Starting phenix.real_space_refine on Wed Feb 4 05:09:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m31_63595/02_2026/9m31_63595.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m31_63595/02_2026/9m31_63595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m31_63595/02_2026/9m31_63595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m31_63595/02_2026/9m31_63595.map" model { file = "/net/cci-nas-00/data/ceres_data/9m31_63595/02_2026/9m31_63595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m31_63595/02_2026/9m31_63595.cif" } resolution = 2.86 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= 0.014 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 P 50 5.49 5 Mg 1 5.21 5 S 28 5.16 5 C 5360 2.51 5 N 1515 2.21 5 O 1790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8744 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 945, 7661 Classifications: {'peptide': 945} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 927} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1082 Classifications: {'RNA': 51} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 21, 'rna3p_pyr': 19} Link IDs: {'rna2p': 11, 'rna3p': 39} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.96, per 1000 atoms: 0.22 Number of scatterers: 8744 At special positions: 0 Unit cell: (83.22, 95.265, 121.545, 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) S 28 16.00 P 50 15.00 Mg 1 11.99 O 1790 8.00 N 1515 7.00 C 5360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.74 Conformation dependent library (CDL) restraints added in 248.8 milliseconds 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1798 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 3 sheets defined 68.5% alpha, 3.7% beta 3 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 7 through 13 removed outlier: 3.623A pdb=" N GLY A 11 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 118 through 149 removed outlier: 3.720A pdb=" N VAL A 122 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 149 " --> pdb=" O ASN A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 171 Processing helix chain 'A' and resid 172 through 180 removed outlier: 3.669A pdb=" N ARG A 176 " --> pdb=" O GLU A 173 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ALA A 177 " --> pdb=" O HIS A 174 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 180 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 201 Processing helix chain 'A' and resid 202 through 207 removed outlier: 4.147A pdb=" N GLY A 206 " --> pdb=" O PRO A 203 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 207 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 224 through 243 removed outlier: 3.659A pdb=" N VAL A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 286 removed outlier: 3.629A pdb=" N ILE A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A 282 " --> pdb=" O ARG A 278 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 291 through 303 Processing helix chain 'A' and resid 305 through 308 Processing helix chain 'A' and resid 309 through 318 Processing helix chain 'A' and resid 328 through 338 removed outlier: 3.996A pdb=" N LEU A 332 " --> pdb=" O ASN A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 348 Processing helix chain 'A' and resid 348 through 353 removed outlier: 3.543A pdb=" N PHE A 352 " --> pdb=" O ASN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 382 Processing helix chain 'A' and resid 393 through 404 removed outlier: 3.557A pdb=" N GLY A 404 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 424 removed outlier: 3.626A pdb=" N LYS A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG A 424 " --> pdb=" O ASN A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 434 Processing helix chain 'A' and resid 438 through 446 removed outlier: 4.386A pdb=" N ARG A 442 " --> pdb=" O ASN A 439 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU A 443 " --> pdb=" O LYS A 440 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 445 " --> pdb=" O ARG A 442 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 446 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 474 removed outlier: 3.653A pdb=" N MET A 474 " --> pdb=" O TYR A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 505 Proline residue: A 503 - end of helix Processing helix chain 'A' and resid 512 through 519 removed outlier: 5.012A pdb=" N PHE A 517 " --> pdb=" O GLU A 514 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 518 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 535 removed outlier: 3.802A pdb=" N ILE A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 556 removed outlier: 3.642A pdb=" N LEU A 556 " --> pdb=" O ALA A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 573 removed outlier: 3.639A pdb=" N PHE A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 610 through 