Starting phenix.real_space_refine on Wed Feb 4 03:28:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lj4_63132/02_2026/9lj4_63132.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lj4_63132/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9lj4_63132/02_2026/9lj4_63132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lj4_63132/02_2026/9lj4_63132.map" model { file = "/net/cci-nas-00/data/ceres_data/9lj4_63132/02_2026/9lj4_63132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lj4_63132/02_2026/9lj4_63132.cif" } 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-2.0-5952/lib/python3.9/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: 2.31, per 1000 atoms: 0.27 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 153.3 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: 1.40 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: 1.64 Time building geometry restraints manager: 0.84 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=" C THR A 52 " pdb=" N GLN A 53 " ideal model delta sigma weight residual 1.331 1.298 0.033 1.59e-02 3.96e+03 4.41e+00 bond pdb=" C3' DG D 10 " pdb=" O3' DG D 10 " ideal model delta sigma weight residual 1.422 1.470 -0.048 3.00e-02 1.11e+03 2.61e+00 bond pdb=" CB ASP A 353 " pdb=" CG ASP A 353 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.87e+00 bond pdb=" SD MET A 15 " pdb=" CE MET A 15 " ideal model delta sigma weight residual 1.791 1.759 0.032 2.50e-02 1.60e+03 1.63e+00 bond pdb=" O3' C B 153 " pdb=" P C B 154 " ideal model delta sigma weight residual 1.607 1.589 0.018 1.50e-02 4.44e+03 1.47e+00 ... (remaining 9265 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 13437 3.49 - 6.98: 107 6.98 - 10.47: 9 10.47 - 13.96: 3 13.96 - 17.45: 1 Bond angle restraints: 13557 Sorted by residual: angle pdb=" C THR A 52 " pdb=" N GLN A 53 " pdb=" CA GLN A 53 " ideal model delta sigma weight residual 122.38 139.83 -17.45 2.90e+00 1.19e-01 3.62e+01 angle pdb=" CA ARG A 270 " pdb=" CB ARG A 270 " pdb=" CG ARG A 270 " ideal model delta sigma weight residual 114.10 122.75 -8.65 2.00e+00 2.50e-01 1.87e+01 angle pdb=" C3' U B 191 " pdb=" O3' U B 191 " pdb=" P U B 192 " ideal model delta sigma weight residual 120.20 126.38 -6.18 1.50e+00 4.44e-01 1.70e+01 angle pdb=" C GLY A 391 " pdb=" N LYS A 392 " pdb=" CA LYS A 392 " ideal model delta sigma weight residual 121.54 129.29 -7.75 1.91e+00 2.74e-01 1.65e+01 angle pdb=" CB MET A 201 " pdb=" CG MET A 201 " pdb=" SD MET A 201 " ideal model delta sigma weight residual 112.70 124.81 -12.11 3.00e+00 1.11e-01 1.63e+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: 1472 0.063 - 0.125: 150 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: 1.210 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.720 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 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 : 0.005 0.048 9274 Z= 0.272 Angle : 0.839 17.446 13560 Z= 0.422 Chirality : 0.042 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 covalent geometry : bond 0.00533 ( 9270) covalent geometry : angle 0.83636 (13557) hydrogen bonds : bond 0.11730 ( 318) hydrogen bonds : angle 5.81994 ( 717) metal coordination : bond 0.00788 ( 4) metal coordination : angle 4.29995 ( 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: 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: 0.1142 time to fit residues: 10.7573 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 : 0.143 ------------------------------------------------------------------------------- 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: 7.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 overall best weight: 5.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3796 r_free = 0.3796 target = 0.074859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.048098 restraints weight = 38661.799| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.00 r_work: 0.2851 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 9274 Z= 0.329 Angle : 0.721 9.021 13560 Z= 0.372 Chirality : 0.040 0.273 1645 Planarity : 0.005 0.072 926 Dihedral : 25.064 179.141 3845 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.75 % Favored : 88.44 % Rotamer: Outliers : 6.76 % Allowed : 30.07 % 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: -1.37 (0.38), residues: 493 helix: 1.04 (0.39), residues: 158 sheet: -1.53 (0.60), residues: 86 loop : -2.03 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 368 TYR 0.012 0.002 TYR A 327 PHE 0.012 0.002 PHE A 152 TRP 0.008 0.001 TRP A 209 HIS 0.003 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00640 ( 9270) covalent geometry : angle 0.72084 (13557) hydrogen bonds : bond 0.07355 ( 318) hydrogen bonds : angle 4.12330 ( 717) metal coordination : bond 0.01198 ( 4) metal coordination : angle 2.03054 ( 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 80 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 51 time to evaluate : 0.134 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: 0.8253 (OUTLIER) cc_final: 0.6583 (m100) REVERT: A 278 TRP cc_start: 0.8591 (t-100) cc_final: 0.8139 (t-100) REVERT: A 282 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.8944 (pp) REVERT: A 363 ARG cc_start: 0.7005 (ttt180) cc_final: 0.6524 (ttt-90) REVERT: A 374 ASP cc_start: 0.9020 (t0) cc_final: 0.8787 (t0) REVERT: A 386 ARG cc_start: 0.8606 (mtm-85) cc_final: 0.8260 (mtm-85) REVERT: A 469 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8664 (m-10) outliers start: 29 outliers final: 19 residues processed: 74 average time/residue: 0.1305 time to fit residues: 12.1130 Evaluate side-chains 73 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 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 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 282 LEU Chi-restraints excluded: chain A residue 294 HIS 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 61 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3772 r_free = 0.3772 target = 0.073849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.046681 restraints weight = 37999.337| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.00 r_work: 0.2820 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 9274 Z= 0.405 Angle : 0.781 14.463 13560 Z= 0.400 Chirality : 0.043 0.273 1645 Planarity : 0.006 0.068 926 Dihedral : 25.212 178.848 3832 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.81 % Allowed : 11.97 % Favored : 87.22 % Rotamer: Outliers : 8.86 % Allowed : 27.51 % 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: -1.56 (0.38), residues: 493 helix: 0.77 (0.38), residues: 158 sheet: -1.56 (0.61), residues: 86 loop : -2.10 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 368 TYR 0.013 0.002 TYR A 327 PHE 0.012 0.002 PHE A 152 TRP 0.011 0.002 TRP A 209 HIS 0.005 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00792 ( 9270) covalent geometry : angle 0.78065 (13557) hydrogen bonds : bond 0.07710 ( 318) hydrogen bonds : angle 4.29895 ( 717) metal coordination : bond 0.02300 ( 4) metal coordination : angle 2.15567 ( 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 89 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 51 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ASN cc_start: 0.8294 (t0) cc_final: 0.7972 (t0) REVERT: A 209 TRP cc_start: 0.8296 (OUTLIER) cc_final: 0.6568 (m100) REVERT: A 261 ARG cc_start: 0.7980 (ttm-80) cc_final: 0.7498 (mtm-85) REVERT: A 278 TRP cc_start: 0.8534 (t-100) cc_final: 0.8077 (t-100) REVERT: A 282 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.8911 (pp) REVERT: A 386 ARG cc_start: 0.8613 (mtm-85) cc_final: 0.8348 (mtm-85) REVERT: A 469 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.8659 (m-10) outliers start: 38 outliers final: 24 residues processed: 84 average time/residue: 0.1220 time to fit residues: 13.2536 Evaluate side-chains 78 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 51 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 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 209 TRP 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 469 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 29 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3783 r_free = 0.3783 target = 0.074258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.047376 restraints weight = 37708.025| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.90 r_work: 0.2843 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 9274 Z= 0.339 Angle : 0.720 9.742 13560 Z= 0.372 Chirality : 0.040 0.269 1645 Planarity : 0.005 0.063 926 Dihedral : 25.166 178.706 3829 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.81 % Allowed : 9.94 % Favored : 89.25 % Rotamer: Outliers : 7.23 % Allowed : 29.60 % 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: -1.45 (0.38), residues: 493 helix: 0.91 (0.38), residues: 159 sheet: -1.52 (0.60), residues: 86 loop : -2.07 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 270 TYR 0.014 0.002 TYR A 340 PHE 0.011 0.002 PHE A 40 TRP 0.011 0.002 TRP A 209 HIS 0.006 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00660 ( 9270) covalent geometry : angle 0.71987 (13557) hydrogen bonds : bond 0.06790 ( 318) hydrogen bonds : angle 4.12649 ( 717) metal coordination : bond 0.01869 ( 4) metal coordination : angle 1.09810 ( 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 84 