Starting phenix.real_space_refine on Wed Feb 4 17:03:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6i_62128/02_2026/9k6i_62128.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6i_62128/02_2026/9k6i_62128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k6i_62128/02_2026/9k6i_62128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6i_62128/02_2026/9k6i_62128.map" model { file = "/net/cci-nas-00/data/ceres_data/9k6i_62128/02_2026/9k6i_62128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6i_62128/02_2026/9k6i_62128.cif" } resolution = 3.6 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= 0.000 sd= 0.021 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 Zn 1 6.06 5 P 54 5.49 5 S 45 5.16 5 C 7252 2.51 5 N 2003 2.21 5 O 2209 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11564 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1270, 10469 Classifications: {'peptide': 1270} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 50, 'TRANS': 1219} Chain: "B" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 404 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "C" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "D" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 210 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "F" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'RNA': 12} Modifications used: {'rna3p_pyr': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9255 SG CYS A1130 48.686 79.042 97.781 1.00 73.81 S ATOM 9290 SG CYS A1134 48.846 77.226 101.108 1.00 86.54 S ATOM 9396 SG CYS A1147 50.971 75.968 98.396 1.00 61.13 S Time building chain proxies: 2.76, per 1000 atoms: 0.24 Number of scatterers: 11564 At special positions: 0 Unit cell: (105, 124, 114, 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) Zn 1 29.99 S 45 16.00 P 54 15.00 O 2209 8.00 N 2003 7.00 C 7252 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: 0.97 Conformation dependent library (CDL) restraints added in 558.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1134 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1147 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1130 " pdb="ZN ZN A1301 " - pdb=" NE2 HIS A1142 " Number of angles added : 3 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2450 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 9 sheets defined 58.6% alpha, 10.8% beta 12 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 20 through 35 removed outlier: 3.782A pdb=" N HIS A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 54 removed outlier: 4.358A pdb=" N HIS A 52 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 54 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 162 through 175 Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.729A pdb=" N LEU A 257 " --> pdb=" O ASN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 277 Processing helix chain 'A' and resid 283 through 311 Processing helix chain 'A' and resid 311 through 331 Processing helix chain 'A' and resid 333 through 369 removed outlier: 3.758A pdb=" N ARG A 369 " --> pdb=" O TRP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 382 Processing helix chain 'A' and resid 403 through 419 removed outlier: 3.558A pdb=" N TYR A 419 " --> pdb=" O TYR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 removed outlier: 3.751A pdb=" N TYR A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 454 through 465 Processing helix chain 'A' and resid 477 through 484 removed outlier: 3.745A pdb=" N TYR A 481 " --> pdb=" O THR A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 503 Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 537 through 553 Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 572 through 589 removed outlier: 3.866A pdb=" N ILE A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 607 Processing helix chain 'A' and resid 609 through 620 Processing helix chain 'A' and resid 624 through 634 Processing helix chain 'A' and resid 663 through 682 removed outlier: 3.591A pdb=" N VAL A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 730 removed outlier: 4.337A pdb=" N GLN A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 728 " --> pdb=" O ASN A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 776 through 778 No H-bonds generated for 'chain 'A' and resid 776 through 778' Processing helix chain 'A' and resid 779 through 785 Processing helix chain 'A' and resid 785 through 799 Processing helix chain 'A' and resid 805 through 816 Processing helix chain 'A' and resid 816 through 828 removed outlier: 4.227A pdb=" N LYS A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 849 removed outlier: 3.766A pdb=" N PHE A 837 " --> pdb=" O PRO A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 862 Processing helix chain 'A' and resid 864 through 868 Processing helix chain 