Starting phenix.real_space_refine on Thu Jul 2 16:51:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8r_44356/07_2026/9b8r_44356.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8r_44356/07_2026/9b8r_44356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b8r_44356/07_2026/9b8r_44356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8r_44356/07_2026/9b8r_44356.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b8r_44356/07_2026/9b8r_44356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8r_44356/07_2026/9b8r_44356.map" } resolution = 3.5 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= 0.002 sd= 0.047 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 Fe 4 7.16 5 P 22 5.49 5 S 47 5.16 5 C 5939 2.51 5 N 1590 2.21 5 O 1823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 103 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9425 Number of models: 1 Model: "" Number of chains: 4 Chain: "P" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 248 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "E" Number of atoms: 8967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8967 Classifications: {'peptide': 1119} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1066} Chain breaks: 2 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 4, 'ASP:plan': 3, 'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5209 SG CYS E 665 45.858 64.745 17.877 1.00 81.51 S ATOM 5297 SG CYS E 677 52.149 64.661 17.029 1.00 87.54 S ATOM 6033 SG CYS E 763 51.160 66.480 22.121 1.00 94.87 S ATOM 5226 SG CYS E 668 49.284 70.341 17.828 1.00 78.76 S Time building chain proxies: 2.12, per 1000 atoms: 0.22 Number of scatterers: 9425 At special positions: 0 Unit cell: (100.188, 110.952, 106.812, 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) Fe 4 26.01 S 47 16.00 P 22 15.00 O 1823 8.00 N 1590 7.00 C 5939 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 358.6 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 E1401 " pdb="FE4 SF4 E1401 " - pdb=" SG CYS E 668 " pdb="FE1 SF4 E1401 " - pdb=" SG CYS E 665 " pdb="FE2 SF4 E1401 " - pdb=" SG CYS E 677 " pdb="FE3 SF4 E1401 " - pdb=" SG CYS E 763 " Number of angles added : 12 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 13 sheets defined 49.2% alpha, 17.6% beta 5 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'E' and resid 27 through 50 Processing helix chain 'E' and resid 65 through 69 removed outlier: 3.549A pdb=" N ILE E 69 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 147 No H-bonds generated for 'chain 'E' and resid 145 through 147' Processing helix chain 'E' and resid 148 through 160 Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 195 through 216 Proline residue: E 208 - end of helix Processing helix chain 'E' and resid 234 through 237 Processing helix chain 'E' and resid 248 through 257 Processing helix chain 'E' and resid 354 through 370 Processing helix chain 'E' and resid 382 through 394 Processing helix chain 'E' and resid 397 through 403 Processing helix chain 'E' and resid 422 through 429 Processing helix chain 'E' and resid 433 through 437 removed outlier: 3.773A pdb=" N GLN E 437 " --> pdb=" O GLN E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 447 Processing helix chain 'E' and resid 455 through 466 removed outlier: 4.670A pdb=" N THR E 460 " --> pdb=" O PRO E 456 " (cutoff:3.500A) Proline residue: E 461 - end of helix removed outlier: 4.164A pdb=" N PHE E 464 " --> pdb=" O THR E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 466 through 488 Processing helix chain 'E' and resid 488 through 498 removed outlier: 3.517A pdb=" N PHE E 492 " --> pdb=" O TYR E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 510 Processing helix chain 'E' and resid 511 through 527 Processing helix chain 'E' and resid 577 through 598 Proline residue: E 589 - end of helix Processing helix chain 'E' and resid 603 through 607 Processing helix chain 'E' and resid 609 through 627 Processing helix chain 'E' and resid 643 through 653 Processing helix chain 'E' and resid 661 through 668 Processing helix chain 'E' and resid 693 through 706 removed outlier: 3.770A pdb=" N ASN E 706 " --> pdb=" O ARG E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 727 through 747 Processing helix chain 'E' and resid 769 through 798 removed outlier: 3.974A pdb=" N ILE E 798 " --> pdb=" O ASN E 794 " (cutoff:3.500A) Processing helix chain 'E' and resid 806 through 834 removed outlier: 3.523A pdb=" N LYS E 810 " --> pdb=" O ARG E 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 843 through 869 removed outlier: 3.633A pdb=" N ILE E 849 " --> pdb=" O GLU E 845 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG E 867 " --> pdb=" O ALA E 863 " (cutoff:3.500A) Processing helix chain 'E' and resid 905 through 919 removed outlier: 3.967A pdb=" N LEU E 910 " --> pdb=" O PRO E 906 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG E 913 " --> pdb=" O MET E 909 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR E 919 " --> pdb=" O HIS E 915 " (cutoff:3.500A) Processing helix chain 'E' and resid 993 through 1003 Processing helix chain 'E' and resid 1004 through 1008 Processing helix chain 'E' and resid 1011 through 1032 