Starting phenix.real_space_refine on Fri Oct 23 00:24:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/23vu_69297/10_2026/23vu_69297.cif Found real_map, /net/cci-nas-00/data/ceres_data/23vu_69297/10_2026/23vu_69297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/23vu_69297/10_2026/23vu_69297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/23vu_69297/10_2026/23vu_69297.map" model { file = "/net/cci-nas-00/data/ceres_data/23vu_69297/10_2026/23vu_69297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/23vu_69297/10_2026/23vu_69297.cif" } resolution = 2.69 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.027 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 104 5.49 5 Mg 2 5.21 5 S 20 5.16 5 C 4062 2.51 5 N 1273 2.21 5 O 1573 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7035 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4839 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 28, 'TRANS': 565} Chain: "B" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1152 Classifications: {'RNA': 54} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 3, 'rna3p_pur': 22, 'rna3p_pyr': 22} Link IDs: {'rna2p': 10, 'rna3p': 43} Chain: "C" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 723 Unusual residues: {' GS': 3, ' SC': 1} Classifications: {'DNA': 31, 'undetermined': 4} Link IDs: {'rna3p': 27, None: 7} Not linked: pdbres="PST C -25 " pdbres=" SC C -24 " Not linked: pdbres=" SC C -24 " pdbres=" GS C -23 " Not linked: pdbres=" GS C -23 " pdbres="PST C -22 " Not linked: pdbres="PST C -21 " pdbres=" GS C -20 " Not linked: pdbres=" GS C -20 " pdbres="PST C -19 " ... (remaining 2 not shown) Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Chain: "D" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 318 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4438 SG CYS A 552 12.935 23.273 63.173 1.00 46.11 S ATOM 4463 SG CYS A 555 9.480 23.610 62.224 1.00 57.02 S ATOM 4578 SG CYS A 570 10.853 25.284 65.381 1.00 56.24 S ATOM 4596 SG CYS A 573 10.300 21.640 65.394 1.00 59.65 S Time building chain proxies: 1.58, per 1000 atoms: 0.22 Number of scatterers: 7035 At special positions: 0 Unit cell: (93.375, 82.17, 96.1762, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 20 16.00 P 104 15.00 Mg 2 11.99 O 1573 8.00 N 1273 7.00 C 4062 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 270.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 703 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 552 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 555 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 573 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 570 " Number of angles added : 6 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1130 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 4 sheets defined 54.4% alpha, 14.6% beta 37 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 27 through 63 removed outlier: 3.993A pdb=" N LEU A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 95 removed outlier: 4.076A pdb=" N GLY A 67 " --> pdb=" O HIS A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 133 removed outlier: 3.514A pdb=" N GLU A 117 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 137 through 155 removed outlier: 3.719A pdb=" N LEU A 141 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 169 Processing helix chain 'A' and resid 169 through 182 removed outlier: 3.858A pdb=" N PHE A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS A 180 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 219 removed outlier: 3.502A pdb=" N PHE A 219 " --> pdb=" O ASP A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 390 removed outlier: 3.636A pdb=" N LYS A 383 " --> pdb=" O ASP A 379 " (cutoff:3.500A) Proline residue: A 386 - end of helix removed outlier: 3.788A pdb=" N ASP A 390 " --> pdb=" O PRO A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 412 Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 439 through 484 Proline residue: A 445 - end of helix removed outlier: 5.469A pdb=" N ARG A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ARG