Starting phenix.real_space_refine on Thu Jul 2 12:45:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lj4_63132/07_2026/9lj4_63132.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lj4_63132/07_2026/9lj4_63132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lj4_63132/07_2026/9lj4_63132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lj4_63132/07_2026/9lj4_63132.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lj4_63132/07_2026/9lj4_63132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lj4_63132/07_2026/9lj4_63132.map" } resolution = 3.09 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= 0.001 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 219 5.49 5 Mg 2 5.21 5 S 27 5.16 5 C 4590 2.51 5 N 1610 2.21 5 O 2190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8639 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3984 Classifications: {'peptide': 495} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 473} Chain: "B" Number of atoms: 4061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 4061 Classifications: {'RNA': 190} Modifications used: {'rna2p_pur': 19, 'rna2p_pyr': 13, 'rna3p_pur': 85, 'rna3p_pyr': 73} Link IDs: {'rna2p': 32, 'rna3p': 157} Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 238 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "D" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 353 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1878 SG CYS A 234 11.888 20.626 58.913 1.00349.39 S ATOM 1903 SG CYS A 237 8.675 21.104 56.849 1.00351.09 S ATOM 2131 SG CYS A 265 11.252 18.159 56.216 1.00343.71 S Time building chain proxies: 1.53, per 1000 atoms: 0.18 Number of scatterers: 8639 At special positions: 0 Unit cell: (93.408, 115.092, 128.436, 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 27 16.00 P 219 15.00 Mg 2 11.99 O 2190 8.00 N 1610 7.00 C 4590 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: 0.67 Conformation dependent library (CDL) restraints added in 109.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 268 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 234 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 265 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 237 " Number of angles added : 3 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 924 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 7 sheets defined 32.7% alpha, 14.1% beta 71 base pairs and 128 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 removed outlier: 3.542A pdb=" N ARG A 24 " --> pdb=" O CYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 108 removed outlier: 4.512A pdb=" N LYS A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 121 Processing helix chain 'A' and resid 163 through 184 Processing helix chain 'A' and resid 221 through 230 removed outlier: 3.585A pdb=" N ALA A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 265 through 275 Processing helix chain 'A' and resid 275 through 293 removed outlier: 3.566A pdb=" N GLY A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR A 293 " --> pdb=" O MET A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 314 Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 322 through 334 removed outlier: 3.624A pdb=" N HIS A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 351 removed outlier: 4.288A pdb=" N TYR A 344 " --> pdb=" O TYR A 340 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 414 removed outlier: 3.570A pdb=" N ALA A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 6.582A pdb=" N TYR A 5 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU A 44 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE A 7 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR A 41 " --> pdb=" O VAL A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 208 removed outlier: 7.191A pdb=" N GLN A 207 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL A 189 " --> pdb=" O CYS A 319 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N THR A 321 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU A 191 " --> pdb=" O THR A 321 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU A 57 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N GLU A 192 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE A 59 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 69 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 79 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N TYR A 365 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN A 80 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL A 367 