removed outlier: 3.709A pdb=" N VAL E1022 " --> pdb=" O ALA E1018 " (cutoff:3.500A) Processing helix chain 'E' and resid 1038 through 1047 Processing helix chain 'E' and resid 1055 through 1060 removed outlier: 3.750A pdb=" N GLU E1060 " --> pdb=" O LYS E1057 " (cutoff:3.500A) Processing helix chain 'E' and resid 1064 through 1078 Processing helix chain 'E' and resid 1079 through 1083 Processing helix chain 'E' and resid 1110 through 1114 Processing helix chain 'E' and resid 1115 through 1128 Processing helix chain 'E' and resid 1136 through 1141 Processing helix chain 'E' and resid 1142 through 1158 Processing helix chain 'E' and resid 1158 through 1165 Processing helix chain 'E' and resid 1177 through 1184 Processing sheet with id=AA1, first strand: chain 'E' and resid 75 through 78 removed outlier: 3.746A pdb=" N ARG E 75 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TRP E 264 " --> pdb=" O ASP E 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 81 through 87 removed outlier: 3.525A pdb=" N PHE E 129 " --> pdb=" O PHE E 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 166 through 172 removed outlier: 6.889A pdb=" N THR E 187 " --> pdb=" O CYS E 143 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N CYS E 143 " --> pdb=" O THR E 187 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP E 241 " --> pdb=" O ALA E 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 335 through 336 removed outlier: 6.869A pdb=" N GLY E 319 " --> pdb=" O THR E 348 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N PHE E 350 " --> pdb=" O GLY E 319 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU E 321 " --> pdb=" O PHE E 350 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU E 352 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N THR E 323 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N MET E 309 " --> pdb=" O ASN E 324 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU E 292 " --> pdb=" O MET E 309 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE E 311 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASP E 290 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR E 313 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA E 288 " --> pdb=" O TYR E 313 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE E 315 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL E 286 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N MET E 287 " --> pdb=" O SER E 375 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE E 374 " --> pdb=" O MET E 420 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 405 through 406 Processing sheet with id=AA6, first strand: chain 'E' and resid 542 through 543 Processing sheet with id=AA7, first strand: chain 'E' and resid 558 through 560 removed outlier: 6.926A pdb=" N TRP E 880 " --> pdb=" O LEU E 872 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU E 874 " --> pdb=" O GLY E 878 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY E 878 " --> pdb=" O LEU E 874 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE E 636 " --> pdb=" O PRO E 949 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 564 through 567 Processing sheet with id=AA9, first strand: chain 'E' and resid 572 through 575 Processing sheet with id=AB1, first strand: chain 'E' and resid 708 through 710 Processing sheet with id=AB2, first strand: chain 'E' and resid 890 through 894 Processing sheet with id=AB3, first strand: chain 'E' and resid 920 through 928 removed outlier: 4.044A pdb=" N GLN E 922 " --> pdb=" O HIS E 937 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N HIS E 937 " --> pdb=" O GLN E 922 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLN E 924 " --> pdb=" O GLU E 935 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLU E 935 " --> pdb=" O GLN E 924 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU E 926 " --> pdb=" O ILE E 933 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE E 933 " --> pdb=" O LEU E 926 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 991 through 992 removed outlier: 4.049A pdb=" N ASN E1049 " --> pdb=" O GLU E 991 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1329 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 3464 1.40 - 1.62: 6138 1.62 - 1.83: 72 1.83 - 2.05: 0 2.05 - 2.27: 12 Bond restraints: 9686 Sorted by residual: bond pdb=" C PRO E 949 " pdb=" N TYR E 950 " ideal model delta sigma weight residual 1.331 1.563 -0.232 1.30e-02 5.92e+03 3.18e+02 bond pdb=" C GLU E 766 " pdb=" N ASN E 767 " ideal model delta sigma weight residual 1.331 1.555 -0.224 2.07e-02 2.33e+03 1.18e+02 bond pdb=" C1' DG P 3 " pdb=" N9 DG P 3 " ideal model delta sigma weight residual 1.468 1.352 0.116 1.40e-02 5.10e+03 6.87e+01 bond pdb=" N ILE E1107 " pdb=" CA ILE E1107 " ideal model delta sigma weight residual 1.462 1.403 0.059 1.01e-02 9.80e+03 3.36e+01 bond pdb=" C1' DC T 12 " pdb=" N1 DC T 12 " ideal model delta sigma weight residual 1.468 1.548 -0.080 1.40e-02 5.10e+03 3.26e+01 ... (remaining 9681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 11829 2.81 - 5.62: 1283 5.62 - 8.43: 72 8.43 - 11.24: 13 11.24 - 14.04: 5 Bond angle restraints: 13202 Sorted by residual: angle pdb=" O GLU E 