Starting phenix.real_space_refine on Thu Aug 6 18:34:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nvu_49856/08_2026/9nvu_49856.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nvu_49856/08_2026/9nvu_49856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nvu_49856/08_2026/9nvu_49856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nvu_49856/08_2026/9nvu_49856.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nvu_49856/08_2026/9nvu_49856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nvu_49856/08_2026/9nvu_49856.map" } resolution = 2.71 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= 0.024 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 228 5.49 5 Mg 4 5.21 5 S 29 5.16 5 C 5249 2.51 5 N 1763 2.21 5 O 2380 1.98 5 H 7515 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s 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: 17170 Number of models: 1 Model: "" Number of chains: 7 Chain: "N" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 857 Classifications: {'DNA': 27} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 26} Chain: "P" Number of atoms: 9878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 9878 Classifications: {'peptide': 603} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 575} Chain: "T" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 1243 Classifications: {'DNA': 39} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 38} Chain: "W" Number of atoms: 5186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 5186 Classifications: {'RNA': 162} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 14, 'rna3p_pur': 72, 'rna3p_pyr': 66} Link IDs: {'rna2p': 24, 'rna3p': 137} Chain breaks: 2 Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "W" 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 6503 SG CYS P 342 12.880 90.185 64.769 1.00 86.94 S ATOM 6943 SG CYS P 371 17.295 91.098 65.045 1.00 92.50 S ATOM 6990 SG CYS P 374 15.624 88.964 67.223 1.00 92.25 S ATOM 3459 SG CYS P 158 51.532 77.898 32.476 1.00 85.56 S ATOM 3508 SG CYS P 161 54.652 78.362 30.877 1.00 87.50 S ATOM 4959 SG CYS P 245 51.805 80.944 30.511 1.00 85.75 S Time building chain proxies: 3.33, per 1000 atoms: 0.19 Number of scatterers: 17170 At special positions: 0 Unit cell: (80.025, 126.225, 137.775, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 29 16.00 P 228 15.00 Mg 4 11.99 O 2380 8.00 N 1763 7.00 C 5249 6.00 H 7515 1.00 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: 1.48 Conformation dependent library (CDL) restraints added in 338.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN P 703 " pdb="ZN ZN P 703 " - pdb=" SG CYS P 374 " pdb="ZN ZN P 703 " - pdb=" SG CYS P 342 " pdb="ZN ZN P 703 " - pdb=" SG CYS P 371 " pdb=" ZN P 704 " pdb="ZN ZN P 704 " - pdb=" ND1 HIS P 248 " pdb="ZN ZN P 704 " - pdb=" SG CYS P 161 " pdb="ZN ZN P 704 " - pdb=" SG CYS P 245 " pdb="ZN ZN P 704 " - pdb=" SG CYS P 158 " Number of angles added : 3 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1126 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 6 sheets defined 41.0% alpha, 13.9% beta 77 base pairs and 149 stacking pairs defined. Time for finding SS restraints: 3.23 Creating SS restraints... Processing helix chain 'P' and resid 18 through 28 Processing helix chain 'P' and resid 86 through 88 No H-bonds generated for 'chain 'P' and resid 86 through 88' Processing helix chain 'P' and resid 89 through 120 Processing helix chain 'P' and resid 171 through 181 removed outlier: 3.700A pdb=" N ILE P 179 " --> pdb=" O LEU P 175 " (cutoff:3.500A) Processing helix chain 'P' and resid 186 through 200 Processing helix chain 'P' and resid 201 through 217 Processing helix chain 'P' and resid 226 through 233 Processing helix chain 'P' and resid 245 through 250 removed outlier: 3.802A pdb=" N ALA P 250 " --> pdb=" O LYS P 246 " (cutoff:3.500A) Processing helix chain 'P' and resid 253 through 257 Processing helix chain 'P' and resid 266 through 284 removed outlier: 3.772A pdb=" N PHE P 280 " --> pdb=" O HIS P 276 " (cutoff:3.500A) Processing helix chain 'P' and resid 300 through 305 Processing helix chain 'P' and resid 310 through 314 Processing helix chain 'P' and resid 326 through 335 Processing helix chain 'P' and resid 355 through 359 removed outlier: 4.024A pdb=" N ARG P 359 " --> pdb=" O ARG P 356 " (cutoff:3.500A) Processing helix chain 'P' and resid 363 through 365 No H-bonds generated for 'chain 'P' and resid 363 through 365' Processing helix chain 'P' and resid 371 through 381 Processing helix chain 'P' and resid 381 through 392 removed outlier: 4.005A