Starting phenix.real_space_refine on Fri Jul 3 06:17:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9klp_62412/07_2026/9klp_62412.cif Found real_map, /net/cci-nas-00/data/ceres_data/9klp_62412/07_2026/9klp_62412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9klp_62412/07_2026/9klp_62412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9klp_62412/07_2026/9klp_62412.map" model { file = "/net/cci-nas-00/data/ceres_data/9klp_62412/07_2026/9klp_62412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9klp_62412/07_2026/9klp_62412.cif" } resolution = 2.87 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= 0.024 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 Ca 6 9.91 5 P 127 5.49 5 S 32 5.16 5 C 7445 2.51 5 N 2306 2.21 5 O 2653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12569 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1268, 9858 Classifications: {'peptide': 1268} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 55, 'TRANS': 1212} Chain breaks: 10 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 16, 'GLN:plan1': 3, 'ARG:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 127 Chain: "B" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1878 Inner-chain residues flagged as termini: ['pdbres=" C B 82 "'] Classifications: {'RNA': 88} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 6, 'rna3p_pur': 38, 'rna3p_pyr': 35} Link IDs: {'rna2p': 15, 'rna3p': 72} Chain: "C" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 406 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 421 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' CA': 4} Chain breaks: 4 Time building chain proxies: 2.45, per 1000 atoms: 0.19 Number of scatterers: 12569 At special positions: 0 Unit cell: (106.449, 118.916, 131.383, 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) Ca 6 19.99 S 32 16.00 P 127 15.00 O 2653 8.00 N 2306 7.00 C 7445 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: 0.98 Conformation dependent library (CDL) restraints added in 403.0 milliseconds 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 7 sheets defined 52.8% alpha, 9.9% beta 27 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 24 through 52 Processing helix chain 'A' and resid 53 through 54 No H-bonds generated for 'chain 'A' and resid 53 through 54' Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 70 through 85 Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 106 through 125 Processing helix chain 'A' and resid 128 through 144 removed outlier: 5.405A pdb=" N ALA A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N SER A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 168 Processing helix chain 'A' and resid 174 through 179 removed outlier: 3.599A pdb=" N ASP A 178 " --> pdb=" O ASP A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 214 through 228 removed outlier: 3.544A pdb=" N LYS A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 251 removed outlier: 4.078A pdb=" N THR A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 269 Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 278 through 286 removed outlier: 3.868A pdb=" N VAL A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.841A pdb=" N ASN A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 330 removed outlier: 3.766A pdb=" N LEU A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU A 329 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 352 removed outlier: 3.565A pdb=" N ARG A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.900A pdb=" N THR A 369 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER A 370 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 371 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 372 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 416 removed outlier: 3.593A pdb=" N PHE A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 removed outlier: 3.505A pdb=" N ARG A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 622 Processing helix chain 'A' and resid 641 through 647 Processing helix chain 'A' and resid 674 through 686 removed outlier: 3.608A pdb=" N LEU A 678 " --> pdb=" O PRO A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 703 Processing helix chain 'A' and resid 720 through 726 removed outlier: 3.999A pdb=" N SER A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 730 Processing helix chain 'A' and resid 742 through 746 removed outlier: 4.301A pdb=" N LYS