Starting phenix.real_space_refine on Thu Aug 6 21:26:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cf3_45528/08_2026/9cf3_45528.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cf3_45528/08_2026/9cf3_45528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cf3_45528/08_2026/9cf3_45528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cf3_45528/08_2026/9cf3_45528.map" model { file = "/net/cci-nas-00/data/ceres_data/9cf3_45528/08_2026/9cf3_45528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cf3_45528/08_2026/9cf3_45528.cif" } resolution = 3.2 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= 0.050 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: 6 Type Number sf(0) Gaussians P 98 5.49 5 S 35 5.16 5 C 5573 2.51 5 N 1629 2.21 5 O 1933 1.98 5 H 8383 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 17651 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2426 Classifications: {'peptide': 162} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 151} Chain: "N" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 350 Classifications: {'DNA': 11} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 10} Chain: "P" Number of atoms: 12097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 12097 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 26, 'TRANS': 699} Chain breaks: 1 Chain: "T" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 991 Classifications: {'DNA': 31} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 30} Chain breaks: 1 Chain: "W" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1787 Classifications: {'DNA': 15, 'RNA': 41} Modifications used: {'3*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p_pur': 18, 'rna3p_pyr': 16} Link IDs: {'rna2p': 7, 'rna3p': 48} Time building chain proxies: 2.98, per 1000 atoms: 0.17 Number of scatterers: 17651 At special positions: 0 Unit cell: (81.675, 119.625, 123.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 98 15.00 O 1933 8.00 N 1629 7.00 C 5573 6.00 H 8383 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: 1.53 Conformation dependent library (CDL) restraints added in 664.8 milliseconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1684 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 7 sheets defined 51.9% alpha, 12.3% beta 36 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'B' and resid 27 through 40 Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 133 through 143 removed outlier: 3.647A pdb=" N LEU B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 114 through 118 Processing helix chain 'P' and resid 119 through 121 No H-bonds generated for 'chain 'P' and resid 119 through 121' Processing helix chain 'P' and resid 122 through 155 removed outlier: 3.662A pdb=" N LEU P 126 " --> pdb=" O TYR P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 160 through 164 removed outlier: 3.542A pdb=" N ILE P 164 " --> pdb=" O ASN P 161 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 176 removed outlier: 3.637A pdb=" N LEU P 176 " --> pdb=" O VAL P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 187 removed outlier: 3.669A pdb=" N ARG P 186 " --> pdb=" O ASN P 183 " (cutoff:3.500A) Processing helix chain 'P' and resid 188 through 210 removed outlier: 3.974A pdb=" N HIS P 201 " --> pdb=" O LEU P 197 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP P 203 " --> pdb=" O GLY P 199 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ALA P 204 " --> pdb=" O LYS P 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 255 removed outlier: 3.545A pdb=" N ALA P 228 " --> pdb=" O LEU P 224 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS P 229 " --> pdb=" O TYR P 225 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLY P 243 " --> pdb=" O LYS P 239 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN P 244 " --> pdb=" O ALA P 240 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG P 245 " --> pdb=" O HIS P 241 " (cutoff:3.500A) Processing helix chain 'P' and resid 255 through 270 Processing helix chain 'P' and resid 273 through 285 Processing helix chain 'P' and resid 285 through 298 Processing helix chain 'P' and resid 308 through 320 Processing helix chain 'P' and resid 332 through 340 removed outlier: 3.866A pdb=" N VAL P 338 " --> pdb=" O PHE P 334 " (cutoff:3.500A) Processing helix chain 'P' and resid 341 through 343 No H-bonds generated for 'chain 'P' and resid 341 through 