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLN A 82 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLN A 369 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ARG A 84 " --> pdb=" O GLN A 369 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 131 removed outlier: 3.704A pdb=" N LYS A 129 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 246 Processing sheet with id=AA5, first strand: chain 'A' and resid 393 through 396 removed outlier: 6.928A pdb=" N TYR A 387 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 386 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 452 through 454 removed outlier: 6.587A pdb=" N ILE A 444 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 461 through 462 137 hydrogen bonds defined for protein. 387 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 181 hydrogen bonds 330 hydrogen bond angles 0 basepair planarities 71 basepair parallelities 128 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1192 1.33 - 1.45: 3594 1.45 - 1.57: 4007 1.57 - 1.69: 435 1.69 - 1.81: 42 Bond restraints: 9270 Sorted by residual: bond pdb=" C3' DC D 18 " pdb=" C2' DC D 18 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" N3 C B 46 " pdb=" C4 C B 46 " ideal model delta sigma weight residual 1.335 1.314 0.021 7.00e-03 2.04e+04 8.85e+00 bond pdb=" C1' DC D 22 " pdb=" N1 DC D 22 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.43e+00 bond pdb=" C3' DG D 9 " pdb=" C2' DG D 9 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.29e+00 bond pdb=" C3' DA C 28 " pdb=" O3' DA C 28 " ideal model delta sigma weight residual 1.435 1.398 0.037 1.30e-02 5.92e+03 8.25e+00 ... (remaining 9265 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 13436 3.49 - 6.98: 108 6.98 - 10.47: 9 10.47 - 13.96: 3 13.96 - 17.45: 1 Bond angle restraints: 13557 Sorted by residual: angle pdb=" C1' U B 171 " pdb=" N1 U B 171 " pdb=" C2 U B 171 " ideal model delta sigma weight residual 117.70 127.21 -9.51 1.20e+00 6.94e-01 6.28e+01 angle pdb=" N1 C B 46 " pdb=" C2 C B 46 " pdb=" O2 C B 46 " ideal model delta sigma weight residual 118.90 123.18 -4.28 6.00e-01 2.78e+00 5.08e+01 angle pdb=" O2 C B 46 " pdb=" C2 C B 46 " pdb=" N3 C B 46 " ideal model delta sigma weight residual 121.90 116.96 4.94 7.00e-01 2.04e+00 4.98e+01 angle pdb=" C1' U B 190 " pdb=" N1 U B 190 " pdb=" C2 U B 190 " ideal model delta sigma weight residual 117.70 125.54 -7.84 1.20e+00 6.94e-01 4.27e+01 angle pdb=" C1' C B 46 " pdb=" N1 C B 46 " pdb=" C2 C B 46 " ideal model delta sigma weight residual 118.80 125.68 -6.88 1.10e+00 8.26e-01 3.91e+01 ... (remaining 13552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 5019 35.94 - 71.87: 657 71.87 - 107.81: 69 107.81 - 143.75: 3 143.75 - 179.68: 5 Dihedral angle restraints: 5753 sinusoidal: 4315 harmonic: 1438 Sorted by residual: dihedral pdb=" O4' C B 46 " pdb=" C1' C B 46 " pdb=" N1 C B 46 " pdb=" C2 C B 46 " ideal model delta sinusoidal sigma weight residual -160.00 -9.02 -150.98 1 1.50e+01 4.44e-03 8.00e+01 dihedral pdb=" O4' U B 94 " pdb=" C1' U B 94 " pdb=" N1 U B 94 " pdb=" C2 U B 94 " ideal model delta sinusoidal sigma weight residual 232.00 54.16 177.84 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 190 " pdb=" C1' U B 190 " pdb=" N1 U B 190 " pdb=" C2 U B 190 " ideal model delta sinusoidal sigma weight residual 200.00 77.94 122.06 1 1.50e+01 4.44e-03 6.53e+01 ... (remaining 5750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1448 0.063 - 0.125: 174 0.125 - 0.188: 18 0.188 - 0.250: 3 0.250 - 0.313: 2 Chirality restraints: 1645 Sorted by residual: chirality pdb=" C1' G B 33 " pdb=" O4' G B 33 " pdb=" C2' G B 33 " pdb=" N9 G B 33 " both_signs ideal model delta sigma weight residual False 2.44 2.12 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C3' A B 83 " pdb=" C4' A B 83 " pdb=" O3' A B 83 " pdb=" C2' A B 83 " both_signs ideal model delta sigma weight residual False -2.48 -2.21 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C3' U B 29 " pdb=" C4' U B 29 " pdb=" O3' U B 29 " pdb=" C2' U B 29 " both_signs ideal model delta sigma weight residual False -2.48 -2.28 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1642 not shown) Planarity restraints: 926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 38 " -0.050 5.00e-02 4.00e+02 7.63e-02 9.31e+00 pdb=" N PRO A 39 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G B 33 " -0.031 2.00e-02 2.50e+03 1.52e-02 6.94e+00 pdb=" N9 G B 33 " 0.037 2.00e-02 2.50e+03 pdb=" C8 G B 33 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G B 33 