'A' and resid 874 through 893 removed outlier: 4.203A pdb=" N THR A 886 " --> pdb=" O THR A 882 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ALA A 887 " --> pdb=" O VAL A 883 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TRP A 888 " --> pdb=" O THR A 884 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR A 889 " --> pdb=" O LYS A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 947 Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 970 through 981 Processing helix chain 'A' and resid 984 through 989 removed outlier: 3.802A pdb=" N ILE A 988 " --> pdb=" O THR A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 994 Processing helix chain 'A' and resid 998 through 1007 removed outlier: 3.884A pdb=" N MET A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A1007 " --> pdb=" O ALA A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1021 Processing helix chain 'A' and resid 1022 through 1030 Processing helix chain 'A' and resid 1034 through 1042 removed outlier: 3.756A pdb=" N PHE A1040 " --> pdb=" O TRP A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1061 Processing helix chain 'A' and resid 1067 through 1076 Processing helix chain 'A' and resid 1081 through 1095 Processing helix chain 'A' and resid 1098 through 1110 removed outlier: 3.800A pdb=" N ARG A1102 " --> pdb=" O SER A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1123 Processing helix chain 'A' and resid 1139 through 1145 Processing helix chain 'A' and resid 1150 through 1164 Processing helix chain 'A' and resid 1172 through 1178 Processing helix chain 'A' and resid 1181 through 1185 removed outlier: 4.032A pdb=" N LYS A1185 " --> pdb=" O ASN A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1207 Processing helix chain 'A' and resid 1215 through 1238 Processing helix chain 'A' and resid 1239 through 1257 removed outlier: 6.225A pdb=" N LYS A1249 " --> pdb=" O GLY A1245 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU A1250 " --> pdb=" O THR A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1266 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 65 removed outlier: 3.750A pdb=" N LYS A 61 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N VAL A 38 " --> pdb=" O HIS A 7 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR A 9 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N CYS A 40 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU A 11 " --> pdb=" O CYS A 40 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N GLN A 42 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU A 13 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ARG A 238 " --> pdb=" O CYS A 217 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N CYS A 217 " --> pdb=" O ARG A 238 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 91 removed outlier: 6.838A pdb=" N LYS A 101 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE A 89 " --> pdb=" O MET A 99 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N MET A 99 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ARG A 91 " --> pdb=" O TYR A 97 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N TYR A 97 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N LEU A 141 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR A 110 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N MET A 143 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEU A 112 " --> pdb=" O MET A 143 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASP A 145 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE A 114 " --> pdb=" O ASP A 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 193 through 195 Processing sheet with id=AA4, first strand: chain 'A' and resid 393 through 394 removed outlier: 3.660A pdb=" N THR A 401 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 530 through 536 removed outlier: 6.460A pdb=" N ALA A 512 " --> pdb=" O ASN A 640 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE A 642 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE A 514 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 530 through 536 removed outlier: 6.460A pdb=" N ALA A 512 " --> pdb=" O ASN A 640 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE A 642 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE A 514 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 697 through 700 removed outlier: 3.846A pdb=" N MET A 704 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A 739 " --> pdb=" O SER A 598 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 688 through 690 Processing sheet with id=AA9, first strand: chain 'A' and resid 765 through 768 560 hydrogen bonds defined for protein. 