Starting phenix.real_space_refine on Wed Aug 5 05:31:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lj4_63132/08_2026/9lj4_63132.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lj4_63132/08_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_63132/08_2026/9lj4_63132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lj4_63132/08_2026/9lj4_63132.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lj4_63132/08_2026/9lj4_63132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lj4_63132/08_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-2.2rc3-6140/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: 1.46, per 1000 atoms: 0.17 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: 0.63 Conformation dependent library (CDL) restraints added in 97.3 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: 1.11 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: 1.69 Time building geometry restraints manager: 0.81 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: 13430 3.49 - 6.98: 114 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=" O4' G B 33 " pdb=" C1' G B 33 " pdb=" N9 G B 33 " ideal model delta sigma weight residual 108.20 114.12 -5.92 8.00e-01 1.56e+00 5.48e+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 ... (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 - 0.062: 1247 0.062 - 0.124: 274 0.124 - 0.187: 118 0.187 - 0.249: 4 0.249 - 0.311: 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 2.42e+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: 1.490 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: 0.180 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.480 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.260 ------------------------------------------------------------------------------- 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= 0.504 Angle : 0.977 17.446 13560 Z= 0.771 Chirality : 0.060 0.311 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 0.00572 / 0.50 ( 9270) covalent geometry : angle 0.97518 / 0.77 (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 : 0.180 Fit side-chains revert: symmetry clash 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 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: 0.0972 time to fit residues: 9.3027 Evaluate side-chains 71 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.137 ------------------------------------------------------------------------------- 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 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: 30.0000 chunk 62 optimal weight: 50.0000 chunk 51 optimal weight: 40.0000 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 30.0000 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 382 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.075944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.048859 restraints weight = 37925.402| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.85 r_work: 0.2854 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.0748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9274 Z= 0.285 Angle : 0.703 8.329 13560 Z= 0.389 Chirality : 0.045 0.281 1645 Planarity : 0.006 0.073 926 Dihedral : 24.988 179.669 3841 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.81 % Allowed : 11.16 % Favored : 88.03 % Rotamer: Outliers : 5.83 % Allowed : 30.54 % Favored : 63.64 % 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: -1.51 (0.38), residues: 493 helix: 0.71 (0.39), residues: 166 sheet: -1.59 (0.60), residues: 87 loop : -2.04 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 270 TYR 0.012 0.002 TYR A 327 PHE 0.014 0.002 PHE A 329 TRP 0.007 0.001 TRP A 209 HIS 0.004 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.29 ( 9270) covalent geometry : angle 0.70232 / 0.39 (13557) hydrogen bonds : bond 0.08071 / 5.43 ( 318) hydrogen bonds : angle 4.31021 / 2.81 ( 717) metal coordination : bond 0.01358 / 0.68 ( 4) metal coordination : angle 2.23583 / 1.21 ( 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: 25 poor density : 50 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7873 (tm-30) REVERT: A 209 TRP cc_start: 0.8193 (OUTLIER) cc_final: 0.6880 (m100) REVERT: A 278 TRP cc_start: 0.8607 (t-100) cc_final: 0.8162 (t-100) REVERT: A 282 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.8962 (pp) REVERT: A 363 ARG cc_start: 0.7008 (ttt180) cc_final: 0.6508 (ttt-90) REVERT: A 374 ASP cc_start: 0.9052 (t0) cc_final: 0.8812 (t0) REVERT: A 386 ARG cc_start: 0.8573 (mtm-85) cc_final: 0.8256 (mtm-85) REVERT: A 469 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8636 (m-10) outliers start: 25 outliers final: 17 residues processed: 70 average time/residue: 0.0981 time to fit residues: 8.8392 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 : 0.212 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 491 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 61 optimal weight: 40.0000 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: 4.9990 chunk 21 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 4 optimal weight: 9.9990 chunk 55 optimal weight: 40.0000 chunk 52 optimal weight: 20.0000 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 376 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.075306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.048679 restraints weight = 37703.890| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.76 r_work: 