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G B 33 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B 33 " -0.012 2.00e-02 2.50e+03 pdb=" O6 G B 33 " 0.003 2.00e-02 2.50e+03 pdb=" N1 G B 33 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G B 33 " -0.007 2.00e-02 2.50e+03 pdb=" N2 G B 33 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G B 33 " 0.014 2.00e-02 2.50e+03 pdb=" C4 G B 33 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 34 " -0.025 2.00e-02 2.50e+03 1.47e-02 6.50e+00 pdb=" N9 G B 34 " 0.020 2.00e-02 2.50e+03 pdb=" C8 G B 34 " -0.016 2.00e-02 2.50e+03 pdb=" N7 G B 34 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G B 34 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B 34 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G B 34 " -0.003 2.00e-02 2.50e+03 pdb=" N1 G B 34 " -0.014 2.00e-02 2.50e+03 pdb=" C2 G B 34 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G B 34 " -0.008 2.00e-02 2.50e+03 pdb=" N3 G B 34 " 0.012 2.00e-02 2.50e+03 pdb=" C4 G B 34 " 0.029 2.00e-02 2.50e+03 ... (remaining 923 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 636 2.71 - 3.26: 8365 3.26 - 3.81: 17880 3.81 - 4.35: 20933 4.35 - 4.90: 28862 Nonbonded interactions: 76676 Sorted by model distance: nonbonded pdb=" N7 G B 48 " pdb="MG MG B 501 " model vdw 2.164 2.250 nonbonded pdb=" CD2 HIS A 273 " pdb="MG MG A 602 " model vdw 2.228 2.390 nonbonded pdb=" CE1 HIS A 245 " pdb="MG MG A 602 " model vdw 2.268 2.390 nonbonded pdb=" N2 G B 133 " pdb=" O2 U B 142 " model vdw 2.329 2.496 nonbonded pdb=" N2 G B 136 " pdb=" O2 U B 140 " model vdw 2.356 2.496 ... (remaining 76671 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: 0.970 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: 0.020 Set scattering table: 0.020 Process input model: 9.250 Find NCS groups from input model: 0.020 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 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 : 0.006 0.041 9274 Z= 0.478 Angle : 0.857 17.446 13560 Z= 0.672 Chirality : 0.044 0.313 1645 Planarity : 0.006 0.076 926 Dihedral : 24.732 179.682 4829 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.75 % Favored : 88.44 % Rotamer: Outliers : 4.90 % Allowed : 31.70 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.64 (0.38), residues: 493 helix: 0.18 (0.38), residues: 167 sheet: -1.30 (0.66), residues: 77 loop : -1.94 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 270 TYR 0.014 0.002 TYR A 327 PHE 0.013 0.002 PHE A 152 TRP 0.007 0.001 TRP A 209 HIS 0.010 0.002 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.48 ( 9270) covalent geometry : angle 0.85469 / 0.67 (13557) hydrogen bonds : bond 0.11730 / 7.49 ( 318) hydrogen bonds : angle 5.81994 / 3.89 ( 717) metal coordination : bond 0.00788 / 0.39 ( 4) metal coordination : angle 4.29995 / 2.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.9103 (ptt90) cc_final: 0.8443 (ppt170) REVERT: A 37 ARG cc_start: 0.9082 (mtm110) cc_final: 0.8606 (tpp80) REVERT: A 146 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8834 (ptp-110) REVERT: A 192 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7839 (tm-30) REVERT: A 278 TRP cc_start: 0.8621 (t-100) cc_final: 0.8209 (t-100) REVERT: A 282 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.8996 (pp) REVERT: A 363 ARG cc_start: 0.6876 (ttt180) cc_final: 0.6624 (ttt-90) REVERT: A 374 ASP cc_start: 0.8977 (t0) cc_final: 0.8657 (t0) REVERT: A 386 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.8118 (mtm-85) REVERT: A 469 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8515 (m-10) outliers start: 21 outliers final: 16 residues processed: 74 average time/residue: 0.1193 time to fit residues: 11.3060 Evaluate side-chains 72 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 405 LYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 469 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 40.0000 chunk 51 optimal weight: 30.0000 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 overall best weight: 5.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 376 GLN A 382 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.075803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.048642 restraints weight = 37973.988| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.05 r_work: 0.2850 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9274 Z= 0.303 Angle : 0.666 8.678 13560 Z= 0.383 Chirality : 0.043 0.290 1645 Planarity : 0.006 0.073 926 Dihedral : 25.089 179.869 3845 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.81 % Allowed : 11.16 % Favored : 88.03 % Rotamer: Outliers : 6.06 % Allowed : 30.77 % Favored : 63.