343' Processing helix chain 'P' and resid 344 through 358 Processing helix chain 'P' and resid 381 through 388 removed outlier: 4.311A pdb=" N TYR P 386 " --> pdb=" O LYS P 382 " (cutoff:3.500A) Processing helix chain 'P' and resid 396 through 398 No H-bonds generated for 'chain 'P' and resid 396 through 398' Processing helix chain 'P' and resid 399 through 406 removed outlier: 3.586A pdb=" N ARG P 406 " --> pdb=" O ASN P 402 " (cutoff:3.500A) Processing helix chain 'P' and resid 419 through 423 Processing helix chain 'P' and resid 466 through 470 Processing helix chain 'P' and resid 471 through 476 Processing helix chain 'P' and resid 477 through 479 No H-bonds generated for 'chain 'P' and resid 477 through 479' Processing helix chain 'P' and resid 512 through 516 Processing helix chain 'P' and resid 516 through 529 Processing helix chain 'P' and resid 531 through 542 Processing helix chain 'P' and resid 550 through 574 removed outlier: 3.523A pdb=" N VAL P 564 " --> pdb=" O ALA P 560 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ASP P 566 " --> pdb=" O ALA P 562 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE P 567 " --> pdb=" O SER P 563 " (cutoff:3.500A) Processing helix chain 'P' and resid 622 through 628 removed outlier: 3.714A pdb=" N LYS P 626 " --> pdb=" O ASP P 622 " (cutoff:3.500A) Processing helix chain 'P' and resid 628 through 639 removed outlier: 4.016A pdb=" N THR P 632 " --> pdb=" O HIS P 628 " (cutoff:3.500A) Processing helix chain 'P' and resid 640 through 645 Processing helix chain 'P' and resid 648 through 665 Processing helix chain 'P' and resid 668 through 679 removed outlier: 3.891A pdb=" N LYS P 672 " --> pdb=" O GLU P 668 " (cutoff:3.500A) Processing helix chain 'P' and resid 680 through 684 Processing helix chain 'P' and resid 686 through 713 Processing helix chain 'P' and resid 738 through 747 Processing helix chain 'P' and resid 780 through 786 removed outlier: 3.879A pdb=" N GLU P 785 " --> pdb=" O HIS P 782 " (cutoff:3.500A) Processing helix chain 'P' and resid 800 through 804 removed outlier: 3.994A pdb=" N LEU P 804 " --> pdb=" O MET P 801 " (cutoff:3.500A) Processing helix chain 'P' and resid 818 through 837 Processing sheet with id=AA1, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.797A pdb=" N ARG B 53 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N GLN B 109 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 128 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N MET B 98 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 126 " --> pdb=" O MET B 98 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL B 19 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ALA B 10 " --> pdb=" O PRO B 14 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY B 16 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 158 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU B 9 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL B 156 " --> pdb=" O GLU B 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 107 through 113 removed outlier: 3.513A pdb=" N LEU P 440 " --> pdb=" O THR P 429 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N THR P 429 " --> pdb=" O LEU P 440 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N GLN P 442 " --> pdb=" O GLN P 427 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N GLN P 427 " --> pdb=" O GLN P 442 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 177 through 178 Processing sheet with id=AA4, first strand: chain 'P' and resid 507 through 511 removed outlier: 5.918A pdb=" N VAL P 483 " --> pdb=" O VAL P 720 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N GLY P 722 " --> pdb=" O VAL P 483 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N MET P 485 " --> pdb=" O GLY P 722 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 591 through 593 removed outlier: 3.522A pdb=" N ALA P 607 " --> pdb=" O LEU P 599 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR P 601 " --> pdb=" O PHE P 605 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N PHE P 605 " --> pdb=" O TYR P 601 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 770 through 772 Processing sheet with id=AA7, first strand: chain 'P' and resid 775 through 777 342 hydrogen bonds defined for protein. 