Starting phenix.real_space_refine on Fri Sep 11 10:34:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m31_63595/09_2026/9m31_63595.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m31_63595/09_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_63595/09_2026/9m31_63595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m31_63595/09_2026/9m31_63595.map" model { file = "/net/cci-nas-00/data/ceres_data/9m31_63595/09_2026/9m31_63595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m31_63595/09_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 1.88, 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: 0.91 Conformation dependent library (CDL) restraints added in 203.8 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: 0.90 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: 1.53 Time building geometry restraints manager: 1.13 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=" N9 A B 9 " pdb=" C4 A B 9 " ideal model delta sigma weight residual 1.374 1.388 -0.014 6.00e-03 2.78e+04 5.38e+00 bond pdb=" N9 A B -4 " pdb=" C4 A B -4 " ideal model delta sigma weight residual 1.374 1.384 -0.010 6.00e-03 2.78e+04 2.70e+00 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=" N9 A B -23 " pdb=" C4 A B -23 " ideal model delta sigma weight residual 1.374 1.367 0.007 6.00e-03 2.78e+04 1.32e+00 ... (remaining 9005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 11813 1.10 - 2.19: 390 2.19 - 3.29: 153 3.29 - 4.38: 12 4.38 - 5.48: 6 Bond angle restraints: 12374 Sorted by residual: angle pdb=" O5' C B 13 " pdb=" C5' C B 13 " pdb=" C4' C B 13 " ideal model delta sigma weight residual 109.40 112.91 -3.51 8.00e-01 1.56e+00 1.92e+01 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=" O5' C B 18 " pdb=" C5' C B 18 " pdb=" C4' C B 18 " ideal model delta sigma weight residual 109.40 112.43 -3.03 8.00e-01 1.56e+00 1.43e+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=" O5' C B -18 " pdb=" C5' C B -18 " pdb=" C4' C B -18 " ideal model delta sigma weight residual 109.40 112.27 -2.87 8.00e-01 1.56e+00 1.28e+01 ... (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 - 0.028: 778 0.028 - 0.056: 387 0.056 - 0.084: 138 0.084 - 0.112: 33 0.112 - 0.140: 50 Chirality restraints: 1386 Sorted by residual: chirality pdb=" C2' A B -2 " pdb=" C3' A B -2 " pdb=" O2' A B -2 " pdb=" C1' A B -2 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" C2' C B -13 " pdb=" C3' C B -13 " pdb=" O2' C B -13 " pdb=" C1' C B -13 " both_signs ideal model delta sigma weight residual False -2.62 -2.75 0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" C2' G B -10 " pdb=" C3' G B -10 " pdb=" O2' G B -10 " pdb=" C1' G B -10 " both_signs ideal model delta sigma weight residual False -2.62 -2.75 0.14 2.00e-01 2.50e+01 4.61e-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: 2.230 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: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.400 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 0.036 9010 Z= 0.194 Angle : 0.525 5.479 12374 Z= 0.355 Chirality : 0.044 0.140 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/Z covalent geometry : bond 0.00355 / 0.19 ( 9010) covalent geometry : angle 0.52531 / 0.36 (12374) hydrogen bonds : bond 0.19817 / 13.06 ( 425) hydrogen bonds : angle 5.48554 / 3.89 ( 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 : 0.267 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: 0.6269 (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: 0.7709 (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: 0.6650 time to fit residues: 152.3507 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 : 0.292 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.3980 chunk 45 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3380 r_free = 0.3380 target = 0.107669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.095288 restraints weight = 12340.445| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.58 r_work: 0.3081 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-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: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9010 Z= 0.209 Angle : 0.519 