1599 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3247 1.34 - 1.45: 2107 1.45 - 1.57: 6388 1.57 - 1.69: 104 1.69 - 1.81: 71 Bond restraints: 11917 Sorted by residual: bond pdb=" N LEU A 663 " pdb=" CA LEU A 663 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.33e-02 5.65e+03 5.00e+00 bond pdb=" CA HIS A 910 " pdb=" CB HIS A 910 " ideal model delta sigma weight residual 1.528 1.570 -0.042 2.61e-02 1.47e+03 2.56e+00 bond pdb=" CB GLN A 925 " pdb=" CG GLN A 925 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.01e+00 bond pdb=" C LEU A 663 " pdb=" O LEU A 663 " ideal model delta sigma weight residual 1.236 1.254 -0.017 1.32e-02 5.74e+03 1.71e+00 bond pdb=" CA ASP A1171 " pdb=" CB ASP A1171 " ideal model delta sigma weight residual 1.531 1.550 -0.019 1.46e-02 4.69e+03 1.66e+00 ... (remaining 11912 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 16069 1.94 - 3.88: 182 3.88 - 5.81: 27 5.81 - 7.75: 8 7.75 - 9.69: 6 Bond angle restraints: 16292 Sorted by residual: angle pdb=" CA GLN A 925 " pdb=" CB GLN A 925 " pdb=" CG GLN A 925 " ideal model delta sigma weight residual 114.10 123.79 -9.69 2.00e+00 2.50e-01 2.35e+01 angle pdb=" CB GLN A 925 " pdb=" CG GLN A 925 " pdb=" CD GLN A 925 " ideal model delta sigma weight residual 112.60 119.32 -6.72 1.70e+00 3.46e-01 1.56e+01 angle pdb=" N TRP A1247 " pdb=" CA TRP A1247 " pdb=" C TRP A1247 " ideal model delta sigma weight residual 112.94 117.31 -4.37 1.41e+00 5.03e-01 9.62e+00 angle pdb=" CB MET A 99 " pdb=" CG MET A 99 " pdb=" SD MET A 99 " ideal model delta sigma weight residual 112.70 121.74 -9.04 3.00e+00 1.11e-01 9.07e+00 angle pdb=" N ILE A 911 " pdb=" CA ILE A 911 " pdb=" C ILE A 911 " ideal model delta sigma weight residual 112.12 109.61 2.51 8.40e-01 1.42e+00 8.96e+00 ... (remaining 16287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6265 17.95 - 35.90: 679 35.90 - 53.84: 234 53.84 - 71.79: 73 71.79 - 89.74: 11 Dihedral angle restraints: 7262 sinusoidal: 3500 harmonic: 3762 Sorted by residual: dihedral pdb=" CB GLU A 328 " pdb=" CG GLU A 328 " pdb=" CD GLU A 328 " pdb=" OE1 GLU A 328 " ideal model delta sinusoidal sigma weight residual 0.00 -88.99 88.99 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA ASN A 254 " pdb=" CB ASN A 254 " pdb=" CG ASN A 254 " pdb=" OD1 ASN A 254 " ideal model delta sinusoidal sigma weight residual -90.00 -157.65 67.65 2 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CB GLU A1261 " pdb=" CG GLU A1261 " pdb=" CD GLU A1261 " pdb=" OE1 GLU A1261 " ideal model delta sinusoidal sigma weight residual 0.00 -87.37 87.37 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 7259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1506 0.051 - 0.101: 261 0.101 - 0.152: 58 0.152 - 0.203: 2 0.203 - 0.254: 1 Chirality restraints: 1828 Sorted by residual: chirality pdb=" CG LEU A1161 " pdb=" CB LEU A1161 " pdb=" CD1 LEU A1161 " pdb=" CD2 LEU A1161 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA TRP A1247 " pdb=" N TRP A1247 " pdb=" C TRP A1247 " pdb=" CB TRP A1247 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CG LEU A 915 " pdb=" CB LEU A 915 " pdb=" CD1 LEU A 915 " pdb=" CD2 LEU A 915 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 1825 not shown) Planarity restraints: 1848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 925 " 0.014 2.00e-02 2.50e+03 2.93e-02 8.60e+00 pdb=" C GLN A 925 " -0.051 2.00e-02 2.50e+03 pdb=" O GLN A 925 " 0.020 2.00e-02 2.50e+03 pdb=" N TRP A 926 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 261 " -0.016 2.00e-02 2.50e+03 1.49e-02 5.58e+00 pdb=" CG TRP A 261 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 261 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 261 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 261 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 261 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 261 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 261 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 261 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 261 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 30 " 0.014 2.00e-02 2.50e+03 1.44e-02 5.15e+00 pdb=" CG TRP A 30 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP A 30 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 30 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 30 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 30 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 30 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 30 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 30 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 30 " 0.001 2.00e-02 2.50e+03 ... (remaining 1845 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 4104 2.89 - 3.39: 11587 3.39 - 3.89: 20404 3.89 - 4.40: 22389 4.40 - 4.90: 36592 Nonbonded interactions: 95076 Sorted by model distance: nonbonded pdb=" O LEU A 317 " pdb=" CD1 LEU A 321 " model vdw 2.383 3.460 nonbonded pdb=" O GLN A 925 " pdb=" OE1 GLN A 925 " model vdw 2.390 