766 " pdb=" C GLU E 766 " pdb=" N ASN E 767 " ideal model delta sigma weight residual 122.95 111.71 11.24 1.24e+00 6.50e-01 8.21e+01 angle pdb=" N LEU E 122 " pdb=" CA LEU E 122 " pdb=" C LEU E 122 " ideal model delta sigma weight residual 111.75 100.75 11.00 1.28e+00 6.10e-01 7.38e+01 angle pdb=" N PRO E 656 " pdb=" CA PRO E 656 " pdb=" C PRO E 656 " ideal model delta sigma weight residual 114.98 103.71 11.27 1.46e+00 4.69e-01 5.96e+01 angle pdb=" CA ASP E 151 " pdb=" CB ASP E 151 " pdb=" CG ASP E 151 " ideal model delta sigma weight residual 112.60 120.19 -7.59 1.00e+00 1.00e+00 5.76e+01 angle pdb=" C LYS E 751 " pdb=" CA LYS E 751 " pdb=" CB LYS E 751 " ideal model delta sigma weight residual 112.09 102.10 9.99 1.43e+00 4.89e-01 4.88e+01 ... (remaining 13197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 5142 16.90 - 33.81: 450 33.81 - 50.71: 136 50.71 - 67.62: 54 67.62 - 84.52: 10 Dihedral angle restraints: 5792 sinusoidal: 2496 harmonic: 3296 Sorted by residual: dihedral pdb=" CA ARG E 749 " pdb=" C ARG E 749 " pdb=" N VAL E 750 " pdb=" CA VAL E 750 " ideal model delta harmonic sigma weight residual -180.00 -139.78 -40.22 0 5.00e+00 4.00e-02 6.47e+01 dihedral pdb=" CA ARG E 672 " pdb=" C ARG E 672 " pdb=" N PRO E 673 " pdb=" CA PRO E 673 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA PRO E 634 " pdb=" C PRO E 634 " pdb=" N LEU E 635 " pdb=" CA LEU E 635 " ideal model delta harmonic sigma weight residual 180.00 154.41 25.59 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 5789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1186 0.127 - 0.254: 215 0.254 - 0.380: 29 0.380 - 0.507: 4 0.507 - 0.634: 7 Chirality restraints: 1441 Sorted by residual: chirality pdb=" P DC P 1 " pdb=" OP1 DC P 1 " pdb=" OP2 DC P 1 " pdb=" O5' DC P 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" P DT T 3 " pdb=" OP1 DT T 3 " pdb=" OP2 DT T 3 " pdb=" O5' DT T 3 " both_signs ideal model delta sigma weight residual True 2.34 -2.95 -0.62 2.00e-01 2.50e+01 9.55e+00 chirality pdb=" P DG P 6 " pdb=" OP1 DG P 6 " pdb=" OP2 DG P 6 " pdb=" O5' DG P 6 " both_signs ideal model delta sigma weight residual True 2.34 -2.93 -0.59 2.00e-01 2.50e+01 8.84e+00 ... (remaining 1438 not shown) Planarity restraints: 1628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 81 " -0.052 2.00e-02 2.50e+03 1.03e-01 1.07e+02 pdb=" C ASN E 81 " 0.179 2.00e-02 2.50e+03 pdb=" O ASN E 81 " -0.070 2.00e-02 2.50e+03 pdb=" N MET E 82 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 949 " -0.046 2.00e-02 2.50e+03 9.21e-02 8.49e+01 pdb=" C PRO E 949 " 0.159 2.00e-02 2.50e+03 pdb=" O PRO E 949 " -0.067 2.00e-02 2.50e+03 pdb=" N TYR E 950 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 485 " -0.119 2.00e-02 2.50e+03 6.35e-02 8.07e+01 pdb=" CG TYR E 485 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR E 485 " 0.070 2.00e-02 2.50e+03 pdb=" CD2 TYR E 485 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR E 485 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR E 485 " 0.042 2.00e-02 2.50e+03 pdb=" CZ TYR E 485 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 485 " -0.087 2.00e-02 2.50e+03 ... (remaining 1625 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 572 2.74 - 3.28: 9248 3.28 - 3.82: 15270 3.82 - 4.36: 20063 4.36 - 4.90: 31911 Nonbonded interactions: 77064 Sorted by model distance: nonbonded pdb=" O GLU E 845 " pdb=" N ALA E 847 " model vdw 2.205 3.120 nonbonded pdb=" O LEU E 815 " pdb=" OG SER E 818 " model vdw 2.283 3.040 nonbonded pdb=" O GLU E 845 " pdb=" N GLY E 848 " model vdw 2.290 3.120 nonbonded pdb=" N ARG E 260 " pdb=" OH TYR E 265 " model vdw 2.291 3.120 nonbonded pdb=" O GLU E 124 " pdb=" N GLY E 126 " model vdw 2.296 3.120 ... (remaining 77059 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 group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.990 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5638 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 : 0.016 0.534 9690 Z= 0.938 Angle : 1.856 38.405 13214 Z= 1.171 Chirality : 0.107 0.634 1441 Planarity : 0.016 0.177 1628 Dihedral : 15.435 84.520 3662 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 1.08 % Allowed : 4.31 % Favored : 94.61 % Rotamer: Outliers : 2.06 % Allowed : 4.42 % Favored : 93.52 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.71 (0.23), residues: 1113 helix: -0.90 (0.21), residues: 459 sheet: -0.93 (0.35), residues: 197 loop : -1.29 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG E 781 TYR 0.119 0.018 TYR E 485 PHE 0.071 0.010 PHE E 347 TRP 0.106 0.016 TRP E 384 HIS 0.021 0.005 HIS E 388 Details of bonding type rmsd/Z covalent geometry : bond 0.01458 / 0.92 ( 9686) covalent geometry : angle 1.75383 / 1.17 (13202) hydrogen bonds : bond 0.18761 / 20.43 ( 488) hydrogen bonds : angle 7.33997 / 7.74 ( 1353) metal coordination : bond 0.32326 / 15.27 ( 4) metal coordination : angle 20.24678 / 36.