pdb=" N MET P 391 " --> pdb=" O SER P 387 " (cutoff:3.500A) Processing helix chain 'P' and resid 399 through 420 removed outlier: 3.548A pdb=" N VAL P 404 " --> pdb=" O GLY P 400 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE P 409 " --> pdb=" O LEU P 405 " (cutoff:3.500A) Proline residue: P 410 - end of helix Processing helix chain 'P' and resid 429 through 439 Processing helix chain 'P' and resid 444 through 454 Processing helix chain 'P' and resid 511 through 524 Processing helix chain 'P' and resid 524 through 533 Processing sheet with id=AA1, first strand: chain 'P' and resid 4 through 6 removed outlier: 6.160A pdb=" N TYR P 4 " --> pdb=" O ILE P 41 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU P 43 " --> pdb=" O TYR P 4 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU P 6 " --> pdb=" O LEU P 43 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLN P 42 " --> pdb=" O ALA P 33 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ALA P 33 " --> pdb=" O GLN P 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 424 through 428 removed outlier: 6.333A pdb=" N VAL P 55 " --> pdb=" O VAL P 289 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU P 295 " --> pdb=" O GLN P 59 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY P 79 " --> pdb=" O ALA P 70 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ARG P 72 " --> pdb=" O GLU P 77 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLU P 77 " --> pdb=" O ARG P 72 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N PHE P 469 " --> pdb=" O LEU P 78 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ARG P 80 " --> pdb=" O PHE P 469 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE P 471 " --> pdb=" O ARG P 80 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N HIS P 82 " --> pdb=" O ILE P 471 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLN P 473 " --> pdb=" O HIS P 82 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ILE P 84 " --> pdb=" O GLN P 473 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU P 470 " --> pdb=" O VAL P 602 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 349 through 352 Processing sheet with id=AA4, first strand: chain 'P' and resid 482 through 485 removed outlier: 3.554A pdb=" N HIS P 484 " --> pdb=" O TYR P 543 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 495 through 498 removed outlier: 5.258A pdb=" N THR P 496 " --> pdb=" O LEU P 492 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU P 492 " --> pdb=" O THR P 496 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 585 through 586 removed outlier: 3.562A pdb=" N GLY P 567 " --> pdb=" O ARG P 576 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL P 555 " --> pdb=" O LEU P 593 " (cutoff:3.500A) 201 hydrogen bonds defined for protein. 567 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 193 hydrogen bonds 374 hydrogen bond angles 0 basepair planarities 77 basepair parallelities 149 stacking parallelities Total time for adding SS restraints: 4.00 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 7501 1.12 - 1.29: 1030 1.29 - 1.47: 4825 1.47 - 1.65: 4423 1.65 - 1.82: 44 Bond restraints: 17823 Sorted by residual: bond pdb=" C8 A W -14 " pdb=" H8 A W -14 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" C6 DT N 14 " pdb=" H6 DT N 14 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N6 A W 63 " pdb=" H61 A W 63 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" CE1 HIS P 352 " pdb=" HE1 HIS P 352 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N ILE P 471 " pdb=" H ILE P 471 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 17818 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 28184 2.83 - 5.66: 3387 5.66 - 8.49: 577 8.49 - 11.32: 28 11.32 - 14.15: 16 Bond angle restraints: 32192 Sorted by residual: angle pdb=" O5' DC N 9 " pdb=" C5' DC N 9 " pdb=" C4' DC N 9 " ideal model delta sigma weight residual 109.40 119.04 -9.64 8.00e-01 1.56e+00 1.45e+02 angle pdb=" O5' DT T 0 " pdb=" C5' DT T 0 " pdb=" C4' DT T 0 " ideal model delta sigma weight residual 109.40 118.89 -9.49 8.00e-01 1.56e+00 1.41e+02 angle pdb=" O5' DC T 20 " pdb=" C5' DC T 20 " pdb=" C4' DC T 20 " ideal model delta sigma weight residual 109.40 118.38 -8.98 8.00e-01 1.56e+00 1.26e+02 angle pdb=" O5' U W -16 " pdb=" C5' U W -16 " pdb=" C4' U W -16 " ideal model delta sigma weight residual 109.40 118.30 -8.90 8.00e-01 1.56e+00 1.24e+02 angle pdb=" N6 A W 57 " pdb=" C6 A W 57 " pdb=" N1 A W 57 " ideal model delta sigma weight residual 118.60 112.45 6.15 6.00e-01 2.78e+00 1.05e+02 ... (remaining 