619 removed outlier: 3.643A pdb=" N HIS A 615 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU A 616 " --> pdb=" O ALA A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 633 Processing helix chain 'A' and resid 641 through 654 removed outlier: 3.552A pdb=" N GLN A 645 " --> pdb=" O ASN A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 675 Processing helix chain 'A' and resid 678 through 683 Processing helix chain 'A' and resid 684 through 689 Processing helix chain 'A' and resid 695 through 744 removed outlier: 3.635A pdb=" N GLU A 699 " --> pdb=" O ASN A 695 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 744 " --> pdb=" O TYR A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 766 removed outlier: 3.972A pdb=" N GLY A 766 " --> pdb=" O LYS A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 792 removed outlier: 3.566A pdb=" N LYS A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 805 removed outlier: 3.828A pdb=" N ASN A 803 " --> pdb=" O LYS A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 826 removed outlier: 3.516A pdb=" N ALA A 813 " --> pdb=" O ASP A 809 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN A 821 " --> pdb=" O THR A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 848 removed outlier: 3.713A pdb=" N ILE A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 844 " --> pdb=" O VAL A 840 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 847 " --> pdb=" O ARG A 843 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 864 Processing helix chain 'A' and resid 869 through 874 removed outlier: 3.797A pdb=" N TYR A 873 " --> pdb=" O TYR A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 899 removed outlier: 3.534A pdb=" N TYR A 889 " --> pdb=" O GLN A 885 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 898 " --> pdb=" O ILE A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 918 removed outlier: 3.651A pdb=" N GLU A 909 " --> pdb=" O GLY A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 929 Processing helix chain 'A' and resid 930 through 933 Processing helix chain 'A' and resid 935 through 942 Processing helix chain 'A' and resid 944 through 948 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 20 removed outlier: 8.187A pdb=" N VAL A 14 " --> pdb=" O PHE A 29 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE A 29 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL A 24 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE A 40 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N MET A 26 " --> pdb=" O GLU A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 59 Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 215 417 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 8 hydrogen bonds 16 hydrogen bond angles 0 basepair planarities 3 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 1.57 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2284 1.33 - 1.45: 1872 1.45 - 1.57: 4706 1.57 - 1.69: 100 1.69 - 1.81: 48 Bond restraints: 9010 Sorted by residual: bond pdb=" C HIS A 714 " pdb=" O HIS A 714 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.42e+00 bond pdb=" C TYR A 708 " pdb=" O TYR A 708 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.41e+00 bond pdb=" C ILE A 722 " pdb=" O ILE A 722 " ideal model delta sigma weight residual 1.237 1.250 -0.012 1.17e-02 7.31e+03 1.12e+00 bond pdb=" C ASN A 718 " pdb=" O ASN A 718 " ideal model delta sigma weight residual 1.237 1.246 -0.010 1.17e-02 7.31e+03 6.84e-01 bond pdb=" C VAL A 711 " pdb=" O VAL A 711 " ideal model delta sigma weight residual 1.237 1.246 -0.009 1.13e-02 7.83e+03 6.70e-01 ... (remaining 9005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 11963 1.10 - 2.19: 337 2.19 - 3.29: 57 3.29 - 4.38: 11 4.38 - 5.48: 6 Bond angle restraints: 12374 Sorted by residual: angle pdb=" CA PRO A 503 " pdb=" N PRO A 503 " pdb=" CD PRO A 503 " ideal model delta sigma weight residual 112.00 106.63 5.37 1.40e+00 5.10e-01 1.47e+01 angle pdb=" N ALA A 953 " pdb=" CA ALA A 953 " pdb=" C ALA A 953 " ideal model delta sigma weight residual 114.56 109.86 4.70 1.27e+00 6.20e-01 1.37e+01 angle pdb=" CA TYR A 708 " pdb=" CB TYR A 708 " pdb=" CG TYR A 708 " ideal model delta sigma weight residual 113.90 118.39 -4.49 1.80e+00 3.09e-01 6.23e+00 angle pdb=" CA ALA A 953 " pdb=" C ALA A 953 " pdb=" N ALA A 954 " ideal model delta sigma weight residual 119.26 116.45 2.81 1.14e+00 7.69e-01 6.06e+00 angle pdb=" N TYR A 900 " pdb=" CA TYR A 900 " pdb=" C TYR A 900 " ideal model delta sigma weight residual 113.18 109.98 3.20 1.33e+00 5.65e-01 5.80e+00 ... (remaining 12369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 5329 35.90 - 71.80: 162 71.80 - 107.70: 25 107.70 - 143.60: 0 143.60 - 179.50: 1 Dihedral angle restraints: 5517 sinusoidal: 2723 harmonic: 2794 Sorted by residual: dihedral