A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS A 461 " --> pdb=" O TYR A 457 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 501 removed outlier: 4.093A pdb=" N ILE A 499 " --> pdb=" O ASN A 495 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 521 Processing helix chain 'A' and resid 521 through 537 Processing helix chain 'A' and resid 579 through 602 Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 199 removed outlier: 4.641A pdb=" N ASN A 284 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 12.241A pdb=" N PHE A 296 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR A 298 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY A 19 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL A 264 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG A 247 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG A 239 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG A 249 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 203 Processing sheet with id=AA3, first strand: chain 'A' and resid 351 through 354 removed outlier: 4.472A pdb=" N LYS A 336 " --> pdb=" O ARG A 327 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ARG A 327 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL A 338 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLU A 492 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU A 324 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE A 489 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL A 543 " --> pdb=" O ILE A 489 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A 491 " --> pdb=" O VAL A 543 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 567 through 569 292 hydrogen bonds defined for protein. 855 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 91 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 2829 1.39 - 1.56: 4323 1.56 - 1.73: 199 1.73 - 1.90: 16 1.90 - 2.08: 8 Bond restraints: 7375 Sorted by residual: bond pdb=" OP1 SC C -24 " pdb=" P SC C -24 " ideal model delta sigma weight residual 1.600 1.493 0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" P PST C -21 " pdb=" OP1 PST C -21 " ideal model delta sigma weight residual 1.595 1.495 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" P PST C -25 " pdb=" OP1 PST C -25 " ideal model delta sigma weight residual 1.595 1.500 0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" P PST C -22 " pdb=" OP1 PST C -22 " ideal model delta sigma weight residual 1.595 1.500 0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" P PST C -19 " pdb=" OP1 PST C -19 " ideal model delta sigma weight residual 1.595 1.501 0.094 2.00e-02 2.50e+03 2.21e+01 ... (remaining 7370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 9102 1.85 - 3.70: 1146 3.70 - 5.55: 118 5.55 - 7.40: 28 7.40 - 9.25: 8 Bond angle restraints: 10402 Sorted by residual: angle pdb=" C1' G B -12 " pdb=" N9 G B -12 " pdb=" C8 G B -12 " ideal model delta sigma weight residual 127.00 136.20 -9.20 1.30e+00 5.92e-01 5.01e+01 angle pdb=" N9 G B -12 " pdb=" C4 G B -12 " pdb=" N3 G B -12 " ideal model delta sigma weight residual 126.00 121.81 4.19 6.00e-01 2.78e+00 4.87e+01 angle pdb=" C1' G B -12 " pdb=" N9 G B -12 " pdb=" C4 G B -12 " ideal model delta sigma weight residual 126.50 118.63 7.87 1.30e+00 5.92e-01 3.66e+01 angle pdb=" N PRO A 64 " pdb=" CA PRO A 64 " pdb=" C PRO A 64 " ideal model delta sigma weight residual 110.70 117.91 -7.21 1.22e+00 6.72e-01 3.49e+01 angle pdb=" O3' G B -13 " pdb=" C3' G B -13 " pdb=" C2' G B -13 " ideal model delta sigma weight residual 113.70 104.45 9.25 1.60e+00 3.91e-01 3.34e+01 ... (remaining 10397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.29: 3907 23.29 - 46.57: 435 46.57 - 69.86: 192 69.86 - 93.15: 21 93.15 - 116.43: 1 Dihedral angle restraints: 4556 sinusoidal: 2814 harmonic: 1742 Sorted by residual: dihedral pdb=" O4' G B -10 " pdb=" C4' G B -10 " pdb=" C3' G B -10 " pdb=" C2' G B -10 " ideal model delta sinusoidal sigma weight residual 24.00 -12.44 36.44 1 8.00e+00 1.56e-02 2.93e+01 dihedral pdb=" CA ARG A 414 " pdb=" C ARG A 414 " pdb=" N ALA A 415 " pdb=" CA ALA A 415 " ideal model delta harmonic