0.2871 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9274 Z= 0.256 Angle : 0.665 7.847 13560 Z= 0.369 Chirality : 0.043 0.256 1645 Planarity : 0.005 0.067 926 Dihedral : 25.022 178.481 3831 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.81 % Allowed : 11.16 % Favored : 88.03 % Rotamer: Outliers : 7.69 % Allowed : 29.14 % 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: -1.34 (0.38), residues: 493 helix: 1.10 (0.39), residues: 158 sheet: -1.55 (0.60), residues: 87 loop : -2.03 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 270 TYR 0.012 0.002 TYR A 340 PHE 0.017 0.002 PHE A 40 TRP 0.009 0.001 TRP A 209 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.26 ( 9270) covalent geometry : angle 0.66415 / 0.37 (13557) hydrogen bonds : bond 0.07585 / 5.12 ( 318) hydrogen bonds : angle 4.21223 / 2.75 ( 717) metal coordination : bond 0.01711 / 0.86 ( 4) metal coordination : angle 2.20264 / 1.17 ( 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 85 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 52 time to evaluate : 0.124 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 209 TRP cc_start: 0.8252 (OUTLIER) cc_final: 0.6575 (m100) REVERT: A 278 TRP cc_start: 0.8590 (t-100) cc_final: 0.8116 (t-100) REVERT: A 282 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.8949 (pp) REVERT: A 363 ARG cc_start: 0.6954 (ttt180) cc_final: 0.6482 (ttt-90) REVERT: A 374 ASP cc_start: 0.9027 (t0) cc_final: 0.8759 (t0) REVERT: A 386 ARG cc_start: 0.8596 (mtm-85) cc_final: 0.8346 (mtm-85) REVERT: A 469 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8646 (m-10) outliers start: 33 outliers final: 23 residues processed: 81 average time/residue: 0.0912 time to fit residues: 9.6256 Evaluate side-chains 76 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 29 optimal weight: 10.0000 chunk 69 optimal weight: 50.0000 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 68 optimal weight: 30.0000 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 overall best weight: 6.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.074624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.047870 restraints weight = 38853.131| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.87 r_work: 0.2845 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9274 Z= 0.312 Angle : 0.714 8.067 13560 Z= 0.392 Chirality : 0.046 0.263 1645 Planarity : 0.006 0.067 926 Dihedral : 25.091 178.415 3831 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.81 % Allowed : 11.76 % Favored : 87.42 % Rotamer: Outliers : 7.93 % Allowed : 29.60 % 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: -1.50 (0.38), residues: 493 helix: 0.89 (0.38), residues: 158 sheet: -1.52 (0.61), residues: 86 loop : -2.11 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 131 TYR 0.012 0.002 TYR A 327 PHE 0.016 0.002 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 0.00560 / 0.31 ( 9270) covalent geometry : angle 0.71346 / 0.39 (13557) hydrogen bonds : bond 0.08259 / 5.59 ( 318) hydrogen bonds : angle 4.29666 / 2.80 ( 717) metal coordination : bond 0.02321 / 1.16 ( 4) metal coordination : angle 1.74581 / 0.96 ( 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 86 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 52 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ASN cc_start: 0.8317 (t0) cc_final: 0.7965 (t0) REVERT: A 208 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8325 (ttp-110) REVERT: A 209 TRP cc_start: 0.8268 (OUTLIER) cc_final: 0.6659 (m100) REVERT: A 282 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.8951 (pp) REVERT: A 386 ARG cc_start: 0.8615 (mtm-85) cc_final: 0.8368 (mtm-85) REVERT: A 469 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8671 (m-10) outliers start: 34 outliers final: 23 residues processed: 82 average time/residue: 0.0971 time to fit residues: 10.3285 Evaluate side-chains 77 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 50 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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 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 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 405 LYS 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: 9.9990 chunk 56 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 24 optimal weight: 30.0000 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.075278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.048540 restraints weight = 38166.015| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.79 r_work: 0.2866 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9274 Z= 0.239 Angle : 0.656 9.277 13560 Z= 0.364 Chirality : 0.042 0.247 1645 Planarity : 0.005 0.063 926 Dihedral : 25.077 178.235 3829 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.75 % Favored : 88.44 % Rotamer: Outliers : 8.39 % Allowed : 29.14 % 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: -1.41 (0.38), residues: 493 helix: 1.02 (0.38), residues: 159 sheet: -1.54 (0.59), residues: 87 loop : -2.08 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 131 TYR 0.012 0.002 TYR A 340 PHE 0.012 0.002 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 0.00430 / 0.24 ( 9270) covalent geometry : angle 0.65524 / 0.36 (13557) hydrogen bonds : bond 0.07240 / 4.88 ( 318) hydrogen bonds : angle 4.18040 / 2.73 ( 717) metal coordination : bond 0.01901 / 0.95 ( 4) metal coordination : angle 1.54437 / 0.83 ( 