32187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.27: 7500 35.27 - 70.53: 749 70.53 - 105.79: 66 105.79 - 141.06: 2 141.06 - 176.32: 8 Dihedral angle restraints: 8325 sinusoidal: 6320 harmonic: 2005 Sorted by residual: dihedral pdb=" O4' U W 102 " pdb=" C1' U W 102 " pdb=" N1 U W 102 " pdb=" C2 U W 102 " ideal model delta sinusoidal sigma weight residual 200.00 43.54 156.46 1 1.50e+01 4.44e-03 8.18e+01 dihedral pdb=" C5' C W 69 " pdb=" C4' C W 69 " pdb=" C3' C W 69 " pdb=" O3' C W 69 " ideal model delta sinusoidal sigma weight residual 147.00 87.71 59.29 1 8.00e+00 1.56e-02 7.34e+01 dihedral pdb=" C4' C W 116 " pdb=" C3' C W 116 " pdb=" C2' C W 116 " pdb=" C1' C W 116 " ideal model delta sinusoidal sigma weight residual -35.00 17.02 -52.02 1 8.00e+00 1.56e-02 5.77e+01 ... (remaining 8322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 1488 0.124 - 0.247: 287 0.247 - 0.371: 28 0.371 - 0.494: 5 0.494 - 0.618: 3 Chirality restraints: 1811 Sorted by residual: chirality pdb=" C3' A W 70 " pdb=" C4' A W 70 " pdb=" O3' A W 70 " pdb=" C2' A W 70 " both_signs ideal model delta sigma weight residual False -2.74 -2.13 -0.62 2.00e-01 2.50e+01 9.54e+00 chirality pdb=" C3' DT N -5 " pdb=" C4' DT N -5 " pdb=" O3' DT N -5 " pdb=" C2' DT N -5 " both_signs ideal model delta sigma weight residual False -2.73 -2.16 -0.57 2.00e-01 2.50e+01 8.02e+00 chirality pdb=" C3' U W 82 " pdb=" C4' U W 82 " pdb=" O3' U W 82 " pdb=" C2' U W 82 " both_signs ideal model delta sigma weight residual False -2.48 -1.97 -0.51 2.00e-01 2.50e+01 6.40e+00 ... (remaining 1808 not shown) Planarity restraints: 1825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U W 84 " -0.401 2.00e-02 2.50e+03 1.52e-01 6.94e+02 pdb=" N1 U W 84 " 0.053 2.00e-02 2.50e+03 pdb=" C2 U W 84 " 0.121 2.00e-02 2.50e+03 pdb=" O2 U W 84 " 0.164 2.00e-02 2.50e+03 pdb=" N3 U W 84 " 0.021 2.00e-02 2.50e+03 pdb=" C4 U W 84 " -0.064 2.00e-02 2.50e+03 pdb=" O4 U W 84 " -0.194 2.00e-02 2.50e+03 pdb=" C5 U W 84 " 0.040 2.00e-02 2.50e+03 pdb=" C6 U W 84 " 0.104 2.00e-02 2.50e+03 pdb=" H5 U W 84 " 0.031 2.00e-02 2.50e+03 pdb=" H3 U W 84 " -0.004 2.00e-02 2.50e+03 pdb=" H6 U W 84 " 0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG P 109 " 0.529 9.50e-02 1.11e+02 2.43e-01 6.58e+02 pdb=" NE ARG P 109 " 0.186 2.00e-02 2.50e+03 pdb=" CZ ARG P 109 " 0.084 2.00e-02 2.50e+03 pdb=" NH1 ARG P 109 " 0.043 2.00e-02 2.50e+03 pdb=" NH2 ARG P 109 " 0.026 2.00e-02 2.50e+03 pdb="HH11 ARG P 109 " -0.263 2.00e-02 2.50e+03 pdb="HH12 ARG P 109 " 0.032 2.00e-02 2.50e+03 pdb="HH21 ARG P 109 " -0.318 2.00e-02 2.50e+03 pdb="HH22 ARG P 109 " 0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U W 117 " -0.308 2.00e-02 2.50e+03 1.34e-01 5.36e+02 pdb=" N1 U W 117 " -0.042 2.00e-02 2.50e+03 pdb=" C2 U W 117 " 0.047 2.00e-02 2.50e+03 pdb=" O2 U W 117 " 0.234 2.00e-02 2.50e+03 pdb=" N3 U W 117 " -0.036 2.00e-02 2.50e+03 pdb=" C4 U W 117 " -0.074 2.00e-02 2.50e+03 pdb=" O4 U W 117 " -0.150 2.00e-02 2.50e+03 pdb=" C5 U W 117 " 0.029 2.00e-02 2.50e+03 pdb=" C6 U W 117 " 0.062 2.00e-02 2.50e+03 pdb=" H5 U W 117 " 0.077 2.00e-02 2.50e+03 pdb=" H3 U W 117 " 0.017 2.00e-02 2.50e+03 pdb=" H6 U W 117 " 0.145 2.00e-02 2.50e+03 ... (remaining 1822 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1034 2.18 - 2.78: 25911 2.78 - 3.39: 45024 3.39 - 3.99: 64035 3.99 - 4.60: 92293 Nonbonded interactions: 228297 Sorted by model distance: nonbonded pdb=" HG SER P 511 " pdb=" OD2 ASP P 514 " model vdw 1.573 2.450 nonbonded pdb=" OE2 GLU P 77 " pdb=" HG1 THR P 466 " model vdw 1.593 2.450 nonbonded pdb=" O THR P 486 " pdb=" HG SER P 540 " model vdw 1.593 2.450 nonbonded pdb=" HG1 THR P 16 " pdb=" OP1 A W 184 " model vdw 1.600 2.450 nonbonded pdb=" OP2 DC N -3 " pdb=" HG1 THR P 64 " model vdw 1.621 2.450 ... (remaining 228292 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: 2.590 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: 0.100 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 23.450 Find NCS groups from input model: 0.050 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: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 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 : 0.017 0.656 10315 Z= 1.269 Angle : 1.967 25.756 14971 Z= 1.965 Chirality : 0.100 0.618 1811 Planarity : 0.028 0.212 1080 Dihedral : 22.138 176.323 5164 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.19 % Allowed : 0.57 % Favored : 99.24 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 7.41 % 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: -0.83 (0.32), residues: 601 helix: -0.53 (0.31), residues: 221 sheet: -0.00 (0.65), residues: 57 loop : -0.56 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG P 23 TYR 0.158 0.020 TYR P 574 PHE 0.068 0.015 PHE P 301 TRP 0.041 0.020 TRP P 515 HIS 0.028 0.005 HIS P 445 Details of bonding type rmsd/Z covalent geometry : bond 0.01323 / 1.22 (10308) covalent geometry : angle 1.94160 / 1.96 (14968) hydrogen bonds : bond 0.15344 / 16.78 ( 394) hydrogen bonds : angle 6.34601 / 8.62 ( 941) metal coordination : bond 0.39216 / 31.88 ( 7) metal coordination : angle 22.48539 / 43.