sigma weight residual -180.00 -153.73 -26.27 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" C4' G B -10 " pdb=" C3' G B -10 " pdb=" C2' G B -10 " pdb=" C1' G B -10 " ideal model delta sinusoidal sigma weight residual -35.00 -0.84 -34.16 1 8.00e+00 1.56e-02 2.59e+01 ... (remaining 4553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 634 0.054 - 0.107: 373 0.107 - 0.161: 128 0.161 - 0.214: 23 0.214 - 0.268: 16 Chirality restraints: 1174 Sorted by residual: chirality pdb=" P G B -22 " pdb=" OP1 G B -22 " pdb=" OP2 G B -22 " pdb=" O5' G B -22 " both_signs ideal model delta sigma weight residual True 2.41 -2.68 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" P G B -2 " pdb=" OP1 G B -2 " pdb=" OP2 G B -2 " pdb=" O5' G B -2 " both_signs ideal model delta sigma weight residual True 2.41 -2.67 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" P G B 9 " pdb=" OP1 G B 9 " pdb=" OP2 G B 9 " pdb=" O5' G B 9 " both_signs ideal model delta sigma weight residual True 2.41 -2.66 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 1171 not shown) Planarity restraints: 973 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA C -16 " -0.056 2.00e-02 2.50e+03 2.38e-02 1.56e+01 pdb=" N9 DA C -16 " 0.046 2.00e-02 2.50e+03 pdb=" C8 DA C -16 " 0.013 2.00e-02 2.50e+03 pdb=" N7 DA C -16 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA C -16 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA C -16 " -0.019 2.00e-02 2.50e+03 pdb=" N6 DA C -16 " -0.012 2.00e-02 2.50e+03 pdb=" N1 DA C -16 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA C -16 " 0.012 2.00e-02 2.50e+03 pdb=" N3 DA C -16 " 0.010 2.00e-02 2.50e+03 pdb=" C4 DA C -16 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA C -7 " 0.049 2.00e-02 2.50e+03 2.19e-02 1.32e+01 pdb=" N9 DA C -7 " -0.046 2.00e-02 2.50e+03 pdb=" C8 DA C -7 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA C -7 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA C -7 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA C -7 " 0.016 2.00e-02 2.50e+03 pdb=" N6 DA C -7 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA C -7 " 0.008 2.00e-02 2.50e+03 pdb=" C2 DA C -7 " -0.009 2.00e-02 2.50e+03 pdb=" N3 DA C -7 " -0.010 2.00e-02 2.50e+03 pdb=" C4 DA C -7 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B -28 " 0.045 2.00e-02 2.50e+03 1.97e-02 1.17e+01 pdb=" N9 G B -28 " -0.025 2.00e-02 2.50e+03 pdb=" C8 G B -28 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G B -28 " -0.010 2.00e-02 2.50e+03 pdb=" C5 G B -28 " -0.013 2.00e-02 2.50e+03 pdb=" C6 G B -28 " 0.018 2.00e-02 2.50e+03 pdb=" O6 G B -28 " 0.007 2.00e-02 2.50e+03 pdb=" N1 G B -28 " 0.018 2.00e-02 2.50e+03 pdb=" C2 G B -28 " -0.006 2.00e-02 2.50e+03 pdb=" N2 G B -28 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G B -28 " -0.029 2.00e-02 2.50e+03 pdb=" C4 G B -28 " -0.012 2.00e-02 2.50e+03 ... (remaining 970 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 70 2.62 - 3.19: 5317 3.19 - 3.76: 12002 3.76 - 4.33: 17111 4.33 - 4.90: 24907 Nonbonded interactions: 59407 Sorted by model distance: nonbonded pdb=" OD1 ASP A 323 " pdb="MG MG A 702 " model vdw 2.052 2.170 nonbonded pdb=" OH TYR A 305 " pdb=" OP1 DC C 0 " model vdw 2.127 3.040 nonbonded pdb=" OE2 GLU A 492 " pdb="MG MG A 702 " model vdw 2.186 2.170 nonbonded pdb=" OD1 ASP A 580 " pdb="MG MG A 701 " model vdw 2.224 2.170 nonbonded pdb=" OP1 GS C -23 " pdb="MG MG A 701 " model vdw 2.285 2.170 ... (remaining 59402 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.190 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.660 Find NCS groups from input model: 0.030 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 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 : 0.008 0.107 7386 Z= 0.549 Angle : 1.278 9.254 10408 Z= 0.842 Chirality : 0.075 0.268 1174 Planarity : 0.006 0.032 973 Dihedral : 20.801 116.433 3426 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.55 % Favored : 96.28 % Rotamer: Outliers : 1.34 % Allowed : 7.28 % Favored : 91.38 % 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: -3.49 (0.27), residues: 592 helix: -3.24 (0.19), residues: 302 sheet: 0.79 (0.51), residues: 82 loop : -1.83 (0.32), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 455 TYR 0.031 0.004 TYR A 448 PHE 0.022 0.004 PHE A 363 TRP 0.026 0.006 TRP A 449 HIS 0.006 0.002 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00828 / 0.53 ( 7375) covalent geometry : angle 1.27515 / 0.84 (10402) hydrogen bonds : bond 0.20928 / 14.05 ( 383) hydrogen bonds : angle 7.33837 / 5.21 ( 1033) metal coordination : bond 0.05303 / 2.73 ( 4) metal coordination : angle 3.77548 / 2.00 ( 6) Misc. bond : bond 0.04284 / 2.09 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.264 Fit side-chains REVERT: A 154 ARG cc_start: 0.8309 (ttp-110) cc_final: 0.7388 (mpt-90) REVERT: A 155 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7931 (pt0) REVERT: A 180 LYS cc_start: 0.8543 (mmtt) cc_final: 0.8266 (mtmt) REVERT: A 208 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7847 (ttpt) REVERT: A 333 LYS cc_start: 0.8604 (ptmt) cc_final: 0.8381 (tmtm) REVERT: A 387 LEU cc_start: 0.9005 (mt) cc_final: 0.8763 (mt) REVERT: A 481 ARG cc_start: 0.8914 (ttp80) cc_final: 0.8380 (ttm-80) REVERT: A 512 LYS cc_start: 0.8333 (mttt) cc_final: 0.7737 (mppt) outliers start: 7 outliers final: 2 residues processed: 86 average time/residue: 0.7749 time to fit residues: 69.1896 Evaluate side-chains 53 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 350 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 27] chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 397 ASN A 531 ASN A 544 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.130855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.104727 restraints weight = 7085.348| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.00 r_work: 0.3059 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7386 Z= 0.209 Angle : 0.698 8.901 10408 Z= 0.393 Chirality : 0.049 0.217 1174 Planarity : 0.006 0.049 973 Dihedral : 22.011 101.816 2158 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.26 % Allowed : 12.07 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.31), residues: 592 helix: 0.10 (0.27), residues: 306 sheet: 1.40 (0.57), residues: 73 loop : -1.04 (0.36), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 247 TYR 0.015 0.002 TYR A 272 PHE 0.021 0.002 PHE A 363 TRP 0.021 0.003 TRP A 449 HIS 0.005 0.002 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.21 ( 7375) covalent geometry : angle 0.69546 / 0.39 (10402) hydrogen bonds : bond 0.07707 / 5.01 ( 383) hydrogen bonds : angle 4.43422 / 3.15 ( 1033) metal coordination : bond 0.00475 / 0.24 ( 4) metal coordination : angle 2.72583 / 1.27 ( 6) Misc. bond : bond 0.00513 / 0.27 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.223 Fit side-chains REVERT: A 112 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7615 (mm-30) REVERT: A 208 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7764 (ttpt) REVERT: A 328 GLU cc_start: 0.7683 (tt0) cc_final: 0.7440 (pt0) REVERT: A 512 LYS cc_start: 0.8187 (mttt) cc_final: 0.7357 (mptt) outliers start: 17 outliers final: 7 residues processed: 64 average time/residue: 0.8362 time to fit residues: 55.5205 Evaluate side-chains 57 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 389 LYS Chi-restraints excluded: chain A residue 557 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: [40, 43, 3, 54, 13, 49, 47, 30, 16, 48, 36] chunk 40 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 477 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.129254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.104518 restraints weight = 7025.770| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 0.91 r_work: 0.3015 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 7386 Z= 0.262 Angle : 0.726 9.221 10408 Z= 0.398 Chirality : 0.052 0.232 1174 Planarity : 0.006 0.051 973 Dihedral : 22.004 101.187 2158 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.21 % Allowed : 13.22 % Favored : 82.57 % 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: 1.01 (0.33), residues: 592 helix: 1.33 (0.29), residues: 306 sheet: 1.49 (0.58), residues: 74 loop : -0.55 (0.38), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 249 TYR 0.014 0.002 TYR A 272 PHE 0.025 0.003 PHE A 363 TRP 0.016 0.003 TRP A 568 HIS 0.005 0.002 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.26 ( 7375) covalent geometry : angle 0.72341 / 0.40 (10402) hydrogen bonds : bond 0.07439 / 4.82 ( 383) hydrogen bonds : angle 4.28461 / 3.04 ( 1033) metal coordination : bond 0.00371 / 0.19 ( 4) metal coordination : angle 2.87730 / 1.40 ( 6) Misc. bond : bond 0.00193 / 0.11 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 45 time to evaluate : 0.228 Fit side-chains REVERT: A 70 MET cc_start: 0.8270 (mmm) cc_final: 0.7990 (mtp) REVERT: A 112 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7694 (mm-30) REVERT: A 208 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7785 (ttpt) REVERT: A 359 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8785 (tmm) REVERT: A 512 LYS cc_start: 0.8152 (mttt) cc_final: 0.7367 (mptt) outliers start: 22 outliers final: 9 residues processed: 61 average time/residue: 0.7656 time to fit residues: 48.6259 Evaluate side-chains 56 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 557 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: [2, 39, 14, 28, 54, 31, 38, 47, 63, 50, 46] chunk 2 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 38 optimal weight: 30.0000 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.132020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.105638 restraints weight = 7123.260| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.06 r_work: 0.3069 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7386 Z= 0.169 Angle : 0.593 7.143 10408 Z= 0.337 Chirality : 0.044 0.199 1174 Planarity : 0.005 0.053 973 Dihedral : 21.769 100.506 2158 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.83 % Allowed : 13.79 % Favored : 82.38 % 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: 1.69 (0.33), residues: 592 helix: 2.03 (0.29), residues: 308 sheet: 1.58 (0.57), residues: 74 loop : -0.42 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 72 TYR 0.011 0.001 TYR A 272 PHE 0.016 0.002 PHE A 363 TRP 0.013 0.002 TRP A 568 HIS 0.003 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 ( 7375) covalent geometry : angle 0.59016 / 0.34 (10402) hydrogen bonds : bond 0.06056 / 3.93 ( 383) hydrogen bonds : angle 4.05266 / 2.88 ( 1033) metal coordination : bond 0.00242 / 0.12 ( 4) metal coordination : angle 2.51962 / 1.25 ( 6) Misc. bond : bond 0.00080 / 0.05 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.221 Fit side-chains REVERT: A 70 MET cc_start: 0.8239 (mmm) cc_final: 0.7976 (mtp) REVERT: A 112 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7659 (mm-30) REVERT: A 208 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7787 (ttpt) REVERT: A 512 LYS cc_start: 0.8167 (mttt) cc_final: 0.7353 (mptt) outliers start: 20 outliers final: 8 residues processed: 69 average time/residue: 0.7535 time to fit residues: 54.2287 Evaluate side-chains 62 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 597 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: [62, 13, 66, 33, 26, 37, 21, 14, 7, 5, 42] chunk 62 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 66 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 0.0070 chunk 37 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 HIS A 544 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.130901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104398 restraints weight = 7070.679| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.00 r_work: 0.3044 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7386 Z= 0.197 Angle : 0.622 7.925 10408 Z= 0.348 Chirality : 0.046 0.215 1174 Planarity : 0.005 0.054 973 Dihedral : 21.718 100.550 2158 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.26 % Allowed : 14.94 % Favored : 81.80 % 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: 1.94 (0.34), residues: 592 helix: 2.23 (0.29), residues: 308 sheet: 1.43 (0.55), residues: 79 loop : -0.23 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 249 TYR 0.011 0.002 TYR A 272 PHE 0.019 0.002 PHE A 363 