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 88 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 52 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.5398 (mtt180) REVERT: A 203 ASN cc_start: 0.8231 (t0) cc_final: 0.7922 (t0) REVERT: A 208 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8330 (ttp-170) REVERT: A 209 TRP cc_start: 0.8261 (OUTLIER) cc_final: 0.6584 (m100) REVERT: A 261 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7483 (mtm-85) REVERT: A 278 TRP cc_start: 0.8251 (t-100) cc_final: 0.7896 (t-100) REVERT: A 279 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8910 (mt-10) REVERT: A 282 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.8932 (pp) REVERT: A 386 ARG cc_start: 0.8625 (mtm-85) cc_final: 0.8356 (mtm-85) REVERT: A 469 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8643 (m-10) outliers start: 36 outliers final: 23 residues processed: 82 average time/residue: 0.1002 time to fit residues: 10.5786 Evaluate side-chains 81 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 52 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 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 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 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 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 445 LEU 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: 6.9990 chunk 40 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 68 optimal weight: 30.0000 chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 59 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.075369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.048668 restraints weight = 38186.775| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.82 r_work: 0.2869 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9274 Z= 0.235 Angle : 0.647 10.263 13560 Z= 0.360 Chirality : 0.041 0.245 1645 Planarity : 0.005 0.061 926 Dihedral : 25.011 178.567 3828 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.81 % Allowed : 11.76 % Favored : 87.42 % Rotamer: Outliers : 7.46 % Allowed : 30.30 % 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: -1.33 (0.38), residues: 493 helix: 1.07 (0.39), residues: 159 sheet: -1.44 (0.60), residues: 86 loop : -2.05 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 33 TYR 0.012 0.002 TYR A 340 PHE 0.010 0.002 PHE A 152 TRP 0.011 0.002 TRP A 209 HIS 0.004 0.001 HIS A 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.24 ( 9270) covalent geometry : angle 0.64647 / 0.36 (13557) hydrogen bonds : bond 0.07161 / 4.83 ( 318) hydrogen bonds : angle 4.10470 / 2.67 ( 717) metal coordination : bond 0.02404 / 1.20 ( 4) metal coordination : angle 1.88443 / 0.97 ( 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: 32 poor density : 54 time to evaluate : 0.188 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 15 MET cc_start: 0.8554 (mpp) cc_final: 0.8318 (mpp) REVERT: A 151 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.5390 (mtt180) REVERT: A 203 ASN cc_start: 0.8259 (t0) cc_final: 0.7982 (t0) REVERT: A 208 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8362 (ttp-110) REVERT: A 209 TRP cc_start: 0.8229 (OUTLIER) cc_final: 0.6472 (m100) REVERT: A 261 ARG cc_start: 0.7928 (ttm-80) cc_final: 0.7428 (mtm-85) REVERT: A 278 TRP cc_start: 0.8260 (t-100) cc_final: 0.7922 (t-100) REVERT: A 279 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8903 (mt-10) REVERT: A 282 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.8950 (pp) REVERT: A 386 ARG cc_start: 0.8624 (mtm-85) cc_final: 0.8354 (mtm-85) REVERT: A 469 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8670 (m-10) outliers start: 32 outliers final: 24 residues processed: 82 average time/residue: 0.0946 time to fit residues: 9.9728 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 : 0.124 ------------------------------------------------------------------------------- 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 132 LEU 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 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 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 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 331 GLU Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 437 SER 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: 3.9990 chunk 49 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 37 optimal weight: 0.2980 chunk 24 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.075912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.049447 restraints weight = 37311.680| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.76 r_work: 0.2897 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9274 Z= 0.188 Angle : 0.619 10.608 13560 Z= 0.344 Chirality : 0.039 0.230 1645 Planarity : 0.005 0.058 926 Dihedral : 24.941 179.187 3824 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.55 % Favored : 88.64 % Rotamer: Outliers : 7.93 % Allowed : 30.30 % Favored : 61.77 % 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: 1.24 (0.39), residues: 159 sheet: -1.37 (0.60), residues: 86 loop : -2.01 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 270 TYR 0.014 0.002 TYR A 340 PHE 0.010 0.001 PHE A 152 TRP 0.007 0.001 TRP A 209 HIS 0.004 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.19 ( 9270) covalent geometry : angle 0.61799 / 0.34 (13557) hydrogen bonds : bond 0.06539 / 4.41 ( 318) hydrogen bonds : angle 3.97583 / 2.60 ( 717) metal coordination : bond 0.02019 / 1.01 ( 4) metal coordination : angle 2.45451 / 1.27 ( 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 87 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 53 time to evaluate : 0.213 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: 0.8409 (OUTLIER) cc_final: 0.5328 (mtt180) REVERT: A 203 ASN cc_start: 0.8273 (t0) cc_final: 0.8015 (t0) REVERT: A 208 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8385 (ttp-170) REVERT: A 209 TRP cc_start: 0.8194 (OUTLIER) cc_final: 0.7437 (m100) REVERT: A 261 ARG cc_start: 0.7991 (ttm-80) cc_final: 0.7491 (mtm-85) REVERT: A 278 TRP cc_start: 0.8294 (t-100) cc_final: 0.7960 (t-100) REVERT: A 279 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8906 (mt-10) REVERT: A 282 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.8922 (pp) REVERT: A 469 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8623 (m-10) outliers start: 34 outliers final: 25 residues processed: 83 average time/residue: 0.1011 time to fit residues: 10.9056 Evaluate side-chains 83 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 52 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 17 THR 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 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 208 ARG Chi-restraints excluded: chain A residue 209 TRP Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 237 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 331 GLU Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 405 LYS 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: 1.9990 chunk 59 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 55 optimal weight: 30.0000 chunk 19 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.076810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.050041 restraints weight = 36383.128| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.77 r_work: 0.2892 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9274 Z= 0.196 Angle : 0.613 11.219 13560 Z= 0.343 Chirality : 0.039 0.231 1645 Planarity : 0.006 0.072 926 Dihedral : 24.864 179.519 3824 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.81 % Allowed : 11.36 % Favored : 87.83 % Rotamer: Outliers : 8.39 % Allowed : 31.00 % Favored : 60.61 % 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: 1.21 (0.39), residues: 159 sheet: -1.31 (0.61), residues: 86 loop : -2.00 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG A 270 TYR 0.014 0.001 TYR A 340 PHE 0.010 0.001 PHE A 152 TRP 0.009 0.002 TRP A 209 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.20 ( 9270) covalent geometry : angle 0.61227 / 0.34 (13557) hydrogen bonds : bond 0.06641 / 4.49 ( 318) hydrogen bonds : angle 3.93466 / 2.57 ( 717) metal coordination : bond 0.01575 / 0.79 ( 4) metal coordination : angle 1.90331 / 0.96 ( 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 89 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 53 time to evaluate : 0.161 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: 0.8416 (OUTLIER) cc_final: 0.5341 (mtt180) REVERT: A 203 ASN cc_start: 0.8288 (t0) cc_final: 0.7920 (t0) REVERT: A 208 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8320 (ttp-170) REVERT: A 209 TRP cc_start: 0.8212 (OUTLIER) cc_final: 0.7614 (m100) REVERT: A 261 ARG cc_start: 0.7992 (ttm-80) cc_final: 0.7473 (mtm-85) REVERT: A 278 TRP cc_start: 0.8285 (t-100) cc_final: 0.7983 (t-100) REVERT: A 279 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8838 (mt-10) REVERT: A 469 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8718 (m-10) outliers start: 36 outliers final: 27 residues processed: 86 average time/residue: 0.1011 time to fit residues: 11.2337 Evaluate side-chains 84 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 52 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 17 THR 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 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 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 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 331 GLU Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 359 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 30.0000 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.0570 chunk 61 optimal weight: 40.0000 chunk 13 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 overall best weight: 1.7904 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.078185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.051887 restraints weight = 37049.782| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.73 r_work: 0.2966 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9274 Z= 0.136 Angle : 0.592 12.830 13560 Z= 0.330 Chirality : 0.036 0.216 1645 Planarity : 0.005 0.055 926 Dihedral : 24.763 179.871 3824 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.53 % Favored : 89.86 % Rotamer: Outliers : 6.29 % Allowed : 33.33 % Favored : 60.37 % 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: -0.98 (0.39), residues: 493 helix: 1.46 (0.40), residues: 158 sheet: -1.13 (0.62), residues: 86 loop : -1.95 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 270 TYR 0.014 0.001 TYR A 340 PHE 0.010 0.002 PHE A 152 TRP 0.007 0.001 TRP A 209 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.14 ( 9270) covalent geometry : angle 0.59205 / 0.33 (13557) hydrogen bonds : bond 0.05892 / 3.98 ( 318) hydrogen bonds : angle 