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 7 ASP cc_start: 0.6484 (t0) cc_final: 0.6249 (t0) REVERT: P 11 LYS cc_start: 0.7682 (mttt) cc_final: 0.7477 (mptt) REVERT: P 51 ILE cc_start: 0.8047 (mt) cc_final: 0.7812 (mp) REVERT: P 108 GLU cc_start: 0.6616 (mm-30) cc_final: 0.6362 (mm-30) REVERT: P 294 VAL cc_start: 0.7721 (t) cc_final: 0.7373 (p) REVERT: P 338 LYS cc_start: 0.7928 (mttt) cc_final: 0.7598 (mtmm) REVERT: P 356 ARG cc_start: 0.6904 (mtp180) cc_final: 0.6572 (mtp180) REVERT: P 366 ASN cc_start: 0.7514 (t0) cc_final: 0.7006 (t0) REVERT: P 458 LYS cc_start: 0.7611 (mttt) cc_final: 0.7381 (mttt) REVERT: P 470 GLU cc_start: 0.6701 (mm-30) cc_final: 0.5468 (mm-30) REVERT: P 510 ASP cc_start: 0.8092 (m-30) cc_final: 0.7844 (m-30) REVERT: P 517 VAL cc_start: 0.7526 (t) cc_final: 0.7233 (m) REVERT: P 518 ASP cc_start: 0.7523 (m-30) cc_final: 0.7318 (m-30) REVERT: P 522 GLU cc_start: 0.7517 (tp30) cc_final: 0.6920 (tp30) REVERT: P 525 LYS cc_start: 0.7303 (mttt) cc_final: 0.6886 (mtpp) REVERT: P 529 ASP cc_start: 0.7366 (m-30) cc_final: 0.7041 (m-30) REVERT: P 541 THR cc_start: 0.7455 (m) cc_final: 0.7075 (p) REVERT: P 561 LYS cc_start: 0.7809 (mttt) cc_final: 0.7428 (mtpp) REVERT: P 573 LYS cc_start: 0.7790 (mttt) cc_final: 0.7497 (mttm) REVERT: P 589 LYS cc_start: 0.8114 (mttt) cc_final: 0.7775 (mtpt) outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 1.2982 time to fit residues: 221.8640 Evaluate side-chains 136 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 65 ASN ** P 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 407 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.135992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.105309 restraints weight = 32130.434| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.07 r_work: 0.3161 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10315 Z= 0.218 Angle : 0.841 9.190 14971 Z= 0.503 Chirality : 0.056 0.444 1811 Planarity : 0.008 0.079 1080 Dihedral : 24.059 176.643 3899 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.46 % Allowed : 8.32 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.23 (0.33), residues: 601 helix: 0.52 (0.33), residues: 222 sheet: 0.29 (0.63), residues: 66 loop : -0.70 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 80 TYR 0.015 0.002 TYR P 4 PHE 0.019 0.002 PHE P 263 TRP 0.006 0.002 TRP P 515 HIS 0.008 0.002 HIS P 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.22 (10308) covalent geometry : angle 0.83823 / 0.50 (14968) hydrogen bonds : bond 0.07451 / 8.11 ( 394) hydrogen bonds : angle 4.65217 / 6.30 ( 941) metal coordination : bond 0.01773 / 1.07 ( 7) metal coordination : angle 4.48051 / 8.78 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 114 ARG cc_start: 0.7810 (mtm110) cc_final: 0.7397 (mtm110) REVERT: P 294 VAL cc_start: 0.8468 (t) cc_final: 0.8208 (p) REVERT: P 310 LYS cc_start: 0.8026 (mptt) cc_final: 0.7790 (mptt) REVERT: P 356 ARG cc_start: 0.7497 (mtp180) cc_final: 0.7250 (mtp180) REVERT: P 366 ASN cc_start: 0.8000 (t0) cc_final: 0.7436 (t0) REVERT: P 470 GLU cc_start: 0.7718 (mm-30) cc_final: 0.6521 (mm-30) REVERT: P 565 MET cc_start: 0.8298 (ttm) cc_final: 0.8062 (ttm) REVERT: P 591 ARG cc_start: 0.8029 (mtp85) cc_final: 0.7801 (mmm-85) outliers start: 13 outliers final: 7 residues processed: 143 average time/residue: 1.2912 time to fit residues: 195.7768 Evaluate side-chains 137 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 30 GLN Chi-restraints excluded: chain P residue 130 ILE Chi-restraints excluded: chain P residue 408 ILE Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain P residue 426 VAL Chi-restraints excluded: chain P residue 569 ILE Chi-restraints excluded: chain P residue 588 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 26 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 65 ASN P 276 HIS P 407 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.133892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.103277 restraints weight = 32283.507| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.06 