Starting phenix.real_space_refine on Thu Mar 13 15:45:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yo3_33980/03_2025/7yo3_33980.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yo3_33980/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yo3_33980/03_2025/7yo3_33980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yo3_33980/03_2025/7yo3_33980.map" model { file = "/net/cci-nas-00/data/ceres_data/7yo3_33980/03_2025/7yo3_33980.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yo3_33980/03_2025/7yo3_33980.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.61, per 1000 atoms: 0.63 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: 2.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.05 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: 2.84 Time building geometry restraints manager: 2.70 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: 1.790 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.630 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.930 ------------------------------------------------------------------------------- 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 9164 Z= 0.284 Angle : 0.672 7.570 12455 Z= 0.400 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.001 TRP B 116 HIS 0.004 0.001 HIS A 771 PHE 0.025 0.001 PHE A 511 TYR 0.023 0.002 TYR B 266 ARG 0.004 0.000 ARG A 20 *********************** 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 : 0.965 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: 0.7019 (p) outliers start: 2 outliers final: 0 residues processed: 201 average time/residue: 0.2527 time to fit residues: 67.0570 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 : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 0.0470 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4307 r_free = 0.4307 target = 0.214419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.178905 restraints weight = 10756.650| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 1.73 r_work: 0.3639 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9164 Z= 0.275 Angle : 0.641 7.326 12455 Z= 0.329 Chirality : 0.044 0.151 1436 Planarity : 0.005 0.066 1574 Dihedral : 4.196 16.954 1229 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.06 % Allowed : 9.47 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1130 helix: 0.93 (0.24), residues: 479 sheet: -0.34 (0.55), residues: 105 loop : -0.29 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 215 HIS 0.009 0.002 HIS A 771 PHE 0.028 0.002 PHE A1000 TYR 0.023 0.003 TYR A1032 ARG 0.004 0.001 ARG B 217 *********************** 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 143 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.7126 (mmm) cc_final: 0.6856 (mmm) REVERT: A 201 ARG cc_start: 0.6771 (ttm-80) cc_final: 0.6166 (ttm170) REVERT: A 453 LYS cc_start: 0.6658 (mppt) cc_final: 0.6014 (ttmt) REVERT: A 477 TRP cc_start: 0.6109 (t60) cc_final: 0.5737 (t60) REVERT: A 886 THR cc_start: 0.8108 (m) cc_final: 0.7852 (m) REVERT: A 930 ASN cc_start: 0.7681 (OUTLIER) cc_final: 0.7178 (p0) REVERT: A 933 ILE cc_start: 0.7868 (mm) cc_final: 0.7520 (tt) REVERT: A 949 LEU cc_start: 0.8119 (tp) cc_final: 0.7870 (mt) REVERT: A 955 GLU cc_start: 0.5596 (mp0) cc_final: 0.5123 (mp0) REVERT: A 1007 TYR cc_start: 0.5301 (OUTLIER) cc_final: 0.4476 (m-80) REVERT: B 124 LEU cc_start: 0.5778 (OUTLIER) cc_final: 0.5573 (tp) outliers start: 20 outliers final: 10 residues processed: 139 average time/residue: 0.2350 time to fit residues: 44.2532 Evaluate side-chains 114 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 196 SER Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 755 VAL 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 1007 TYR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 131 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 49 optimal weight: 10.0000 chunk 38 optimal weight: 0.0370 chunk 75 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4309 r_free = 0.4309 target = 0.214888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.178230 restraints weight = 10953.308| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.72 r_work: 0.3617 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9164 Z= 0.151 Angle : 0.499 6.846 12455 Z= 0.258 Chirality : 0.040 0.143 1436 Planarity : 0.004 0.057 1574 Dihedral : 3.799 15.403 1229 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.16 % Allowed : 12.24 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1130 helix: 1.26 (0.24), residues: 481 sheet: -0.26 (0.55), residues: 105 loop : -0.16 (0.29), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 215 HIS 0.005 0.001 HIS A 771 PHE 0.017 0.001 PHE A1000 TYR 0.010 0.001 TYR A1032 ARG 0.007 0.000 ARG B 99 *********************** 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 129 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 1.158 Fit