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.42 (0.38), residues: 493 helix: 0.88 (0.39), residues: 160 sheet: -1.54 (0.60), residues: 86 loop : -2.00 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 270 TYR 0.012 0.002 TYR A 327 PHE 0.013 0.002 PHE A 152 TRP 0.008 0.001 TRP A 209 HIS 0.004 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.30 ( 9270) covalent geometry : angle 0.66570 / 0.38 (13557) hydrogen bonds : bond 0.08045 / 5.45 ( 318) hydrogen bonds : angle 4.28037 / 2.79 ( 717) metal coordination : bond 0.01454 / 0.73 ( 4) metal coordination : angle 2.25611 / 1.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 49 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8874 (ptp-110) REVERT: A 209 TRP cc_start: 0.8197 (OUTLIER) cc_final: 0.6879 (m100) REVERT: A 278 TRP cc_start: 0.8596 (t-100) cc_final: 0.8143 (t-100) REVERT: A 282 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8964 (pp) REVERT: A 363 ARG cc_start: 0.7039 (ttt180) cc_final: 0.6551 (ttt-90) REVERT: A 374 ASP cc_start: 0.9052 (t0) cc_final: 0.8816 (t0) REVERT: A 469 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8642 (m-10) outliers start: 26 outliers final: 16 residues processed: 70 average time/residue: 0.1260 time to fit residues: 11.2154 Evaluate side-chains 70 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 209 TRP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 405 LYS Chi-restraints excluded: chain A residue 469 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 61 optimal weight: 30.0000 chunk 53 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 39 optimal weight: 0.0020 chunk 4 optimal weight: 9.9990 chunk 55 optimal weight: 30.0000 chunk 52 optimal weight: 20.0000 overall best weight: 6.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.074753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.047933 restraints weight = 38050.614| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.04 r_work: 0.2846 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9274 Z= 0.324 Angle : 0.660 8.105 13560 Z= 0.382 Chirality : 0.043 0.289 1645 Planarity : 0.006 0.069 926 Dihedral : 25.163 178.500 3835 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.81 % Allowed : 11.97 % Favored : 87.22 % Rotamer: Outliers : 8.86 % Allowed : 27.97 % Favored : 63.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.47 (0.38), residues: 493 helix: 0.93 (0.38), residues: 158 sheet: -1.57 (0.60), residues: 87 loop : -2.07 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 270 TYR 0.012 0.002 TYR A 327 PHE 0.017 0.002 PHE A 40 TRP 0.009 0.002 TRP A 209 HIS 0.005 0.002 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.32 ( 9270) covalent geometry : angle 0.65869 / 0.38 (13557) hydrogen bonds : bond 0.08048 / 5.45 ( 318) hydrogen bonds : angle 4.31913 / 2.81 ( 717) metal coordination : bond 0.02102 / 1.06 ( 4) metal coordination : angle 2.55267 / 1.35 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 53 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.9072 (mtm110) cc_final: 0.8558 (tpp80) REVERT: A 209 TRP cc_start: 0.8220 (OUTLIER) cc_final: 0.6805 (m100) REVERT: A 278 TRP cc_start: 0.8558 (t-100) cc_final: 0.8095 (t-100) REVERT: A 282 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.8955 (pp) REVERT: A 289 MET cc_start: 0.9089 (tpt) cc_final: 0.8832 (tpt) REVERT: A 363 ARG cc_start: 0.7029 (ttt180) cc_final: 0.6545 (ttt-90) REVERT: A 374 ASP cc_start: 0.9056 (t0) cc_final: 0.8819 (t0) REVERT: A 386 ARG cc_start: 0.8540 (mtm-85) cc_final: 0.8188 (mtm-85) REVERT: A 469 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8649 (m-10) outliers start: 38 outliers final: 28 residues processed: 84 average time/residue: 0.1154 time to fit residues: 12.4687 Evaluate side-chains 81 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 50 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 209 TRP Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 405 LYS Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 491 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 29 optimal weight: 8.9990 chunk 69 optimal weight: 50.0000 chunk 23 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 13 optimal weight: 0.4980 chunk 68 optimal weight: 30.0000 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.075146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.048306 restraints weight = 38822.766| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.97 r_work: 0.2856 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9274 Z= 0.270 Angle : 0.627 8.080 13560 Z= 0.363 Chirality : 0.041 0.285 1645 Planarity : 0.005 0.065 926 Dihedral : 25.181 178.763 3831 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.81 % Allowed : 11.16 % Favored : 88.03 % Rotamer: Outliers : 9.09 % Allowed : 27.97 % Favored : 62.