r_work: 0.3118 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 10315 Z= 0.268 Angle : 0.749 7.562 14971 Z= 0.451 Chirality : 0.052 0.494 1811 Planarity : 0.006 0.073 1080 Dihedral : 23.899 165.192 3899 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.40 % Allowed : 11.72 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.23 (0.33), residues: 601 helix: 0.74 (0.33), residues: 227 sheet: 0.26 (0.64), residues: 66 loop : -0.91 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 101 TYR 0.019 0.002 TYR P 4 PHE 0.017 0.003 PHE P 556 TRP 0.006 0.001 TRP P 515 HIS 0.012 0.002 HIS P 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.27 (10308) covalent geometry : angle 0.74718 / 0.45 (14968) hydrogen bonds : bond 0.06330 / 6.96 ( 394) hydrogen bonds : angle 4.34160 / 5.80 ( 941) metal coordination : bond 0.01049 / 0.59 ( 7) metal coordination : angle 3.68441 / 7.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 294 VAL cc_start: 0.8454 (t) cc_final: 0.8240 (p) REVERT: P 295 GLU cc_start: 0.8004 (tt0) cc_final: 0.6889 (tt0) REVERT: P 356 ARG cc_start: 0.7551 (mtp180) cc_final: 0.7280 (mtp180) REVERT: P 366 ASN cc_start: 0.8089 (t0) cc_final: 0.7406 (t0) REVERT: P 470 GLU cc_start: 0.7668 (mm-30) cc_final: 0.6529 (mm-30) REVERT: P 514 ASP cc_start: 0.8021 (m-30) cc_final: 0.7754 (m-30) REVERT: P 522 GLU cc_start: 0.7742 (tp30) cc_final: 0.7311 (tp30) REVERT: P 532 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8128 (mtm-85) outliers start: 18 outliers final: 8 residues processed: 134 average time/residue: 1.3391 time to fit residues: 189.2220 Evaluate side-chains 132 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 17 CYS Chi-restraints excluded: chain P residue 30 GLN Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 130 ILE Chi-restraints excluded: chain P residue 408 ILE Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain P residue 426 VAL Chi-restraints excluded: chain P residue 532 ARG Chi-restraints excluded: chain P residue 569 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 22 optimal weight: 20.0000 chunk 56 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.135984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105580 restraints weight = 32097.477| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.05 r_work: 0.3168 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10315 Z= 0.186 Angle : 0.645 7.503 14971 Z= 0.389 Chirality : 0.045 0.353 1811 Planarity : 0.006 0.066 1080 Dihedral : 23.938 165.306 3899 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.65 % Allowed : 12.48 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.00 (0.33), residues: 601 helix: 1.11 (0.34), residues: 228 sheet: 0.33 (0.65), residues: 66 loop : -0.92 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 80 TYR 0.014 0.001 TYR P 4 PHE 0.013 0.002 PHE P 263 TRP 0.007 0.001 TRP P 430 HIS 0.010 0.002 HIS P 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.19 (10308) covalent geometry : angle 0.64326 / 0.39 (14968) hydrogen bonds : bond 0.05550 / 6.05 ( 394) hydrogen bonds : angle 4.07706 / 5.49 ( 941) metal coordination : bond 0.01954 / 0.86 ( 7) metal coordination : angle 3.81264 / 7.41 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 63 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7999 (ttt180) REVERT: P 294 VAL cc_start: 0.8457 (t) cc_final: 0.8241 (p) REVERT: P 356 ARG cc_start: 0.7525 (mtp180) cc_final: 0.7263 (mtp180) REVERT: P 470 GLU cc_start: 0.7655 (mm-30) cc_final: 0.6583 (mm-30) REVERT: P 532 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8183 (mtm-85) outliers start: 14 outliers final: 9 residues processed: 124 average time/residue: 1.3983 time to fit residues: 183.4197 Evaluate side-chains 132 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 17 CYS Chi-restraints excluded: chain P residue 27 LYS Chi-restraints excluded: chain P residue 63 ARG Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 408 ILE Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain P residue 426 VAL Chi-restraints excluded: chain P residue 461 GLU Chi-restraints excluded: chain P residue 467 GLU Chi-restraints excluded: chain P residue 532 ARG Chi-restraints excluded: chain P residue 569 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 50 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 57 optimal weight: 0.0470 chunk 69 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 406 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.136880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.106486 restraints weight = 