5.478 12374 Z= 0.293 Chirality : 0.041 0.146 1386 Planarity : 0.004 0.072 1409 Dihedral : 16.463 178.902 1819 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.71 % Allowed : 11.14 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.27), residues: 939 helix: 1.42 (0.21), residues: 562 sheet: -0.08 (1.07), residues: 23 loop : -1.02 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 899 TYR 0.017 0.002 TYR A 708 PHE 0.020 0.002 PHE A 884 TRP 0.008 0.001 TRP A 256 HIS 0.009 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 ( 9010) covalent geometry : angle 0.51915 / 0.29 (12374) hydrogen bonds : bond 0.08289 / 5.68 ( 425) hydrogen bonds : angle 4.47324 / 3.11 ( 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 211 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 0.312 Fit side-chains REVERT: A 18 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8584 (mt) REVERT: A 171 ASP cc_start: 0.7669 (p0) cc_final: 0.7397 (p0) REVERT: A 173 GLU cc_start: 0.7688 (mp0) cc_final: 0.7213 (mp0) REVERT: A 175 HIS cc_start: 0.8258 (m90) cc_final: 0.7911 (m90) REVERT: A 183 ASP cc_start: 0.7138 (t70) cc_final: 0.6901 (t0) REVERT: A 190 LYS cc_start: 0.7235 (mttt) cc_final: 0.6891 (mttt) REVERT: A 210 GLN cc_start: 0.8327 (mm-40) cc_final: 0.7935 (mm-40) REVERT: A 353 ASP cc_start: 0.7362 (m-30) cc_final: 0.6996 (m-30) REVERT: A 559 ASN cc_start: 0.8200 (t0) cc_final: 0.7883 (t0) REVERT: A 686 SER cc_start: 0.8144 (t) cc_final: 0.7877 (p) REVERT: A 785 ARG cc_start: 0.7773 (mtm180) cc_final: 0.7568 (mtm180) REVERT: A 916 ASP cc_start: 0.7542 (m-30) cc_final: 0.7178 (m-30) REVERT: A 923 ARG cc_start: 0.7341 (mpt180) cc_final: 0.7141 (mpt180) REVERT: A 955 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8176 (mttt) outliers start: 14 outliers final: 8 residues processed: 201 average time/residue: 0.7160 time to fit residues: 151.2018 Evaluate side-chains 203 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 193 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 391 SER 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: 2.9990 chunk 46 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 64 optimal weight: 0.0030 chunk 86 optimal weight: 0.9980 chunk 8 optimal weight: 0.0000 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 ASN A 328 ASN A 819 GLN ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.108652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.096537 restraints weight = 12252.436| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.60 r_work: 0.3106 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9010 Z= 0.139 Angle : 0.446 4.700 12374 Z= 0.258 Chirality : 0.037 0.131 1386 Planarity : 0.003 0.051 1409 Dihedral : 16.202 178.704 1817 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.45 % Allowed : 13.83 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.27), residues: 939 helix: 1.71 (0.22), residues: 563 sheet: 0.01 (1.01), residues: 18 loop : -0.99 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 899 TYR 0.016 0.001 TYR A 708 PHE 0.014 0.001 PHE A 884 TRP 0.005 0.001 TRP A 256 HIS 0.004 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 9010) covalent geometry : angle 0.44563 / 0.26 (12374) hydrogen bonds : bond 0.06907 / 4.77 ( 425) hydrogen bonds : angle 4.18040 / 2.91 ( 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 216 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 0.304 Fit side-chains REVERT: A 18 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8565 (mt) REVERT: A 171 ASP cc_start: 0.7625 (p0) cc_final: 0.7372 (p0) REVERT: A 173 GLU cc_start: 0.7719 (mp0) cc_final: 0.7187 (mp0) REVERT: A 190 LYS cc_start: 0.7230 (mttt) cc_final: 0.6799 (mttm) REVERT: A 210 GLN cc_start: 0.8299 (mm-40) cc_final: 0.7906 (mm-40) REVERT: A 353 ASP cc_start: 0.7439 (m-30) cc_final: 0.7058 (m-30) REVERT: A 396 ASP cc_start: 0.7590 (m-30) cc_final: 0.7292 (m-30) REVERT: A 559 ASN cc_start: 0.8206 (t0) cc_final: 0.7882 (t0) REVERT: A 686 SER cc_start: 0.8150 (t) cc_final: 0.7924 (p) REVERT: A 785 ARG cc_start: 0.7748 (mtm180) cc_final: 0.7494 (mtm180) REVERT: A 788 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7349 (tp30) REVERT: A 916 ASP cc_start: 0.7561 (m-30) cc_final: 0.7169 (m-30) REVERT: A 955 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8120 (mttt) outliers start: 20 outliers final: 8 residues processed: 202 average time/residue: 0.6736 time to fit residues: 143.0645 Evaluate side-chains 204 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 194 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 344 GLU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 805 ILE 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: 0.6980 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 30 optimal weight: 0.0570 chunk 23 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 ASN A 897 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.107463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.095294 restraints weight = 12546.979| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.61 r_work: 0.3085 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | 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: 4 | |-----------------------------------------------------------------------------| |-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: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9010 Z= 0.186 Angle : 0.473 4.882 12374 Z= 0.270 Chirality : 0.039 0.136 1386 Planarity : 0.003 0.042 1409 Dihedral : 16.151 178.697 1817 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.82 % Allowed : 15.18 % Favored : 82.01 % 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: 1.04 (0.27), residues: 939 helix: 1.75 (0.22), residues: 562 sheet: -0.09 (1.07), residues: 23 loop : -1.01 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 725 TYR 0.017 0.002 TYR A 708 PHE 0.014 0.002 PHE A 884 TRP 0.008 0.001 TRP A 256 HIS 0.008 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 ( 9010) covalent geometry : angle 0.47343 / 0.27 (12374) hydrogen bonds : bond 0.07285 / 5.04 ( 425) hydrogen bonds : angle 4.22107 / 2.94 ( 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 220 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.247 Fit side-chains REVERT: A 18 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8583 (mt) REVERT: A 171 ASP cc_start: 0.7660 (p0) cc_final: 0.7303 (p0) REVERT: A 173 GLU cc_start: 0.7761 (mp0) cc_final: 0.7228 (mp0) REVERT: A 190 LYS cc_start: 0.7226 (mttt) cc_final: 0.6939 (mttm) REVERT: A 210 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7933 (mm-40) REVERT: A 353 ASP cc_start: 0.7481 (m-30) cc_final: 0.7082 (m-30) REVERT: A 396 ASP cc_start: 0.7593 (m-30) cc_final: 0.7309 (m-30) REVERT: A 510 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8360 (mttp) REVERT: A 559 ASN cc_start: 0.8222 (t0) cc_final: 0.7907 (t0) REVERT: A 785 ARG cc_start: 0.7761 (mtm180) cc_final: 0.7520 (mtm180) REVERT: A 788 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7369 (tp30) REVERT: A 916 ASP cc_start: 0.7527 (m-30) cc_final: 0.7134 (m-30) REVERT: A 955 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8182 (mttt) outliers start: 23 outliers final: 14 residues processed: 205 average time/residue: 0.7056 time to fit residues: 151.9440 Evaluate side-chains 214 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 344 GLU 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 512 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 656 LYS Chi-restraints excluded: chain A residue 805 ILE 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: 0.7980 chunk 72 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 78 optimal weight: 0.3980 chunk 83 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 ASN A 897 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.107280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.094743 restraints weight = 12482.170| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.69 r_work: 0.3071 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9010 Z= 0.185 Angle : 0.472 5.015 12374 Z= 0.268 Chirality : 0.039 0.135 1386 Planarity : 0.003 0.038 1409 Dihedral : 16.130 178.591 1817 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.06 % Allowed : 15.67 % 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: 1.06 (0.27), residues: 