A 746 " --> pdb=" O ILE A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 752 Processing helix chain 'A' and resid 783 through 794 Processing helix chain 'A' and resid 868 through 882 Processing helix chain 'A' and resid 887 through 895 Processing helix chain 'A' and resid 900 through 914 Processing helix chain 'A' and resid 936 through 966 removed outlier: 4.121A pdb=" N LYS A 953 " --> pdb=" O ARG A 949 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS A 955 " --> pdb=" O ALA A 951 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 959 " --> pdb=" O HIS A 955 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR A 966 " --> pdb=" O ALA A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 988 removed outlier: 3.862A pdb=" N SER A 988 " --> pdb=" O ASP A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1015 Processing helix chain 'A' and resid 1021 through 1031 removed outlier: 3.621A pdb=" N LYS A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1035 Processing helix chain 'A' and resid 1054 through 1072 Proline residue: A1066 - end of helix Processing helix chain 'A' and resid 1075 through 1108 removed outlier: 4.058A pdb=" N LYS A1098 " --> pdb=" O ALA A1094 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A1107 " --> pdb=" O MET A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1115 Processing helix chain 'A' and resid 1116 through 1120 removed outlier: 3.941A pdb=" N ILE A1119 " --> pdb=" O THR A1116 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A1120 " --> pdb=" O PRO A1117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1116 through 1120' Processing helix chain 'A' and resid 1126 through 1140 removed outlier: 3.700A pdb=" N LEU A1130 " --> pdb=" O SER A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'A' and resid 1162 through 1190 Processing helix chain 'A' and resid 1234 through 1241 removed outlier: 3.913A pdb=" N GLY A1238 " --> pdb=" O ARG A1234 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A1239 " --> pdb=" O GLU A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1258 removed outlier: 4.311A pdb=" N LYS A1246 " --> pdb=" O TRP A1242 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS A1248 " --> pdb=" O SER A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1309 Processing helix chain 'A' and resid 1311 through 1326 removed outlier: 3.523A pdb=" N ARG A1315 " --> pdb=" O THR A1311 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN A1326 " --> pdb=" O GLU A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1360 removed outlier: 3.591A pdb=" N LYS A1359 " --> pdb=" O PRO A1356 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1374 Processing helix chain 'A' and resid 1457 through 1479 removed outlier: 3.635A pdb=" N ASN A1467 " --> pdb=" O LYS A1463 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A1468 " --> pdb=" O GLU A1464 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A1469 " --> pdb=" O VAL A1465 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A1470 " --> pdb=" O GLU A1466 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 560 through 562 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 90 removed outlier: 3.746A pdb=" N ALA A 101 " --> pdb=" O TRP A 153 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASN A 155 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE A 99 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 635 through 637 Processing sheet with id=AA4, first strand: chain 'A' and resid 805 through 812 removed outlier: 21.778A pdb=" N GLU A 824 " --> pdb=" O PHE A 854 " (cutoff:3.500A) removed outlier: 17.424A pdb=" N PHE A 854 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 13.618A pdb=" N SER A 826 " --> pdb=" O ARG A 852 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N ARG A 852 " --> pdb=" O SER A 826 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N VAL A 828 " --> pdb=" O LEU A 850 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ALA A 848 " --> pdb=" O MET A 782 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N MET A 782 " --> pdb=" O ALA A 848 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LEU A 850 " --> pdb=" O GLU A 780 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLU A 780 " --> pdb=" O LEU A 850 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG A 852 " --> pdb=" O VAL A 778 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 774 " --> pdb=" O ILE A 856 