Starting phenix.real_space_refine on Wed Aug 5 09:59:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8r_44356/08_2026/9b8r_44356.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8r_44356/08_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_44356/08_2026/9b8r_44356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8r_44356/08_2026/9b8r_44356.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b8r_44356/08_2026/9b8r_44356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8r_44356/08_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-2.2rc3-6140/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: 2.02, per 1000 atoms: 0.21 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: 0.85 Conformation dependent library (CDL) restraints added in 273.3 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: 1.04 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: 1.60 Time building geometry restraints manager: 1.14 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: 11828 2.81 - 5.62: 1284 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: 0.000 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 11.480 Find NCS groups from input model: 0.180 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: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.450 ------------------------------------------------------------------------------- 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= 0.939 Angle : 1.857 38.405 13214 Z= 1.172 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 1.75422 / 1.17 (13202) hydrogen bonds : bond 0.18761 / 20.50 ( 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 : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.4962 (OUTLIER) cc_final: 0.4686 (t80) REVERT: E 86 LEU cc_start: 0.8801 (tp) cc_final: 0.8510 (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: 0.6211 (m) REVERT: E 645 TYR cc_start: 0.7523 (m-10) cc_final: 0.7164 (m-10) REVERT: E 926 LEU cc_start: 0.6822 (tt) cc_final: 0.6606 (tp) outliers start: 20 outliers final: 3 residues processed: 313 average time/residue: 0.0989 time to fit residues: 41.0288 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 : 0.329 ------------------------------------------------------------------------------- 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: 0.8980 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 0.3980 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 E 997 ASN E1062 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.168957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.137408 restraints weight = 19993.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.141273 restraints weight = 9617.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.143761 restraints weight = 6092.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.145110 restraints weight = 4648.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.146098 restraints weight = 4005.235| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9690 Z= 0.172 Angle : 0.855 35.947 13214 Z= 0.391 Chirality : 0.046 0.247 1441 Planarity : 0.005 0.066 1628 Dihedral : 13.955 80.384 1463 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.88 % Favored : 97.04 % Rotamer: Outliers : 2.98 % Allowed : 13.68 % Favored : 83.33 % 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: 0.21 (0.25), residues: 1113 helix: 1.00 (0.24), residues: 471 sheet: -0.12 (0.36), residues: 184 loop : -0.57 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 653 TYR 0.019 0.002 TYR E 412 PHE 0.036 0.002 PHE E 381 TRP 0.020 0.003 TRP E1143 HIS 0.006 0.001 HIS E 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 ( 9686) covalent geometry : angle 0.72073 / 0.39 (13202) hydrogen bonds : bond 0.05970 / 6.56 ( 488) hydrogen bonds : angle 5.64759 / 5.81 ( 1353) metal coordination : bond 0.01564 / 0.75 ( 4) metal coordination : angle 15.29278 / 24.85 ( 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 189 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5384 (OUTLIER) cc_final: 0.5038 (t80) REVERT: E 86 LEU cc_start: 0.8716 (tp) cc_final: 0.8515 (mp) REVERT: E 207 ARG cc_start: 0.7197 (ppt170) cc_final: 0.6624 (ppt170) REVERT: E 265 TYR cc_start: 0.6488 (m-80) cc_final: 0.6084 (m-80) outliers start: 29 outliers final: 18 residues processed: 183 average time/residue: 0.0907 time to fit residues: 23.1552 Evaluate side-chains 139 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 89 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 45 optimal weight: 0.0980 chunk 58 optimal weight: 0.0020 chunk 41 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 83 HIS E 572 ASN E 997 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.167604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.139012 restraints weight = 19680.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.140658 restraints weight = 9796.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.142169 restraints weight = 6930.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.142705 restraints weight = 5387.