side-chains REVERT: A 453 LYS cc_start: 0.6523 (mppt) cc_final: 0.5974 (ttmt) REVERT: A 477 TRP cc_start: 0.6160 (t60) cc_final: 0.5769 (t60) REVERT: A 505 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8329 (t) REVERT: A 739 MET cc_start: 0.7000 (ttt) cc_final: 0.6620 (ttm) REVERT: A 886 THR cc_start: 0.8189 (m) cc_final: 0.7932 (m) REVERT: A 930 ASN cc_start: 0.7476 (OUTLIER) cc_final: 0.6936 (p0) REVERT: A 933 ILE cc_start: 0.7848 (mm) cc_final: 0.7499 (tt) REVERT: A 955 GLU cc_start: 0.5611 (mp0) cc_final: 0.5202 (mp0) REVERT: A 1007 TYR cc_start: 0.5229 (OUTLIER) cc_final: 0.4697 (m-80) REVERT: A 1047 ASP cc_start: 0.6234 (t0) cc_final: 0.5956 (t0) REVERT: B 230 LEU cc_start: 0.5993 (pp) cc_final: 0.5791 (pp) outliers start: 21 outliers final: 12 residues processed: 123 average time/residue: 0.2449 time to fit residues: 42.4975 Evaluate side-chains 111 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 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 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 1007 TYR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 107 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.4218 r_free = 0.4218 target = 0.205192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.169770 restraints weight = 10680.253| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.60 r_work: 0.3516 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9164 Z= 0.365 Angle : 0.714 7.569 12455 Z= 0.371 Chirality : 0.048 0.191 1436 Planarity : 0.006 0.060 1574 Dihedral : 4.840 23.676 1229 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.09 % Allowed : 15.64 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.25), residues: 1130 helix: 0.56 (0.24), residues: 480 sheet: -0.49 (0.53), residues: 103 loop : -0.59 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 477 HIS 0.014 0.002 HIS A 771 PHE 0.028 0.003 PHE A1000 TYR 0.021 0.003 TYR A 48 ARG 0.010 0.001 ARG B 157 *********************** 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 150 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.909 Fit side-chains REVERT: A 201 ARG cc_start: 0.7214 (ttm-80) cc_final: 0.6812 (ttm170) REVERT: A 481 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7239 (t70) REVERT: A 778 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7580 (mt) REVERT: A 930 ASN cc_start: 0.7835 (OUTLIER) cc_final: 0.7268 (p0) REVERT: A 931 ASP cc_start: 0.6889 (p0) cc_final: 0.6588 (t0) REVERT: A 933 ILE cc_start: 0.8041 (mm) cc_final: 0.7793 (tt) REVERT: A 955 GLU cc_start: 0.6016 (mp0) cc_final: 0.5714 (mp0) REVERT: A 1000 PHE cc_start: 0.4535 (OUTLIER) cc_final: 0.2320 (p90) REVERT: A 1007 TYR cc_start: 0.5155 (OUTLIER) cc_final: 0.4634 (m-80) REVERT: B 126 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6337 (tt) outliers start: 30 outliers final: 15 residues processed: 142 average time/residue: 0.2104 time to fit residues: 41.9431 Evaluate side-chains 127 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 901 THR Chi-restraints excluded: chain A residue 930 ASN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1007 TYR Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 127 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 106 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4256 r_free = 0.4256 target = 0.209297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.173317 restraints weight = 10772.482| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.59 r_work: 0.3564 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9164 Z= 0.148 Angle : 0.509 6.858 12455 Z= 0.261 Chirality : 0.040 0.144 1436 Planarity : 0.004 0.058 1574 Dihedral : 4.036 15.657 1229 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.47 % Allowed : 16.98 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1130 helix: 0.99 (0.24), residues: 488 sheet: -0.42 (0.53), residues: 105 loop : -0.45 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 767 HIS 0.006 0.001 HIS A 771 PHE 0.017 0.001 PHE A 120 TYR 0.011 0.001 TYR A 145 ARG 0.007 0.001 ARG B 294 *********************** 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 139 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.983 Fit side-chains REVERT: A 201 ARG cc_start: 0.7048 (ttm-80) cc_final: 0.6399 (ttm170) REVERT: A 265 ASN cc_start: 0.7237 (m-40) cc_final: 0.6426 (t0) REVERT: A 453 LYS cc_start: 0.6947 (mppt) cc_final: 0.6730 (mtmm) REVERT: A 477 TRP cc_start: 0.6138 (t60) cc_final: 0.5901 (t60) REVERT: A 481 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7068 (t70) REVERT: A 536 MET cc_start: 0.7796 (tpp) cc_final: 0.7530 (tpp) REVERT: A 739 MET cc_start: 0.7061 (ttt) cc_final: 0.6611 (ttm) REVERT: A 778 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7465 (mt) REVERT: A 930 ASN cc_start: 0.7417 (OUTLIER) cc_final: 0.7077 (p0) REVERT: A 949 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7830 (tt) REVERT: A 1000 PHE cc_start: 0.4385 (OUTLIER) cc_final: 0.2431 (p90) REVERT: A 1002 LYS cc_start: 0.6365 (mttp) cc_final: 0.6137 (tptt) REVERT: A 1007 TYR cc_start: 0.5138 (OUTLIER) cc_final: 0.4695 (m-80) REVERT: B 230 LEU cc_start: 0.6077 (pp) cc_final: 0.5843 (pp) outliers start: 24 outliers final: 12 residues processed: 133 average time/residue: 0.2045 time to fit residues: 38.6784 Evaluate side-chains 123 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 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 751 LEU 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 112 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 216 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 92 optimal weight: 0.0870 chunk 52 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.208602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.172923 restraints weight = 10735.729| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 1.58 r_work: 0.3566 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9164 Z= 0.171 Angle : 0.509 6.319 12455 Z= 0.261 Chirality : 0.040 0.150 1436 Planarity : 0.004 0.058 1574 Dihedral : 3.939 16.040 1229 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.37 % Allowed : 18.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.26), residues: 1130 helix: 1.10 (0.24), residues: 488 sheet: -0.33 (0.54), residues: 103 loop : -0.41 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 93 HIS 0.004 0.001 HIS A 771 PHE 0.017 0.001 PHE A 120 TYR 0.012 0.002 TYR A 928 ARG 0.005 0.000 ARG B 113 *********************** 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 128 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.939 Fit side-chains REVERT: A 201 ARG cc_start: 0.7071 (ttm-80) cc_final: 0.6518 (ttm170) REVERT: A 265 ASN cc_start: 0.7244 (m-40) cc_final: 0.6446 (t0) REVERT: A 453 LYS cc_start: 0.6813 (mppt) cc_final: 0.6577 (mtmm) REVERT: A 477 TRP cc_start: 0.6200 (t60) cc_final: 0.5953 (t60) REVERT: A 778 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7452 (mt) REVERT: A 886 THR cc_start: 0.8665 (m) cc_final: 0.8451 (m) REVERT: A 949 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7854 (tt) REVERT: A 955 GLU cc_start: 0.5244 (mp0) cc_final: 0.4943 (mp0) REVERT: A 1000 PHE cc_start: 0.4450 (OUTLIER) cc_final: 0.2159 (p90) REVERT: A 1007 TYR cc_start: 0.5128 (OUTLIER) cc_final: 0.4695 (m-80) REVERT: B 126 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6403 (tt) REVERT: B 230 LEU cc_start: 0.6001 (pp) cc_final: 0.5737 (pp) outliers start: 23 outliers final: 16 residues processed: 123 average time/residue: 0.2135 time to fit residues: 37.9699 Evaluate side-chains 121 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR 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 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 751 LEU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 778 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 112 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 277 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 44 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.205768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.169828 restraints weight = 10755.835| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.67 r_work: 0.3531 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9164 Z= 0.270 Angle : 0.585 6.796 12455 Z= 0.302 Chirality : 0.043 0.167 1436 Planarity : 0.005 0.060 1574 Dihedral : 4.294 19.781 1229 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.98 % Allowed : 18.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.26), residues: 1130 helix: 0.91 (0.24), residues: 481 sheet: -0.34 (0.53), residues: 103 loop : -0.47 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 215 HIS 0.005 0.001 HIS A 254 PHE 0.021 0.002 PHE A 511 TYR 0.015 0.002 TYR A 928 ARG 0.004 0.001 ARG A 974 *********************** 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 133 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 1.013 Fit side-chains REVERT: A 201 ARG cc_start: 0.7224 (ttm-80) cc_final: 0.6675 (ttm170) REVERT: A 265 ASN cc_start: 0.7325 (m-40) cc_final: 0.6501 (t0) REVERT: A 339 VAL cc_start: 0.8398 (OUTLIER) cc_final: 0.8094 (t) REVERT: A 481 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7189 (t70) REVERT: A 778 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7678 (mt) REVERT: A 886 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8499 (m) REVERT: A 949 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7846 (tt) REVERT: A 955 GLU cc_start: 0.5428 (mp0) cc_final: 0.5065 (mp0) REVERT: A 1000 PHE cc_start: 0.4595 (OUTLIER) cc_final: 0.2780 (p90) REVERT: A 1002 LYS cc_start: 0.6998 (tptt) cc_final: 0.6698 (mttp) REVERT: A 1007 TYR cc_start: 0.5123 (OUTLIER) cc_final: 0.4647 (m-80) REVERT: B 126 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6538 (tt) REVERT: B 230 LEU cc_start: 0.6023 (pp) cc_final: 0.5747 (pp) REVERT: B 295 ARG cc_start: 0.6150 (ttp80) cc_final: 0.5777 (ttp-110) outliers start: 29 outliers final: 18 residues processed: 125 average time/residue: 0.2108 time to fit residues: 37.3405 Evaluate side-chains 126 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR 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 506 MET Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 886 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 B residue 112 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 216 LEU 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 109 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 12 optimal weight: 0.1980 chunk 80 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.207024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.177502 restraints weight = 10944.483| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 1.43 r_work: 0.3638 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9164 Z= 0.200 Angle : 0.533 6.698 12455 Z= 0.275 Chirality : 0.041 0.153 1436 Planarity : 0.004 0.060 1574 Dihedral : 4.085 16.740 1229 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.98 % Allowed : 18.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.26), residues: 1130 helix: 1.07 (0.24), residues: 483 sheet: -0.25 (0.53), residues: 103 loop : -0.49 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 93 HIS 0.005 0.001 HIS A 771 PHE 0.035 0.002 PHE A 692 TYR 0.013 0.002 TYR A 928 ARG 0.004 0.000 ARG B 294 *********************** 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 139 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.913 Fit side-chains REVERT: A 201 ARG cc_start: 0.7047 (ttm-80) cc_final: 0.6494 (ttm170) REVERT: A 477 TRP cc_start: 0.5822 (t60) cc_final: 0.5604 (t60) REVERT: A 481 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.6947 (t70) REVERT: A 778 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7511 (mt) REVERT: A 886 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8417 (m) REVERT: A 930 ASN cc_start: 0.7650 (OUTLIER) cc_final: 0.7206 (p0) REVERT: A 949 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7712 (tt) REVERT: A 955 GLU cc_start: 0.5298 (mp0) cc_final: 0.4854 (mp0) REVERT: A 1000 PHE cc_start: 0.4472 (OUTLIER) cc_final: 0.2791 (p90) REVERT: A 1007 TYR cc_start: 0.5347 (OUTLIER) cc_final: 0.4778 (m-80) REVERT: B 126 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6541 (tt) REVERT: B 230 LEU cc_start: 0.5905 (pp) cc_final: 0.5620 (pp) REVERT: B 295 ARG cc_start: 0.6078 (ttp80) cc_final: 0.5819 (ttp-110) outliers start: 29 outliers final: 18 residues processed: 130 average time/residue: 0.2124 time to fit residues: 38.9951 Evaluate side-chains 131 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 337 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 505 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 886 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 71 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 130 GLN 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 84 optimal weight: 8.9990 chunk 56 optimal weight: 0.0970 chunk 94 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 65 optimal weight: 0.0020 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 0.4980 chunk 89 optimal weight: 20.0000 overall best weight: 0.4588 ------------------------------------------------------------------------------- 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 = 0.4256 r_free = 0.4256 target = 0.209245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.179608 restraints weight = 10747.859| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 1.48 r_work: 0.3660 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9164 Z= 0.128 Angle : 0.484 6.616 12455 Z= 0.248 Chirality : 0.040 0.161 1436 Planarity : 0.004 0.058 1574 Dihedral : 3.817 15.175 1229 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.26 % Allowed : 19.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1130 helix: 1.32 (0.25), residues: 484 sheet: -0.16 (0.53), residues: 103 loop : -0.33 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 93 HIS 0.003 0.001 HIS A 464 PHE 0.029 0.001 PHE A 692 TYR 0.010 0.001 TYR A 145 ARG 0.004 0.000 ARG B 294 *********************** 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 126 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.948 Fit side-chains REVERT: A 201 ARG cc_start: 0.6984 (ttm-80) cc_final: 0.6431 (ttm170) REVERT: A 265 ASN cc_start: 0.7208 (m-40) cc_final: 0.6394 (t0) REVERT: A 481 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.6864 (t70) REVERT: A 565 MET cc_start: 0.7222 (ttm) cc_final: 0.6943 (tpp) REVERT: A 778 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7448 (mt) REVERT: A 886 THR cc_start: 0.8704 (m) cc_final: 0.8446 (m) REVERT: A 930 ASN cc_start: 0.7500 (OUTLIER) cc_final: 0.7279 (p0) REVERT: A 949 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7719 (tt) REVERT: A 955 GLU cc_start: 0.5350 (mp0) cc_final: 0.4871 (mp0) REVERT: A 1000 PHE cc_start: 0.4452 (OUTLIER) cc_final: 0.2273 (p90) REVERT: A 1007 TYR cc_start: 0.5283 (OUTLIER) cc_final: 0.4753 (m-80) REVERT: B 126 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6584 (tt) REVERT: B 230 LEU cc_start: 0.5960 (pp) cc_final: 0.5701 (pp) REVERT: B 295 ARG cc_start: 0.6029 (ttp80) cc_final: 0.5808 (ttp-110) outliers start: 22 outliers final: 14 residues processed: 121 average time/residue: 0.2209 time to fit residues: 38.8342 Evaluate side-chains 122 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 196 SER 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 751 LEU 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 949 LEU 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 65 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 130 GLN 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 101 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 24 optimal weight: 0.0470 chunk 26 optimal weight: 0.7980 overall best weight: 1.3280 ------------------------------------------------------------------------------- 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 = 0.4238 r_free = 0.4238 target = 0.207288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.177800 restraints weight = 10870.002| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 1.44 r_work: 0.3630 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9164 Z= 0.178 Angle : 0.522 6.924 12455 Z= 0.268 Chirality : 0.041 0.160 1436 Planarity : 0.004 0.058 1574 Dihedral : 3.933 16.685 1229 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.57 % Allowed : 19.75 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 1130 helix: 1.26 (0.24), residues: 485 sheet: -0.19 (0.53), residues: 103 loop : -0.38 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 93 HIS 0.005 0.001 HIS A 254 PHE 0.027 0.001 PHE A 692 TYR 0.013 0.002 TYR A 928 ARG 0.003 0.000 ARG B 294 ********************** 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 128 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.977 Fit side-chains REVERT: A 201 ARG cc_start: 0.7042 (ttm-80) cc_final: 0.6497 (ttm170) REVERT: A 265 ASN cc_start: 0.7139 (m-40) cc_final: 0.6367 (t0) REVERT: A 481 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.6938 (t0) REVERT: A 565 MET cc_start: 0.7239 (ttm) cc_final: 0.7010 (tpp) REVERT: A 778 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7509 (mt) REVERT: A 886 THR cc_start: 0.8733 (m) cc_final: 0.8477 (m) REVERT: A 930 ASN cc_start: 0.7562 (OUTLIER) cc_final: 0.7143 (p0) REVERT: A 949 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7742 (tt) REVERT: A 955 GLU cc_start: 0.5463 (mp0) cc_final: 0.4958 (mp0) REVERT: A 1000 PHE cc_start: 0.4655 (OUTLIER) cc_final: 0.2422 (p90) REVERT: A 1007 TYR cc_start: 0.5293 (OUTLIER) cc_final: 0.4733 (m-80) REVERT: A 1053 MET cc_start: 0.4340 (ppp) cc_final: 0.3957 (ppp) REVERT: B 126 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6617 (tt) REVERT: B 295 ARG cc_start: 0.6039 (ttp80) cc_final: 0.5792 (ttp-110) outliers start: 25 outliers final: 16 residues processed: 123 average time/residue: 0.2147 time to fit residues: 37.5301 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 : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR 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 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 580 LEU Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 751 LEU 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 949 LEU 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 65 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 130 GLN 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 89 optimal weight: 20.0000 chunk 111 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.4227 r_free = 0.4227 target = 0.206228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.176551 restraints weight = 10824.832| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 1.40 r_work: 0.3626 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9164 Z= 0.213 Angle : 0.565 7.047 12455 Z= 0.290 Chirality : 0.042 0.161 1436 Planarity : 0.004 0.060 1574 Dihedral : 4.132 16.572 1229 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.67 % Allowed : 19.55 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 1130 helix: 1.14 (0.24), residues: 485 sheet: -0.23 (0.52), residues: 103 loop : -0.43 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 93 HIS 0.006 0.001 HIS A 771 PHE 0.027 0.002 PHE A 692 TYR 0.013 0.002 TYR A 928 ARG 0.003 0.000 ARG A 974 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5189.56 seconds wall clock time: 92 minutes 25.26 seconds (5545.26 seconds total)