pdb=" O4' C B 10 " pdb=" C1' C B 10 " pdb=" N1 C B 10 " pdb=" C2 C B 10 " ideal model delta sinusoidal sigma weight residual 232.00 52.50 179.50 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 12 " pdb=" C1' U B 12 " pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sinusoidal sigma weight residual -128.00 -71.52 -56.48 1 1.70e+01 3.46e-03 1.49e+01 dihedral pdb=" CA GLU A 754 " pdb=" C GLU A 754 " pdb=" N LYS A 755 " pdb=" CA LYS A 755 " ideal model delta harmonic sigma weight residual 180.00 162.34 17.66 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 5514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 811 0.027 - 0.054: 382 0.054 - 0.080: 141 0.080 - 0.107: 36 0.107 - 0.134: 16 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA THR A 162 " pdb=" N THR A 162 " pdb=" C THR A 162 " pdb=" CB THR A 162 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE A 68 " pdb=" N ILE A 68 " pdb=" C ILE A 68 " pdb=" CB ILE A 68 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA ILE A 46 " pdb=" N ILE A 46 " pdb=" C ILE A 46 " pdb=" CB ILE A 46 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 1383 not shown) Planarity restraints: 1409 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 502 " -0.079 5.00e-02 4.00e+02 1.17e-01 2.17e+01 pdb=" N PRO A 503 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO A 503 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 503 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 305 " 0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO A 306 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 306 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 306 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 930 " -0.024 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO A 931 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 931 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 931 " -0.020 5.00e-02 4.00e+02 ... (remaining 1406 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 63 2.63 - 3.20: 7491 3.20 - 3.76: 12816 3.76 - 4.33: 18655 4.33 - 4.90: 30183 Nonbonded interactions: 69208 Sorted by model distance: nonbonded pdb=" OP1 U B -7 " pdb="MG MG B 101 " model vdw 2.062 2.170 nonbonded pdb=" O2' U B 12 " pdb=" OP2 A B 14 " model vdw 2.165 3.040 nonbonded pdb=" O ASN A 245 " pdb=" NH2 ARG A 254 " model vdw 2.266 3.120 nonbonded pdb=" OE1 GLN A 121 " pdb=" O2' U B -8 " model vdw 2.281 3.040 nonbonded pdb=" O TYR A 470 " pdb=" OG1 THR A 473 " model vdw 2.286 3.040 ... (remaining 69203 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=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.260 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 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 : 0.003 0.036 9010 Z= 0.157 Angle : 0.461 5.479 12374 Z= 0.267 Chirality : 0.037 0.134 1386 Planarity : 0.004 0.117 1409 Dihedral : 16.354 179.501 3719 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: 0.24 (0.26), residues: 939 helix: 0.98 (0.21), residues: 558 sheet: -0.20 (1.06), residues: 23 loop : -1.10 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 775 TYR 0.020 0.002 TYR A 920 PHE 0.012 0.001 PHE A 365 TRP 0.007 0.001 TRP A 256 HIS 0.005 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9010) covalent geometry : angle 0.46077 (12374) hydrogen bonds : bond 0.19817 ( 425) hydrogen bonds : angle 5.48554 ( 1219) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.240 Fit side-chains REVERT: A 183 ASP cc_start: 0.6851 (t70) cc_final: 0.6621 (t0) REVERT: A 190 LYS cc_start: 0.6972 (mttt) cc_final: 0.6690 (mttt) REVERT: A 210 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7504 (mm-40) REVERT: A 350 LYS cc_start: 0.7608 (pttt) cc_final: 0.7388 (pttt) REVERT: A 353 ASP cc_start: 0.6565 (m-30) cc_final: 0.6270 (m-30) REVERT: A 559 ASN cc_start: 0.7420 (t0) cc_final: 0.7201 (t0) REVERT: A 660 LYS cc_start: 0.7924 (mttm) cc_final: 0.7710 (mttt) REVERT: A 686 SER cc_start: 0.7833 (t) cc_final: 0.7502 (p) REVERT: A 851 ASN cc_start: 0.8444 (m-40) cc_final: 0.8195 (m-40) REVERT: A 909 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6583 (tm-30) REVERT: A 916 ASP cc_start: 0.7058 (m-30) cc_final: 0.6743 (m-30) REVERT: A 923 ARG cc_start: 0.6816 (mpt180) cc_final: 0.6547 (mpt180) outliers start: 0 outliers final: 1 residues processed: 218 average time/residue: 0.7221 time to fit residues: 164.9205 Evaluate side-chains 198 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 328 ASN A 797 ASN A 915 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.107430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.095096 restraints weight = 12377.306| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.58 r_work: 0.3076 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9010 Z= 0.230 Angle : 0.539 6.137 12374 Z= 0.295 Chirality : 0.041 0.159 