978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 90 hydrogen bonds 176 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 4.10 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8366 1.03 - 1.23: 53 1.23 - 1.42: 4148 1.42 - 1.62: 5433 1.62 - 1.81: 53 Bond restraints: 18053 Sorted by residual: bond pdb=" C3' DT T 0 " pdb=" C2' DT T 0 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C1' DC N -8 " pdb=" N1 DC N -8 " ideal model delta sigma weight residual 1.468 1.515 -0.047 1.40e-02 5.10e+03 1.14e+01 bond pdb=" C3' DG T 8 " pdb=" C2' DG T 8 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DT N -3 " pdb=" C2' DT N -3 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.33e+00 bond pdb=" C1' DC T 4 " pdb=" N1 DC T 4 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.77e+00 ... (remaining 18048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 32294 2.37 - 4.75: 309 4.75 - 7.12: 11 7.12 - 9.49: 9 9.49 - 11.86: 19 Bond angle restraints: 32642 Sorted by residual: angle pdb=" O4' U W 30 " pdb=" C1' U W 30 " pdb=" N1 U W 30 " ideal model delta sigma weight residual 108.50 117.35 -8.85 7.00e-01 2.04e+00 1.60e+02 angle pdb=" C2' A W 32 " pdb=" C1' A W 32 " pdb=" N9 A W 32 " ideal model delta sigma weight residual 112.00 119.05 -7.05 1.10e+00 8.26e-01 4.11e+01 angle pdb=" O4' A W 28 " pdb=" C1' A W 28 " pdb=" N9 A W 28 " ideal model delta sigma weight residual 108.50 104.20 4.30 7.00e-01 2.04e+00 3.77e+01 angle pdb=" C2' U W 30 " pdb=" C1' U W 30 " pdb=" N1 U W 30 " ideal model delta sigma weight residual 112.00 118.42 -6.42 1.10e+00 8.26e-01 3.41e+01 angle pdb=" O5' U W 31 " pdb=" C5' U W 31 " pdb=" C4' U W 31 " ideal model delta sigma weight residual 109.40 113.55 -4.15 8.00e-01 1.56e+00 2.69e+01 ... (remaining 32637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 7889 35.59 - 71.18: 361 71.18 - 106.78: 24 106.78 - 142.37: 9 142.37 - 177.96: 6 Dihedral angle restraints: 8289 sinusoidal: 5163 harmonic: 3126 Sorted by residual: dihedral pdb=" C4' A W 7 " pdb=" C3' A W 7 " pdb=" C2' A W 7 " pdb=" C1' A W 7 " ideal model delta sinusoidal sigma weight residual -35.00 37.48 -72.48 1 8.00e+00 1.56e-02 1.05e+02 dihedral pdb=" C5' A W 7 " pdb=" C4' A W 7 " pdb=" C3' A W 7 " pdb=" O3' A W 7 " ideal model delta sinusoidal sigma weight residual 147.00 74.96 72.04 1 8.00e+00 1.56e-02 1.04e+02 dihedral pdb=" O4' A W 7 " pdb=" C4' A W 7 " pdb=" C3' A W 7 " pdb=" C2' A W 7 " ideal model delta sinusoidal sigma weight residual 24.00 -39.54 63.54 1 8.00e+00 1.56e-02 8.32e+01 ... (remaining 8286 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 1410 0.114 - 0.229: 72 0.229 - 0.343: 7 0.343 - 0.458: 8 0.458 - 0.572: 1 Chirality restraints: 1498 Sorted by residual: chirality pdb=" C1' U W 30 " pdb=" O4' U W 30 " pdb=" C2' U W 30 " pdb=" N1 U W 30 " both_signs ideal model delta sigma weight residual False 2.47 1.90 0.57 2.00e-01 2.50e+01 8.18e+00 chirality pdb=" P DT N -1 " pdb=" OP1 DT N -1 " pdb=" OP2 DT N -1 " pdb=" O5' DT N -1 " both_signs ideal model delta sigma weight residual True 2.34 -2.77 -0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" P DA T 1 " pdb=" OP1 DA T 1 " pdb=" OP2 DA T 1 " pdb=" O5' DA T 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.77 -0.43 2.00e-01 2.50e+01 4.62e+00 ... (remaining 1495 not shown) Planarity restraints: 2290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U W 30 " 0.033 2.00e-02 2.50e+03 2.13e-02 1.36e+01 pdb=" N1 U W 30 " -0.026 2.00e-02 2.50e+03 pdb=" C2 U W 30 " -0.032 2.00e-02 2.50e+03 pdb=" O2 U W 30 " -0.001 2.00e-02 2.50e+03 pdb=" N3 U W 30 " 0.035 2.00e-02 2.50e+03 pdb=" C4 U W 30 " -0.028 2.00e-02 2.50e+03 pdb=" O4 U W 30 " 0.024 2.00e-02 2.50e+03 pdb=" C5 U W 30 " -0.007 2.00e-02 2.50e+03 pdb=" C6 U W 30 " 0.001 2.00e-02 2.50e+03 pdb=" H5 U W 30 " -0.000 2.00e-02 2.50e+03 pdb=" H3 U W 30 " -0.002 2.00e-02 2.50e+03 pdb=" H6 U W 30 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A W 32 " -0.031 2.00e-02 2.50e+03 1.89e-02 1.17e+01 pdb=" N9 A W 32 " 0.030 2.00e-02 2.50e+03 pdb=" C8 A W 32 " -0.000 2.00e-02 2.50e+03 pdb=" N7 A W 32 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A W 32 " 0.004 2.00e-02 2.50e+03 pdb=" C6 A W 32 " 0.008 2.00e-02 2.50e+03 pdb=" N6 A W 32 " -0.004 2.00e-02 2.50e+03 pdb=" N1 A W 32 " -0.039 2.00e-02 2.50e+03 pdb=" C2 A W 32 " 0.034 2.00e-02 2.50e+03 pdb=" N3 A W 32 " -0.000 2.00e-02 2.50e+03 pdb=" C4 A W 32 " -0.000 2.00e-02 2.50e+03 pdb=" H8 A W 32 " 0.001 2.00e-02 2.50e+03 pdb=" H2 A W 32 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS P 738 