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 300 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.4962 (OUTLIER) cc_final: 0.4688 (t80) REVERT: E 86 LEU cc_start: 0.8801 (tp) cc_final: 0.8513 (mp) REVERT: E 242 ILE cc_start: 0.8427 (pt) cc_final: 0.8189 (mt) REVERT: E 265 TYR cc_start: 0.6297 (m-80) cc_final: 0.5525 (m-80) REVERT: E 604 VAL cc_start: 0.6580 (m) cc_final: 0.6207 (m) REVERT: E 645 TYR cc_start: 0.7523 (m-10) cc_final: 0.7167 (m-10) REVERT: E 926 LEU cc_start: 0.6822 (tt) cc_final: 0.6605 (tp) outliers start: 20 outliers final: 3 residues processed: 313 average time/residue: 0.1201 time to fit residues: 49.8234 Evaluate side-chains 160 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 156 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 TYR Chi-restraints excluded: chain E residue 689 PHE Chi-restraints excluded: chain E residue 827 LEU Chi-restraints excluded: chain E residue 1038 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.0010 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 0.3980 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 211 GLN E 572 ASN E 638 HIS E 794 ASN E 823 HIS E1062 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.166930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.135111 restraints weight = 20028.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.138850 restraints weight = 9867.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.141240 restraints weight = 6356.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.142672 restraints weight = 4900.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.143426 restraints weight = 4212.229| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9690 Z= 0.178 Angle : 0.865 37.247 13214 Z= 0.394 Chirality : 0.046 0.257 1441 Planarity : 0.005 0.063 1628 Dihedral : 13.876 81.142 1463 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.61 % Favored : 97.30 % Rotamer: Outliers : 2.98 % Allowed : 13.48 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.17 (0.25), residues: 1113 helix: 0.99 (0.24), residues: 472 sheet: -0.27 (0.35), residues: 193 loop : -0.55 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 988 TYR 0.019 0.002 TYR E 412 PHE 0.036 0.002 PHE E 381 TRP 0.021 0.002 TRP E1143 HIS 0.006 0.001 HIS E 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 ( 9686) covalent geometry : angle 0.72653 / 0.39 (13202) hydrogen bonds : bond 0.05881 / 6.42 ( 488) hydrogen bonds : angle 5.64142 / 5.81 ( 1353) metal coordination : bond 0.01147 / 0.56 ( 4) metal coordination : angle 15.60398 / 25.14 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5417 (OUTLIER) cc_final: 0.5070 (t80) REVERT: E 265 TYR cc_start: 0.6595 (m-80) cc_final: 0.6087 (m-80) REVERT: E 381 PHE cc_start: 0.7602 (t80) cc_final: 0.7323 (t80) REVERT: E 834 VAL cc_start: 0.8431 (p) cc_final: 0.8125 (p) REVERT: E 957 SER cc_start: 0.7861 (t) cc_final: 0.7576 (p) outliers start: 29 outliers final: 19 residues processed: 186 average time/residue: 0.1005 time to fit residues: 26.1594 Evaluate side-chains 139 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 TYR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 413 LYS Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 474 SER Chi-restraints excluded: chain E residue 572 ASN Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 954 ILE Chi-restraints excluded: chain E residue 1083 LYS Chi-restraints excluded: chain E residue 1092 ILE Chi-restraints excluded: chain E residue 1154 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 111 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 88 optimal weight: 0.0070 chunk 78 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 41 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 83 HIS E 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.166468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.137151 restraints weight = 19789.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.139629 restraints weight = 9895.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.141083 restraints weight = 6739.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.141109 restraints weight = 5421.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.141575 restraints weight = 5057.005| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9690 Z= 0.143 Angle : 0.743 33.071 13214 Z= 0.342 Chirality : 0.043 0.165 1441 Planarity : 0.004 0.060 1628 Dihedral : 13.364 66.771 1456 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.43 % Favored : 97.48 % Rotamer: Outliers : 2.67 % Allowed : 15.23 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.55 (0.25), residues: 1113 helix: 1.25 (0.24), residues: 472 sheet: -0.06 (0.36), residues: 188 loop : -0.28 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E1138 TYR 0.013 0.001 TYR E 313 PHE 0.022 0.002 PHE E 984 TRP 0.013 0.001 TRP E1143 HIS 0.003 0.001 HIS E 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 9686) covalent geometry : angle 0.63767 / 0.34 (13202) hydrogen bonds : bond 0.04936 / 5.43 ( 488) hydrogen bonds : angle 5.41969 / 5.60 ( 1353) metal coordination : bond 0.00668 / 0.49 ( 4) metal coordination : angle 12.64818 / 19.