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 53 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.5482 (mtt180) REVERT: A 203 ASN cc_start: 0.8220 (t0) cc_final: 0.7927 (t0) REVERT: A 208 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8296 (ttp-170) REVERT: A 209 TRP cc_start: 0.8254 (OUTLIER) cc_final: 0.6524 (m100) REVERT: A 250 ARG cc_start: 0.9164 (ttp80) cc_final: 0.8960 (ttp80) REVERT: A 261 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7456 (mtm-85) REVERT: A 278 TRP cc_start: 0.8505 (t-100) cc_final: 0.8074 (t-100) REVERT: A 279 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8915 (mt-10) REVERT: A 282 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.8941 (pp) REVERT: A 386 ARG cc_start: 0.8625 (mtm-85) cc_final: 0.8346 (mtm-85) REVERT: A 469 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.8730 (m-10) outliers start: 31 outliers final: 20 residues processed: 80 average time/residue: 0.1456 time to fit residues: 14.6585 Evaluate side-chains 77 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 51 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 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 222 VAL 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 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: 10.0000 chunk 53 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3803 r_free = 0.3803 target = 0.075337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.048521 restraints weight = 37707.478| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.78 r_work: 0.2874 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9274 Z= 0.267 Angle : 0.682 9.846 13560 Z= 0.350 Chirality : 0.038 0.262 1645 Planarity : 0.005 0.060 926 Dihedral : 25.111 179.805 3828 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 17.24 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: -1.31 (0.38), residues: 493 helix: 1.14 (0.39), residues: 159 sheet: -1.48 (0.60), residues: 86 loop : -2.06 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 33 TYR 0.016 0.002 TYR A 340 PHE 0.010 0.001 PHE A 152 TRP 0.011 0.002 TRP A 209 HIS 0.004 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 9270) covalent geometry : angle 0.68210 (13557) hydrogen bonds : bond 0.06103 ( 318) hydrogen bonds : angle 3.98456 ( 717) metal coordination : bond 0.01903 ( 4) metal coordination : angle 1.17828 ( 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 85 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 53 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6639 (mtm-85) REVERT: A 37 ARG cc_start: 0.9118 (mtm110) cc_final: 0.8518 (tpp80) REVERT: A 53 GLN cc_start: 0.6712 (OUTLIER) cc_final: 0.6158 (mp10) REVERT: A 151 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.5455 (mtt180) REVERT: A 203 ASN cc_start: 0.8286 (t0) cc_final: 0.7964 (t0) REVERT: A 208 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8319 (ttp-170) REVERT: A 209 TRP cc_start: 0.8274 (OUTLIER) cc_final: 0.6442 (m100) REVERT: A 261 ARG cc_start: 0.7960 (ttm-80) cc_final: 0.7441 (mtm-85) REVERT: A 278 TRP cc_start: 0.8470 (t-100) cc_final: 0.8040 (t-100) REVERT: A 279 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8912 (mt-10) REVERT: A 282 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.8937 (pp) REVERT: A 469 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8657 (m-10) outliers start: 32 outliers final: 21 residues processed: 81 average time/residue: 0.1465 time to fit residues: 15.0693 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 : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 53 GLN 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 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 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 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: 8.9990 chunk 40 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3794 r_free = 0.3794 target = 0.074924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.048035 restraints weight = 37993.225| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.89 r_work: 0.2858 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 9274 Z= 0.318 Angle : 0.705 9.784 13560 Z= 0.364 Chirality : 0.040 0.263 1645 Planarity : 0.005 0.059 926 Dihedral : 25.109 179.806 3824 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.95 % Favored : 88.24 % Rotamer: Outliers : 9.09 % Allowed : 29.14 % 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: -1.38 (0.38), residues: 493 helix: 1.06 (0.38), residues: 159 sheet: -1.51 (0.59), residues: 86 loop : -2.08 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 33 TYR 0.016 0.002 TYR A 340 PHE 0.011 0.001 PHE A 152 TRP 0.011 