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.38), residues: 493 helix: 1.06 (0.39), residues: 158 sheet: -1.58 (0.60), residues: 87 loop : -2.07 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 270 TYR 0.012 0.002 TYR A 340 PHE 0.017 0.002 PHE A 40 TRP 0.010 0.001 TRP A 209 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.27 ( 9270) covalent geometry : angle 0.62686 / 0.36 (13557) hydrogen bonds : bond 0.07415 / 5.02 ( 318) hydrogen bonds : angle 4.20730 / 2.76 ( 717) metal coordination : bond 0.01686 / 0.85 ( 4) metal coordination : angle 1.75930 / 0.95 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 51 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.9084 (mtm110) cc_final: 0.8547 (tpp80) REVERT: A 203 ASN cc_start: 0.8328 (t0) cc_final: 0.7973 (t0) REVERT: A 208 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8333 (ttp-170) REVERT: A 209 TRP cc_start: 0.8247 (OUTLIER) cc_final: 0.6627 (m100) REVERT: A 261 ARG cc_start: 0.8054 (ttm-80) cc_final: 0.7612 (mtm-85) REVERT: A 278 TRP cc_start: 0.8557 (t-100) cc_final: 0.8088 (t-100) REVERT: A 282 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.8913 (pp) REVERT: A 363 ARG cc_start: 0.7054 (ttt180) cc_final: 0.6796 (ttt-90) REVERT: A 374 ASP cc_start: 0.9041 (t0) cc_final: 0.8797 (t0) REVERT: A 386 ARG cc_start: 0.8540 (mtm-85) cc_final: 0.8264 (mtm-85) REVERT: A 469 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8677 (m-10) outliers start: 39 outliers final: 25 residues processed: 85 average time/residue: 0.1093 time to fit residues: 12.0992 Evaluate side-chains 80 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 51 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 209 TRP Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 405 LYS Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 469 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 4 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 24 optimal weight: 30.0000 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.074572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.047770 restraints weight = 38360.203| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.99 r_work: 0.2839 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9274 Z= 0.326 Angle : 0.661 8.313 13560 Z= 0.382 Chirality : 0.043 0.284 1645 Planarity : 0.006 0.066 926 Dihedral : 25.206 178.600 3829 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.81 % Allowed : 12.78 % Favored : 86.41 % Rotamer: Outliers : 8.86 % Allowed : 28.67 % Favored : 62.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.53 (0.38), residues: 493 helix: 0.86 (0.38), residues: 158 sheet: -1.60 (0.60), residues: 86 loop : -2.11 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 270 TYR 0.012 0.002 TYR A 340 PHE 0.014 0.002 PHE A 40 TRP 0.011 0.002 TRP A 209 HIS 0.008 0.002 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.33 ( 9270) covalent geometry : angle 0.66060 / 0.38 (13557) hydrogen bonds : bond 0.08080 / 5.48 ( 318) hydrogen bonds : angle 4.32496 / 2.83 ( 717) metal coordination : bond 0.02486 / 1.25 ( 4) metal coordination : angle 2.03655 / 1.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 51 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.5405 (mtt180) REVERT: A 203 ASN cc_start: 0.8297 (t0) cc_final: 0.8013 (t0) REVERT: A 208 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8235 (ttp-110) REVERT: A 209 TRP cc_start: 0.8251 (OUTLIER) cc_final: 0.6572 (m100) REVERT: A 261 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7514 (mtm-85) REVERT: A 278 TRP cc_start: 0.8547 (t-100) cc_final: 0.8133 (t-100) REVERT: A 279 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8908 (mt-10) REVERT: A 282 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.8927 (pp) REVERT: A 386 ARG cc_start: 0.8575 (mtm-85) cc_final: 0.8371 (mtm-85) REVERT: A 469 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.8646 (m-10) outliers start: 38 outliers final: 28 residues processed: 84 average time/residue: 0.1169 time to fit residues: 12.6429 Evaluate side-chains 85 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 51 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 209 