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.142994 restraints weight = 5016.928| |-----------------------------------------------------------------------------| r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9690 Z= 0.142 Angle : 0.735 32.036 13214 Z= 0.340 Chirality : 0.043 0.166 1441 Planarity : 0.004 0.059 1628 Dihedral : 13.419 69.331 1456 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.16 % Favored : 97.75 % Rotamer: Outliers : 2.37 % Allowed : 14.92 % Favored : 82.72 % 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: 1.26 (0.24), residues: 472 sheet: -0.05 (0.36), residues: 188 loop : -0.29 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 653 TYR 0.012 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 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 9686) covalent geometry : angle 0.63583 / 0.34 (13202) hydrogen bonds : bond 0.04863 / 5.35 ( 488) hydrogen bonds : angle 5.42040 / 5.62 ( 1353) metal coordination : bond 0.00687 / 0.48 ( 4) metal coordination : angle 12.27709 / 19.28 ( 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 152 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5344 (OUTLIER) cc_final: 0.5034 (t80) REVERT: E 265 TYR cc_start: 0.6780 (m-80) cc_final: 0.6223 (m-80) REVERT: E 992 LEU cc_start: 0.5694 (OUTLIER) cc_final: 0.5136 (mt) outliers start: 23 outliers final: 16 residues processed: 150 average time/residue: 0.0885 time to fit residues: 19.2360 Evaluate side-chains 127 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 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 873 GLU Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 992 LEU 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: 5.9990 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 0.0270 chunk 66 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- 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 = 0.4310 r_free = 0.4310 target = 0.164094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.134201 restraints weight = 20141.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.135971 restraints weight = 10521.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.137576 restraints weight = 7476.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.137955 restraints weight = 5895.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.137907 restraints weight = 5494.069| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9690 Z= 0.145 Angle : 0.700 29.516 13214 Z= 0.322 Chirality : 0.042 0.157 1441 Planarity : 0.004 0.065 1628 Dihedral : 13.275 71.549 1456 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.47 % Allowed : 16.36 % Favored : 81.17 % 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: 0.83 (0.26), residues: 1113 helix: 1.47 (0.24), residues: 473 sheet: -0.14 (0.36), residues: 197 loop : 0.01 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 207 TYR 0.017 0.001 TYR E 742 PHE 0.018 0.002 PHE E 830 TRP 0.011 0.001 TRP E1143 HIS 0.003 0.001 HIS E1176 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 9686) covalent geometry : angle 0.61296 / 0.32 (13202) hydrogen bonds : bond 0.04458 / 4.90 ( 488) hydrogen bonds : angle 5.24462 / 5.44 ( 1353) metal coordination : bond 0.00787 / 0.64 ( 4) metal coordination : angle 11.26614 / 17.32 ( 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 146 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5421 (OUTLIER) cc_final: 0.5110 (t80) REVERT: E 265 TYR cc_start: 0.7055 (m-80) cc_final: 0.6451 (m-80) REVERT: E 557 HIS cc_start: 0.7500 (t70) cc_final: 0.6852 (t70) REVERT: E 613 ILE cc_start: 0.7908 (mm) cc_final: 0.7486 (mt) REVERT: E 957 SER cc_start: 0.7933 (t) cc_final: 0.7703 (p) REVERT: E 980 GLU cc_start: 0.6508 (mt-10) cc_final: 0.6286 (mt-10) REVERT: E 992 LEU cc_start: 0.5988 (OUTLIER) cc_final: 0.5777 (tt) REVERT: E 1087 LEU cc_start: 0.4420 (tt) cc_final: 0.3842 (mp) outliers start: 24 outliers final: 19 residues processed: 143 average time/residue: 0.0769 time to fit residues: 16.2737 Evaluate side-chains 129 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 397 ASP 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 584 LEU Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 992 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 33 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 1 optimal weight: 30.0000 chunk 50 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 29 ASN ** E 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.155733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.125076 restraints weight = 20193.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.127462 restraints weight = 10557.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.128712 restraints weight = 7065.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.128991 restraints weight = 5791.