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ARG A 762 " --> pdb=" O ALA A1216 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE A1218 " --> pdb=" O ARG A 762 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU A 764 " --> pdb=" O ILE A1218 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N GLU A1220 " --> pdb=" O LEU A 764 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N VAL A 766 " --> pdb=" O GLU A1220 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 969 through 972 Processing sheet with id=AA6, first strand: chain 'A' and resid 1338 through 1341 Processing sheet with id=AA7, first strand: chain 'A' and resid 1387 through 1391 504 hydrogen bonds defined for protein. 1437 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2398 1.33 - 1.45: 3721 1.45 - 1.57: 6665 1.57 - 1.68: 251 1.68 - 1.80: 51 Bond restraints: 13086 Sorted by residual: bond pdb=" C3' DT D 12 " pdb=" O3' DT D 12 " ideal model delta sigma weight residual 1.435 1.394 0.041 1.30e-02 5.92e+03 9.75e+00 bond pdb=" O4' DT D 12 " pdb=" C1' DT D 12 " ideal model delta sigma weight residual 1.420 1.391 0.029 1.10e-02 8.26e+03 6.73e+00 bond pdb=" N1 C B 8 " pdb=" C6 C B 8 " ideal model delta sigma weight residual 1.367 1.352 0.015 6.00e-03 2.78e+04 6.46e+00 bond pdb=" C3' DT D 13 " pdb=" O3' DT D 13 " ideal model delta sigma weight residual 1.435 1.402 0.033 1.30e-02 5.92e+03 6.26e+00 bond pdb=" N7 G B 32 " pdb=" C5 G B 32 " ideal model delta sigma weight residual 1.388 1.373 0.015 6.00e-03 2.78e+04 6.19e+00 ... (remaining 13081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 17809 1.83 - 3.66: 439 3.66 - 5.49: 34 5.49 - 7.32: 12 7.32 - 9.15: 2 Bond angle restraints: 18296 Sorted by residual: angle pdb=" O4' DG D 11 " pdb=" C4' DG D 11 " pdb=" C3' DG D 11 " ideal model delta sigma weight residual 106.00 102.64 3.36 6.00e-01 2.78e+00 3.14e+01 angle pdb=" N3 DT D 12 " pdb=" C4 DT D 12 " pdb=" O4 DT D 12 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT D 13 " pdb=" C4 DT D 13 " pdb=" O4 DT D 13 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT C 33 " pdb=" C4 DT C 33 " pdb=" O4 DT C 33 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT D 15 " pdb=" C4 DT D 15 " pdb=" O4 DT D 15 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 ... (remaining 18291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.91: 7176 27.91 - 55.81: 548 55.81 - 83.72: 150 83.72 - 111.62: 4 111.62 - 139.53: 1 Dihedral angle restraints: 7879 sinusoidal: 4225 harmonic: 3654 Sorted by residual: dihedral pdb=" CA GLN A1362 " pdb=" C GLN A1362 " pdb=" N ALA A1363 " pdb=" CA ALA A1363 " ideal model delta harmonic sigma weight residual -180.00 -158.73 -21.27 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA PRO A 973 " pdb=" C PRO A 973 " pdb=" N GLY A 974 " pdb=" CA GLY A 974 " ideal model delta harmonic sigma weight residual 180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA THR A 380 " pdb=" C THR A 380 " pdb=" N ALA A 381 " pdb=" CA ALA A 381 " ideal model delta harmonic sigma weight residual -180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 7876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2048 0.123 - 0.246: 22 0.246 - 0.369: 0 0.369 - 0.492: 1 0.492 - 0.616: 3 Chirality restraints: 2074 Sorted by residual: chirality pdb=" P DT D 24 " pdb=" OP1 DT D 24 " pdb=" OP2 DT D 24 " pdb=" O5' DT D 24 " both_signs ideal model delta sigma weight residual True 2.34 -2.95 -0.62 2.00e-01 2.50e+01 9.47e+00 chirality pdb=" P DT D 16 " pdb=" OP1 DT D 16 " pdb=" OP2 DT D 16 " pdb=" O5' DT D 16 " both_signs ideal model delta sigma weight residual True 2.34 -2.93 -0.59 2.00e-01 2.50e+01 8.84e+00 chirality pdb=" P DT D 26 " pdb=" OP1 DT D 26 " pdb=" OP2 DT D 26 " pdb=" O5' DT D 26 " both_signs ideal model delta sigma weight residual True 2.34 -2.92 -0.58 2.00e-01 2.50e+01 8.54e+00 ... (remaining 2071 not shown) Planarity restraints: 1893 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A1002 " -0.019 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C TYR A1002 " 0.064 2.00e-02 2.50e+03 pdb=" O TYR A1002 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU A1003 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1458 " -0.026 2.00e-02 2.50e+03 2.55e-02 1.30e+01 pdb=" CG TYR A1458 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR A1458 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A1458 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR A1458 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A1458 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A1458 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A1458 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 845 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO A 846 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 846 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 846 " -0.026 5.00e-02 4.00e+02 ... (remaining 1890 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 32 2.44 - 3.06: 7608 3.06 - 3.67: 18329 3.67 - 4.29: 27554 4.29 - 4.90: 45142 Nonbonded interactions: 98665 Sorted by model distance: nonbonded pdb="CA CA B 202 " pdb="CA CA B 204 " model vdw 1.830 3.460 nonbonded pdb="CA CA B 201 " pdb="CA CA B 203 " model vdw 1.854 3.460 nonbonded pdb="CA CA A1501 " pdb="CA CA A1502 " model vdw 1.984 3.460 nonbonded pdb=" OE1 GLU A1228 " pdb=" OG SER A1271 " model vdw 2.189 3.040 nonbonded pdb=" OG SER A 276 " pdb=" OD1 ASN A 278 " model vdw 2.199 3.040 ... (remaining 98660 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.620 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 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 : 0.007 0.041 13086 Z= 0.437 Angle : 0.660 9.152 18296 Z= 0.435 Chirality : 0.049 0.616 2074 Planarity : 0.005 0.051 1893 Dihedral : 18.916 139.530 5511 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.41 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.24), residues: 1246 helix: 1.57 (0.22), residues: 601 sheet: 0.05 (0.42), residues: 133 loop : -0.93 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 74 TYR 0.063 0.002 TYR A1458 PHE 0.018 0.002 PHE A 43 TRP 0.013 0.002 TRP A 30 HIS 0.006 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00700 / 0.44 (13086) covalent geometry : angle 0.66018 / 0.43 (18296) hydrogen bonds : bond 0.18323 / 12.59 ( 570) hydrogen bonds : angle 5.88184 / 4.47 ( 1561) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.258 Fit side-chains REVERT: A 1006 MET cc_start: 0.8533 (tmm) cc_final: 0.8201 (tmm) REVERT: A 1064 MET cc_start: 0.8636 (mmp) cc_final: 0.8203 (mpm) REVERT: A 1159 GLU cc_start: 0.8363 (tp30) cc_final: 0.8136 (pm20) REVERT: A 1322 GLU cc_start: 0.8975 (tp30) cc_final: 0.8406 (tp30) REVERT: A 1326 GLN cc_start: 0.7365 (pm20) cc_final: 0.6831 (pm20) REVERT: A 1335 MET cc_start: 0.6497 (tpp) cc_final: 0.6289 (tpp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.7586 time to fit residues: 58.6699 Evaluate side-chains 47 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.0010 chunk 55 optimal weight: 0.7980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.111101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.076509 restraints weight = 22489.156| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.44 r_work: 0.2917 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13086 Z= 0.132 Angle : 0.541 9.687 18296 Z= 0.303 Chirality : 0.039 0.407 2074 Planarity : 0.004 0.038 1893 Dihedral : 19.964 141.251 3201 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.37 % Favored : 96.55 % Rotamer: Outliers : 0.10 % Allowed : 8.07 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.24), residues: 1246 helix: 1.99 (0.21), residues: 601 sheet: 0.31 (0.43), residues: 134 loop : -1.01 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 74 TYR 0.016 0.002 TYR A1458 PHE 0.008 0.001 PHE A1136 TRP 0.011 0.001 TRP A 30 HIS 0.003 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.13 (13086) covalent geometry : angle 0.54051 / 0.30 (18296) hydrogen bonds : bond 0.06398 / 4.50 ( 570) hydrogen bonds : angle 4.13710 / 3.12 ( 1561) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.346 Fit side-chains REVERT: A 136 MET cc_start: 0.9126 (mmm) cc_final: 0.8839 (mmt) REVERT: A 960 ARG cc_start: 0.7637 (ttp80) cc_final: 0.7309 (tmt90) REVERT: A 1020 ARG cc_start: 0.8076 (mtm110) cc_final: 0.7869 (ptp-110) REVERT: A 1038 TYR cc_start: 0.7634 (t80) cc_final: 0.7372 (t80) REVERT: A 1064 MET cc_start: 0.8658 (mmp) cc_final: 0.8136 (mpm) REVERT: A 1135 GLU cc_start: 0.8637 (tp30) cc_final: 0.8258 (tp30) REVERT: A 1159 GLU cc_start: 0.8433 (tp30) cc_final: 0.8117 (pm20) outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 0.6958 time to fit residues: 39.6239 Evaluate side-chains 46 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 47 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 95 optimal