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C LYS P 738 " 0.037 2.00e-02 2.50e+03 pdb=" O LYS P 738 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY P 739 " -0.013 2.00e-02 2.50e+03 ... (remaining 2287 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.88: 87 1.88 - 2.56: 14671 2.56 - 3.24: 53844 3.24 - 3.92: 66159 3.92 - 4.60: 107176 Nonbonded interactions: 241937 Sorted by model distance: nonbonded pdb="HE21 GLN P 221 " pdb=" OH TYR P 225 " model vdw 1.194 2.450 nonbonded pdb=" HG3 GLN P 221 " pdb=" CE2 TYR P 225 " model vdw 1.295 2.970 nonbonded pdb=" O THR P 759 " pdb="HD21 ASN P 825 " model vdw 1.609 2.450 nonbonded pdb=" HZ3 LYS P 400 " pdb=" O GLN P 427 " model vdw 1.611 2.450 nonbonded pdb=" O THR P 539 " pdb=" HG SER P 542 " model vdw 1.622 2.450 ... (remaining 241932 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: 1.710 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: 0.040 Set scattering table: 0.030 Process input model: 18.980 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: 0.000 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: 22.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 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 : 0.003 0.047 9670 Z= 0.288 Angle : 0.787 11.863 13460 Z= 0.565 Chirality : 0.061 0.572 1498 Planarity : 0.003 0.037 1368 Dihedral : 18.408 177.959 4055 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.30), residues: 882 helix: 2.73 (0.27), residues: 384 sheet: 2.12 (0.65), residues: 60 loop : 0.42 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 490 TYR 0.008 0.001 TYR P 613 PHE 0.007 0.001 PHE B 111 TRP 0.006 0.001 TRP P 724 HIS 0.003 0.001 HIS P 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.29 ( 9670) covalent geometry : angle 0.78658 / 0.56 (13460) hydrogen bonds : bond 0.14134 / 9.01 ( 432) hydrogen bonds : angle 5.87688 / 4.06 ( 1154) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 LEU cc_start: 0.7214 (mp) cc_final: 0.6502 (mp) REVERT: B 98 MET cc_start: 0.7007 (mmm) cc_final: 0.6665 (mmt) REVERT: P 342 GLU cc_start: 0.7427 (pm20) cc_final: 0.7226 (pm20) REVERT: P 380 ASP cc_start: 0.6928 (t70) cc_final: 0.6655 (t70) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2988 time to fit residues: 78.4007 Evaluate side-chains 106 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 220 GLN P 284 ASN ** P 598 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 = 0.4079 r_free = 0.4079 target = 0.141297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.112769 restraints weight = 47105.483| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.03 r_work: 0.3559 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9670 Z= 0.177 Angle : 0.642 9.581 13460 Z= 0.374 Chirality : 0.045 0.227 1498 Planarity : 0.004 0.037 1368 Dihedral : 22.795 177.229 2197 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.14 % Allowed : 7.95 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.29), residues: 882 helix: 2.14 (0.26), residues: 386 sheet: 1.83 (0.60), residues: 58 loop : 0.20 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 412 TYR 0.010 0.001 TYR B 5 PHE 0.024 0.001 PHE B 111 TRP 0.005 0.001 TRP P 724 HIS 0.011 0.001 HIS P 671 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 ( 9670) covalent geometry : angle 0.64204 / 0.37 (13460) hydrogen bonds : bond 0.06121 / 4.27 ( 432) hydrogen bonds : angle 5.04921 / 3.57 ( 1154) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ASP cc_start: 0.6501 (m-30) cc_final: 0.6220 (m-30) outliers start: 9 outliers final: 7 residues processed: 101 average time/residue: 0.1994 time to fit residues: 29.0280 Evaluate side-chains 92 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 308 ASP Chi-restraints excluded: chain P residue 677 SER Chi-restraints excluded: chain P residue 678 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 13 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 161 ASN P 284 ASN P 513 ASN P 817 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.134765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.106740 restraints weight = 46520.054| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.91 r_work: 0.3482 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9670 Z= 0.237 Angle : 0.653 7.887 13460 Z= 0.380 Chirality : 0.046 0.244 1498 Planarity : 0.005 0.044 1368 Dihedral : 22.966 175.632 2197 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.39 % Allowed : 8.96 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.28), residues: 882 helix: 1.69 (0.26), residues: 386 sheet: 0.72 (0.58), residues: 65 loop : -0.09 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 688 TYR 0.011 0.002 TYR B 5 PHE 0.017 0.002 PHE B 111 TRP 0.007 0.001 TRP P 724 HIS 0.004 0.001 HIS P 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.24 ( 9670) covalent geometry : angle 0.65315 / 0.38 (13460) hydrogen bonds : bond 0.06268 / 4.39 ( 432) hydrogen bonds : angle 4.98041 / 3.49 ( 1154) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 TYR cc_start: 0.6859 (p90) cc_final: 0.6644 (p90) REVERT: B 7 ASP cc_start: 0.6353 (m-30) cc_final: 0.5922 (m-30) outliers start: 11 outliers final: 8 residues processed: 99 average time/residue: 0.2075 time to fit residues: 29.4548 Evaluate side-chains 87 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain P residue 308 ASP Chi-restraints excluded: chain P residue 677 SER Chi-restraints excluded: chain P residue 678 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 30 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 631 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 = 0.4009 r_free = 0.4009 target = 0.135846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.106776 restraints weight = 47199.484| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.10 r_work: 0.3469 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9670 Z= 0.178 Angle : 0.607 8.251 13460 Z= 0.354 Chirality : 0.043 0.224 1498 Planarity : 0.004 0.034 1368 Dihedral : 23.016 175.707 2197 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.39 % Allowed : 10.10 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.28), residues: 882 helix: 1.65 (0.26), residues: 392 sheet: 0.51 (0.60), residues: 63 loop : -0.16 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 520 TYR 0.009 0.001 TYR P 205 PHE 0.015 0.001 PHE B 111 TRP 0.004 0.001 TRP P 724 HIS 0.006 0.001 HIS P 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 ( 9670) covalent geometry : angle 0.60728 / 0.35 (13460) hydrogen bonds : bond 0.05901 / 4.18 ( 432) hydrogen bonds : angle 4.83608 / 3.41 ( 1154) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ASP cc_start: 0.6001 (m-30) cc_final: 0.5672 (m-30) outliers start: 11 outliers final: 9 residues processed: 94 average time/residue: 0.2061 time to fit residues: 27.9873 Evaluate side-chains 89 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 308 ASP Chi-restraints excluded: chain P residue 590 ASP Chi-restraints excluded: chain P residue 677 SER Chi-restraints excluded: chain P residue 678 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 28 optimal weight: 0.1980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 284 ASN P 316 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.135649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.106798 restraints weight = 46882.740| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.07 r_work: 0.3468 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9670 Z= 0.159 Angle : 0.580 8.940 13460 Z= 0.338 Chirality : 0.042 0.225 1498 Planarity : 0.004 0.034 1368 Dihedral : 22.986 176.229 2197 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.39 % Allowed : 10.10 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.28), residues: 882 helix: 1.83 (0.26), residues: 386 sheet: 0.52 (0.59), residues: 65 loop : -0.19 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 153 TYR 0.015 0.001 TYR B 5 PHE 0.022 0.001 PHE P 158 TRP 0.004 0.001 TRP P 724 HIS 0.009 0.001 HIS P 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 ( 9670) covalent geometry : angle 0.57966 / 0.34 (13460) hydrogen bonds : bond 0.05784 / 4.11 ( 432) hydrogen bonds : angle 4.69310 / 3.31 ( 1154) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ASP cc_start: 0.6167 (m-30) cc_final: 0.5900 (m-30) REVERT: B 32 GLU cc_start: 0.8254 (tp30) cc_final: 0.7901 (tp30) REVERT: P 158 PHE cc_start: 0.7503 (t80) cc_final: 0.7214 (t80) outliers start: 11 outliers final: 9 residues processed: 92 average time/residue: 0.2003 time to fit residues: 26.8850 Evaluate side-chains 90 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 308 ASP Chi-restraints excluded: chain P residue 327 THR Chi-restraints excluded: chain P residue 496 MET Chi-restraints excluded: chain P residue 677 SER Chi-restraints excluded: chain P residue 699 