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.129534 restraints weight = 5536.831| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9690 Z= 0.197 Angle : 0.749 30.078 13214 Z= 0.349 Chirality : 0.045 0.169 1441 Planarity : 0.005 0.062 1628 Dihedral : 13.202 72.308 1456 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.40 % Allowed : 16.36 % Favored : 80.25 % 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: 0.71 (0.26), residues: 1113 helix: 1.34 (0.24), residues: 476 sheet: -0.22 (0.37), residues: 193 loop : -0.02 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 968 TYR 0.021 0.002 TYR E 833 PHE 0.020 0.002 PHE E 784 TRP 0.011 0.002 TRP E 683 HIS 0.008 0.002 HIS E 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 ( 9686) covalent geometry : angle 0.66417 / 0.35 (13202) hydrogen bonds : bond 0.04760 / 5.20 ( 488) hydrogen bonds : angle 5.21168 / 5.41 ( 1353) metal coordination : bond 0.01380 / 1.08 ( 4) metal coordination : angle 11.49775 / 17.29 ( 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 150 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5655 (OUTLIER) cc_final: 0.5364 (t80) REVERT: E 265 TYR cc_start: 0.7588 (m-80) cc_final: 0.7123 (m-80) REVERT: E 904 SER cc_start: 0.8498 (t) cc_final: 0.8220 (p) REVERT: E 957 SER cc_start: 0.8157 (t) cc_final: 0.7864 (p) REVERT: E 968 ARG cc_start: 0.8282 (mtt90) cc_final: 0.7940 (mtt90) REVERT: E 1042 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7931 (tt) REVERT: E 1087 LEU cc_start: 0.4690 (tt) cc_final: 0.4160 (mt) outliers start: 33 outliers final: 23 residues processed: 141 average time/residue: 0.0762 time to fit residues: 15.8162 Evaluate side-chains 128 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 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 470 LEU Chi-restraints excluded: chain E residue 474 SER Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain E residue 572 ASN Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 699 MET 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 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: 1.9990 chunk 52 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 59 optimal weight: 0.0970 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.156396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.125925 restraints weight = 19957.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.128606 restraints weight = 10211.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.129600 restraints weight = 6947.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.129735 restraints weight = 5783.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.129915 restraints weight = 5302.952| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9690 Z= 0.141 Angle : 0.684 27.456 13214 Z= 0.315 Chirality : 0.043 0.185 1441 Planarity : 0.004 0.041 1628 Dihedral : 13.100 71.596 1456 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.78 % Allowed : 18.00 % Favored : 79.22 % 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: 0.87 (0.26), residues: 1113 helix: 1.48 (0.24), residues: 476 sheet: -0.15 (0.37), residues: 192 loop : 0.05 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 968 TYR 0.013 0.001 TYR E 842 PHE 0.017 0.001 PHE E 139 TRP 0.011 0.001 TRP E1143 HIS 0.003 0.001 HIS E1176 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 9686) covalent geometry : angle 0.59959 / 0.31 (13202) hydrogen bonds : bond 0.04346 / 4.76 ( 488) hydrogen bonds : angle 5.10316 / 5.28 ( 1353) metal coordination : bond 0.00855 / 0.66 ( 4) metal coordination : angle 10.93001 / 16.75 ( 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 138 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5563 (OUTLIER) cc_final: 0.5246 (t80) REVERT: E 265 TYR cc_start: 0.7534 (m-80) cc_final: 0.7065 (m-80) REVERT: E 613 ILE cc_start: 0.8018 (mm) cc_final: 0.7616 (mt) REVERT: E 904 SER cc_start: 0.8574 (t) cc_final: 0.8230 (p) REVERT: E 957 SER cc_start: 0.8253 (t) cc_final: 0.7930 (p) REVERT: E 982 LYS cc_start: 0.8098 (mmtt) cc_final: 0.7541 (mmtt) REVERT: E 1042 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7890 (tt) REVERT: E 1087 LEU cc_start: 0.4647 (tt) cc_final: 0.4154 (mt) outliers start: 27 outliers final: 19 residues processed: 131 average time/residue: 0.0710 time to fit residues: 13.6270 Evaluate side-chains 121 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 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 474 SER 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 879 ILE 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: 9.9990 chunk 23 optimal weight: 0.0570 chunk 1 optimal weight: 30.0000 chunk 87 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- 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 = 0.4196 r_free = 0.4196 target = 0.154869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.123858 restraints weight = 20188.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.126410 restraints weight = 10137.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.128001 restraints weight = 6675.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.127852 restraints weight = 5751.