31936.367| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.05 r_work: 0.3175 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10315 Z= 0.159 Angle : 0.601 7.486 14971 Z= 0.364 Chirality : 0.042 0.357 1811 Planarity : 0.005 0.058 1080 Dihedral : 23.879 167.593 3899 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.27 % Allowed : 13.99 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.18 (0.34), residues: 601 helix: 1.44 (0.34), residues: 226 sheet: 0.32 (0.65), residues: 66 loop : -0.94 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 114 TYR 0.012 0.001 TYR P 4 PHE 0.011 0.001 PHE P 263 TRP 0.006 0.001 TRP P 430 HIS 0.007 0.001 HIS P 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.16 (10308) covalent geometry : angle 0.59912 / 0.36 (14968) hydrogen bonds : bond 0.05168 / 5.69 ( 394) hydrogen bonds : angle 3.92796 / 5.23 ( 941) metal coordination : bond 0.01816 / 0.78 ( 7) metal coordination : angle 3.76264 / 7.33 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.296 Fit side-chains REVERT: P 92 LYS cc_start: 0.8290 (tppt) cc_final: 0.8089 (tttp) REVERT: P 294 VAL cc_start: 0.8469 (t) cc_final: 0.8219 (p) REVERT: P 356 ARG cc_start: 0.7538 (mtp180) cc_final: 0.7283 (mtp180) REVERT: P 532 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8230 (mtm-85) outliers start: 12 outliers final: 8 residues processed: 121 average time/residue: 1.3837 time to fit residues: 177.3244 Evaluate side-chains 121 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 17 CYS Chi-restraints excluded: chain P residue 30 GLN Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 402 THR Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain P residue 426 VAL Chi-restraints excluded: chain P residue 461 GLU Chi-restraints excluded: chain P residue 467 GLU Chi-restraints excluded: chain P residue 532 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 70 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 406 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.132220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.101247 restraints weight = 31758.874| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.09 r_work: 0.3097 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.127 10315 Z= 0.402 Angle : 0.762 9.258 14971 Z= 0.444 Chirality : 0.054 0.483 1811 Planarity : 0.007 0.064 1080 Dihedral : 23.960 169.170 3899 Min Nonbonded Distance : 1.597 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.84 % Allowed : 14.56 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.25 (0.33), residues: 601 helix: 0.99 (0.34), residues: 226 sheet: 0.21 (0.66), residues: 60 loop : -1.12 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 101 TYR 0.020 0.003 TYR P 4 PHE 0.019 0.003 PHE P 556 TRP 0.009 0.002 TRP P 515 HIS 0.011 0.003 HIS P 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00805 / 0.40 (10308) covalent geometry : angle 0.76149 / 0.44 (14968) hydrogen bonds : bond 0.06740 / 7.31 ( 394) hydrogen bonds : angle 4.16347 / 5.47 ( 941) metal coordination : bond 0.01334 / 1.08 ( 7) metal coordination : angle 2.59857 / 4.83 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: P 63 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8065 (ttt180) REVERT: P 294 VAL cc_start: 0.8492 (t) cc_final: 0.8244 (p) REVERT: P 356 ARG cc_start: 0.7637 (mtp180) cc_final: 0.7358 (mtp180) REVERT: P 532 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8173 (mtm-85) outliers start: 15 outliers final: 11 residues processed: 117 average time/residue: 1.3615 time to fit residues: 168.6484 Evaluate side-chains 126 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 17 CYS Chi-restraints excluded: chain P residue 30 GLN Chi-restraints excluded: chain P residue 63 ARG Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 130 ILE Chi-restraints excluded: chain P residue 402 THR Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain P residue 426 VAL Chi-restraints excluded: chain P residue 461 GLU Chi-restraints excluded: chain P residue 467 GLU Chi-restraints excluded: chain P residue 489 THR Chi-restraints excluded: chain P residue 532 ARG Chi-restraints excluded: chain P residue 569 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 5 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 366 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 = 0.3719 r_free = 0.3719 target = 0.135792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105189 restraints weight = 31787.974| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.05 r_work: 0.3148 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10315 Z= 