0.002 TRP A 209 HIS 0.006 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00622 ( 9270) covalent geometry : angle 0.70458 (13557) hydrogen bonds : bond 0.06588 ( 318) hydrogen bonds : angle 4.07592 ( 717) metal coordination : bond 0.02123 ( 4) metal coordination : angle 2.10619 ( 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 92 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 53 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.6121 (mp10) REVERT: A 151 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.5426 (mtt180) REVERT: A 203 ASN cc_start: 0.8230 (t0) cc_final: 0.7979 (t0) REVERT: A 208 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8256 (ttp-110) REVERT: A 209 TRP cc_start: 0.8314 (OUTLIER) cc_final: 0.6466 (m100) REVERT: A 261 ARG cc_start: 0.7959 (ttm-80) cc_final: 0.7424 (mtm-85) REVERT: A 278 TRP cc_start: 0.8462 (t-100) cc_final: 0.8047 (t-100) REVERT: A 279 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8839 (mt-10) REVERT: A 469 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8707 (m-10) outliers start: 39 outliers final: 27 residues processed: 88 average time/residue: 0.1370 time to fit residues: 15.3860 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 : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 53 GLN 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 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 437 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 493 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 30 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3822 r_free = 0.3822 target = 0.076202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.049510 restraints weight = 37839.454| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.81 r_work: 0.2901 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9274 Z= 0.208 Angle : 0.657 11.419 13560 Z= 0.337 Chirality : 0.036 0.255 1645 Planarity : 0.005 0.056 926 Dihedral : 25.053 179.266 3824 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.34 % Favored : 88.84 % Rotamer: Outliers : 8.39 % Allowed : 29.84 % 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: -1.17 (0.39), residues: 493 helix: 1.22 (0.39), residues: 159 sheet: -1.31 (0.61), residues: 86 loop : -1.98 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 33 TYR 0.015 0.002 TYR A 340 PHE 0.010 0.001 PHE A 152 TRP 0.010 0.001 TRP A 209 HIS 0.005 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 9270) covalent geometry : angle 0.65655 (13557) hydrogen bonds : bond 0.05462 ( 318) hydrogen bonds : angle 3.89086 ( 717) metal coordination : bond 0.01175 ( 4) metal coordination : angle 0.80711 ( 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 93 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 57 time to evaluate : 0.218 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: 0.9121 (mtm110) cc_final: 0.8525 (tpp80) REVERT: A 53 GLN cc_start: 0.6797 (OUTLIER) cc_final: 0.6381 (mp10) REVERT: A 151 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.5428 (mtt180) REVERT: A 203 ASN cc_start: 0.8240 (t0) cc_final: 0.7921 (t0) REVERT: A 209 TRP cc_start: 0.8342 (OUTLIER) cc_final: 0.6281 (m100) REVERT: A 278 TRP cc_start: 0.8480 (t-100) cc_final: 0.8081 (t-100) REVERT: A 279 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8841 (mt-10) REVERT: A 386 ARG cc_start: 0.8448 (mtm-85) cc_final: 0.8200 (mtm-85) REVERT: A 449 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7942 (tm-30) REVERT: A 469 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8686 (m-10) outliers start: 36 outliers final: 25 residues processed: 89 average time/residue: 0.1425 time to fit residues: 15.9425 Evaluate side-chains 84 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 53 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 53 GLN 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 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 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 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 449 GLU 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: 8.9990 chunk 59 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3801 r_free = 0.3801 target = 0.075239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.048452 restraints weight = 37997.538| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.82 r_work: 0.2867 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1831 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= 0.310 Angle : 0.719 12.677 13560 Z= 0.368 Chirality : 0.040 0.256 1645 Planarity : 0.005 0.056 926 Dihedral : 25.071 179.612 3824 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.81 % Allowed : 