1386 Planarity : 0.004 0.074 1409 Dihedral : 16.472 178.034 1819 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.59 % Allowed : 11.51 % Favored : 86.90 % 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 (0.27), residues: 939 helix: 1.40 (0.21), residues: 561 sheet: -0.04 (1.07), residues: 23 loop : -1.04 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 899 TYR 0.017 0.002 TYR A 708 PHE 0.016 0.002 PHE A 884 TRP 0.009 0.002 TRP A 256 HIS 0.009 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00534 ( 9010) covalent geometry : angle 0.53949 (12374) hydrogen bonds : bond 0.07965 ( 425) hydrogen bonds : angle 4.45060 ( 1219) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 0.203 Fit side-chains REVERT: A 18 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8547 (mt) REVERT: A 173 GLU cc_start: 0.7683 (mp0) cc_final: 0.7156 (mp0) REVERT: A 183 ASP cc_start: 0.7005 (t70) cc_final: 0.6742 (t0) REVERT: A 190 LYS cc_start: 0.7262 (mttt) cc_final: 0.6882 (mttm) REVERT: A 210 GLN cc_start: 0.8305 (mm-40) cc_final: 0.7918 (mm-40) REVERT: A 353 ASP cc_start: 0.7393 (m-30) cc_final: 0.7040 (m-30) REVERT: A 396 ASP cc_start: 0.7594 (m-30) cc_final: 0.7310 (m-30) REVERT: A 429 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.7893 (mm) REVERT: A 559 ASN cc_start: 0.8208 (t0) cc_final: 0.7900 (t0) REVERT: A 686 SER cc_start: 0.8117 (t) cc_final: 0.7855 (p) REVERT: A 916 ASP cc_start: 0.7547 (m-30) cc_final: 0.7199 (m-30) REVERT: A 923 ARG cc_start: 0.7377 (mpt180) cc_final: 0.7139 (mpt180) REVERT: A 955 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8189 (mttt) outliers start: 13 outliers final: 9 residues processed: 203 average time/residue: 0.6302 time to fit residues: 134.4361 Evaluate side-chains 208 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain A residue 955 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 94 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 819 GLN A 915 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.106112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.094024 restraints weight = 12280.989| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.58 r_work: 0.3064 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 9010 Z= 0.236 Angle : 0.527 5.664 12374 Z= 0.289 Chirality : 0.041 0.163 1386 Planarity : 0.004 0.056 1409 Dihedral : 16.274 177.457 1819 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.06 % Allowed : 12.97 % Favored : 83.97 % 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: 0.75 (0.27), residues: 939 helix: 1.50 (0.22), residues: 561 sheet: -0.03 (1.06), residues: 23 loop : -1.10 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 589 TYR 0.017 0.002 TYR A 708 PHE 0.015 0.002 PHE A 884 TRP 0.009 0.002 TRP A 256 HIS 0.009 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00553 ( 9010) covalent geometry : angle 0.52702 (12374) hydrogen bonds : bond 0.07904 ( 425) hydrogen bonds : angle 4.37349 ( 1219) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 202 time to evaluate : 0.249 Fit side-chains REVERT: A 18 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8546 (mt) REVERT: A 171 ASP cc_start: 0.7707 (p0) cc_final: 0.7504 (p0) REVERT: A 173 GLU cc_start: 0.7738 (mp0) cc_final: 0.7200 (mp0) REVERT: A 190 LYS cc_start: 0.7248 (mttt) cc_final: 0.6943 (mttm) REVERT: A 210 GLN cc_start: 0.8327 (mm-40) cc_final: 0.7936 (mm-40) REVERT: A 353 ASP cc_start: 0.7478 (m-30) cc_final: 0.7095 (m-30) REVERT: A 451 ARG cc_start: 0.8143 (ptm-80) cc_final: 0.7849 (ptm-80) REVERT: A 510 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8343 (mttp) REVERT: A 559 ASN cc_start: 0.8229 (t0) cc_final: 0.7912 (t0) REVERT: A 738 GLN cc_start: 0.8573 (tp40) cc_final: 0.8323 (tp40) REVERT: A 788 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7382 (tp30) REVERT: A 864 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7861 (mt) REVERT: A 916 ASP cc_start: 0.7521 (m-30) cc_final: 0.7104 (m-30) REVERT: A 923 ARG cc_start: 0.7446 (mpt180) cc_final: 0.7215 (mpt180) REVERT: A 955 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8169 (mmtt) outliers start: 25 outliers final: 12 residues processed: 211 average time/residue: 0.6615 time to fit residues: 147.0138 Evaluate side-chains 217 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain A residue 955 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 77 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 76 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN A 328 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.106965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.094839 restraints weight = 12581.256| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.61 r_work: 0.3075 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9010 Z= 0.187 Angle : 0.489 5.686 12374 Z= 0.270 Chirality : 0.039 0.154 1386 Planarity : 0.003 0.046 1409 Dihedral : 16.193 177.057 1817 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.79 % Allowed : 13.83 % Favored : 82.37 % 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: 0.95 (0.27), residues: 939 helix: 1.69 (0.22), residues: 562 sheet: -0.03 (1.06), residues: 23 loop : -1.08 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 899 TYR 0.017 0.002 TYR A 708 PHE 0.015 0.001 PHE A 884 TRP 0.008 0.001 TRP A 256 HIS 0.007 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 9010) covalent geometry : angle 0.48915 (12374) hydrogen bonds : bond 0.07182 ( 425) hydrogen bonds : angle 4.25151 ( 1219) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.298 Fit side-chains REVERT: A 18 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8553 (mt) REVERT: A 171 ASP cc_start: 0.7753 (p0) cc_final: 0.7444 (p0) REVERT: A 173 GLU cc_start: 0.7775 (mp0) cc_final: 0.7233 (mp0) REVERT: A 190 LYS cc_start: 0.7222 (mttt) cc_final: 0.6925 (mttm) REVERT: A 210 GLN cc_start: 0.8315 (mm-40) cc_final: 0.7906 (mm-40) REVERT: A 353 ASP cc_start: 0.7379 (m-30) cc_final: 0.6965 (m-30) REVERT: A 451 ARG cc_start: 0.8160 (ptm-80) cc_final: 0.7853 (ptm-80) REVERT: A 510 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8362 (mttp) REVERT: A 559 ASN cc_start: 0.8220 (t0) cc_final: 0.7901 (t0) REVERT: A 750 LYS cc_start: 0.8262 (mmmm) cc_final: 0.8053 (mmmm) REVERT: A 788 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7432 (tp30) REVERT: A 916 ASP cc_start: 0.7527 (m-30) cc_final: 0.7174 (m-30) REVERT: A 923 ARG cc_start: 0.7510 (mpt180) cc_final: 0.7242 (mpt180) REVERT: A 955 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8151 (mmtt) outliers start: 31 outliers final: 18 residues processed: 206 average time/residue: 0.6286 time to fit residues: 136.2658 Evaluate side-chains 220 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 753 GLU Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain A residue 955 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 89 optimal weight: 0.0980 chunk 72 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 78 optimal weight: 0.0370 chunk 83 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN A 328 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.107632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.095269 restraints weight = 12544.592| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.68 r_work: 0.3070 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9010 Z= 0.150 Angle : 0.462 5.654 12374 Z= 0.255 Chirality : 0.037 0.146 1386 Planarity : 0.003 0.038 1409 Dihedral : 16.112 176.546 1817 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.67 % Allowed : 15.06 % Favored : 81.27 % 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: 1.14 (0.27), residues: 939 helix: 1.85 (0.22), residues: 563 sheet: -0.07 (1.05), residues: 23 loop : -1.01 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 899 TYR 0.017 0.001 TYR A 708 PHE 0.014 0.001 PHE A 884 TRP 0.007 0.001 TRP A 256 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9010) covalent geometry : angle 0.46220 (12374) hydrogen bonds : bond 0.06544 ( 425) hydrogen bonds : angle 4.10469 ( 1219) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 0.203 Fit side-chains REVERT: A 18 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8533 (mt) REVERT: A 47 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7414 (ttm110) REVERT: A 171 ASP cc_start: 0.7728 (p0) cc_final: 0.7382 (p0) REVERT: A 173 GLU cc_start: 0.7794 (mp0) cc_final: 0.7249 (mp0) REVERT: A 190 LYS cc_start: 0.7169 (mttt) cc_final: 0.6919 (mttm) REVERT: A 210 GLN cc_start: 0.8270 (mm-40) cc_final: 0.7874 (mm-40) REVERT: A 353 ASP cc_start: 0.7433 (m-30) cc_final: 0.7001 (m-30) REVERT: A 372 ILE cc_start: 0.8686 (mm) cc_final: 0.8485 (mp) REVERT: A 451 ARG cc_start: 0.8167 (ptm-80) cc_final: 0.7846 (ptm-80) REVERT: A 559 ASN cc_start: 0.8265 (t0) cc_final: 0.7933 (t0) REVERT: A 788 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7413 (tp30) REVERT: A 810 GLU cc_start: 0.6766 (tm-30) cc_final: 0.6456 (tm-30) REVERT: A 916 ASP cc_start: 0.7516 (m-30) cc_final: 0.7183 (m-30) REVERT: A 923 ARG cc_start: 0.7504 (mpt180) cc_final: 0.7252 (mpt180) REVERT: A 955 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8159 (mmtt) outliers start: 30 outliers final: 18 residues processed: 208 average time/residue: 0.5839 time to fit residues: 127.7294 Evaluate side-chains 217 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 753 GLU Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 797 ASN Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain A residue 955 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 82 optimal weight: 0.2980 chunk 40 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.106856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.094633 