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.128111 restraints weight = 5416.695| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.5537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9690 Z= 0.158 Angle : 0.691 26.838 13214 Z= 0.319 Chirality : 0.043 0.202 1441 Planarity : 0.004 0.039 1628 Dihedral : 13.116 73.078 1456 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.09 % Allowed : 18.42 % Favored : 78.50 % 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: 0.90 (0.26), residues: 1113 helix: 1.52 (0.24), residues: 476 sheet: -0.09 (0.37), residues: 192 loop : 0.02 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 968 TYR 0.014 0.001 TYR E 842 PHE 0.015 0.002 PHE E 139 TRP 0.010 0.001 TRP E1143 HIS 0.004 0.001 HIS E 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 9686) covalent geometry : angle 0.61088 / 0.32 (13202) hydrogen bonds : bond 0.04371 / 4.79 ( 488) hydrogen bonds : angle 5.08533 / 5.25 ( 1353) metal coordination : bond 0.00944 / 0.69 ( 4) metal coordination : angle 10.70886 / 16.40 ( 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: 30 poor density : 113 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5574 (OUTLIER) cc_final: 0.5237 (t80) REVERT: E 904 SER cc_start: 0.8644 (t) cc_final: 0.8293 (p) REVERT: E 957 SER cc_start: 0.8278 (t) cc_final: 0.7942 (p) REVERT: E 1042 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7965 (tt) REVERT: E 1087 LEU cc_start: 0.4393 (tt) cc_final: 0.3920 (mt) REVERT: E 1091 TYR cc_start: 0.6330 (p90) cc_final: 0.5978 (p90) outliers start: 30 outliers final: 19 residues processed: 135 average time/residue: 0.0649 time to fit residues: 12.8896 Evaluate side-chains 126 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 38 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 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 366 ILE 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 879 ILE 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: 0.8980 chunk 12 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 65 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4200 r_free = 0.4200 target = 0.155271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.124563 restraints weight = 20236.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.126835 restraints weight = 10182.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.127562 restraints weight = 7250.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.128002 restraints weight = 5988.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.127973 restraints weight = 5543.204| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.5710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9690 Z= 0.133 Angle : 0.679 25.549 13214 Z= 0.310 Chirality : 0.043 0.162 1441 Planarity : 0.003 0.030 1628 Dihedral : 13.120 73.741 1456 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.26 % Allowed : 19.75 % Favored : 77.98 % 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: 1.64 (0.24), residues: 471 sheet: -0.03 (0.37), residues: 190 loop : 0.05 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 968 TYR 0.027 0.002 TYR E 449 PHE 0.017 0.001 PHE E 139 TRP 0.012 0.001 TRP E1026 HIS 0.005 0.001 HIS E 921 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 9686) covalent geometry : angle 0.60289 / 0.31 (13202) hydrogen bonds : bond 0.04232 / 4.63 ( 488) hydrogen bonds : angle 5.02820 / 5.18 ( 1353) metal coordination : bond 0.00732 / 0.54 ( 4) metal coordination : angle 10.38365 / 16.03 ( 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 130 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5590 (OUTLIER) cc_final: 0.5247 (t80) REVERT: E 207 ARG cc_start: 0.7280 (ptt180) cc_final: 0.6919 (ptt180) REVERT: E 904 SER cc_start: 0.8690 (t) cc_final: 0.8326 (p) REVERT: E 957 SER cc_start: 0.8255 (t) cc_final: 0.7931 (p) REVERT: E 968 ARG cc_start: 0.8040 (mtt90) cc_final: 0.7653 (mtt90) REVERT: E 1042 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7918 (tt) REVERT: E 1087 LEU cc_start: 0.4205 (tt) cc_final: 0.3787 (mt) REVERT: E 1091 TYR cc_start: 0.6285 (p90) cc_final: 0.5919 (p90) REVERT: E 1164 LEU cc_start: 0.8399 (pp) cc_final: 0.8178 (mt) outliers start: 22 outliers final: 16 residues processed: 126 average time/residue: 0.0676 time to fit residues: 12.4869 Evaluate side-chains 122 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 94 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 0.0980 chunk 13 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.155848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.125420 restraints weight = 20138.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.126917 restraints weight = 10076.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.129079 restraints weight = 6987.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.128766 restraints weight = 5673.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.128921 restraints weight = 5557.505| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.5771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9690 Z= 0.122 Angle : 0.681 24.534 13214 Z= 0.312 Chirality : 0.043 0.200 1441 Planarity : 0.003 0.038 1628 Dihedral : 13.121 74.422 1456 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.26 % Allowed : 19.65 % 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: 1.05 (0.26), residues: 1113 helix: 1.68 (0.24), residues: 471 sheet: -0.02 (0.37), residues: 190 loop : 0.09 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 968 TYR 0.025 0.001 TYR E 449 PHE 0.017 0.001 PHE E 139 TRP 0.012 0.001 TRP E1143 HIS 0.002 0.001 HIS E 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 9686) covalent geometry : angle 0.60854 / 0.31 (13202) hydrogen bonds : bond 0.04129 / 4.56 ( 488) hydrogen bonds : angle 5.05335 / 5.22 ( 1353) metal coordination : bond 0.00474 / 0.34 ( 4) metal coordination : angle 10.14291 / 15.79 ( 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 129 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5585 (OUTLIER) cc_final: 0.5241 (t80) REVERT: E 192 SER cc_start: 0.7275 (OUTLIER) cc_final: 0.6795 (t) REVERT: E 904 SER cc_start: 0.8666 (t) cc_final: 0.8290 (p) REVERT: E 957 SER cc_start: 0.8224 (t) cc_final: 0.7884 (p) REVERT: E 968 ARG cc_start: 0.8086 (mtt90) cc_final: 0.7663 (mtt90) REVERT: E 1042 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.8011 (tp) REVERT: E 1087 LEU cc_start: 0.4265 (tt) cc_final: 0.3868 (mt) REVERT: E 1091 TYR cc_start: 0.6347 (p90) cc_final: 0.6043 (p90) outliers start: 22 outliers final: 17 residues processed: 126 average time/residue: 0.0685 time to fit residues: 12.9150 Evaluate side-chains 121 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 192 SER 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 366 ILE 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 1042 LEU Chi-restraints excluded: chain E residue 1092 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: 9.9990 chunk 32 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 0.0070 chunk 78 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.157036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.124463 restraints weight = 20163.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.127747 restraints weight = 9913.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.129838 restraints weight = 6503.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.131030 restraints weight = 5121.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.131780 restraints weight = 4505.619| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9690 Z= 0.118 Angle : 0.667 23.010 13214 Z= 0.307 Chirality : 0.042 0.153 1441 Planarity : 0.003 0.036 1628 Dihedral : 13.082 73.146 1456 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.16 % Allowed : 19.96 % Favored : 77.88 % 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: 1.12 (0.26), residues: 1113 helix: 1.70 (0.24), residues: 472 sheet: -0.02 (0.37), residues: 189 loop : 0.19 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 968 TYR 0.020 0.001 TYR E 449 PHE 0.017 0.001 PHE E 139 TRP 0.013 0.001 TRP E1143 HIS 0.002 0.001 HIS E 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 9686) covalent geometry : angle 0.59925 / 0.31 (13202) hydrogen bonds : bond 0.03957 / 4.39 ( 488) hydrogen bonds : angle 5.03117 / 5.17 ( 1353) metal coordination : bond 0.00406 / 0.32 ( 4) metal coordination : angle 9.74617 / 15.33 ( 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 128 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5690 (OUTLIER) cc_final: 0.5340 (t80) REVERT: E 192 SER cc_start: 0.7211 (OUTLIER) cc_final: 0.6774 (t) REVERT: E 846 MET cc_start: 0.8336 (ptm) cc_final: 0.8074 (ppp) REVERT: E 904 SER cc_start: 0.8607 (t) cc_final: 0.8196 (p) REVERT: E 957 SER cc_start: 0.8193 (t) cc_final: 0.7888 (p) REVERT: E 968 ARG cc_start: 0.8123 (mtt90) cc_final: 0.7741 (mtt90) REVERT: E 1042 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.8011 (tp) REVERT: E 1087 LEU cc_start: 0.4464 (tt) cc_final: 0.4081 (mt) REVERT: E 1091 TYR cc_start: 0.6326 (p90) cc_final: 0.6074 (p90) outliers start: 21 outliers final: 17 residues processed: 124 average time/residue: 0.0644 time to fit residues: 11.9448 Evaluate side-chains 120 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 192 SER 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 572 ASN Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 819 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 1186 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.148324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.117503 restraints weight = 20214.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.119981 restraints weight = 10543.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.121003 restraints weight = 7246.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.121238 restraints weight = 6043.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.121450 restraints weight = 5699.188| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.6332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 9690 Z= 0.305 Angle : 0.848 29.796 13214 Z= 0.400 Chirality : 0.050 0.217 1441 Planarity : 0.005 0.074 1628 Dihedral : 13.154 71.709 1456 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.47 % Allowed : 20.27 % Favored : 77.26 % 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: 0.61 (0.26), residues: 1113 helix: 1.31 (0.24), residues: 469 sheet: -0.29 (0.37), residues: 192 loop : -0.11 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 361 TYR 0.021 0.002 TYR E 449 PHE 0.027 0.002 PHE E 574 TRP 0.021 0.002 TRP E1026 HIS 0.008 0.002 HIS E 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00716 / 0.30 ( 9686) covalent geometry : angle 0.77382 / 0.40 (13202) hydrogen bonds : bond 0.05218 / 5.66 ( 488) hydrogen bonds : angle 5.28750 / 5.47 ( 1353) metal coordination : bond 0.02024 / 1.28 ( 4) metal coordination : angle 11.49646 / 17.20 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1489.24 seconds wall clock time: 26 minutes 18.55 seconds (1578.55 seconds total)