939 helix: 1.79 (0.22), residues: 561 sheet: -0.08 (1.06), residues: 23 loop : -1.04 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 899 TYR 0.017 0.002 TYR A 708 PHE 0.014 0.002 PHE A 884 TRP 0.007 0.001 TRP A 256 HIS 0.007 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 ( 9010) covalent geometry : angle 0.47176 / 0.27 (12374) hydrogen bonds : bond 0.07244 / 5.02 ( 425) hydrogen bonds : angle 4.20442 / 2.93 ( 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 220 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.263 Fit side-chains REVERT: A 18 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8578 (mt) REVERT: A 171 ASP cc_start: 0.7699 (p0) cc_final: 0.7306 (p0) REVERT: A 173 GLU cc_start: 0.7812 (mp0) cc_final: 0.7271 (mp0) REVERT: A 190 LYS cc_start: 0.7259 (mttt) cc_final: 0.7020 (mttm) REVERT: A 210 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7905 (mm-40) REVERT: A 353 ASP cc_start: 0.7519 (m-30) cc_final: 0.7098 (m-30) REVERT: A 378 VAL cc_start: 0.7879 (OUTLIER) cc_final: 0.7629 (p) REVERT: A 396 ASP cc_start: 0.7636 (m-30) cc_final: 0.7263 (m-30) REVERT: A 510 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8378 (mttp) REVERT: A 559 ASN cc_start: 0.8241 (t0) cc_final: 0.7914 (t0) REVERT: A 738 GLN cc_start: 0.8568 (tp40) cc_final: 0.8280 (tp-100) REVERT: A 785 ARG cc_start: 0.7769 (mtm180) cc_final: 0.7480 (mtm180) REVERT: A 788 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7402 (tp30) REVERT: A 916 ASP cc_start: 0.7549 (m-30) cc_final: 0.7165 (m-30) REVERT: A 955 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8200 (mttt) outliers start: 25 outliers final: 15 residues processed: 204 average time/residue: 0.6632 time to fit residues: 142.4624 Evaluate side-chains 216 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 344 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 391 SER 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 671 LYS Chi-restraints excluded: chain A residue 754 GLU 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: 0.8980 chunk 50 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 ASN A 897 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.106608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.094369 restraints weight = 12530.766| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.62 r_work: 0.3067 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9010 Z= 0.217 Angle : 0.496 5.061 12374 Z= 0.279 Chirality : 0.041 0.140 1386 Planarity : 0.003 0.037 1409 Dihedral : 16.118 178.517 1817 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.67 % Allowed : 15.42 % Favored : 80.91 % 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: 1.00 (0.27), residues: 939 helix: 1.75 (0.22), residues: 561 sheet: -0.07 (1.06), residues: 23 loop : -1.09 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 899 TYR 0.017 0.002 TYR A 708 PHE 0.016 0.002 PHE A 884 TRP 0.008 0.002 TRP A 256 HIS 0.009 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.22 ( 9010) covalent geometry : angle 0.49561 / 0.28 (12374) hydrogen bonds : bond 0.07593 / 5.25 ( 425) hydrogen bonds : angle 4.26737 / 2.98 ( 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 225 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.308 Fit side-chains REVERT: A 18 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8570 (mt) REVERT: A 163 VAL cc_start: 0.8213 (t) cc_final: 0.7846 (m) REVERT: A 171 ASP cc_start: 0.7714 (p0) cc_final: 0.7295 (p0) REVERT: A 173 GLU cc_start: 0.7807 (mp0) cc_final: 0.7268 (mp0) REVERT: A 190 LYS cc_start: 0.7262 (mttt) cc_final: 0.7019 (mttm) REVERT: A 210 GLN cc_start: 0.8308 (mm-40) cc_final: 0.7890 (mm-40) REVERT: A 353 ASP cc_start: 0.7524 (m-30) cc_final: 0.7088 (m-30) REVERT: A 510 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8356 (mttp) REVERT: A 559 ASN cc_start: 0.8228 (t0) cc_final: 0.7902 (t0) REVERT: A 785 ARG cc_start: 0.7758 (mtm180) cc_final: 0.7483 (mtm180) REVERT: A 788 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7409 (tp30) REVERT: A 916 ASP cc_start: 0.7535 (m-30) cc_final: 0.7169 (m-30) REVERT: A 955 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8187 (mmtt) outliers start: 30 outliers final: 19 residues processed: 208 average time/residue: 0.6864 time to fit residues: 150.3044 Evaluate side-chains 218 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 344 GLU 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 510 LYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 671 LYS Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 754 GLU 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: 0.8980 chunk 1 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 ASN A 328 ASN A 897 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.106115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.093830 restraints weight = 12612.033| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.63 r_work: 0.3056 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9010 Z= 0.240 Angle : 0.520 6.040 12374 Z= 0.292 Chirality : 0.042 0.139 1386 Planarity : 0.003 0.037 1409 Dihedral : 16.117 178.416 1817 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.30 % Allowed : 16.03 % 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: 0.93 (0.27), residues: 939 helix: 1.69 (0.22), residues: 561 sheet: -0.09 (1.06), residues: 23 loop : -1.11 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 899 TYR 0.016 0.002 TYR A 708 PHE 0.017 0.002 PHE A 884 TRP 0.009 0.002 TRP A 256 HIS 0.010 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.24 ( 9010) covalent geometry : angle 0.52007 / 0.29 (12374) hydrogen bonds : bond 0.07837 / 5.42 ( 425) hydrogen bonds : angle 4.32032 / 3.01 ( 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 225 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 0.358 Fit side-chains REVERT: A 18 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8555 (mt) REVERT: A 163 VAL cc_start: 0.8214 (t) cc_final: 0.7852 (m) REVERT: A 171 ASP cc_start: 0.7729 (p0) cc_final: 0.7277 (p0) REVERT: A 173 GLU cc_start: 0.7820 (mp0) cc_final: 0.7275 (mp0) REVERT: A 190 LYS cc_start: 0.7253 (mttt) cc_final: 0.7006 (mttm) REVERT: A 210 GLN cc_start: 0.8302 (mm-40) cc_final: 0.7911 (mm-40) REVERT: A 353 ASP cc_start: 0.7440 (m-30) cc_final: 0.7002 (m-30) REVERT: A 451 ARG cc_start: 0.8187 (ptm-80) cc_final: 0.7884 (ptm-80) REVERT: A 559 ASN cc_start: 0.8236 (t0) cc_final: 0.7900 (t0) REVERT: A 738 GLN cc_start: 0.8567 (tp40) cc_final: 0.8265 (tp-100) REVERT: A 785 ARG cc_start: 0.7762 (mtm180) cc_final: 0.7480 (mtm180) REVERT: A 788 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7418 (tp30) REVERT: A 916 ASP cc_start: 0.7511 (m-30) cc_final: 0.7157 (m-30) REVERT: A 955 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8212 (mmtt) outliers start: 27 outliers final: 19 residues processed: 208 average time/residue: 0.7205 time to fit residues: 157.5059 Evaluate side-chains 219 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 340 LYS Chi-restraints excluded: chain A residue 344 GLU 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 530 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 848 ARG 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: 0.0030 chunk 87 optimal weight: 0.0970 chunk 92 optimal weight: 0.3980 chunk 46 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 43 optimal weight: 0.0870 chunk 34 optimal weight: 0.0050 chunk 22 optimal weight: 0.7980 overall best weight: 0.1180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 GLN A 328 ASN ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.098347 restraints weight = 12437.065| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.62 r_work: 0.3133 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1819 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= 0.114 Angle : 0.442 5.947 12374 Z= 0.255 Chirality : 0.036 0.129 1386 Planarity : 0.003 0.041 1409 Dihedral : 16.071 178.617 1817 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.20 % Allowed : 17.63 % Favored : 80.17 % 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: 1.38 (0.28), residues: 939 helix: 2.05 (0.22), residues: 564 sheet: 0.13 (1.00), residues: 18 loop : -0.93 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 899 TYR 0.018 0.001 TYR A 801 PHE 0.010 0.001 PHE A 884 TRP 0.004 0.001 