TRP 0.012 0.002 TRP A 568 HIS 0.004 0.001 HIS A 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.20 ( 7375) covalent geometry : angle 0.61880 / 0.35 (10402) hydrogen bonds : bond 0.06182 / 4.01 ( 383) hydrogen bonds : angle 4.04187 / 2.88 ( 1033) metal coordination : bond 0.00269 / 0.14 ( 4) metal coordination : angle 2.69735 / 1.32 ( 6) Misc. bond : bond 0.00059 / 0.03 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.207 Fit side-chains REVERT: A 70 MET cc_start: 0.8278 (mmm) cc_final: 0.8052 (mtp) REVERT: A 208 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7907 (ttpt) REVERT: A 512 LYS cc_start: 0.8175 (mttt) cc_final: 0.7469 (mptt) outliers start: 17 outliers final: 11 residues processed: 66 average time/residue: 0.7500 time to fit residues: 51.5619 Evaluate side-chains 62 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 597 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: [22, 8, 53, 32, 48, 9, 19, 23, 27, 67, 34] chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 HIS A 544 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.130131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.104082 restraints weight = 7118.147| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.03 r_work: 0.3040 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7386 Z= 0.233 Angle : 0.658 8.128 10408 Z= 0.364 Chirality : 0.048 0.235 1174 Planarity : 0.006 0.054 973 Dihedral : 21.752 100.526 2158 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.83 % Allowed : 15.33 % Favored : 80.84 % 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: 1.94 (0.34), residues: 592 helix: 2.20 (0.29), residues: 307 sheet: 1.37 (0.54), residues: 79 loop : -0.13 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 249 TYR 0.010 0.002 TYR A 272 PHE 0.016 0.002 PHE A 363 TRP 0.013 0.003 TRP A 568 HIS 0.004 0.001 HIS A 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.23 ( 7375) covalent geometry : angle 0.65497 / 0.36 (10402) hydrogen bonds : bond 0.06495 / 4.21 ( 383) hydrogen bonds : angle 4.09475 / 2.92 ( 1033) metal coordination : bond 0.00394 / 0.20 ( 4) metal coordination : angle 2.79583 / 1.36 ( 6) Misc. bond : bond 0.00101 / 0.05 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.181 Fit side-chains REVERT: A 61 LYS cc_start: 0.8228 (mtpm) cc_final: 0.7774 (mppt) REVERT: A 70 MET cc_start: 0.8240 (mmm) cc_final: 0.7985 (mtp) REVERT: A 208 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7789 (ttpt) REVERT: A 209 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8347 (tppt) REVERT: A 512 LYS cc_start: 0.8143 (mttt) cc_final: 0.7365 (mptt) outliers start: 20 outliers final: 11 residues processed: 63 average time/residue: 0.8002 time to fit residues: 52.4434 Evaluate side-chains 62 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 597 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: [64, 33, 50, 59, 45, 41, 1, 56, 24, 30, 13] chunk 64 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.131729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.105253 restraints weight = 7129.545| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.06 r_work: 0.3055 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7386 Z= 0.171 Angle : 0.593 7.103 10408 Z= 0.335 Chirality : 0.044 0.215 1174 Planarity : 0.005 0.054 973 Dihedral : 21.640 100.618 2158 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.64 % Allowed : 15.71 % Favored : 80.65 % 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: 2.10 (0.34), residues: 592 helix: 2.39 (0.29), residues: 308 sheet: 1.44 (0.54), residues: 79 loop : -0.18 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 249 TYR 0.009 0.001 TYR A 272 PHE 0.018 0.002 PHE A 363 TRP 0.012 0.002 TRP A 568 HIS 0.003 0.001 HIS A 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 ( 7375) covalent geometry : angle 0.58987 / 0.34 (10402) hydrogen bonds : bond 0.05860 / 3.80 ( 383) hydrogen bonds : angle 3.99401 / 2.84 ( 1033) metal coordination : bond 0.00225 / 0.12 ( 4) metal coordination : angle 2.76745 / 1.39 ( 6) Misc. bond : bond 0.00066 / 0.03 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.222 