Starting phenix.real_space_refine on Wed Aug 5 22:10:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6i_62128/08_2026/9k6i_62128.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6i_62128/08_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_62128/08_2026/9k6i_62128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6i_62128/08_2026/9k6i_62128.map" model { file = "/net/cci-nas-00/data/ceres_data/9k6i_62128/08_2026/9k6i_62128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6i_62128/08_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-2.2rc3-6140/lib/python3.11/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: 2.45, per 1000 atoms: 0.21 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: 0.85 Conformation dependent library (CDL) restraints added in 473.6 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: 1.27 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: 3.02 Time building geometry restraints manager: 1.19 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=" C3' DT C 30 " pdb=" C2' DT C 30 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.16e+00 bond pdb=" C1' DC B 15 " pdb=" N1 DC B 15 " ideal model delta sigma weight residual 1.468 1.505 -0.037 1.40e-02 5.10e+03 6.98e+00 bond pdb=" C1' DC B 20 " pdb=" N1 DC B 20 " ideal model delta sigma weight residual 1.468 1.503 -0.035 1.40e-02 5.10e+03 6.34e+00 bond pdb=" C1' DT C 22 " pdb=" N1 DT C 22 " ideal model delta sigma weight residual 1.468 1.502 -0.034 1.40e-02 5.10e+03 5.92e+00 bond pdb=" C1' DT C 24 " pdb=" N1 DT C 24 " ideal model delta sigma weight residual 1.468 1.501 -0.033 1.40e-02 5.10e+03 5.67e+00 ... (remaining 11912 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 15985 1.94 - 3.88: 266 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=" N3 DT C 30 " pdb=" C4 DT C 30 " pdb=" O4 DT C 30 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT C 29 " pdb=" C4 DT C 29 " pdb=" O4 DT C 29 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT C 19 " pdb=" C4 DT C 19 " pdb=" O4 DT C 19 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT C 26 " pdb=" C4 DT C 26 " pdb=" O4 DT C 26 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 ... (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: 1457 0.051 - 0.101: 298 0.101 - 0.152: 70 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: 3.940 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.690 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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= 0.236 Angle : 0.609 9.690 16295 Z= 0.394 Chirality : 0.043 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/Z covalent geometry : bond 0.00338 / 0.23 (11917) covalent geometry : angle 0.60656 / 0.39 (16292) hydrogen bonds : bond 0.13501 / 8.98 ( 578) hydrogen bonds : angle 6.08439 / 4.37 ( 1647) metal coordination : bond 0.13726 / 6.86 ( 4) metal coordination : angle 4.34238 / 2.30 ( 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 : 0.413 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: 0.1049 time to fit residues: 20.0082 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 : 0.393 ------------------------------------------------------------------------------- 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: 7.9990 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... A 19 ASN A1077 ASN A1127 ASN ** A1142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.166510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.119427 restraints weight = 17529.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.119169 restraints weight = 12045.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.120484 restraints weight = 9192.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.120875 restraints weight = 7251.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.121143 restraints weight = 6812.960| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11921 Z= 0.149 Angle : 0.544 7.962 16295 Z= 0.291 Chirality : 0.041 0.174 1828 Planarity : 0.003 0.041 1848 Dihedral : 16.318 78.043 2071 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.49 % Allowed : 12.63 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.24), residues: 1268 helix: 1.75 (0.21), residues: 671 sheet: 0.71 (0.51), residues: 107 loop : 0.35 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1132 TYR 0.013 0.001 TYR A 879 PHE 0.016 0.002 PHE A 741 TRP 0.022 0.001 TRP A 261 HIS 0.013 0.001 HIS A1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (11917) covalent geometry : angle 0.53998 / 0.29 (16292) hydrogen bonds : bond 0.04264 / 2.95 ( 578) hydrogen bonds : angle 4.76636 / 3.48 ( 1647) metal coordination : bond 0.01646 / 0.82 ( 4) metal coordination : angle 4.73155 / 2.52 ( 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 147 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.7368 (OUTLIER) cc_final: 0.7110 (p) REVERT: A 16 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7660 (m110) REVERT: A 338 GLN cc_start: 0.8345 (mt0) cc_final: 0.8128 (mp10) REVERT: A 354 LYS cc_start: 0.7902 (ttmt) cc_final: 0.7681 (tppt) REVERT: A 468 LYS cc_start: 0.7787 (tptp) cc_final: 0.7295 (tptt) REVERT: A 834 MET cc_start: 0.7768 (mmm) cc_final: 0.7540 (tpt) REVERT: A 918 ASP cc_start: 0.8143 (t0) cc_final: 0.7910 (t0) REVERT: A 939 ASN cc_start: 0.7887 (OUTLIER) cc_final: 0.7520 (m110) REVERT: A 1002 MET cc_start: 0.8150 (mpp) cc_final: 0.7066 (ttm) REVERT: A 1174 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8132 (mm) REVERT: A 1224 TRP cc_start: 0.8206 (OUTLIER) cc_final: 0.6396 (m-90) REVERT: A 1229 MET cc_start: 0.8228 (mmp) cc_final: 0.7691 (mmt) outliers start: 29 outliers final: 19 residues processed: 136 average time/residue: 0.0928 time to fit residues: 18.4305 Evaluate side-chains 135 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 16 ASN 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 625 THR 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 1150 VAL Chi-restraints excluded: chain A residue 1161 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 115 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 130 optimal weight: 8.9990 chunk 117 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1127 ASN ** A1142 HIS ** 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 = 0.4152 r_free = 0.4152 target = 0.171007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.125652 restraints weight = 17458.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.124579 restraints weight = 14925.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.125600 restraints weight = 11926.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.126255 restraints weight = 9280.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.126361 restraints weight = 8512.175| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11921 Z= 0.155 Angle : 0.523 7.387 16295 Z= 0.278 Chirality : 0.041 0.152 1828 Planarity : 0.003 0.039 1848 Dihedral : 16.239 78.846 2065 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.92 % Allowed : 12.54 % Favored : 84.54 % 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: 1.75 (0.21), residues: 672 sheet: 0.79 (0.51), residues: 107 loop : 0.32 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1132 TYR 0.012 0.001 TYR A 436 PHE 0.018 0.002 PHE A 491 TRP 0.024 0.002 TRP A 30 HIS 0.008 0.001 HIS A1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (11917) covalent geometry : angle 0.52069 / 0.28 (16292) hydrogen bonds : bond 0.03966 / 2.78 ( 578) hydrogen bonds : angle 4.51832 / 3.30 ( 1647) metal coordination : bond 0.01228 / 0.61 ( 4) metal coordination : angle 3.80044 / 2.02 ( 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: 34 poor density : 122 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.7077 (OUTLIER) cc_final: 0.6820 (p) REVERT: A 834 MET cc_start: 0.7751 (mmm) cc_final: 0.7417 (tpt) REVERT: A 918 ASP cc_start: 0.8088 (t0) cc_final: 0.7718 (t0) REVERT: A 939 ASN cc_start: 0.7978 (OUTLIER) cc_final: 0.7646 (m110) REVERT: A 1224 TRP cc_start: 0.8259 (OUTLIER) cc_final: 0.6775 (m-90) outliers start: 34 outliers final: 22 residues processed: 146 average time/residue: 0.0909 time to fit residues: 19.3341 Evaluate side-chains 139 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 446 VAL 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 792 ILE Chi-restraints excluded: chain A residue 804 CYS 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 986 GLN Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1224 TRP Chi-restraints excluded: chain A residue 1250 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 17 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 0.0170 chunk 13 optimal weight: 7.9990 chunk 90 optimal weight: 0.0670 chunk 111 optimal weight: 0.0970 chunk 82 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 ASN A 254 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.172880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.126098 restraints weight = 17452.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.125186 restraints weight = 10211.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.125748 restraints weight = 9719.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.127085 restraints weight = 8274.