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5336 (OUTLIER) cc_final: 0.5022 (t80) REVERT: E 265 TYR cc_start: 0.6831 (m-80) cc_final: 0.6301 (m-80) REVERT: E 381 PHE cc_start: 0.7550 (t80) cc_final: 0.7323 (t80) REVERT: E 557 HIS cc_start: 0.7393 (t70) cc_final: 0.6906 (t70) REVERT: E 834 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.8195 (p) REVERT: E 957 SER cc_start: 0.7861 (t) cc_final: 0.7581 (p) outliers start: 26 outliers final: 17 residues processed: 152 average time/residue: 0.0899 time to fit residues: 20.0141 Evaluate side-chains 134 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 TYR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 413 LYS Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 474 SER Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 834 VAL Chi-restraints excluded: chain E residue 873 GLU Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 1092 ILE Chi-restraints excluded: chain E residue 1154 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 42 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 38 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 6 optimal weight: 0.4980 chunk 98 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1176 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.162590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.132426 restraints weight = 20164.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.134464 restraints weight = 10156.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.136769 restraints weight = 7097.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.136634 restraints weight = 5747.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.136818 restraints weight = 5347.780| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9690 Z= 0.147 Angle : 0.718 30.217 13214 Z= 0.328 Chirality : 0.043 0.158 1441 Planarity : 0.005 0.073 1628 Dihedral : 13.251 68.445 1456 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.98 % Allowed : 15.74 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.77 (0.26), residues: 1113 helix: 1.40 (0.24), residues: 473 sheet: -0.20 (0.36), residues: 197 loop : 0.01 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 207 TYR 0.021 0.002 TYR E 449 PHE 0.016 0.002 PHE E 464 TRP 0.011 0.001 TRP E1143 HIS 0.003 0.001 HIS E1176 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 9686) covalent geometry : angle 0.62950 / 0.33 (13202) hydrogen bonds : bond 0.04516 / 4.98 ( 488) hydrogen bonds : angle 5.23657 / 5.43 ( 1353) metal coordination : bond 0.00839 / 0.68 ( 4) metal coordination : angle 11.50428 / 17.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5480 (OUTLIER) cc_final: 0.5178 (t80) REVERT: E 265 TYR cc_start: 0.7136 (m-80) cc_final: 0.6563 (m-80) REVERT: E 557 HIS cc_start: 0.7400 (t70) cc_final: 0.6825 (t70) REVERT: E 613 ILE cc_start: 0.7938 (mm) cc_final: 0.7524 (mt) REVERT: E 649 MET cc_start: 0.8548 (mtp) cc_final: 0.8329 (mtp) REVERT: E 690 PHE cc_start: 0.6966 (m-80) cc_final: 0.6624 (m-10) REVERT: E 882 ILE cc_start: 0.9098 (pt) cc_final: 0.8384 (mm) REVERT: E 957 SER cc_start: 0.7954 (t) cc_final: 0.7667 (p) REVERT: E 1052 MET cc_start: 0.5714 (mtp) cc_final: 0.5358 (mtm) REVERT: E 1087 LEU cc_start: 0.4392 (tt) cc_final: 0.3751 (mt) outliers start: 29 outliers final: 18 residues processed: 146 average time/residue: 0.0919 time to fit residues: 19.4267 Evaluate side-chains 130 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 TYR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 413 LYS Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 572 ASN Chi-restraints excluded: chain E residue 771 VAL Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 1092 ILE Chi-restraints excluded: chain E residue 1154 ILE Chi-restraints excluded: chain E residue 1186 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 33 optimal weight: 0.7980 chunk 102 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 1 optimal weight: 30.0000 chunk 50 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 36 optimal weight: 0.3980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 29 ASN ** E 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1176 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.157247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.126050 restraints weight = 20317.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.129212 restraints weight = 10129.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.129538 restraints weight = 6529.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.130098 restraints weight = 6198.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.130037 restraints weight = 5600.521| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9690 Z= 0.179 Angle : 0.743 29.428 13214 Z= 0.343 Chirality : 0.045 0.266 1441 Planarity : 0.005 0.069 1628 Dihedral : 13.162 67.537 1456 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.88 % Allowed : 17.08 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.70 (0.26), residues: 1113 helix: 1.32 (0.24), residues: 476 sheet: -0.25 (0.37), residues: 193 loop : 0.01 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 988 TYR 0.012 0.002 TYR E 485 PHE 0.018 0.002 PHE E 784 TRP 0.012 0.001 TRP E 791 HIS 0.006 0.001 HIS E 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 ( 9686) covalent geometry : angle 0.66007 / 0.34 (13202) hydrogen bonds : bond 0.04665 / 5.14 ( 488) hydrogen bonds : angle 5.19274 / 5.34 ( 1353) metal coordination : bond 0.01155 / 0.91 ( 4) metal coordination : angle 11.31830 / 17.