11.16 % Favored : 88.03 % Rotamer: Outliers : 8.16 % Allowed : 30.77 % 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: -1.31 (0.38), residues: 493 helix: 1.17 (0.39), residues: 158 sheet: -1.43 (0.60), residues: 86 loop : -2.09 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 33 TYR 0.015 0.002 TYR A 340 PHE 0.011 0.001 PHE A 152 TRP 0.009 0.002 TRP A 209 HIS 0.005 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00605 ( 9270) covalent geometry : angle 0.71908 (13557) hydrogen bonds : bond 0.06543 ( 318) hydrogen bonds : angle 4.15263 ( 717) metal coordination : bond 0.02409 ( 4) metal coordination : angle 1.54702 ( 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 90 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 55 time to evaluate : 0.211 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 53 GLN cc_start: 0.6784 (OUTLIER) cc_final: 0.6273 (mp10) REVERT: A 151 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.5450 (mtt180) REVERT: A 203 ASN cc_start: 0.8181 (t0) cc_final: 0.7919 (t0) REVERT: A 209 TRP cc_start: 0.8361 (OUTLIER) cc_final: 0.6396 (m100) REVERT: A 261 ARG cc_start: 0.7270 (mmm-85) cc_final: 0.7046 (mmm-85) REVERT: A 278 TRP cc_start: 0.8527 (t-100) cc_final: 0.8084 (t-100) REVERT: A 279 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8825 (mt-10) REVERT: A 341 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8870 (mm) REVERT: A 386 ARG cc_start: 0.8450 (mtm-85) cc_final: 0.8191 (mtm-85) REVERT: A 449 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8029 (tm-30) REVERT: A 469 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8634 (m-10) outliers start: 35 outliers final: 24 residues processed: 86 average time/residue: 0.1292 time to fit residues: 14.1485 Evaluate side-chains 85 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 54 time to evaluate : 0.137 ------------------------------------------------------------------------------- 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 53 GLN 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 141 THR 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 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 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 341 LEU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 449 GLU 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: 8.9990 chunk 45 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 GLN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.077807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.051148 restraints weight = 36542.588| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.81 r_work: 0.2929 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9274 Z= 0.165 Angle : 0.656 13.708 13560 Z= 0.333 Chirality : 0.036 0.248 1645 Planarity : 0.005 0.054 926 Dihedral : 24.965 178.977 3822 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.81 % Allowed : 9.13 % Favored : 90.06 % Rotamer: Outliers : 6.76 % Allowed : 32.17 % 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: -1.05 (0.39), residues: 493 helix: 1.39 (0.40), residues: 159 sheet: -1.17 (0.62), residues: 86 loop : -1.99 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 33 TYR 0.011 0.001 TYR A 387 PHE 0.009 0.001 PHE A 152 TRP 0.008 0.001 TRP A 209 HIS 0.005 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9270) covalent geometry : angle 0.65638 (13557) hydrogen bonds : bond 0.05138 ( 318) hydrogen bonds : angle 3.89471 ( 717) metal coordination : bond 0.01204 ( 4) metal coordination : angle 0.76117 ( 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 86 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 0.232 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: 0.9109 (mtm110) cc_final: 0.8557 (tpp80) REVERT: A 95 LYS cc_start: 0.9215 (tppt) cc_final: 0.9010 (tptt) REVERT: A 151 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.5375 (mtt180) REVERT: A 203 ASN cc_start: 0.8175 (t0) cc_final: 0.7882 (t0) REVERT: A 209 TRP cc_start: 0.8395 (OUTLIER) cc_final: 0.6329 (m100) REVERT: A 278 TRP cc_start: 0.8526 (t-100) cc_final: 0.8091 (t-100) REVERT: A 279 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8825 (mt-10) REVERT: A 289 MET cc_start: 0.9116 (tpt) cc_final: 0.8766 (tpt) REVERT: A 386 ARG cc_start: 0.8499 (mtm-85) cc_final: 0.8221 (mtm-85) REVERT: A 449 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7965 (tm-30) REVERT: A 461 ARG cc_start: 0.8277 (tpt90) cc_final: 0.7732 (tpt90) REVERT: A 469 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8602 (m-10) outliers start: 29 outliers final: 20 residues processed: 84 average time/residue: 0.1344 time to fit residues: 14.4255 Evaluate side-chains 