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.127043 restraints weight = 7160.706| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11921 Z= 0.118 Angle : 0.510 7.929 16295 Z= 0.271 Chirality : 0.041 0.219 1828 Planarity : 0.003 0.041 1848 Dihedral : 16.206 79.740 2065 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.49 % Allowed : 13.14 % Favored : 84.36 % 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: 1.77 (0.24), residues: 1268 helix: 1.82 (0.21), residues: 665 sheet: 0.88 (0.52), residues: 107 loop : 0.48 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 337 TYR 0.021 0.001 TYR A 260 PHE 0.020 0.001 PHE A 491 TRP 0.021 0.001 TRP A 30 HIS 0.006 0.001 HIS A1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (11917) covalent geometry : angle 0.50861 / 0.27 (16292) hydrogen bonds : bond 0.03757 / 2.62 ( 578) hydrogen bonds : angle 4.39616 / 3.21 ( 1647) metal coordination : bond 0.00762 / 0.38 ( 4) metal coordination : angle 3.21325 / 1.71 ( 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 154 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.7397 (OUTLIER) cc_final: 0.7138 (p) REVERT: A 354 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7741 (tppt) REVERT: A 939 ASN cc_start: 0.7968 (OUTLIER) cc_final: 0.7617 (m110) REVERT: A 1224 TRP cc_start: 0.8209 (OUTLIER) cc_final: 0.6821 (m-90) outliers start: 29 outliers final: 18 residues processed: 145 average time/residue: 0.0897 time to fit residues: 19.2176 Evaluate side-chains 134 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 352 THR Chi-restraints excluded: chain A residue 393 ILE 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 777 VAL Chi-restraints excluded: chain A residue 804 CYS 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 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 Chi-restraints excluded: chain A residue 1250 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 52 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 59 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 ASN A 933 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.171453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.126061 restraints weight = 17537.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.122512 restraints weight = 11616.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.123523 restraints weight = 12052.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.123930 restraints weight = 10091.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.124301 restraints weight = 8994.391| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11921 Z= 0.149 Angle : 0.534 7.174 16295 Z= 0.283 Chirality : 0.041 0.197 1828 Planarity : 0.003 0.041 1848 Dihedral : 16.190 79.676 2065 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.26 % Allowed : 12.89 % Favored : 83.85 % 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: 1.70 (0.24), residues: 1268 helix: 1.78 (0.21), residues: 665 sheet: 0.90 (0.52), residues: 107 loop : 0.40 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 337 TYR 0.023 0.001 TYR A 260 PHE 0.018 0.002 PHE A 491 TRP 0.023 0.002 TRP A 30 HIS 0.006 0.001 HIS A1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (11917) covalent geometry : angle 0.53212 / 0.28 (16292) hydrogen bonds : bond 0.03740 / 2.62 ( 578) hydrogen bonds : angle 4.36415 / 3.18 ( 1647) metal coordination : bond 0.00718 / 0.35 ( 4) metal coordination : angle 3.41790 / 1.81 ( 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 166 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.7459 (OUTLIER) cc_final: 0.7190 (p) REVERT: A 336 ARG cc_start: 0.8056 (ttm-80) cc_final: 0.7828 (ttp-110) REVERT: A 338 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7713 (mp10) REVERT: A 354 LYS cc_start: 0.7997 (ttmt) cc_final: 0.7733 (tppt) REVERT: A 918 ASP cc_start: 0.8095 (t0) cc_final: 0.7887 (t0) REVERT: A 939 ASN cc_start: 0.7999 (OUTLIER) cc_final: 0.7664 (m110) REVERT: A 1092 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8104 (mtp) REVERT: A 1224 TRP cc_start: 0.8250 (OUTLIER) cc_final: 0.6904 (m-90) REVERT: A 1227 TYR cc_start: 0.8396 (t80) cc_final: 0.7978 (t80) outliers start: 38 outliers final: 26 residues processed: 154 average time/residue: 0.0852 time to fit residues: 19.6046 Evaluate side-chains 150 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 352 THR 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 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 953 LEU Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 986 GLN 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 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 Chi-restraints excluded: chain A residue 1250 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 120 optimal weight: 0.0980 chunk 32 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 117 optimal weight: 0.0270 chunk 80 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 64 optimal weight: 0.0020 chunk 85 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.2646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4174 r_free = 0.4174 target = 0.173240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.128288 restraints weight = 17573.