TRP A 256 HIS 0.003 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 ( 9010) covalent geometry : angle 0.44234 / 0.26 (12374) hydrogen bonds : bond 0.05806 / 4.04 ( 425) hydrogen bonds : angle 3.96219 / 2.77 ( 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 210 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.350 Fit side-chains REVERT: A 128 ASP cc_start: 0.8007 (m-30) cc_final: 0.7751 (m-30) REVERT: A 163 VAL cc_start: 0.8217 (t) cc_final: 0.7924 (m) REVERT: A 171 ASP cc_start: 0.7692 (p0) cc_final: 0.7240 (p0) REVERT: A 173 GLU cc_start: 0.7783 (mp0) cc_final: 0.7582 (mp0) REVERT: A 210 GLN cc_start: 0.8275 (mm-40) cc_final: 0.7994 (mm-40) REVERT: A 353 ASP cc_start: 0.7430 (m-30) cc_final: 0.6977 (m-30) REVERT: A 559 ASN cc_start: 0.8212 (t0) cc_final: 0.7888 (t0) REVERT: A 750 LYS cc_start: 0.8268 (mmmm) cc_final: 0.8047 (mmmm) REVERT: A 785 ARG cc_start: 0.7718 (mtm180) cc_final: 0.7414 (mtm180) REVERT: A 788 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7418 (tp30) REVERT: A 897 ASN cc_start: 0.7883 (t0) cc_final: 0.7528 (t0) REVERT: A 916 ASP cc_start: 0.7544 (m-30) cc_final: 0.7129 (m-30) REVERT: A 955 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8155 (mttt) outliers start: 18 outliers final: 5 residues processed: 198 average time/residue: 0.7200 time to fit residues: 149.9244 Evaluate side-chains 197 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 191 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 671 LYS Chi-restraints excluded: chain A residue 753 GLU Chi-restraints excluded: chain A residue 918 LYS 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: 0.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 75 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3386 r_free = 0.3386 target = 0.108016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.095849 restraints weight = 12462.222| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.61 r_work: 0.3094 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9010 Z= 0.180 Angle : 0.485 7.217 12374 Z= 0.272 Chirality : 0.039 0.135 1386 Planarity : 0.003 0.038 1409 Dihedral : 16.006 178.301 1817 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.35 % Allowed : 19.46 % 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: 1.33 (0.27), residues: 939 helix: 2.02 (0.22), residues: 562 sheet: 0.03 (1.05), residues: 23 loop : -0.97 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 899 TYR 0.018 0.002 TYR A 801 PHE 0.017 0.002 PHE A 884 TRP 0.006 0.001 TRP A 256 HIS 0.007 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 ( 9010) covalent geometry : angle 0.48499 / 0.27 (12374) hydrogen bonds : bond 0.06690 / 4.65 ( 425) hydrogen bonds : angle 4.06041 / 2.83 ( 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 203 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 192 time to evaluate : 0.310 Fit side-chains REVERT: A 128 ASP cc_start: 0.8021 (m-30) cc_final: 0.7750 (m-30) REVERT: A 163 VAL cc_start: 0.8241 (t) cc_final: 0.7925 (m) REVERT: A 171 ASP cc_start: 0.7713 (p0) cc_final: 0.7255 (p0) REVERT: A 173 GLU cc_start: 0.7730 (mp0) cc_final: 0.7298 (mp0) REVERT: A 210 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7871 (mm-40) REVERT: A 353 ASP cc_start: 0.7434 (m-30) cc_final: 0.6989 (m-30) REVERT: A 372 ILE cc_start: 0.8736 (mm) cc_final: 0.8535 (mp) REVERT: A 451 ARG cc_start: 0.8155 (ptm-80) cc_final: 0.7853 (ptm-80) REVERT: A 559 ASN cc_start: 0.8215 (t0) cc_final: 0.7891 (t0) REVERT: A 750 LYS cc_start: 0.8277 (mmmm) cc_final: 0.8068 (mmmm) REVERT: A 785 ARG cc_start: 0.7757 (mtm180) cc_final: 0.7468 (mtm180) REVERT: A 788 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7435 (tp30) REVERT: A 810 GLU cc_start: 0.6779 (tm-30) cc_final: 0.6494 (tm-30) REVERT: A 912 ASP cc_start: 0.8352 (m-30) cc_final: 0.7765 (m-30) REVERT: A 916 ASP cc_start: 0.7583 (m-30) cc_final: 0.7143 (m-30) REVERT: A 955 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8179 (mmtt) outliers start: 11 outliers final: 8 residues processed: 196 average time/residue: 0.6779 time to fit residues: 139.8337 Evaluate side-chains 199 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 