3.040 nonbonded pdb=" O5' DC B 20 " pdb=" O4' DC B 20 " model vdw 2.570 2.432 nonbonded pdb=" O4' U F 25 " pdb=" C6 U F 25 " model vdw 2.590 2.672 nonbonded pdb=" O4' DC B 15 " pdb=" C6 DC B 15 " model vdw 2.614 2.672 ... (remaining 95071 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: 3.850 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.000 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 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 : 0.004 0.274 11921 Z= 0.136 Angle : 0.568 9.690 16295 Z= 0.301 Chirality : 0.040 0.254 1828 Planarity : 0.003 0.051 1848 Dihedral : 17.232 89.738 4812 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.52 % Allowed : 13.83 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.24), residues: 1268 helix: 1.66 (0.21), residues: 665 sheet: 0.65 (0.51), residues: 107 loop : 0.47 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 26 TYR 0.015 0.001 TYR A 305 PHE 0.029 0.001 PHE A 491 TRP 0.038 0.002 TRP A 30 HIS 0.005 0.001 HIS A1142 Details of bonding type rmsd covalent geometry : bond 0.00279 (11917) covalent geometry : angle 0.56507 (16292) hydrogen bonds : bond 0.13501 ( 578) hydrogen bonds : angle 6.08439 ( 1647) metal coordination : bond 0.13726 ( 4) metal coordination : angle 4.34238 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.7596 (tptp) cc_final: 0.7188 (tptt) REVERT: A 834 MET cc_start: 0.7715 (mmm) cc_final: 0.7465 (tpt) REVERT: A 1145 TRP cc_start: 0.8519 (t-100) cc_final: 0.8239 (t-100) REVERT: A 1229 MET cc_start: 0.8235 (mmp) cc_final: 0.8002 (mmp) outliers start: 6 outliers final: 5 residues processed: 131 average time/residue: 0.1115 time to fit residues: 21.0664 Evaluate side-chains 125 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 986 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A1127 ASN ** A1142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.172411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.126332 restraints weight = 17405.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.124315 restraints weight = 11539.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.125468 restraints weight = 11216.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.126028 restraints weight = 8785.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.126323 restraints weight = 8100.955| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.0771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11921 Z= 0.146 Angle : 0.532 7.683 16295 Z= 0.280 Chirality : 0.040 0.164 1828 Planarity : 0.003 0.044 1848 Dihedral : 16.432 76.509 2071 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.15 % Allowed : 12.80 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.24), residues: 1268 helix: 1.74 (0.21), residues: 672 sheet: 0.72 (0.51), residues: 107 loop : 0.37 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1132 TYR 0.013 0.001 TYR A 879 PHE 0.017 0.001 PHE A 994 TRP 0.020 0.001 TRP A 261 HIS 0.012 0.001 HIS A1142 Details of bonding type rmsd covalent geometry : bond 0.00337 (11917) covalent geometry : angle 0.52845 (16292) hydrogen bonds : bond 0.04039 ( 578) hydrogen bonds : angle 4.65885 ( 1647) metal coordination : bond 0.01886 ( 4) metal coordination : angle 4.31383 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.7324 (OUTLIER) cc_final: 0.7069 (p) REVERT: A 16 ASN cc_start: 0.7889 (m110) cc_final: 0.7673 (m110) REVERT: A 338 GLN cc_start: 0.8289 (mt0) cc_final: 0.8080 (mp10) REVERT: A 918 ASP cc_start: 0.8088 (t0) cc_final: 0.7791 (t0) REVERT: A 939 ASN cc_start: 0.7880 (OUTLIER) cc_final: 0.7526 (m110) REVERT: A 1174 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8203 (mm) REVERT: A 1229 MET cc_start: 0.8189 (mmp) cc_final: 0.7764 (mmt) outliers start: 25 outliers final: 19 residues processed: 136 average time/residue: 0.1047 time to fit residues: 20.7237 Evaluate side-chains 131 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1250 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 115 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A1127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.170895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.124157 restraints weight = 17450.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126297 restraints weight = 12874.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126278 restraints weight = 9903.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.126794 restraints weight = 9577.