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.126318 restraints weight = 11988.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.128190 restraints weight = 11006.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.128581 restraints weight = 8420.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.129253 restraints weight = 8259.134| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11921 Z= 0.107 Angle : 0.507 7.704 16295 Z= 0.267 Chirality : 0.040 0.140 1828 Planarity : 0.003 0.040 1848 Dihedral : 16.154 80.584 2065 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.58 % Allowed : 14.00 % 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: 1.80 (0.24), residues: 1268 helix: 1.85 (0.21), residues: 666 sheet: 1.10 (0.54), residues: 101 loop : 0.44 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 307 TYR 0.023 0.001 TYR A 260 PHE 0.028 0.002 PHE A 994 TRP 0.028 0.001 TRP A1247 HIS 0.005 0.001 HIS A1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (11917) covalent geometry : angle 0.50515 / 0.27 (16292) hydrogen bonds : bond 0.03553 / 2.48 ( 578) hydrogen bonds : angle 4.25818 / 3.11 ( 1647) metal coordination : bond 0.00653 / 0.32 ( 4) metal coordination : angle 2.86720 / 1.52 ( 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 166 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.7049 (OUTLIER) cc_final: 0.6797 (p) REVERT: A 336 ARG cc_start: 0.7857 (ttm-80) cc_final: 0.7484 (ttp-110) REVERT: A 354 LYS cc_start: 0.8033 (ttmt) cc_final: 0.7801 (tppt) REVERT: A 918 ASP cc_start: 0.8078 (t0) cc_final: 0.7794 (t0) REVERT: A 939 ASN cc_start: 0.7911 (OUTLIER) cc_final: 0.7572 (m110) REVERT: A 1092 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.8111 (mtp) REVERT: A 1224 TRP cc_start: 0.8150 (OUTLIER) cc_final: 0.6709 (m-90) REVERT: A 1227 TYR cc_start: 0.8280 (t80) cc_final: 0.7946 (t80) outliers start: 30 outliers final: 17 residues processed: 157 average time/residue: 0.0949 time to fit residues: 21.7996 Evaluate side-chains 149 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 352 THR 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 985 ILE Chi-restraints excluded: chain A residue 993 ASP 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 1213 CYS Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1224 TRP Chi-restraints excluded: chain A residue 1250 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 54 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 0.3980 chunk 94 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.172290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.126976 restraints weight = 17519.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.127315 restraints weight = 13829.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.128120 restraints weight = 11004.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.128441 restraints weight = 8735.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.128691 restraints weight = 7580.012| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1453 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= 0.126 Angle : 0.525 8.850 16295 Z= 0.275 Chirality : 0.040 0.146 1828 Planarity : 0.003 0.039 1848 Dihedral : 16.145 80.543 2064 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.06 % Allowed : 15.38 % Favored : 82.56 % 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: 1.82 (0.21), residues: 667 sheet: 0.90 (0.52), residues: 107 loop : 0.46 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1162 TYR 0.024 0.001 TYR A 260 PHE 0.016 0.001 PHE A 491 TRP 0.022 0.001 TRP A1247 HIS 0.004 0.001 HIS A1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (11917) covalent geometry : angle 0.52327 / 0.27 (16292) hydrogen bonds : bond 0.03591 / 2.51 ( 578) hydrogen bonds : angle 4.23956 / 3.09 ( 1647) metal coordination : bond 0.00661 / 0.32 ( 4) metal coordination : angle 3.30418 / 1.75 ( 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: 24 poor density : 129 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.6997 (OUTLIER) cc_final: 0.6780 (p) REVERT: A 336 ARG cc_start: 0.7855 (ttm-80) cc_final: 0.7566 (ttp-110) REVERT: A 354 LYS cc_start: 0.7998 (ttmt) cc_final: 0.7782 (tppt) REVERT: A 918 ASP cc_start: 0.8076 (t0) cc_final: 0.7796 (t0) REVERT: A 939 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7566 (m110) REVERT: A 1092 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8181 (mtp) REVERT: A 1224 TRP cc_start: 0.8189 (OUTLIER) cc_final: 0.6733 (m-90) REVERT: A 1227 TYR cc_start: 0.8338 (t80) cc_final: 0.7959 (t80) outliers start: 24 outliers final: 17 residues processed: 148 average time/residue: 0.0836 time to fit residues: 18.1031 Evaluate side-chains 144 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 352 THR 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 777 VAL 