0.165 Angle : 0.593 7.516 14971 Z= 0.358 Chirality : 0.041 0.306 1811 Planarity : 0.005 0.062 1080 Dihedral : 23.978 169.303 3899 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.46 % Allowed : 15.12 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.00 (0.34), residues: 601 helix: 1.40 (0.34), residues: 226 sheet: 0.21 (0.66), residues: 66 loop : -1.14 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 80 TYR 0.016 0.001 TYR P 4 PHE 0.011 0.001 PHE P 263 TRP 0.006 0.001 TRP P 430 HIS 0.004 0.001 HIS P 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.17 (10308) covalent geometry : angle 0.59148 / 0.36 (14968) hydrogen bonds : bond 0.05298 / 5.80 ( 394) hydrogen bonds : angle 3.91079 / 5.16 ( 941) metal coordination : bond 0.01856 / 0.85 ( 7) metal coordination : angle 3.47835 / 6.77 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.362 Fit side-chains REVERT: P 294 VAL cc_start: 0.8461 (t) cc_final: 0.8195 (p) REVERT: P 336 ASP cc_start: 0.7524 (m-30) cc_final: 0.7315 (t70) REVERT: P 356 ARG cc_start: 0.7614 (mtp180) cc_final: 0.7346 (mtp180) REVERT: P 532 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8224 (mtm-85) outliers start: 13 outliers final: 11 residues processed: 121 average time/residue: 1.3730 time to fit residues: 175.9537 Evaluate side-chains 124 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 17 CYS Chi-restraints excluded: chain P residue 27 LYS Chi-restraints excluded: chain P residue 30 GLN Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 402 THR Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain P residue 426 VAL Chi-restraints excluded: chain P residue 456 HIS Chi-restraints excluded: chain P residue 461 GLU Chi-restraints excluded: chain P residue 467 GLU Chi-restraints excluded: chain P residue 532 ARG Chi-restraints excluded: chain P residue 569 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 366 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 = 0.3726 r_free = 0.3726 target = 0.136381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.105710 restraints weight = 31822.349| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.06 r_work: 0.3171 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10315 Z= 0.178 Angle : 0.588 7.565 14971 Z= 0.352 Chirality : 0.041 0.331 1811 Planarity : 0.005 0.058 1080 Dihedral : 23.856 169.774 3899 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.65 % Allowed : 15.12 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.13 (0.34), residues: 601 helix: 1.61 (0.34), residues: 226 sheet: 0.22 (0.66), residues: 66 loop : -1.14 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 80 TYR 0.014 0.001 TYR P 4 PHE 0.010 0.001 PHE P 556 TRP 0.006 0.001 TRP P 430 HIS 0.005 0.002 HIS P 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.18 (10308) covalent geometry : angle 0.58685 / 0.35 (14968) hydrogen bonds : bond 0.05083 / 5.58 ( 394) hydrogen bonds : angle 3.83230 / 5.06 ( 941) metal coordination : bond 0.01720 / 0.86 ( 7) metal coordination : angle 2.95177 / 5.71 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: P 294 VAL cc_start: 0.8463 (t) cc_final: 0.8177 (p) REVERT: P 356 ARG cc_start: 0.7617 (mtp180) cc_final: 0.7351 (mtp180) REVERT: P 532 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8249 (mtm-85) outliers start: 14 outliers final: 10 residues processed: 118 average time/residue: 1.3679 time to fit residues: 171.1818 Evaluate side-chains 120 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 17 CYS Chi-restraints excluded: chain P residue 30 GLN Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain P residue 426 VAL Chi-restraints excluded: chain P residue 456 HIS Chi-restraints excluded: chain P residue 461 GLU Chi-restraints excluded: chain P residue 467 GLU Chi-restraints excluded: chain P residue 521 LYS Chi-restraints excluded: chain P residue 532 ARG Chi-restraints excluded: chain P residue 569 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 26 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 152 ASN ** P 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.137551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.107120 restraints weight = 31842.964| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.06 r_work: 0.3207 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10315 Z= 0.148 Angle : 0.558 7.157 14971 Z= 0.336 Chirality : 0.039 0.280 1811 Planarity : 0.005 0.057 1080 Dihedral : 23.809 170.127 3899 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.46 % Allowed : 15.50 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.34), residues: 601 helix: 1.80 (0.34), residues: 226 sheet: 0.21 (0.67), residues: 66 loop : -1.15 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 80 TYR 0.013 0.001 TYR P 4 PHE 0.008 0.001 PHE P 263 TRP 0.007 0.001 TRP P 430 HIS 0.004 0.001 HIS P 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (10308) covalent geometry : angle 0.55588 / 0.34 (14968) hydrogen bonds : bond 0.04878 / 5.36 ( 394) hydrogen bonds : angle 3.75544 / 4.98 ( 941) metal coordination : bond 0.01881 / 0.88 ( 7) metal coordination : angle 3.17488 / 6.