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.126930 restraints weight = 8384.569| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11921 Z= 0.146 Angle : 0.515 7.301 16295 Z= 0.269 Chirality : 0.040 0.145 1828 Planarity : 0.003 0.041 1848 Dihedral : 16.360 75.918 2065 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.58 % Allowed : 12.46 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.24), residues: 1268 helix: 1.84 (0.21), residues: 666 sheet: 0.82 (0.52), residues: 107 loop : 0.41 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 26 TYR 0.012 0.001 TYR A 436 PHE 0.019 0.002 PHE A 491 TRP 0.023 0.002 TRP A 30 HIS 0.008 0.001 HIS A1142 Details of bonding type rmsd covalent geometry : bond 0.00342 (11917) covalent geometry : angle 0.51270 (16292) hydrogen bonds : bond 0.03755 ( 578) hydrogen bonds : angle 4.41748 ( 1647) metal coordination : bond 0.01189 ( 4) metal coordination : angle 3.81710 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.7059 (OUTLIER) cc_final: 0.6819 (p) REVERT: A 918 ASP cc_start: 0.8145 (t0) cc_final: 0.7871 (t0) REVERT: A 939 ASN cc_start: 0.7991 (OUTLIER) cc_final: 0.7690 (m110) REVERT: A 1224 TRP cc_start: 0.8330 (OUTLIER) cc_final: 0.7283 (m-90) outliers start: 30 outliers final: 20 residues processed: 144 average time/residue: 0.0914 time to fit residues: 19.5389 Evaluate side-chains 142 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 871 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1224 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 17 optimal weight: 9.9990 chunk 51 optimal weight: 0.0670 chunk 1 optimal weight: 0.0010 chunk 84 optimal weight: 0.1980 chunk 13 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 82 optimal weight: 0.0670 chunk 125 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 overall best weight: 0.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN A1077 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.173518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.127540 restraints weight = 17397.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.125832 restraints weight = 11373.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.127183 restraints weight = 10571.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.127546 restraints weight = 8241.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.127868 restraints weight = 7810.089| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11921 Z= 0.107 Angle : 0.505 9.407 16295 Z= 0.262 Chirality : 0.039 0.188 1828 Planarity : 0.003 0.039 1848 Dihedral : 16.299 76.646 2065 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.23 % Allowed : 13.14 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.24), residues: 1268 helix: 1.90 (0.21), residues: 664 sheet: 0.90 (0.52), residues: 107 loop : 0.50 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1132 TYR 0.022 0.001 TYR A 260 PHE 0.018 0.001 PHE A 741 TRP 0.019 0.001 TRP A 30 HIS 0.006 0.001 HIS A1142 Details of bonding type rmsd covalent geometry : bond 0.00237 (11917) covalent geometry : angle 0.50288 (16292) hydrogen bonds : bond 0.03492 ( 578) hydrogen bonds : angle 4.27828 ( 1647) metal coordination : bond 0.00957 ( 4) metal coordination : angle 3.13461 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.7335 (OUTLIER) cc_final: 0.7068 (p) REVERT: A 918 ASP cc_start: 0.8049 (t0) cc_final: 0.7821 (t70) REVERT: A 939 ASN cc_start: 0.7923 (OUTLIER) cc_final: 0.7628 (m110) REVERT: A 1224 TRP cc_start: 0.8215 (OUTLIER) cc_final: 0.6869 (m-90) outliers start: 26 outliers final: 14 residues processed: 156 average time/residue: 0.0961 time to fit residues: 21.9278 Evaluate side-chains 140 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1147 CYS Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1213 CYS Chi-restraints excluded: chain A residue 1224 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 52 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 22 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 59 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.171269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.125697 restraints weight = 17528.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.125976 restraints weight = 15485.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126450 restraints weight = 12042.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.127030 restraints weight = 9896.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.127222 restraints weight = 8185.960| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11921 Z= 0.138 Angle : 0.522 7.097 16295 Z= 0.270 Chirality : 0.040 0.169 1828 Planarity : 0.003 0.036 1848 Dihedral : 16.289 75.991 2064 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.41 % Allowed : 14.18 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.24), residues: 1268 helix: 1.85 (0.21), residues: 667 sheet: 0.90 (0.52), residues: 107 loop : 0.47 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 337 TYR 0.022 0.001 TYR A 260 PHE 0.018 0.001 PHE A 367 TRP 0.020 0.001 TRP A 30 HIS 0.005 0.001 HIS A1142 Details of bonding type rmsd covalent geometry : bond 0.00321 (11917) covalent geometry : angle 0.52000 (16292) hydrogen bonds : bond 0.03541 ( 578) hydrogen bonds : angle 4.25490 ( 1647) metal coordination : bond 0.00724 ( 4) metal coordination : angle 3.56904 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.7056 (OUTLIER) cc_final: 0.6850 (p) REVERT: A 918 ASP cc_start: 0.8116 (t0) cc_final: 0.7844 (t70) REVERT: A 939 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7604 (m110) REVERT: A 1224 TRP cc_start: 0.8334 (OUTLIER) cc_final: 0.7110 (m-90) REVERT: A 1262 GLN cc_start: 0.7580 (mt0) cc_final: 0.7253 (mt0) outliers start: 28 outliers final: 14 residues processed: 145 average time/residue: 0.1018 time to fit residues: 21.6945 Evaluate side-chains 137 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1213 CYS Chi-restraints excluded: chain A residue 1224 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 120 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 117 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 89 optimal weight: 0.4980 chunk 106 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN A 960 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.170921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.125492 restraints weight = 17587.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.124384 restraints weight = 14527.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.125590 restraints weight = 11305.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.126216 restraints weight = 8695.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.126398 restraints weight = 7910.076| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11921 Z= 0.140 Angle : 0.528 11.667 16295 Z= 0.272 Chirality : 0.039 0.137 1828 Planarity : 0.003 0.036 1848 Dihedral : 16.265 75.627 2063 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.66 % Allowed : 13.92 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.24), residues: 1268 helix: 1.84 (0.21), residues: 667 sheet: 1.04 (0.53), residues: 101 loop : 0.45 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1132 TYR 0.023 0.001 TYR A 260 PHE 0.018 0.002 PHE A 491 TRP 0.019 0.001 TRP A 30 HIS 0.005 0.001 HIS A1142 Details of bonding type rmsd covalent geometry : bond 0.00326 (11917) covalent geometry : angle 0.52580 (16292) hydrogen bonds : bond 0.03517 ( 578) hydrogen bonds : angle 4.23659 ( 1647) metal coordination : bond 0.00673 ( 4) metal coordination : angle 3.49406 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.7239 (OUTLIER) cc_final: 0.7023 (p) REVERT: A 918 ASP cc_start: 0.8115 (t0) cc_final: 0.7839 (t70) REVERT: A 939 ASN cc_start: 0.8108 (OUTLIER) cc_final: 0.7805 (m110) REVERT: A 1224 TRP cc_start: 0.8348 (OUTLIER) cc_final: 0.7056 (m-90) outliers start: 31 outliers final: 18 residues processed: 154 average time/residue: 0.0921 time to fit residues: 21.3177 Evaluate side-chains 139 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1147 CYS Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1213 CYS Chi-restraints excluded: chain A residue 1224 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 54 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 70 optimal weight: 0.4980 chunk 89 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 12 optimal weight: 0.0370 chunk 48 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.171430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.125233 restraints weight = 17461.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.127107 restraints weight = 13044.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.127747 restraints weight = 9319.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.127797 restraints weight = 8004.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.128152 restraints weight = 7382.522| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11921 Z= 0.126 Angle : 0.532 11.694 16295 Z= 0.272 Chirality : 0.039 0.138 1828 Planarity : 0.003 0.036 1848 Dihedral : 16.249 75.712 2063 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.23 % Allowed : 14.69 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.24), residues: 1268 helix: 1.88 (0.21), residues: 665 sheet: 1.14 (0.54), residues: 101 loop : 0.47 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1162 TYR 0.020 0.001 TYR A 260 PHE 0.015 0.001 PHE A 367 TRP 0.019 0.001 TRP A 30 HIS 0.004 0.001 HIS A1142 Details of bonding type rmsd covalent geometry : bond 0.00298 (11917) covalent geometry : angle 0.52961 (16292) hydrogen bonds : bond 0.03459 ( 578) hydrogen bonds : angle 4.22646 ( 1647) metal coordination : bond 0.00667 ( 4) metal coordination : angle 3.40349 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 LYS cc_start: 0.8822 (tppt) cc_final: 0.8325 (ttmt) REVERT: A 918 ASP cc_start: 0.8092 (t0) cc_final: 0.7823 (t70) REVERT: A 939 ASN cc_start: 0.7946 (OUTLIER) cc_final: 0.7614 (m110) REVERT: A 