restraints weight = 12566.274| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.63 r_work: 0.3067 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9010 Z= 0.198 Angle : 0.501 5.631 12374 Z= 0.274 Chirality : 0.040 0.153 1386 Planarity : 0.003 0.037 1409 Dihedral : 16.098 175.927 1817 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.06 % Allowed : 16.28 % Favored : 80.66 % 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: 1.09 (0.27), residues: 939 helix: 1.81 (0.22), residues: 562 sheet: -0.05 (1.05), residues: 23 loop : -1.03 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 899 TYR 0.018 0.002 TYR A 708 PHE 0.016 0.002 PHE A 884 TRP 0.007 0.001 TRP A 256 HIS 0.008 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 9010) covalent geometry : angle 0.50149 (12374) hydrogen bonds : bond 0.07148 ( 425) hydrogen bonds : angle 4.20642 ( 1219) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.231 Fit side-chains REVERT: A 18 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8554 (mt) REVERT: A 163 VAL cc_start: 0.8317 (t) cc_final: 0.7957 (m) REVERT: A 171 ASP cc_start: 0.7729 (p0) cc_final: 0.7351 (p0) REVERT: A 173 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: A 190 LYS cc_start: 0.7190 (mttt) cc_final: 0.6937 (mttm) REVERT: A 210 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7879 (mm-40) REVERT: A 353 ASP cc_start: 0.7442 (m-30) cc_final: 0.6994 (m-30) REVERT: A 451 ARG cc_start: 0.8172 (ptm-80) cc_final: 0.7845 (ptm-80) REVERT: A 510 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8361 (mttp) REVERT: A 559 ASN cc_start: 0.8233 (t0) cc_final: 0.7917 (t0) REVERT: A 750 LYS cc_start: 0.8256 (mmmm) cc_final: 0.8009 (mmmm) REVERT: A 788 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7436 (tp30) REVERT: A 810 GLU cc_start: 0.6831 (tm-30) cc_final: 0.6556 (tm-30) REVERT: A 916 ASP cc_start: 0.7529 (m-30) cc_final: 0.7146 (m-30) REVERT: A 923 ARG cc_start: 0.7495 (mpt180) cc_final: 0.7216 (mpt180) REVERT: A 955 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8221 (mmtt) outliers start: 25 outliers final: 17 residues processed: 204 average time/residue: 0.5978 time to fit residues: 128.4598 Evaluate side-chains 213 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain A residue 955 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 91 optimal weight: 0.0980 chunk 69 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN A 328 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.107651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.095463 restraints weight = 12614.878| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.63 r_work: 0.3078 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9010 Z= 0.165 Angle : 0.481 5.633 12374 Z= 0.264 Chirality : 0.038 0.149 1386 Planarity : 0.003 0.038 1409 Dihedral : 16.073 175.691 1817 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.30 % Allowed : 16.28 % Favored : 80.42 % 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: 1.19 (0.27), residues: 939 helix: 1.88 (0.22), residues: 563 sheet: -0.06 (1.05), residues: 23 loop : -0.97 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 899 TYR 0.016 0.001 TYR A 708 PHE 0.015 0.001 PHE A 884 TRP 0.007 0.001 TRP A 256 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9010) covalent geometry : angle 0.48102 (12374) hydrogen bonds : bond 0.06721 ( 425) hydrogen bonds : angle 4.13459 ( 1219) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.297 Fit side-chains REVERT: A 18 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8541 (mt) REVERT: A 47 ARG cc_start: 0.7928 (mtm110) cc_final: 0.7411 (ttm110) REVERT: A 163 VAL cc_start: 0.8201 (t) cc_final: 0.7860 (m) REVERT: A 171 ASP cc_start: 0.7737 (p0) cc_final: 0.7309 (p0) REVERT: A 173 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: A 210 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7850 (mm-40) REVERT: A 353 ASP cc_start: 0.7439 (m-30) cc_final: 0.6980 (m-30) REVERT: A 451 ARG cc_start: 0.8182 (ptm-80) cc_final: 0.7855 (ptm-80) REVERT: A 510 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8377 (mttp) REVERT: A 559 ASN cc_start: 0.8243 (t0) cc_final: 0.7927 (t0) REVERT: A 750 LYS cc_start: 0.8258 (mmmm) cc_final: 0.8005 (mmmm) REVERT: A 788 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7436 (tp30) REVERT: A 810 GLU cc_start: 0.6776 (tm-30) cc_final: 0.6492 (tm-30) REVERT: A 916 ASP cc_start: 0.7523 (m-30) cc_final: 0.7145 (m-30) REVERT: A 923 ARG cc_start: 0.7494 (mpt180) cc_final: 0.7253 (mpt180) REVERT: A 955 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8222 (mmtt) outliers start: 27 outliers final: 19 residues processed: 206 average time/residue: 0.6092 time to fit residues: 132.0456 Evaluate side-chains 220 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 