TRP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 268 HIS Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 405 LYS Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 469 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 32 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 68 optimal weight: 30.0000 chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.075926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.049313 restraints weight = 37686.626| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.78 r_work: 0.2887 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9274 Z= 0.189 Angle : 0.595 10.553 13560 Z= 0.342 Chirality : 0.038 0.275 1645 Planarity : 0.005 0.060 926 Dihedral : 25.155 178.975 3829 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.14 % Favored : 89.05 % Rotamer: Outliers : 7.93 % Allowed : 29.84 % Favored : 62.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.26 (0.39), residues: 493 helix: 1.20 (0.40), residues: 159 sheet: -1.49 (0.60), residues: 87 loop : -2.02 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 270 TYR 0.013 0.002 TYR A 340 PHE 0.012 0.001 PHE A 40 TRP 0.010 0.002 TRP A 209 HIS 0.006 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.19 ( 9270) covalent geometry : angle 0.59471 / 0.34 (13557) hydrogen bonds : bond 0.06397 / 4.32 ( 318) hydrogen bonds : angle 4.05892 / 2.66 ( 717) metal coordination : bond 0.00951 / 0.48 ( 4) metal coordination : angle 1.36261 / 0.72 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 52 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.5401 (mtt180) REVERT: A 203 ASN cc_start: 0.8288 (t0) cc_final: 0.8007 (t0) REVERT: A 208 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8426 (ttp-170) REVERT: A 209 TRP cc_start: 0.8238 (OUTLIER) cc_final: 0.7634 (m100) REVERT: A 261 ARG cc_start: 0.7988 (ttm-80) cc_final: 0.7521 (mtm-85) REVERT: A 278 TRP cc_start: 0.8540 (t-100) cc_final: 0.8105 (t-100) REVERT: A 279 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8925 (mt-10) REVERT: A 282 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.8930 (pp) REVERT: A 386 ARG cc_start: 0.8566 (mtm-85) cc_final: 0.8257 (mtm-85) REVERT: A 469 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.8605 (m-10) outliers start: 34 outliers final: 24 residues processed: 81 average time/residue: 0.1246 time to fit residues: 13.0247 Evaluate side-chains 81 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 51 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 209 TRP Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 469 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 30 optimal weight: 0.5980 chunk 49 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 376 GLN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.077252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.050477 restraints weight = 38546.271| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.90 r_work: 0.2931 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9274 Z= 0.168 Angle : 0.576 10.948 13560 Z= 0.331 Chirality : 0.037 0.261 1645 Planarity : 0.005 0.057 926 Dihedral : 25.011 179.758 3824 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.34 % Favored : 88.84 % Rotamer: Outliers : 6.99 % Allowed : 30.77 % Favored : 62.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.13 (0.39), residues: 493 helix: 1.30 (0.40), residues: 159 sheet: -1.32 (0.61), residues: 86 loop : -1.98 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 33 TYR 0.013 0.001 TYR A 340 PHE 0.010 0.002 PHE A 236 TRP 0.007 0.001 TRP A 209 HIS 0.002 0.001 HIS A 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.17 ( 9270) covalent geometry : angle 0.57544 / 0.33 (13557) hydrogen bonds : bond 0.06130 / 4.15 ( 318) hydrogen bonds : angle 3.92182 / 2.57 ( 717) metal coordination : bond 0.01118 / 0.54 ( 4) metal coordination : angle 1.37327 / 0.77 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 53 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.9118 (mtm110) cc_final: 0.8526 (tpp80) REVERT: A 151 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.5345 (mtt180) REVERT: A 203 ASN cc_start: 0.8288 (t0) cc_final: 0.7902 (t0) REVERT: A 208 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8390 (ptm160) REVERT: A 209 TRP cc_start: 0.8265 (OUTLIER) cc_final: 0.7606 (m100) REVERT: A 261 ARG cc_start: 0.7993 (ttm-80) cc_final: 0.7491 (mtm-85) REVERT: A 278 TRP cc_start: 0.8509 (t-100) cc_final: 0.8064 (t-100) REVERT: A 279 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8904 (mt-10) REVERT: A 282 