Fit side-chains REVERT: A 61 LYS cc_start: 0.8169 (mtpm) cc_final: 0.7723 (mppt) REVERT: A 70 MET cc_start: 0.8240 (mmm) cc_final: 0.8002 (mtp) REVERT: A 208 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7812 (ttpt) REVERT: A 328 GLU cc_start: 0.7667 (tt0) cc_final: 0.7398 (pt0) REVERT: A 512 LYS cc_start: 0.8164 (mttt) cc_final: 0.7430 (mptt) REVERT: A 580 ASP cc_start: 0.8226 (m-30) cc_final: 0.7891 (m-30) outliers start: 19 outliers final: 10 residues processed: 67 average time/residue: 0.7115 time to fit residues: 49.7791 Evaluate side-chains 63 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 597 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: [39, 50, 66, 29, 32, 22, 10, 51, 12, 46, 59] chunk 39 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 29 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 12 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 59 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 HIS A 544 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.133182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.107140 restraints weight = 7204.088| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.01 r_work: 0.3094 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7386 Z= 0.147 Angle : 0.562 6.355 10408 Z= 0.320 Chirality : 0.042 0.199 1174 Planarity : 0.005 0.055 973 Dihedral : 21.477 100.693 2158 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.64 % Allowed : 15.52 % Favored : 80.84 % 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: 2.35 (0.34), residues: 592 helix: 2.62 (0.29), residues: 308 sheet: 1.51 (0.54), residues: 79 loop : -0.08 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 72 TYR 0.008 0.001 TYR A 272 PHE 0.012 0.001 PHE A 421 TRP 0.011 0.002 TRP A 568 HIS 0.003 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 ( 7375) covalent geometry : angle 0.55799 / 0.32 (10402) hydrogen bonds : bond 0.05394 / 3.51 ( 383) hydrogen bonds : angle 3.90763 / 2.78 ( 1033) metal coordination : bond 0.00190 / 0.10 ( 4) metal coordination : angle 2.73414 / 1.39 ( 6) Misc. bond : bond 0.00061 / 0.03 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.157 Fit side-chains REVERT: A 61 LYS cc_start: 0.8124 (mtpm) cc_final: 0.7672 (mppt) REVERT: A 208 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7766 (ttpt) REVERT: A 209 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8338 (tppt) REVERT: A 580 ASP cc_start: 0.8205 (m-30) cc_final: 0.7871 (m-30) outliers start: 19 outliers final: 13 residues processed: 69 average time/residue: 0.7628 time to fit residues: 54.8215 Evaluate side-chains 68 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 597 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: [55, 35, 3, 67, 28, 41, 8, 51, 50, 36, 58] chunk 55 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 67 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 544 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106258 restraints weight = 7116.793| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.00 r_work: 0.3072 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7386 Z= 0.163 Angle : 0.573 6.988 10408 Z= 0.324 Chirality : 0.043 0.207 1174 Planarity : 0.005 0.054 973 Dihedral : 21.435 100.534 2158 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.07 % Allowed : 16.28 % Favored : 80.65 % 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: 2.35 (0.34), residues: 592 helix: 2.61 (0.29), residues: 308 sheet: 1.49 (0.53), residues: 79 loop : -0.06 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 72 TYR 0.009 0.001 TYR A 272 PHE 0.015 0.002 PHE A 363 TRP 0.011 0.002 TRP A 449 HIS 0.003 0.001 HIS A 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 ( 7375) covalent geometry : angle 0.56932 / 0.32 (10402) hydrogen bonds : bond 0.05526 / 3.59 ( 383) hydrogen bonds : angle 3.91842 / 2.79 ( 1033) metal coordination : bond 0.00209 / 0.11 ( 4) metal coordination : angle 2.73475 / 1.37 ( 6) Misc. bond : bond 0.00070 / 0.03 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.161 Fit side-chains REVERT: A 61 LYS cc_start: 0.8127 (mtpm) cc_final: 