weight: 0.0270 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.107951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.073417 restraints weight = 22929.009| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.45 r_work: 0.2851 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13086 Z= 0.286 Angle : 0.597 8.936 18296 Z= 0.333 Chirality : 0.043 0.441 2074 Planarity : 0.005 0.049 1893 Dihedral : 19.941 147.497 3201 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.57 % Favored : 95.35 % Rotamer: Outliers : 0.72 % Allowed : 9.19 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.23), residues: 1246 helix: 1.81 (0.21), residues: 602 sheet: 0.14 (0.43), residues: 132 loop : -1.15 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1276 TYR 0.020 0.002 TYR A1458 PHE 0.016 0.002 PHE A 43 TRP 0.015 0.002 TRP A 30 HIS 0.007 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.29 (13086) covalent geometry : angle 0.59707 / 0.33 (18296) hydrogen bonds : bond 0.06933 / 4.92 ( 570) hydrogen bonds : angle 4.14816 / 3.12 ( 1561) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.317 Fit side-chains REVERT: A 625 ASP cc_start: 0.8351 (t0) cc_final: 0.8138 (t0) REVERT: A 1038 TYR cc_start: 0.7723 (t80) cc_final: 0.7472 (t80) REVERT: A 1064 MET cc_start: 0.8701 (mmp) cc_final: 0.8188 (mpm) REVERT: A 1135 GLU cc_start: 0.8642 (tp30) cc_final: 0.8377 (tp30) REVERT: A 1159 GLU cc_start: 0.8406 (tp30) cc_final: 0.8008 (pm20) outliers start: 7 outliers final: 2 residues processed: 55 average time/residue: 0.8098 time to fit residues: 47.6567 Evaluate side-chains 48 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 170 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 26 optimal weight: 4.9990 chunk 95 optimal weight: 0.0170 chunk 21 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.109849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.075137 restraints weight = 22513.865| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.45 r_work: 0.2907 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13086 Z= 0.168 Angle : 0.511 8.926 18296 Z= 0.288 Chirality : 0.038 0.434 2074 Planarity : 0.004 0.039 1893 Dihedral : 19.888 146.916 3201 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.53 % Favored : 96.39 % Rotamer: Outliers : 0.82 % Allowed : 11.64 % Favored : 87.54 % 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: 0.87 (0.24), residues: 1246 helix: 2.08 (0.21), residues: 592 sheet: 0.15 (0.42), residues: 134 loop : -1.12 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 960 TYR 0.015 0.001 TYR A1002 PHE 0.010 0.001 PHE A1416 TRP 0.014 0.001 TRP A 30 HIS 0.004 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (13086) covalent geometry : angle 0.51064 / 0.29 (18296) hydrogen bonds : bond 0.05752 / 4.10 ( 570) hydrogen bonds : angle 3.87787 / 2.92 ( 1561) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.432 Fit side-chains REVERT: A 625 ASP cc_start: 0.8380 (t0) cc_final: 0.8157 (t0) REVERT: A 1006 MET cc_start: 0.7957 (tmm) cc_final: 0.7617 (tmm) REVERT: A 1020 ARG cc_start: 0.8093 (mtm110) cc_final: 0.7879 (ptp-110) REVERT: A 1038 TYR cc_start: 0.7794 (t80) cc_final: 0.7525 (t80) REVERT: A 1064 MET cc_start: 0.8624 (mmp) cc_final: 0.8095 (mpm) REVERT: A 1135 GLU cc_start: 0.8594 (tp30) cc_final: 0.8317 (tp30) REVERT: A 1159 GLU cc_start: 0.8376 (tp30) cc_final: 0.7967 (pm20) outliers start: 8 outliers final: 5 residues processed: 59 average time/residue: 0.7279 time to fit residues: 46.2807 Evaluate side-chains 54 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 812 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 9 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.107120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.072409 restraints weight = 22777.312| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.46 r_work: 0.2854 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 13086 Z= 0.311 Angle : 0.600 8.930 18296 Z= 0.334 Chirality : 0.043 0.443 2074 Planarity : 0.005 0.050 1893 Dihedral : 19.848 150.480 3201 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.57 % Favored : 95.35 % Rotamer: Outliers : 1.23 % Allowed : 13.69 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.23), residues: 1246 helix: 1.72 (0.21), residues: 599 sheet: -0.09 (0.42), residues: 135 loop : -1.22 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 946 TYR 0.014 0.002 TYR A1250 PHE 0.013 0.002 PHE A 