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.8908 (pp) REVERT: A 386 ARG cc_start: 0.8552 (mtm-85) cc_final: 0.8333 (mtm-85) REVERT: A 469 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8536 (m-10) outliers start: 30 outliers final: 22 residues processed: 78 average time/residue: 0.1154 time to fit residues: 11.7026 Evaluate side-chains 81 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 53 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 209 TRP Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 469 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 12 optimal weight: 4.9990 chunk 59 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 0.0070 chunk 9 optimal weight: 0.8980 chunk 55 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 overall best weight: 2.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.077371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.050944 restraints weight = 38336.769| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.77 r_work: 0.2903 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 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 : 0.003 0.034 9274 Z= 0.174 Angle : 0.592 11.734 13560 Z= 0.335 Chirality : 0.037 0.258 1645 Planarity : 0.005 0.056 926 Dihedral : 24.954 179.983 3820 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.81 % Allowed : 9.94 % Favored : 89.25 % Rotamer: Outliers : 7.46 % Allowed : 31.70 % Favored : 60.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.39), residues: 493 helix: 1.42 (0.40), residues: 158 sheet: -1.26 (0.62), residues: 86 loop : -2.03 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 270 TYR 0.013 0.001 TYR A 340 PHE 0.010 0.001 PHE A 152 TRP 0.008 0.001 TRP A 209 HIS 0.003 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.17 ( 9270) covalent geometry : angle 0.59157 / 0.34 (13557) hydrogen bonds : bond 0.06089 / 4.12 ( 318) hydrogen bonds : angle 3.91439 / 2.57 ( 717) metal coordination : bond 0.01795 / 0.90 ( 4) metal coordination : angle 2.20730 / 1.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 54 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.9091 (mtm110) cc_final: 0.8517 (tpp80) REVERT: A 151 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.5368 (mtt180) REVERT: A 203 ASN cc_start: 0.8326 (t0) cc_final: 0.8057 (t0) REVERT: A 209 TRP cc_start: 0.8284 (OUTLIER) cc_final: 0.7760 (m100) REVERT: A 261 ARG cc_start: 0.8018 (ttm-80) cc_final: 0.7510 (mtm-85) REVERT: A 279 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8942 (mt-10) REVERT: A 282 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.8964 (pp) REVERT: A 386 ARG cc_start: 0.8551 (mtm-85) cc_final: 0.8323 (mtm-85) REVERT: A 469 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8669 (m-10) outliers start: 32 outliers final: 24 residues processed: 82 average time/residue: 0.1181 time to fit residues: 12.6282 Evaluate side-chains 82 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 53 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 209 TRP Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 469 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 13 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.077194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.050540 restraints weight = 38190.984| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.90 r_work: 0.2899 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9274 Z= 0.187 Angle : 0.591 12.866 13560 Z= 0.337 Chirality : 0.037 0.257 1645 Planarity : 0.005 0.056 926 Dihedral : 24.931 179.924 3820 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.81 % Allowed : 9.94 % Favored : 89.25 % Rotamer: Outliers : 6.76 % Allowed : 31.93 % Favored : 61.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.10 (0.39), residues: 493 helix: 1.40 (0.40), residues: 158 sheet: -1.23 (0.62), residues: 86 loop : -2.03 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 270 TYR 0.012 0.001 TYR A 340 PHE 0.010 0.001 PHE A 152 TRP 0.009 0.002 TRP A 278 HIS 0.003 0.001 HIS A 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.19 ( 9270) covalent geometry : angle 0.59064 / 0.34 (13557) hydrogen bonds : bond 0.06139 / 4.16 ( 318) hydrogen bonds : angle 3.95259 / 2.59 ( 717) metal coordination : bond 0.01767 / 0.88 ( 4) metal coordination : angle 1.66761 / 0.85 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 53 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.9082 (mtm110) cc_final: 0.8515 (tpp80) REVERT: A 151 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.5380 (mtt180) REVERT: A 203 