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: P 336 ASP cc_start: 0.7513 (t70) cc_final: 0.7248 (t0) REVERT: P 356 ARG cc_start: 0.7579 (mtp180) cc_final: 0.7317 (mtp180) outliers start: 13 outliers final: 9 residues processed: 113 average time/residue: 1.4562 time to fit residues: 174.1682 Evaluate side-chains 121 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 17 CYS Chi-restraints excluded: chain P residue 30 GLN Chi-restraints excluded: chain P residue 398 LYS Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain P residue 456 HIS Chi-restraints excluded: chain P residue 461 GLU Chi-restraints excluded: chain P residue 467 GLU Chi-restraints excluded: chain P residue 525 LYS Chi-restraints excluded: chain P residue 569 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 152 ASN ** P 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.135894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.105302 restraints weight = 31543.418| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.06 r_work: 0.3167 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10315 Z= 0.202 Angle : 0.590 7.894 14971 Z= 0.351 Chirality : 0.041 0.340 1811 Planarity : 0.005 0.056 1080 Dihedral : 23.706 169.781 3899 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.27 % Allowed : 15.88 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.18 (0.34), residues: 601 helix: 1.75 (0.34), residues: 226 sheet: 0.19 (0.65), residues: 66 loop : -1.18 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 80 TYR 0.016 0.002 TYR P 4 PHE 0.013 0.002 PHE P 556 TRP 0.006 0.001 TRP P 430 HIS 0.006 0.002 HIS P 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.20 (10308) covalent geometry : angle 0.58857 / 0.35 (14968) hydrogen bonds : bond 0.05137 / 5.62 ( 394) hydrogen bonds : angle 3.78400 / 4.99 ( 941) metal coordination : bond 0.01696 / 0.96 ( 7) metal coordination : angle 2.76984 / 5.35 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: P 356 ARG cc_start: 0.7608 (mtp180) cc_final: 0.7338 (mtp180) outliers start: 12 outliers final: 10 residues processed: 115 average time/residue: 1.3563 time to fit residues: 165.2577 Evaluate side-chains 117 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 17 CYS Chi-restraints excluded: chain P residue 30 GLN Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 152 ASN Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain P residue 456 HIS Chi-restraints excluded: chain P residue 461 GLU Chi-restraints excluded: chain P residue 467 GLU Chi-restraints excluded: chain P residue 525 LYS Chi-restraints excluded: chain P residue 569 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 39 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 152 ASN ** P 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.135962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.105328 restraints weight = 31754.355| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.06 r_work: 0.3179 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.320 10315 Z= 0.320 Angle : 0.878 59.196 14971 Z= 0.557 Chirality : 0.041 0.339 1811 Planarity : 0.005 0.056 1080 Dihedral : 23.706 169.777 3899 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.70 % Allowed : 17.20 % Favored : 81.10 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 7.41 % 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: 0.19 (0.34), residues: 601 helix: 1.75 (0.34), residues: 226 sheet: 0.18 (0.65), residues: 66 loop : -1.18 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 80 TYR 0.016 0.002 TYR P 4 PHE 0.012 0.002 PHE P 556 TRP 0.006 0.001 TRP P 430 HIS 0.006 0.002 HIS P 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.32 (10308) covalent geometry : angle 0.87672 / 0.56 (14968) hydrogen bonds : bond 0.05134 / 5.61 ( 394) hydrogen bonds : angle 3.78353 / 4.99 ( 941) metal coordination : bond 0.01699 / 0.95 ( 7) metal coordination : angle 2.76923 / 5.35 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6946.14 seconds wall clock time: 118 minutes 1.47 seconds (7081.47 seconds total)