chirality : 0.041 0.158 1436 Planarity : 0.004 0.045 1574 Dihedral : 3.696 15.752 1229 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.95 % Allowed : 18.72 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.26), residues: 1130 helix: 1.39 (0.24), residues: 484 sheet: -0.54 (0.50), residues: 113 loop : -0.10 (0.29), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 103 TYR 0.014 0.002 TYR A 928 PHE 0.016 0.001 PHE A 120 TRP 0.026 0.002 TRP A 93 HIS 0.010 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 9164) covalent geometry : angle 0.51508 / 0.26 (12455) SS BOND : bond 0.00103 / 0.07 ( 4) SS BOND : angle 0.76838 / 0.41 ( 8) hydrogen bonds : bond 0.04071 / 2.63 ( 380) hydrogen bonds : angle 4.14017 / 2.97 ( 1062) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2544.86 seconds wall clock time: 44 minutes 12.47 seconds (2652.47 seconds total)