753 GLU Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 797 ASN Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain A residue 955 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 53 optimal weight: 0.0170 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 0.0050 chunk 46 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 34 optimal weight: 0.0670 chunk 22 optimal weight: 0.9990 overall best weight: 0.2570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.109235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.097095 restraints weight = 12460.312| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.61 r_work: 0.3115 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9010 Z= 0.123 Angle : 0.465 6.346 12374 Z= 0.255 Chirality : 0.036 0.134 1386 Planarity : 0.003 0.039 1409 Dihedral : 16.040 175.672 1817 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.57 % Allowed : 17.50 % Favored : 79.93 % 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: 1.40 (0.28), residues: 939 helix: 2.05 (0.22), residues: 563 sheet: -0.08 (1.05), residues: 23 loop : -0.88 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 899 TYR 0.018 0.001 TYR A 142 PHE 0.012 0.001 PHE A 884 TRP 0.005 0.001 TRP A 256 HIS 0.005 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9010) covalent geometry : angle 0.46514 (12374) hydrogen bonds : bond 0.05907 ( 425) hydrogen bonds : angle 3.98037 ( 1219) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.302 Fit side-chains REVERT: A 18 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8547 (mt) REVERT: A 47 ARG cc_start: 0.7879 (mtm110) cc_final: 0.7370 (ttm110) REVERT: A 128 ASP cc_start: 0.8024 (m-30) cc_final: 0.7751 (m-30) REVERT: A 163 VAL cc_start: 0.8198 (t) cc_final: 0.7900 (m) REVERT: A 171 ASP cc_start: 0.7712 (p0) cc_final: 0.7276 (p0) REVERT: A 173 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: A 210 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7841 (mm-40) REVERT: A 353 ASP cc_start: 0.7411 (m-30) cc_final: 0.6961 (m-30) REVERT: A 451 ARG cc_start: 0.8143 (ptm-80) cc_final: 0.7837 (ptm-80) REVERT: A 452 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8105 (mt) REVERT: A 559 ASN cc_start: 0.8222 (t0) cc_final: 0.7914 (t0) REVERT: A 750 LYS cc_start: 0.8220 (mmmm) cc_final: 0.7984 (mmmm) REVERT: A 788 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7464 (tp30) REVERT: A 805 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8383 (mt) REVERT: A 810 GLU cc_start: 0.6684 (tm-30) cc_final: 0.6406 (tm-30) REVERT: A 916 ASP cc_start: 0.7526 (m-30) cc_final: 0.7085 (m-30) REVERT: A 923 ARG cc_start: 0.7436 (mpt180) cc_final: 0.7211 (mpt180) REVERT: A 955 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8190 (mmtt) outliers start: 21 outliers final: 11 residues processed: 203 average time/residue: 0.6108 time to fit residues: 130.3645 Evaluate side-chains 211 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 753 GLU Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 955 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 18 optimal weight: 0.5980 chunk 1 optimal weight: 0.0870 chunk 79 optimal weight: 1.9990 chunk 29 optimal weight: 0.0970 chunk 28 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 53 optimal weight: 0.0020 chunk 27 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.2564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.109909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.097781 restraints weight = 12469.926| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.60 r_work: 0.3124 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9010 Z= 0.119 Angle : 0.456 7.700 12374 Z= 0.248 Chirality : 0.036 0.132 1386 Planarity : 0.003 0.039 1409 Dihedral : 15.976 175.759 1817 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.08 % Allowed : 18.73 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.28), residues: 939 helix: 2.11 (0.22), residues: 565 sheet: -0.06 (1.06), residues: 23 loop : -0.85 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 899 TYR 0.019 0.001 TYR A 142 PHE 0.013 0.001 PHE A 884 TRP 0.005 0.001 TRP A 256 HIS 0.005 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9010) covalent geometry : angle 0.45647 (12374) hydrogen bonds : bond 0.05622 ( 425) hydrogen bonds : angle 3.89324 ( 1219) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 0.270 Fit side-chains REVERT: A 47 ARG cc_start: 0.7883 (mtm110) cc_final: 0.7345 (ttm110) REVERT: A 128 ASP cc_start: 0.7995 (m-30) cc_final: 0.7722 (m-30) REVERT: A 163 VAL cc_start: 0.8184 (t) cc_final: 0.7927 (m) REVERT: A 171 ASP cc_start: 0.7706 (p0) cc_final: 0.7266 (p0) REVERT: A 173 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: A 210 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7842 (mm-40) REVERT: A 262 LYS cc_start: 