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 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 1213 CYS Chi-restraints excluded: chain A residue 1224 TRP Chi-restraints excluded: chain A residue 1250 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 127 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 101 optimal weight: 0.0270 chunk 128 optimal weight: 9.9990 chunk 38 optimal weight: 0.0470 chunk 75 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 65 optimal weight: 0.0970 chunk 93 optimal weight: 0.4980 chunk 15 optimal weight: 20.0000 overall best weight: 0.2934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 ASN A1262 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.173268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.128314 restraints weight = 17491.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.130754 restraints weight = 13225.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.130981 restraints weight = 9349.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.131374 restraints weight = 8300.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.131281 restraints weight = 7670.871| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11921 Z= 0.111 Angle : 0.537 9.071 16295 Z= 0.278 Chirality : 0.040 0.242 1828 Planarity : 0.003 0.046 1848 Dihedral : 16.095 80.923 2063 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.06 % Allowed : 15.29 % 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: 1.84 (0.24), residues: 1268 helix: 1.85 (0.21), residues: 666 sheet: 1.13 (0.54), residues: 101 loop : 0.50 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A1162 TYR 0.022 0.001 TYR A 260 PHE 0.017 0.001 PHE A 994 TRP 0.025 0.001 TRP A1247 HIS 0.004 0.001 HIS A1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (11917) covalent geometry : angle 0.53560 / 0.28 (16292) hydrogen bonds : bond 0.03535 / 2.45 ( 578) hydrogen bonds : angle 4.19947 / 3.07 ( 1647) metal coordination : bond 0.00606 / 0.30 ( 4) metal coordination : angle 3.01139 / 1.60 ( 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 153 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 918 ASP cc_start: 0.8036 (t0) cc_final: 0.7697 (t0) REVERT: A 939 ASN cc_start: 0.7864 (OUTLIER) cc_final: 0.7530 (m110) REVERT: A 1092 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8110 (mtp) REVERT: A 1224 TRP cc_start: 0.8119 (OUTLIER) cc_final: 0.6786 (m-90) REVERT: A 1227 TYR cc_start: 0.8245 (t80) cc_final: 0.7882 (t80) outliers start: 24 outliers final: 18 residues processed: 148 average time/residue: 0.0768 time to fit residues: 17.1905 Evaluate side-chains 146 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 352 THR 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 777 VAL 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 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 1213 CYS Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1224 TRP Chi-restraints excluded: chain A residue 1250 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 14 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.172095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.126040 restraints weight = 17325.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.128249 restraints weight = 13622.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.128708 restraints weight = 9310.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.128942 restraints weight = 7710.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.129104 restraints weight = 7397.551| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11921 Z= 0.127 Angle : 0.557 12.218 16295 Z= 0.284 Chirality : 0.040 0.181 1828 Planarity : 0.003 0.038 1848 Dihedral : 16.089 80.741 2063 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.89 % Allowed : 15.55 % Favored : 82.56 % 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: 1.83 (0.21), residues: 665 sheet: 1.18 (0.54), residues: 101 loop : 0.47 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1162 TYR 0.020 0.001 TYR A 260 PHE 0.017 0.001 PHE A 491 TRP 0.030 0.001 TRP A 963 HIS 0.004 0.001 HIS A1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (11917) covalent geometry : angle 0.55481 / 0.28 (16292) hydrogen bonds : bond 0.03520 / 2.45 ( 578) hydrogen bonds : angle 4.20922 / 3.07 ( 1647) metal coordination : bond 0.00690 / 0.34 ( 4) metal coordination : angle 3.29242 / 1.74 ( 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 146 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 ARG cc_start: 0.7705 (mtm-85) cc_final: 0.7147 (ttp-170) REVERT: A 338 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7023 (pm20) REVERT: A 354 LYS cc_start: 0.8833 (tppt) cc_final: 0.8323 (ttmt) REVERT: A 918 ASP cc_start: 0.7907 (t0) cc_final: 0.7646 (t0) REVERT: A 939 ASN cc_start: 0.7909 (OUTLIER) cc_final: 0.7581 (m110) REVERT: A 1092 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8147 (mtp) REVERT: A 1224 TRP cc_start: 0.8178 (OUTLIER) cc_final: 0.6839 (m-90) REVERT: A 1227 TYR cc_start: 0.8261 (t80) cc_final: 0.7884 (t80) outliers start: 22 outliers final: 17 residues processed: 141 average time/residue: 0.0946 time to fit residues: 20.0273 Evaluate side-chains 143 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 796 THR Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 993 ASP 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 1213 CYS Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1224 TRP Chi-restraints excluded: chain A residue 1250 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 112 optimal weight: 2.9990 chunk 82 optimal weight: 0.0980 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 ASN A 42 GLN A 497 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.167466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.119047 restraints weight = 17594.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.122201 restraints weight = 11562.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.122879 restraints weight = 7643.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.121949 restraints weight = 6052.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.122487 restraints weight = 6981.226| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 11921 Z= 0.245 Angle : 0.637 11.663 16295 Z= 0.326 Chirality : 0.043 0.156 1828 Planarity : 0.004 0.042 1848 Dihedral : 16.187 78.167 2063 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: 1.44 (0.24), residues: 1268 helix: 1.56 (0.20), residues: 663 sheet: 0.87 (0.53), residues: 101 loop : 0.30 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1162 TYR 0.018 0.002 TYR A 260 PHE 0.015 0.002 PHE A 491 TRP 0.043 0.002 TRP A1247 HIS 0.006 0.001 HIS A1113 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.24 (11917) covalent geometry : angle 0.63417 / 0.33 (16292) hydrogen bonds : bond 0.03925 / 2.76 ( 578) hydrogen bonds : angle 4.39142 / 3.19 ( 1647) metal coordination : bond 0.01938 / 0.96 ( 4) metal coordination : angle 4.10585 / 2.17 ( 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: A 338 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7248 (pm20) REVERT: A 354 LYS cc_start: 0.8831 (tppt) cc_final: 0.8272 (ttmt) REVERT: A 918 ASP cc_start: 0.8125 (t0) cc_final: 0.7757 (t0) REVERT: A 939 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7868 (m110) REVERT: A 1092 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8271 (mtp) REVERT: A 1224 TRP cc_start: 0.8465 (OUTLIER) cc_final: 0.7328 (m-90) outliers start: 23 outliers final: 16 residues processed: 133 average time/residue: 0.0958 time to fit residues: 19.0782 Evaluate side-chains 130 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 760 THR Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 993 ASP 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 1221 LYS Chi-restraints excluded: chain A residue 1224 TRP Chi-restraints excluded: chain A residue 1250 LEU 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: 6.9990 chunk 71 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 127 optimal weight: 20.0000 chunk 114 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 103 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 HIS A 42 GLN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.170163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.124780 restraints weight = 17713.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.123887 restraints weight = 15327.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.125027 restraints weight = 11354.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.125604 restraints weight = 9083.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.125816 restraints weight = 8262.426| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11921 Z= 0.133 Angle : 0.580 12.313 16295 Z= 0.296 Chirality : 0.041 0.239 1828 Planarity : 0.003 0.037 1848 Dihedral : 16.160 79.289 2063 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.63 % Allowed : 15.89 % Favored : 82.47 % 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: 660 sheet: 0.93 (0.53), residues: 101 loop : 0.44 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1162 TYR 0.020 0.001 TYR A 260 PHE 0.018 0.001 PHE A 741 TRP 0.040 0.002 TRP A1247 HIS 0.005 0.001 HIS A1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (11917) covalent geometry : angle 0.57789 / 0.30 (16292) hydrogen bonds : bond 0.03654 / 2.56 ( 578) hydrogen bonds : angle 4.30842 / 3.13 ( 1647) metal coordination : bond 0.00866 / 0.43 ( 4) metal coordination : angle 4.05842 / 2.15 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1616.36 seconds wall clock time: 28 minutes 45.68 seconds (1725.68 seconds total)