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.135652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.106864 restraints weight = 46834.043| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.08 r_work: 0.3466 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9670 Z= 0.158 Angle : 0.580 7.970 13460 Z= 0.334 Chirality : 0.042 0.278 1498 Planarity : 0.004 0.037 1368 Dihedral : 22.857 177.432 2197 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.26 % Allowed : 10.23 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.28), residues: 882 helix: 1.86 (0.26), residues: 386 sheet: 0.48 (0.58), residues: 67 loop : -0.25 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 780 TYR 0.010 0.001 TYR P 205 PHE 0.013 0.001 PHE B 111 TRP 0.004 0.001 TRP P 724 HIS 0.004 0.001 HIS P 671 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 ( 9670) covalent geometry : angle 0.57968 / 0.33 (13460) hydrogen bonds : bond 0.05794 / 4.11 ( 432) hydrogen bonds : angle 4.60363 / 3.26 ( 1154) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 GLU cc_start: 0.8194 (tp30) cc_final: 0.7831 (tp30) outliers start: 10 outliers final: 7 residues processed: 93 average time/residue: 0.1785 time to fit residues: 23.7613 Evaluate side-chains 87 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 327 THR Chi-restraints excluded: chain P residue 677 SER Chi-restraints excluded: chain P residue 699 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 65 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 67 optimal weight: 0.0070 chunk 14 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 overall best weight: 1.0800 ------------------------------------------------------------------------------- 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 = 0.4009 r_free = 0.4009 target = 0.136080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.107353 restraints weight = 47078.617| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.08 r_work: 0.3476 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9670 Z= 0.131 Angle : 0.546 5.940 13460 Z= 0.317 Chirality : 0.040 0.222 1498 Planarity : 0.004 0.035 1368 Dihedral : 22.764 177.651 2197 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.88 % Allowed : 11.11 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.28), residues: 882 helix: 1.96 (0.26), residues: 386 sheet: 0.36 (0.58), residues: 67 loop : -0.23 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 780 TYR 0.009 0.001 TYR P 205 PHE 0.020 0.001 PHE P 158 TRP 0.004 0.001 TRP B 119 HIS 0.004 0.001 HIS P 671 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 ( 9670) covalent geometry : angle 0.54597 / 0.32 (13460) hydrogen bonds : bond 0.05655 / 4.03 ( 432) hydrogen bonds : angle 4.51898 / 3.20 ( 1154) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 GLU cc_start: 0.8179 (tp30) cc_final: 0.7821 (tp30) outliers start: 7 outliers final: 7 residues processed: 86 average time/residue: 0.1693 time to fit residues: 21.1370 Evaluate side-chains 85 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 327 THR Chi-restraints excluded: chain P residue 699 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 88 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 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 = 0.4017 r_free = 0.4017 target = 0.136663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.107926 restraints weight = 47189.808| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.09 r_work: 0.3482 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9670 Z= 0.128 Angle : 0.541 5.879 13460 Z= 0.314 Chirality : 0.040 0.220 1498 Planarity : 0.004 0.034 1368 Dihedral : 22.734 178.039 2197 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.26 % Allowed : 10.73 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.28), residues: 882 helix: 2.02 (0.26), residues: 386 sheet: 0.32 (0.57), residues: 67 loop : -0.23 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 490 TYR 0.009 0.001 TYR P 205 PHE 0.026 0.001 PHE P 158 TRP 0.004 0.001 TRP B 119 HIS 0.004 0.001 HIS P 671 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.13 ( 9670) covalent geometry : angle 0.54105 / 0.31 (13460) hydrogen bonds : bond 0.05626 / 4.01 ( 432) hydrogen bonds : angle 4.45075 / 3.15 ( 1154) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 86 average time/residue: 0.1745 time to fit residues: 21.7920 Evaluate side-chains 86 