0.8430 (ptmm) cc_final: 0.8171 (ptpp) REVERT: A 353 ASP cc_start: 0.7406 (m-30) cc_final: 0.6950 (m-30) REVERT: A 451 ARG cc_start: 0.8126 (ptm-80) cc_final: 0.7827 (ptm-80) REVERT: A 452 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8082 (mt) REVERT: A 559 ASN cc_start: 0.8220 (t0) cc_final: 0.7913 (t0) REVERT: A 750 LYS cc_start: 0.8213 (mmmm) cc_final: 0.7937 (mmmm) REVERT: A 788 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7455 (tp30) REVERT: A 810 GLU cc_start: 0.6652 (tm-30) cc_final: 0.6376 (tm-30) REVERT: A 916 ASP cc_start: 0.7513 (m-30) cc_final: 0.7087 (m-30) REVERT: A 923 ARG cc_start: 0.7467 (mpt180) cc_final: 0.7241 (mpt180) REVERT: A 955 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8207 (mmtt) outliers start: 17 outliers final: 10 residues processed: 198 average time/residue: 0.6010 time to fit residues: 125.2312 Evaluate side-chains 207 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 955 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 36 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 48 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 410 GLN A 897 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.107579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.095025 restraints weight = 12510.744| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.69 r_work: 0.3071 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9010 Z= 0.204 Angle : 0.515 9.544 12374 Z= 0.276 Chirality : 0.040 0.204 1386 Planarity : 0.003 0.037 1409 Dihedral : 15.994 175.880 1817 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.96 % Allowed : 19.34 % Favored : 78.70 % 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: 1.29 (0.27), residues: 939 helix: 1.96 (0.22), residues: 562 sheet: -0.09 (1.06), residues: 23 loop : -0.92 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 899 TYR 0.021 0.002 TYR A 142 PHE 0.016 0.002 PHE A 884 TRP 0.007 0.001 TRP A 256 HIS 0.008 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 9010) covalent geometry : angle 0.51476 (12374) hydrogen bonds : bond 0.06792 ( 425) hydrogen bonds : angle 4.10511 ( 1219) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 0.309 Fit side-chains REVERT: A 163 VAL cc_start: 0.8223 (t) cc_final: 0.7917 (m) REVERT: A 171 ASP cc_start: 0.7752 (p0) cc_final: 0.7310 (p0) REVERT: A 173 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: A 210 GLN cc_start: 0.8275 (mm-40) cc_final: 0.7875 (mm-40) REVERT: A 262 LYS cc_start: 0.8472 (ptmm) cc_final: 0.8200 (ptpp) REVERT: A 353 ASP cc_start: 0.7475 (m-30) cc_final: 0.7021 (m-30) REVERT: A 451 ARG cc_start: 0.8197 (ptm-80) cc_final: 0.7863 (ptm-80) REVERT: A 452 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8106 (mt) REVERT: A 559 ASN cc_start: 0.8275 (t0) cc_final: 0.7963 (t0) REVERT: A 750 LYS cc_start: 0.8245 (mmmm) cc_final: 0.7943 (mmmm) REVERT: A 788 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7482 (tp30) REVERT: A 810 GLU cc_start: 0.6878 (tm-30) cc_final: 0.6571 (tm-30) REVERT: A 916 ASP cc_start: 0.7620 (m-30) cc_final: 0.7108 (m-30) REVERT: A 923 ARG cc_start: 0.7512 (mpt180) cc_final: 0.7229 (mpt180) REVERT: A 955 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8275 (mmtt) outliers start: 16 outliers final: 11 residues processed: 201 average time/residue: 0.6414 time to fit residues: 135.5715 Evaluate side-chains 210 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 196 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 955 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 78 optimal weight: 0.2980 chunk 40 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 27 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 410 GLN A 897 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.107808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.095617 restraints weight = 12314.400| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.59 r_work: 0.3090 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9010 Z= 0.171 Angle : 0.508 11.188 12374 Z= 0.272 Chirality : 0.038 0.140 1386 Planarity : 0.003 0.038 1409 Dihedral : 16.007 175.979 1817 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.71 % Allowed : 19.71 % Favored : 78.58 % 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: 1.31 (0.27), residues: 939 helix: 1.97 (0.22), residues: 562 sheet: -0.05 (1.07), residues: 23 loop : -0.91 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 899 TYR 0.026 0.002 TYR A 142 PHE 0.016 0.001 PHE A 884 TRP 0.006 0.001 TRP A 256 HIS 0.007 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 9010) covalent geometry : angle 0.50784 (12374) hydrogen bonds : bond 0.06609 ( 425) hydrogen bonds : angle 4.11644 ( 1219) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3237.51 seconds wall clock time: 55 minutes 43.06 seconds (3343.06 seconds total)