ASN cc_start: 0.8248 (t0) cc_final: 0.8047 (t0) REVERT: A 209 TRP cc_start: 0.8292 (OUTLIER) cc_final: 0.7773 (m100) REVERT: A 261 ARG cc_start: 0.7975 (ttm-80) cc_final: 0.7448 (mtm-85) REVERT: A 278 TRP cc_start: 0.8263 (t-100) cc_final: 0.7920 (t-100) REVERT: A 279 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8838 (mt-10) REVERT: A 386 ARG cc_start: 0.8547 (mtm-85) cc_final: 0.8315 (mtm-85) REVERT: A 469 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8617 (m-10) outliers start: 29 outliers final: 25 residues processed: 79 average time/residue: 0.1106 time to fit residues: 11.4859 Evaluate side-chains 82 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 53 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 209 TRP Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 469 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 44 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.076579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.049958 restraints weight = 38368.099| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.80 r_work: 0.2911 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9274 Z= 0.179 Angle : 0.598 13.378 13560 Z= 0.338 Chirality : 0.037 0.255 1645 Planarity : 0.005 0.055 926 Dihedral : 24.927 179.863 3819 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.14 % Favored : 89.05 % Rotamer: Outliers : 6.99 % Allowed : 31.93 % Favored : 61.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.08 (0.39), residues: 493 helix: 1.43 (0.41), residues: 158 sheet: -1.22 (0.62), residues: 86 loop : -2.03 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 270 TYR 0.013 0.001 TYR A 340 PHE 0.010 0.001 PHE A 152 TRP 0.008 0.002 TRP A 209 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.18 ( 9270) covalent geometry : angle 0.59721 / 0.34 (13557) hydrogen bonds : bond 0.06031 / 4.08 ( 318) hydrogen bonds : angle 3.92303 / 2.57 ( 717) metal coordination : bond 0.02052 / 1.03 ( 4) metal coordination : angle 1.79968 / 0.91 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 53 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.9081 (mtm110) cc_final: 0.8512 (tpp80) REVERT: A 151 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.5372 (mtt180) REVERT: A 203 ASN cc_start: 0.8281 (t0) cc_final: 0.8071 (t0) REVERT: A 261 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7436 (mtm-85) REVERT: A 278 TRP cc_start: 0.8331 (t-100) cc_final: 0.7991 (t-100) REVERT: A 279 GLU cc_start: 0.9133 (OUTLIER) cc_final: 0.8856 (mt-10) REVERT: A 386 ARG cc_start: 0.8541 (mtm-85) cc_final: 0.8310 (mtm-85) REVERT: A 469 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.8624 (m-10) outliers start: 30 outliers final: 25 residues processed: 80 average time/residue: 0.1263 time to fit residues: 13.1793 Evaluate side-chains 82 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 54 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 469 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 30.0000 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 51 optimal weight: 30.0000 chunk 33 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 55 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 overall best weight: 4.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 376 GLN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.075787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.049173 restraints weight = 38805.859| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.89 r_work: 0.2882 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9274 Z= 0.256 Angle : 0.623 12.985 13560 Z= 0.355 Chirality : 0.040 0.258 1645 Planarity : 0.005 0.057 926 Dihedral : 24.939 179.949 3819 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.81 % Allowed : 11.36 % Favored : 87.83 % Rotamer: Outliers : 6.76 % Allowed : 32.40 % Favored : 60.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.39), residues: 493 helix: 1.29 (0.40), residues: 158 sheet: -1.26 (0.62), residues: 86 loop : -2.07 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 33 TYR 0.013 0.002 TYR A 388 PHE 0.011 0.001 PHE A 152 TRP 0.006 0.001 TRP A 278 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.26 ( 9270) covalent geometry : angle 0.62225 / 0.35 (13557) hydrogen bonds : bond 0.06662 / 4.52 ( 318) hydrogen bonds : angle 4.05597 / 2.66 ( 717) metal coordination : bond 0.02698 / 1.35 ( 4) metal coordination : angle 2.26706 / 1.16 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2604.59 seconds wall clock time: 45 minutes 10.45 seconds (2710.45 seconds total)