78 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 53 GLN 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 151 ARG 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 209 TRP Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 235 LEU 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 445 LEU Chi-restraints excluded: chain A residue 449 GLU 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: 0.4980 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 0.0020 chunk 47 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 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 = 0.3882 r_free = 0.3882 target = 0.078659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.052174 restraints weight = 36795.032| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.80 r_work: 0.2991 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9274 Z= 0.138 Angle : 0.659 16.149 13560 Z= 0.331 Chirality : 0.035 0.238 1645 Planarity : 0.005 0.055 926 Dihedral : 24.836 178.860 3821 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.94 % Favored : 89.45 % Rotamer: Outliers : 6.29 % Allowed : 32.63 % 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: -0.99 (0.39), residues: 493 helix: 1.46 (0.41), residues: 158 sheet: -1.02 (0.63), residues: 86 loop : -2.01 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 33 TYR 0.011 0.001 TYR A 387 PHE 0.009 0.001 PHE A 152 TRP 0.007 0.001 TRP A 478 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9270) covalent geometry : angle 0.65881 (13557) hydrogen bonds : bond 0.05029 ( 318) hydrogen bonds : angle 3.79829 ( 717) metal coordination : bond 0.00647 ( 4) metal coordination : angle 0.76807 ( 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: 27 poor density : 56 time to evaluate : 0.208 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: 0.8954 (ptt90) cc_final: 0.8464 (ppt170) REVERT: A 37 ARG cc_start: 0.9102 (mtm110) cc_final: 0.8597 (tpp80) REVERT: A 53 GLN cc_start: 0.6748 (OUTLIER) cc_final: 0.5965 (mp10) REVERT: A 151 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.5285 (mtt180) REVERT: A 199 MET cc_start: 0.8982 (ppp) cc_final: 0.8462 (ppp) REVERT: A 203 ASN cc_start: 0.8250 (t0) cc_final: 0.8012 (t0) REVERT: A 209 TRP cc_start: 0.8399 (OUTLIER) cc_final: 0.7937 (m100) REVERT: A 278 TRP cc_start: 0.8577 (t-100) cc_final: 0.8101 (t-100) REVERT: A 289 MET cc_start: 0.9052 (tpt) cc_final: 0.8799 (tpt) REVERT: A 386 ARG cc_start: 0.8444 (mtm-85) cc_final: 0.8198 (mtm-85) REVERT: A 449 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7897 (tm-30) REVERT: A 469 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8559 (m-10) outliers start: 27 outliers final: 20 residues processed: 81 average time/residue: 0.1285 time to fit residues: 13.4374 Evaluate side-chains 79 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 53 GLN 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 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 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 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 359 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 449 GLU 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: 20.0000 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 0.0030 chunk 1 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 55 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 overall best weight: 3.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3824 r_free = 0.3824 target = 0.076214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.049602 restraints weight = 37115.404| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.76 r_work: 0.2907 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9274 Z= 0.241 Angle : 0.685 15.464 13560 Z= 0.346 Chirality : 0.037 0.241 1645 Planarity : 0.005 0.056 926 Dihedral : 24.835 178.552 3821 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.81 % Allowed : 9.94 % Favored : 89.25 % Rotamer: Outliers : 6.53 % Allowed : 32.40 % 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: -0.99 (0.39), residues: 493 helix: 1.48 (0.40), residues: 158 sheet: -1.03 (0.63), residues: 86 loop : -2.03 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 33 TYR 0.012 0.002 TYR A 293 PHE 0.011 0.001 PHE A 152 TRP 0.007 0.001 TRP A 209 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 9270) covalent geometry : angle 0.68437 (13557) hydrogen bonds : bond 0.05764 ( 318) hydrogen bonds : angle 3.95024 ( 717) metal coordination : bond 0.01761 ( 4) metal coordination : angle 1.23755 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2981.90 seconds wall clock time: 51 minutes 43.43 seconds (3103.43 seconds total)