0.7721 (mppt) REVERT: A 208 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7842 (ttpt) REVERT: A 209 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8358 (tppt) REVERT: A 359 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.7891 (tmm) REVERT: A 580 ASP cc_start: 0.8368 (m-30) cc_final: 0.8123 (m-30) outliers start: 16 outliers final: 11 residues processed: 65 average time/residue: 0.7923 time to fit residues: 53.5902 Evaluate side-chains 69 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 597 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: [11, 40, 57, 32, 0, 16, 1, 43, 29, 44, 22] chunk 11 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 HIS A 544 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.131335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.104819 restraints weight = 7105.307| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 0.99 r_work: 0.3055 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7386 Z= 0.194 Angle : 0.608 7.716 10408 Z= 0.340 Chirality : 0.045 0.223 1174 Planarity : 0.005 0.054 973 Dihedral : 21.468 100.662 2158 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.07 % Allowed : 16.48 % Favored : 80.46 % 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: 2.25 (0.34), residues: 592 helix: 2.53 (0.29), residues: 308 sheet: 1.41 (0.53), residues: 79 loop : -0.09 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 72 TYR 0.009 0.001 TYR A 272 PHE 0.016 0.002 PHE A 363 TRP 0.011 0.002 TRP A 449 HIS 0.004 0.001 HIS A 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 ( 7375) covalent geometry : angle 0.60450 / 0.34 (10402) hydrogen bonds : bond 0.05911 / 3.83 ( 383) hydrogen bonds : angle 3.97546 / 2.83 ( 1033) metal coordination : bond 0.00282 / 0.14 ( 4) metal coordination : angle 2.75222 / 1.36 ( 6) Misc. bond : bond 0.00096 / 0.05 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1184 Ramachandran restraints generated. 592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.227 Fit side-chains REVERT: A 61 LYS cc_start: 0.8106 (mtpm) cc_final: 0.7644 (mppt) REVERT: A 208 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7773 (ttpt) REVERT: A 209 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8338 (tppt) REVERT: A 359 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.7896 (tmm) REVERT: A 580 ASP cc_start: 0.8244 (m-30) cc_final: 0.7895 (m-30) outliers start: 16 outliers final: 10 residues processed: 67 average time/residue: 0.7613 time to fit residues: 53.1621 Evaluate side-chains 67 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 597 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: [34, 33, 63, 50, 35, 41, 58, 24, 16, 45, 59] chunk 34 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 HIS A 544 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.130395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.103691 restraints weight = 7080.666| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.03 r_work: 0.3038 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7386 Z= 0.221 Angle : 0.645 7.706 10408 Z= 0.358 Chirality : 0.047 0.239 1174 Planarity : 0.006 0.054 973 Dihedral : 21.538 100.612 2158 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.07 % Allowed : 16.28 % Favored : 80.65 % 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: 2.13 (0.34), residues: 592 helix: 2.41 (0.29), residues: 308 sheet: 1.41 (0.53), residues: 79 loop : -0.13 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 249 TYR 0.009 0.002 TYR A 272 PHE 0.018 0.002 PHE A 363 TRP 0.012 0.003 TRP A 568 HIS 0.004 0.001 HIS A 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.22 ( 7375) covalent geometry : angle 0.64171 / 0.36 (10402) hydrogen bonds : bond 0.06299 / 4.08 ( 383) hydrogen bonds : angle 4.04754 / 2.88 ( 1033) metal coordination : bond 0.00343 / 0.17 ( 4) metal coordination : angle 2.70536 / 1.32 ( 6) Misc. bond : bond 0.00107 / 0.05 ( 7) =============================================================================== Job complete usr+sys time: 2348.42 seconds wall clock time: 40 minutes 48.36 seconds (2448.36 seconds total)