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 327 THR Chi-restraints excluded: chain P residue 433 ASP Chi-restraints excluded: chain P residue 699 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.0980 chunk 2 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 161 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.134551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.105839 restraints weight = 47464.416| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.08 r_work: 0.3448 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9670 Z= 0.191 Angle : 0.582 6.436 13460 Z= 0.334 Chirality : 0.041 0.229 1498 Planarity : 0.004 0.032 1368 Dihedral : 22.744 179.389 2197 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.74 % Favored : 96.15 % Rotamer: Outliers : 1.39 % Allowed : 10.48 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.28), residues: 882 helix: 1.83 (0.26), residues: 386 sheet: 0.20 (0.58), residues: 67 loop : -0.38 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 561 TYR 0.014 0.001 TYR B 5 PHE 0.031 0.002 PHE P 158 TRP 0.004 0.001 TRP P 724 HIS 0.005 0.001 HIS P 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 ( 9670) covalent geometry : angle 0.58200 / 0.33 (13460) hydrogen bonds : bond 0.05912 / 4.20 ( 432) hydrogen bonds : angle 4.53165 / 3.21 ( 1154) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.407 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: P 158 PHE cc_start: 0.6845 (t80) cc_final: 0.6624 (t80) outliers start: 11 outliers final: 11 residues processed: 87 average time/residue: 0.1905 time to fit residues: 24.0294 Evaluate side-chains 87 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 327 THR Chi-restraints excluded: chain P residue 433 ASP Chi-restraints excluded: chain P residue 677 SER Chi-restraints excluded: chain P residue 699 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.135024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.106432 restraints weight = 47280.761| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.08 r_work: 0.3454 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9670 Z= 0.150 Angle : 0.557 6.144 13460 Z= 0.321 Chirality : 0.040 0.226 1498 Planarity : 0.004 0.033 1368 Dihedral : 22.724 179.812 2197 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.51 % Favored : 96.37 % Rotamer: Outliers : 0.88 % Allowed : 10.86 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.28), residues: 882 helix: 1.88 (0.26), residues: 385 sheet: 0.16 (0.59), residues: 67 loop : -0.31 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 153 TYR 0.011 0.001 TYR B 5 PHE 0.020 0.001 PHE P 158 TRP 0.004 0.001 TRP P 724 HIS 0.004 0.001 HIS P 671 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 ( 9670) covalent geometry : angle 0.55671 / 0.32 (13460) hydrogen bonds : bond 0.05748 / 4.09 ( 432) hydrogen bonds : angle 4.47739 / 3.17 ( 1154) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 83 average time/residue: 0.1877 time to fit residues: 22.1820 Evaluate side-chains 82 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 327 THR Chi-restraints excluded: chain P residue 433 ASP Chi-restraints excluded: chain P residue 699 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 51 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.134109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.105556 restraints weight = 47526.332| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.08 r_work: 0.3443 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9670 Z= 0.175 Angle : 0.568 6.386 13460 Z= 0.326 Chirality : 0.041 0.230 1498 Planarity : 0.004 0.033 1368 Dihedral : 22.711 179.685 2197 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.74 % Favored : 96.15 % Rotamer: Outliers : 1.01 % Allowed : 11.11 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.28), residues: 882 helix: 1.83 (0.26), residues: 385 sheet: 0.06 (0.59), residues: 67 loop : -0.37 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 780 TYR 0.010 0.001 TYR B 5 PHE 0.016 0.001 PHE P 158 TRP 0.004 0.001 TRP P 724 HIS 0.004 0.001 HIS P 671 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 ( 9670) covalent geometry : angle 0.56808 / 0.33 (13460) hydrogen bonds : bond 0.05854 / 4.16 ( 432) hydrogen bonds : angle 4.50715 / 3.19 ( 1154) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4219.14 seconds wall clock time: 72 minutes 18.44 seconds (4338.44 seconds total)