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5583 (OUTLIER) cc_final: 0.5281 (t80) REVERT: E 265 TYR cc_start: 0.7584 (m-80) cc_final: 0.7084 (m-80) REVERT: E 557 HIS cc_start: 0.7578 (t70) cc_final: 0.6951 (t70) REVERT: E 904 SER cc_start: 0.8555 (t) cc_final: 0.8255 (p) REVERT: E 957 SER cc_start: 0.8175 (t) cc_final: 0.7819 (p) REVERT: E 1042 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7944 (tt) REVERT: E 1087 LEU cc_start: 0.4448 (tt) cc_final: 0.3893 (mt) outliers start: 28 outliers final: 21 residues processed: 142 average time/residue: 0.0859 time to fit residues: 18.1146 Evaluate side-chains 131 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 TYR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 211 GLN Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 572 ASN Chi-restraints excluded: chain E residue 771 VAL Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 827 LEU Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 1042 LEU Chi-restraints excluded: chain E residue 1092 ILE Chi-restraints excluded: chain E residue 1186 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 107 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 0.0370 chunk 65 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 572 ASN E 794 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.159648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.129041 restraints weight = 20192.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.131828 restraints weight = 10089.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.132268 restraints weight = 6637.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.133972 restraints weight = 6031.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.133428 restraints weight = 5436.809| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9690 Z= 0.119 Angle : 0.663 26.320 13214 Z= 0.305 Chirality : 0.042 0.167 1441 Planarity : 0.004 0.043 1628 Dihedral : 13.051 67.315 1456 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.47 % Allowed : 17.39 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.92 (0.26), residues: 1113 helix: 1.50 (0.24), residues: 477 sheet: -0.11 (0.37), residues: 191 loop : 0.09 (0.32), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 988 TYR 0.012 0.001 TYR E1016 PHE 0.013 0.001 PHE E 139 TRP 0.011 0.001 TRP E1143 HIS 0.002 0.001 HIS E 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 9686) covalent geometry : angle 0.58091 / 0.30 (13202) hydrogen bonds : bond 0.04163 / 4.59 ( 488) hydrogen bonds : angle 5.09297 / 5.23 ( 1353) metal coordination : bond 0.00531 / 0.43 ( 4) metal coordination : angle 10.64404 / 16.50 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5578 (OUTLIER) cc_final: 0.5239 (t80) REVERT: E 265 TYR cc_start: 0.7299 (m-80) cc_final: 0.6822 (m-80) REVERT: E 904 SER cc_start: 0.8584 (t) cc_final: 0.8220 (p) REVERT: E 957 SER cc_start: 0.8123 (t) cc_final: 0.7747 (p) REVERT: E 1042 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7921 (tt) REVERT: E 1087 LEU cc_start: 0.4290 (tt) cc_final: 0.3865 (mt) outliers start: 24 outliers final: 18 residues processed: 139 average time/residue: 0.0821 time to fit residues: 17.1609 Evaluate side-chains 123 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 TYR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 211 GLN Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 572 ASN Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 827 LEU Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 1042 LEU Chi-restraints excluded: chain E residue 1092 ILE Chi-restraints excluded: chain E residue 1186 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 1 optimal weight: 40.0000 chunk 87 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 572 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.157259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.126200 restraints weight = 20202.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.129023 restraints weight = 10659.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.129498 restraints weight = 6694.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.129961 restraints weight = 6281.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.130336 restraints weight = 5629.710| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9690 Z= 0.137 Angle : 0.667 25.866 13214 Z= 0.308 Chirality : 0.042 0.167 1441 Planarity : 0.004 0.043 1628 Dihedral : 13.037 68.271 1456 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.98 % Allowed : 18.31 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 1.00 (0.26), residues: 1113 helix: 1.58 (0.24), residues: 476 sheet: -0.07 (0.37), residues: 193 loop : 0.13 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 988 TYR 0.015 0.001 TYR E1016 PHE 0.013 0.001 PHE E 784 TRP 0.011 0.001 TRP E1143 HIS 0.003 0.001 HIS E 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 9686) covalent geometry : angle 0.58925 / 0.31 (13202) hydrogen bonds : bond 0.04171 / 4.56 ( 488) hydrogen bonds : angle 5.04545 / 5.17 ( 1353) metal coordination : bond 0.00771 / 0.58 ( 4) metal coordination : angle 10.40732 / 16.