3.81335 / 2.50 ( 717) metal coordination : bond 0.00918 / 0.46 ( 4) metal coordination : angle 1.15283 / 0.58 ( 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 83 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 56 time to evaluate : 0.177 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: symmetry clash REVERT: A 151 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.5198 (mtt180) REVERT: A 199 MET cc_start: 0.8958 (ppp) cc_final: 0.8473 (ppp) REVERT: A 203 ASN cc_start: 0.8342 (t0) cc_final: 0.8073 (t0) REVERT: A 261 ARG cc_start: 0.8032 (ttm-80) cc_final: 0.7471 (mtm-85) REVERT: A 278 TRP cc_start: 0.8355 (t-100) cc_final: 0.8049 (t-100) REVERT: A 279 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8839 (mt-10) REVERT: A 469 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8510 (m-10) outliers start: 27 outliers final: 19 residues processed: 81 average time/residue: 0.0874 time to fit residues: 9.1942 Evaluate side-chains 78 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 17 THR 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 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 191 LEU Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 237 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 331 GLU Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 437 SER 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: 0.7980 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 16 optimal weight: 0.0970 chunk 49 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.078217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.051926 restraints weight = 37360.288| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.74 r_work: 0.2932 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9274 Z= 0.141 Angle : 0.604 14.479 13560 Z= 0.332 Chirality : 0.036 0.216 1645 Planarity : 0.005 0.067 926 Dihedral : 24.683 179.543 3819 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.34 % Favored : 88.84 % Rotamer: Outliers : 5.13 % Allowed : 34.03 % 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: -0.94 (0.39), residues: 493 helix: 1.52 (0.40), residues: 157 sheet: -1.03 (0.63), residues: 86 loop : -1.97 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 270 TYR 0.013 0.001 TYR A 340 PHE 0.010 0.001 PHE A 152 TRP 0.006 0.001 TRP A 478 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 ( 9270) covalent geometry : angle 0.60346 / 0.33 (13557) hydrogen bonds : bond 0.05937 / 4.02 ( 318) hydrogen bonds : angle 3.82134 / 2.50 ( 717) metal coordination : bond 0.01592 / 0.80 ( 4) metal coordination : angle 1.49773 / 0.76 ( 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 79 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8889 (ptt90) cc_final: 0.8433 (ppt170) REVERT: A 151 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.5220 (mtt180) REVERT: A 203 ASN cc_start: 0.8242 (t0) cc_final: 0.8037 (t0) REVERT: A 261 ARG cc_start: 0.8025 (ttm-80) cc_final: 0.7495 (mtm-85) REVERT: A 278 TRP cc_start: 0.8337 (t-100) cc_final: 0.8022 (t-100) REVERT: A 279 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8844 (mt-10) REVERT: A 386 ARG cc_start: 0.8245 (mtm-85) cc_final: 0.8006 (mtm-85) REVERT: A 469 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8665 (m-10) outliers start: 22 outliers final: 19 residues processed: 77 average time/residue: 0.0864 time to fit residues: 8.7885 Evaluate side-chains 76 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 17 THR 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 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 184 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 237 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 331 GLU Chi-restraints excluded: chain A residue 340 TYR Chi-restraints excluded: chain A residue 437 SER 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: 20.0000 chunk 67 optimal weight: 40.0000 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 51 optimal weight: 40.0000 chunk 33 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 55 optimal weight: 40.0000 chunk 5 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.074789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.047748 restraints weight = 37411.384| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.81 r_work: 0.2851 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 9274 Z= 0.359 Angle : 0.779 13.790 13560 Z= 0.415 Chirality : 0.049 0.274 1645 Planarity : 0.007 0.072 926 Dihedral : 24.835 179.545 3819 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 22.68 Ramachandran Plot: Outliers : 0.81 % Allowed : 13.59 % Favored : 85.60 % Rotamer: Outliers : 6.53 % Allowed : 32.87 % Favored : 60.61 % 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: -1.45 (0.38), residues: 493 helix: 0.92 (0.39), residues: 158 sheet: -1.28 (0.62), residues: 86 loop : -2.16 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 270 TYR 0.013 0.002 TYR A 340 PHE 0.009 0.002 PHE A 329 TRP 0.006 0.002 TRP A 478 HIS 0.006 0.002 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.36 ( 9270) covalent geometry : angle 0.77705 / 0.42 (13557) hydrogen bonds : bond 0.08839 / 6.02 ( 318) hydrogen bonds : angle 4.29377 / 2.79 ( 717) metal coordination : bond 0.03617 / 1.81 ( 4) metal coordination : angle 3.50205 / 1.86 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2097.40 seconds wall clock time: 36 minutes 27.89 seconds (2187.89 seconds total)