190 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 918 LYS 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: 0.9980 chunk 47 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 ASN A 897 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.106120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.093882 restraints weight = 12492.094| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.61 r_work: 0.3059 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- 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: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 9010 Z= 0.255 Angle : 0.549 7.507 12374 Z= 0.304 Chirality : 0.042 0.142 1386 Planarity : 0.004 0.038 1409 Dihedral : 16.047 177.970 1817 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.47 % Allowed : 19.95 % 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: 1.07 (0.27), residues: 939 helix: 1.82 (0.22), residues: 561 sheet: 0.19 (1.07), residues: 23 loop : -1.10 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 899 TYR 0.019 0.002 TYR A 136 PHE 0.019 0.002 PHE A 884 TRP 0.008 0.002 TRP A 256 HIS 0.011 0.002 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.25 ( 9010) covalent geometry : angle 0.54885 / 0.30 (12374) hydrogen bonds : bond 0.07809 / 5.40 ( 425) hydrogen bonds : angle 4.27556 / 2.98 ( 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 209 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 197 time to evaluate : 0.191 Fit side-chains REVERT: A 163 VAL cc_start: 0.8236 (t) cc_final: 0.7894 (m) REVERT: A 171 ASP cc_start: 0.7732 (p0) cc_final: 0.7270 (p0) REVERT: A 173 GLU cc_start: 0.7746 (mp0) cc_final: 0.7317 (mp0) REVERT: A 210 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7883 (mm-40) REVERT: A 353 ASP cc_start: 0.7450 (m-30) cc_final: 0.7009 (m-30) REVERT: A 451 ARG cc_start: 0.8164 (ptm-80) cc_final: 0.7848 (ptm-80) REVERT: A 559 ASN cc_start: 0.8217 (t0) cc_final: 0.7907 (t0) REVERT: A 750 LYS cc_start: 0.8289 (mmmm) cc_final: 0.8080 (mmmm) REVERT: A 785 ARG cc_start: 0.7773 (mtm180) cc_final: 0.7495 (mtm180) REVERT: A 788 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7438 (tp30) REVERT: A 810 GLU cc_start: 0.6983 (tm-30) cc_final: 0.6666 (tm-30) REVERT: A 916 ASP cc_start: 0.7519 (m-30) cc_final: 0.7078 (m-30) REVERT: A 955 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8254 (mmtt) outliers start: 12 outliers final: 8 residues processed: 201 average time/residue: 0.6734 time to fit residues: 142.4708 Evaluate side-chains 206 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 197 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 325 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 805 ILE Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 918 LYS 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: 0.9980 chunk 13 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 ASN A 328 ASN A 410 GLN A 897 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.106987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.094580 restraints weight = 12280.147| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.66 r_work: 0.3067 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 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 = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 9010 Z= 0.196 Angle : 0.512 7.166 12374 Z= 0.288 Chirality : 0.040 0.136 1386 Planarity : 0.003 0.038 1409 Dihedral : 16.043 177.864 1817 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.59 % Allowed : 20.07 % Favored : 78.34 % 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: 1.12 (0.27), residues: 939 helix: 1.86 (0.22), residues: 562 sheet: 0.19 (1.06), residues: 23 loop : -1.07 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 899 TYR 0.025 0.002 TYR A 801 PHE 0.017 0.002 PHE A 534 TRP 0.008 0.001 TRP A 256 HIS 0.008 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 ( 9010) covalent geometry : angle 0.51222 / 0.29 (12374) hydrogen bonds : bond 0.07392 / 5.11 ( 425) hydrogen bonds : angle 4.23251 / 2.95 ( 1219) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3396.47 seconds wall clock time: 58 minutes 33.03 seconds (3513.03 seconds total)