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5548 (OUTLIER) cc_final: 0.5245 (t80) REVERT: E 50 MET cc_start: 0.7130 (mmm) cc_final: 0.6875 (tpp) REVERT: E 265 TYR cc_start: 0.7463 (m-80) cc_final: 0.7032 (m-80) REVERT: E 904 SER cc_start: 0.8624 (t) cc_final: 0.8257 (p) REVERT: E 957 SER cc_start: 0.8239 (t) cc_final: 0.7895 (p) REVERT: E 968 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7726 (mtt90) REVERT: E 1042 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7937 (tt) REVERT: E 1087 LEU cc_start: 0.4335 (tt) cc_final: 0.3900 (mt) outliers start: 29 outliers final: 19 residues processed: 138 average time/residue: 0.0795 time to fit residues: 16.5026 Evaluate side-chains 125 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 TYR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 771 VAL Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 827 LEU Chi-restraints excluded: chain E residue 1042 LEU Chi-restraints excluded: chain E residue 1092 ILE Chi-restraints excluded: chain E residue 1186 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 76 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.4227 r_free = 0.4227 target = 0.157663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.127229 restraints weight = 19946.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.129899 restraints weight = 9838.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.130868 restraints weight = 6366.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.131494 restraints weight = 5776.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.131355 restraints weight = 5237.741| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9690 Z= 0.131 Angle : 0.672 24.903 13214 Z= 0.314 Chirality : 0.042 0.165 1441 Planarity : 0.003 0.032 1628 Dihedral : 13.041 69.473 1456 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.16 % Allowed : 19.44 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 1.01 (0.26), residues: 1113 helix: 1.58 (0.24), residues: 476 sheet: -0.04 (0.38), residues: 193 loop : 0.13 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 207 TYR 0.030 0.002 TYR E 449 PHE 0.012 0.001 PHE E1122 TRP 0.021 0.002 TRP E1026 HIS 0.004 0.001 HIS E 921 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 9686) covalent geometry : angle 0.59856 / 0.31 (13202) hydrogen bonds : bond 0.04129 / 4.54 ( 488) hydrogen bonds : angle 5.06508 / 5.23 ( 1353) metal coordination : bond 0.00647 / 0.49 ( 4) metal coordination : angle 10.15266 / 15.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5506 (OUTLIER) cc_final: 0.5176 (t80) REVERT: E 265 TYR cc_start: 0.7430 (m-80) cc_final: 0.7129 (m-80) REVERT: E 904 SER cc_start: 0.8665 (t) cc_final: 0.8291 (p) REVERT: E 957 SER cc_start: 0.8282 (t) cc_final: 0.7929 (p) REVERT: E 968 ARG cc_start: 0.8144 (mtt90) cc_final: 0.7777 (mtt90) REVERT: E 1042 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7945 (tt) REVERT: E 1087 LEU cc_start: 0.4427 (tt) cc_final: 0.3993 (mt) outliers start: 21 outliers final: 17 residues processed: 129 average time/residue: 0.0839 time to fit residues: 16.1734 Evaluate side-chains 128 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 TYR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 827 LEU Chi-restraints excluded: chain E residue 1042 LEU Chi-restraints excluded: chain E residue 1092 ILE Chi-restraints excluded: chain E residue 1186 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 77 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 13 optimal weight: 0.0030 chunk 76 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 15 optimal weight: 0.0970 overall best weight: 0.7992 ------------------------------------------------------------------------------- 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 = 0.4221 r_free = 0.4221 target = 0.157022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.126580 restraints weight = 20047.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.129375 restraints weight = 9976.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.130264 restraints weight = 6820.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.130524 restraints weight = 5762.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.130749 restraints weight = 5271.874| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9690 Z= 0.118 Angle : 0.649 23.348 13214 Z= 0.301 Chirality : 0.042 0.154 1441 Planarity : 0.004 0.042 1628 Dihedral : 13.027 70.482 1456 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.16 % Allowed : 19.75 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 (0.26), residues: 1113 helix: 1.74 (0.24), residues: 471 sheet: 0.01 (0.37), residues: 190 loop : 0.20 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 207 TYR 0.020 0.001 TYR E 449 PHE 0.014 0.001 PHE E1112 TRP 0.013 0.001 TRP E1143 HIS 0.002 0.001 HIS E 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 9686) covalent geometry : angle 0.57812 / 0.30 (13202) hydrogen bonds : bond 0.03953 / 4.34 ( 488) hydrogen bonds : angle 4.95378 / 5.08 ( 1353) metal coordination : bond 0.00477 / 0.36 ( 4) metal coordination : angle 9.78262 / 15.