1092 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.8054 (mtp) REVERT: A 1224 TRP cc_start: 0.8267 (OUTLIER) cc_final: 0.6964 (m-90) REVERT: A 1227 TYR cc_start: 0.8372 (t80) cc_final: 0.8170 (t80) outliers start: 26 outliers final: 20 residues processed: 145 average time/residue: 0.0963 time to fit residues: 20.7215 Evaluate side-chains 144 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1147 CYS Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1224 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 127 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 38 optimal weight: 0.0670 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 15 optimal weight: 10.0000 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN A 497 GLN A 960 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.168472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.121380 restraints weight = 17518.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.122728 restraints weight = 13943.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.123742 restraints weight = 10030.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.123608 restraints weight = 7995.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.123885 restraints weight = 7618.745| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11921 Z= 0.188 Angle : 0.571 8.450 16295 Z= 0.292 Chirality : 0.041 0.135 1828 Planarity : 0.003 0.035 1848 Dihedral : 16.295 75.459 2063 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.41 % Allowed : 14.78 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.24), residues: 1268 helix: 1.77 (0.21), residues: 663 sheet: 0.93 (0.53), residues: 101 loop : 0.36 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 658 TYR 0.018 0.001 TYR A 260 PHE 0.016 0.002 PHE A 367 TRP 0.019 0.002 TRP A 30 HIS 0.004 0.001 HIS A1113 Details of bonding type rmsd covalent geometry : bond 0.00446 (11917) covalent geometry : angle 0.56903 (16292) hydrogen bonds : bond 0.03703 ( 578) hydrogen bonds : angle 4.31057 ( 1647) metal coordination : bond 0.01085 ( 4) metal coordination : angle 3.74230 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7170 (pm20) REVERT: A 354 LYS cc_start: 0.8801 (tppt) cc_final: 0.8287 (ttmt) REVERT: A 918 ASP cc_start: 0.8183 (t0) cc_final: 0.7921 (t70) REVERT: A 939 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7813 (m110) REVERT: A 1092 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8051 (mtp) REVERT: A 1224 TRP cc_start: 0.8441 (OUTLIER) cc_final: 0.7599 (m-90) REVERT: A 1262 GLN cc_start: 0.7730 (mt0) cc_final: 0.7491 (mt0) outliers start: 28 outliers final: 18 residues processed: 141 average time/residue: 0.1005 time to fit residues: 21.1874 Evaluate side-chains 137 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1147 CYS Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1224 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 112 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 0.0770 chunk 22 optimal weight: 3.9990 chunk 84 optimal weight: 0.0870 chunk 14 optimal weight: 9.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.171051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.126405 restraints weight = 17310.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.124639 restraints weight = 12182.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.125939 restraints weight = 11427.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.126502 restraints weight = 8892.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.126636 restraints weight = 7641.921| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11921 Z= 0.121 Angle : 0.542 8.845 16295 Z= 0.278 Chirality : 0.039 0.163 1828 Planarity : 0.003 0.035 1848 Dihedral : 16.258 76.042 2063 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.06 % Allowed : 15.12 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.24), residues: 1268 helix: 1.87 (0.21), residues: 657 sheet: 1.05 (0.54), residues: 101 loop : 0.48 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 337 TYR 0.018 0.001 TYR A 260 PHE 0.015 0.001 PHE A 741 TRP 0.023 0.001 TRP A 30 HIS 0.005 0.001 HIS A1142 Details of bonding type rmsd covalent geometry : bond 0.00282 (11917) covalent geometry : angle 0.54042 (16292) hydrogen bonds : bond 0.03486 ( 578) hydrogen bonds : angle 4.20759 ( 1647) metal coordination : bond 0.00764 ( 4) metal coordination : angle 3.51039 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 LYS cc_start: 0.8756 (tppt) cc_final: 0.8313 (ttmt) REVERT: A 599 ILE cc_start: 0.8391 (mm) cc_final: 0.7700 (mm) REVERT: A 939 ASN cc_start: 0.8020 (OUTLIER) cc_final: 0.7680 (m110) REVERT: A 1092 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.8085 (mtp) REVERT: A 1224 TRP cc_start: 0.8324 (OUTLIER) cc_final: 0.7207 (m-90) REVERT: A 1262 GLN cc_start: 0.7756 (mt0) cc_final: 0.7512 (mt0) outliers start: 24 outliers final: 18 residues processed: 140 average time/residue: 0.1045 time to fit residues: 21.7281 Evaluate side-chains 137 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1147 CYS Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1224 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 112 optimal weight: 0.0020 chunk 82 optimal weight: 0.4980 chunk 13 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 0.0770 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.6548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 925 GLN ** 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 = 0.4143 r_free = 0.4143 target = 0.170233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.124941 restraints weight = 17449.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.124586 restraints weight = 13131.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.125359 restraints weight = 11610.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.125623 restraints weight = 9286.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.125925 restraints weight = 7707.379| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11921 Z= 0.143 Angle : 0.563 11.893 16295 Z= 0.286 Chirality : 0.040 0.236 1828 Planarity : 0.003 0.035 1848 Dihedral : 16.256 77.078 2063 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.98 % Allowed : 15.38 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.24), residues: 1268 helix: 1.85 (0.21), residues: 655 sheet: 0.97 (0.53), residues: 101 loop : 0.46 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 337 TYR 0.018 0.001 TYR A 879 PHE 0.016 0.001 PHE A 367 TRP 0.028 0.002 TRP A 963 HIS 0.004 0.001 HIS A1142 Details of bonding type rmsd covalent geometry : bond 0.00340 (11917) covalent geometry : angle 0.56093 (16292) hydrogen bonds : bond 0.03569 ( 578) hydrogen bonds : angle 4.23846 ( 1647) metal coordination : bond 0.00692 ( 4) metal coordination : angle 3.49716 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 ASN cc_start: 0.7759 (m-40) cc_final: 0.7535 (t0) REVERT: A 336 ARG cc_start: 0.7840 (mtm-85) cc_final: 0.7398 (ttp-170) REVERT: A 354 LYS cc_start: 0.8739 (tppt) cc_final: 0.8241 (ttmt) REVERT: A 599 ILE cc_start: 0.8377 (mm) cc_final: 0.7732 (mm) REVERT: A 918 ASP cc_start: 0.8001 (t0) cc_final: 0.7677 (t0) REVERT: A 939 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7791 (m110) REVERT: A 1092 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8104 (mtp) REVERT: A 1103 GLU cc_start: 0.7557 (tt0) cc_final: 0.7247 (tt0) REVERT: A 1224 TRP cc_start: 0.8327 (OUTLIER) cc_final: 0.7306 (m-90) REVERT: A 1227 TYR cc_start: 0.8454 (t80) cc_final: 0.7897 (t80) REVERT: A 1262 GLN cc_start: 0.7846 (mt0) cc_final: 0.7607 (mt0) outliers start: 23 outliers final: 18 residues processed: 133 average time/residue: 0.1101 time to fit residues: 21.5281 Evaluate side-chains 133 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1147 CYS Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1224 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 94 optimal weight: 0.6980 chunk 17 optimal weight: 9.9990 chunk 71 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 127 optimal weight: 8.9990 chunk 114 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 925 GLN ** 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 = 0.4141 r_free = 0.4141 target = 0.170084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.123540 restraints weight = 17689.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.126243 restraints weight = 12850.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126462 restraints weight = 8828.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.126456 restraints weight = 7738.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.126674 restraints weight = 7097.683| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11921 Z= 0.140 Angle : 0.556 11.391 16295 Z= 0.283 Chirality : 0.040 0.176 1828 Planarity : 0.003 0.034 1848 Dihedral : 16.270 78.624 2063 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.98 % Allowed : 15.21 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.24), residues: 1268 helix: 1.85 (0.21), residues: 654 sheet: 0.88 (0.54), residues: 101 loop : 0.46 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 337 TYR 0.017 0.001 TYR A 260 PHE 0.016 0.001 PHE A 741 TRP 0.028 0.002 TRP A 963 HIS 0.005 0.001 HIS A1142 Details of bonding type rmsd covalent geometry : bond 0.00333 (11917) covalent geometry : angle 0.55419 (16292) hydrogen bonds : bond 0.03512 ( 578) hydrogen bonds : angle 4.22244 ( 1647) metal coordination : bond 0.00697 ( 4) metal coordination : angle 3.52507 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1830.06 seconds wall clock time: 32 minutes 43.49 seconds (1963.49 seconds total)