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5618 (OUTLIER) cc_final: 0.5295 (t80) REVERT: E 265 TYR cc_start: 0.7403 (m-80) cc_final: 0.7104 (m-80) REVERT: E 420 MET cc_start: 0.9145 (mmt) cc_final: 0.8937 (mmt) REVERT: E 904 SER cc_start: 0.8680 (t) cc_final: 0.8258 (p) REVERT: E 957 SER cc_start: 0.8345 (t) cc_final: 0.8019 (p) REVERT: E 968 ARG cc_start: 0.8181 (mtt90) cc_final: 0.7829 (mtt90) REVERT: E 1042 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8014 (tp) outliers start: 21 outliers final: 17 residues processed: 130 average time/residue: 0.0756 time to fit residues: 14.8964 Evaluate side-chains 119 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 TYR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 827 LEU Chi-restraints excluded: chain E residue 857 ILE Chi-restraints excluded: chain E residue 1042 LEU Chi-restraints excluded: chain E residue 1092 ILE Chi-restraints excluded: chain E residue 1154 ILE Chi-restraints excluded: chain E residue 1186 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 97 optimal weight: 4.9990 chunk 5 optimal weight: 0.0970 chunk 32 optimal weight: 0.4980 chunk 92 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.156941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.124715 restraints weight = 20137.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.128044 restraints weight = 9901.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.130149 restraints weight = 6465.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.131342 restraints weight = 5071.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.131914 restraints weight = 4448.243| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9690 Z= 0.121 Angle : 0.663 23.036 13214 Z= 0.308 Chirality : 0.042 0.153 1441 Planarity : 0.003 0.030 1628 Dihedral : 13.036 73.389 1456 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.06 % Allowed : 19.75 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.26), residues: 1113 helix: 1.70 (0.24), residues: 472 sheet: -0.06 (0.37), residues: 190 loop : 0.23 (0.32), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 968 TYR 0.026 0.001 TYR E 449 PHE 0.012 0.001 PHE E 139 TRP 0.011 0.001 TRP E1143 HIS 0.002 0.001 HIS E 921 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 9686) covalent geometry : angle 0.59620 / 0.31 (13202) hydrogen bonds : bond 0.04009 / 4.41 ( 488) hydrogen bonds : angle 4.96276 / 5.09 ( 1353) metal coordination : bond 0.00487 / 0.34 ( 4) metal coordination : angle 9.64127 / 15.05 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5715 (OUTLIER) cc_final: 0.5327 (t80) REVERT: E 420 MET cc_start: 0.9136 (mmt) cc_final: 0.8921 (mmt) REVERT: E 904 SER cc_start: 0.8647 (t) cc_final: 0.8234 (p) REVERT: E 957 SER cc_start: 0.8365 (t) cc_final: 0.8061 (p) REVERT: E 1042 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8034 (tp) REVERT: E 1087 LEU cc_start: 0.4548 (tt) cc_final: 0.4178 (mt) REVERT: E 1164 LEU cc_start: 0.8359 (pp) cc_final: 0.8135 (mt) outliers start: 20 outliers final: 17 residues processed: 121 average time/residue: 0.0796 time to fit residues: 14.6555 Evaluate side-chains 121 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 TYR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 827 LEU Chi-restraints excluded: chain E residue 1042 LEU Chi-restraints excluded: chain E residue 1092 ILE Chi-restraints excluded: chain E residue 1154 ILE Chi-restraints excluded: chain E residue 1186 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 15 optimal weight: 0.3980 chunk 6 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 overall best weight: 2.2384 ------------------------------------------------------------------------------- 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 = 0.4174 r_free = 0.4174 target = 0.152935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.121967 restraints weight = 20073.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.124047 restraints weight = 10687.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.125202 restraints weight = 7013.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.125773 restraints weight = 6224.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.125671 restraints weight = 5765.747| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.6181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9690 Z= 0.173 Angle : 0.717 26.901 13214 Z= 0.334 Chirality : 0.044 0.156 1441 Planarity : 0.004 0.048 1628 Dihedral : 13.062 74.728 1456 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.26 % Allowed : 19.96 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.26), residues: 1113 helix: 1.64 (0.24), residues: 470 sheet: -0.25 (0.36), residues: 198 loop : 0.14 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 968 TYR 0.025 0.002 TYR E 449 PHE 0.017 0.002 PHE E1122 TRP 0.016 0.002 TRP E1026 HIS 0.005 0.001 HIS E 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 9686) covalent geometry : angle 0.64285 / 0.33 (13202) hydrogen bonds : bond 0.04479 / 4.92 ( 488) hydrogen bonds : angle 5.08841 / 5.20 ( 1353) metal coordination : bond 0.01140 / 0.74 ( 4) metal coordination : angle 10.52159 / 15.91 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1758.41 seconds wall clock time: 31 minutes 12.27 seconds (1872.27 seconds total)