712 TRP 0.014 0.002 TRP A 30 HIS 0.007 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00696 / 0.31 (13086) covalent geometry : angle 0.60044 / 0.33 (18296) hydrogen bonds : bond 0.06681 / 4.75 ( 570) hydrogen bonds : angle 4.05680 / 3.04 ( 1561) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.313 Fit side-chains REVERT: A 625 ASP cc_start: 0.8478 (t0) cc_final: 0.8167 (t0) REVERT: A 1006 MET cc_start: 0.8028 (tmm) cc_final: 0.7652 (tmm) REVERT: A 1038 TYR cc_start: 0.7773 (t80) cc_final: 0.7529 (t80) REVERT: A 1064 MET cc_start: 0.8619 (mmp) cc_final: 0.8178 (mpm) REVERT: A 1135 GLU cc_start: 0.8606 (tp30) cc_final: 0.8380 (tp30) REVERT: A 1159 GLU cc_start: 0.8379 (tp30) cc_final: 0.7947 (pm20) outliers start: 12 outliers final: 8 residues processed: 61 average time/residue: 0.6180 time to fit residues: 40.5904 Evaluate side-chains 57 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1445 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 5 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 131 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.110769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.076358 restraints weight = 22607.672| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.43 r_work: 0.2906 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13086 Z= 0.117 Angle : 0.489 9.053 18296 Z= 0.274 Chirality : 0.036 0.427 2074 Planarity : 0.004 0.040 1893 Dihedral : 19.832 148.666 3201 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.21 % Favored : 96.71 % Rotamer: Outliers : 1.02 % Allowed : 14.71 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.24), residues: 1246 helix: 2.23 (0.22), residues: 592 sheet: 0.11 (0.42), residues: 135 loop : -1.12 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 946 TYR 0.018 0.001 TYR A1002 PHE 0.008 0.001 PHE A1348 TRP 0.014 0.001 TRP A 30 HIS 0.003 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.12 (13086) covalent geometry : angle 0.48884 / 0.27 (18296) hydrogen bonds : bond 0.05222 / 3.74 ( 570) hydrogen bonds : angle 3.73904 / 2.82 ( 1561) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.418 Fit side-chains REVERT: A 625 ASP cc_start: 0.8471 (t0) cc_final: 0.8186 (t0) REVERT: A 1006 MET cc_start: 0.7860 (tmm) cc_final: 0.7404 (tmm) REVERT: A 1020 ARG cc_start: 0.8082 (mtm110) cc_final: 0.7839 (ptp-110) REVERT: A 1038 TYR cc_start: 0.7824 (t80) cc_final: 0.7541 (t80) REVERT: A 1063 LYS cc_start: 0.7809 (mmpt) cc_final: 0.7558 (mtpp) REVERT: A 1064 MET cc_start: 0.8528 (mmp) cc_final: 0.8077 (mpm) REVERT: A 1135 GLU cc_start: 0.8618 (tp30) cc_final: 0.8364 (tp30) outliers start: 10 outliers final: 2 residues processed: 62 average time/residue: 0.7176 time to fit residues: 47.8322 Evaluate side-chains 50 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 690 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.108919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.074423 restraints weight = 22678.283| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.43 r_work: 0.2874 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13086 Z= 0.217 Angle : 0.539 9.803 18296 Z= 0.297 Chirality : 0.039 0.420 2074 Planarity : 0.004 0.044 1893 Dihedral : 19.787 150.710 3201 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.93 % Favored : 95.99 % Rotamer: Outliers : 1.12 % Allowed : 15.32 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.24), residues: 1246 helix: 2.10 (0.21), residues: 593 sheet: -0.05 (0.41), residues: 142 loop : -1.19 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 946 TYR 0.015 0.002 TYR A1002 PHE 0.011 0.001 PHE A 712 TRP 0.013 0.001 TRP A 30 HIS 0.006 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.22 (13086) covalent geometry : angle 0.53853 / 0.30 (18296) hydrogen bonds : bond 0.05788 / 4.15 ( 570) hydrogen bonds : angle 3.83219 / 2.88 ( 1561) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.377 Fit side-chains REVERT: A 624 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9094 (mp) REVERT: A 625 ASP cc_start: 0.8531 (t0) cc_final: 0.8186 (t0) REVERT: A 960 ARG cc_start: 0.7616 (ttp80) cc_final: 0.7079 (tpp80) REVERT: A 1006 MET cc_start: 0.8121 (tmm) cc_final: 0.7529 (tmm) REVERT: A 1038 TYR cc_start: 0.7852 (t80) cc_final: 0.7567 (t80) REVERT: A 1063 LYS cc_start: 0.7844 (mmpt) cc_final: 0.7567 (mtpp) REVERT: A 1064 MET cc_start: 0.8532 (mmp) cc_final: 0.8138 (mpm) REVERT: A 1135 GLU cc_start: 0.8637 (tp30) cc_final: 0.8380 (tp30) REVERT: A 1159 GLU cc_start: 0.8152 (tp30) cc_final: 0.7749 (pm20) REVERT: A 1470 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8200 (mp) outliers start: 11 outliers final: 7 residues processed: 62 average time/residue: 0.7004 time to fit residues: 46.8287 Evaluate side-chains 58 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 1470 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 112 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.108122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.073666 restraints weight = 22632.924| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.43 r_work: 0.2861 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13086 Z= 0.243 Angle : 0.559 10.693 18296 Z= 0.310 Chirality : 0.040 0.426 2074 Planarity : 0.005 0.040 1893 Dihedral : 19.847 152.610 3201 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.65 % Favored : 95.26 % Rotamer: Outliers : 1.33 % Allowed : 15.53 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.23), residues: 1246 helix: 1.96 (0.21), residues: 593 sheet: -0.12 (0.41), residues: 137 loop : -1.26 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 946 TYR 0.014 0.002 TYR A1002 PHE 0.012 0.002 PHE A 712 TRP 0.014 0.001 TRP A 30 HIS 0.005 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.24 (13086) covalent geometry : angle 0.55932 / 0.31 (18296) hydrogen bonds : bond 0.06049 / 4.33 ( 570) hydrogen bonds : angle 3.93470 / 2.95 ( 1561) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.403 Fit side-chains REVERT: A 625 ASP cc_start: 0.8586 (t0) cc_final: 0.8209 (t0) REVERT: A 960 ARG cc_start: 0.7620 (ttp80) cc_final: 0.7099 (tpp80) REVERT: A 1006 MET cc_start: 0.8095 (tmm) cc_final: 0.7796 (tmm) REVERT: A 1020 ARG cc_start: 0.8274 (mtm110) cc_final: 0.7943 (ptp-110) REVERT: A 1038 TYR cc_start: 0.7831 (t80) cc_final: 0.7577 (t80) REVERT: A 1063 LYS cc_start: 0.7854 (mmpt) cc_final: 0.7565 (mtpp) REVERT: A 1064 MET cc_start: 0.8622 (mmp) cc_final: 0.8304 (mpm) REVERT: A 1135 GLU cc_start: 0.8633 (tp30) cc_final: 0.8378 (tp30) REVERT: A 1159 GLU cc_start: 0.8182 (tp30) cc_final: 0.7719 (pm20) outliers start: 13 outliers final: 7 residues processed: 61 average time/residue: 0.7995 time to fit residues: 52.2544 Evaluate side-chains 55 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 812 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 65 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 46 optimal weight: 0.4980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.110716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.076389 restraints weight = 22636.101| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.42 r_work: 0.2905 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13086 Z= 0.125 Angle : 0.505 11.731 18296 Z= 0.275 Chirality : 0.036 0.402 2074 Planarity : 0.004 0.038 1893 Dihedral : 19.845 151.099 3201 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.45 % Favored : 96.47 % Rotamer: Outliers : 1.02 % Allowed : 16.04 % Favored : 82.94 % 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: 1.01 (0.24), residues: 1246 helix: 2.30 (0.22), residues: 592 sheet: -0.03 (0.41), residues: 144 loop : -1.14 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 946 TYR 0.018 0.001 TYR A1002 PHE 0.009 0.001 PHE A 712 TRP 0.014 0.001 TRP A 30 HIS 0.004 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (13086) covalent geometry : angle 0.50536 / 0.28 (18296) hydrogen bonds : bond 0.05059 / 3.62 ( 570) hydrogen bonds : angle 3.70390 / 2.80 ( 1561) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.391 Fit side-chains REVERT: A 322 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8327 (mp0) REVERT: A 625 ASP cc_start: 0.8548 (t0) cc_final: 0.8190 (t0) REVERT: A 960 ARG cc_start: 0.7610 (ttp80) cc_final: 0.7093 (tpp80) REVERT: A 1006 MET cc_start: 0.7984 (tmm) cc_final: 0.7735 (tmm) REVERT: A 1038 TYR cc_start: 0.7863 (t80) cc_final: 0.7552 (t80) REVERT: A 1064 MET cc_start: 0.8505 (mmp) cc_final: 0.8216 (mpm) REVERT: A 1135 GLU cc_start: 0.8633 (tp30) cc_final: 0.8382 (tp30) REVERT: A 1159 GLU cc_start: 0.8160 (tp30) cc_final: 0.7679 (pm20) outliers start: 10 outliers final: 5 residues processed: 63 average time/residue: 0.8157 time to fit residues: 55.1471 Evaluate side-chains 56 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 812 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 130 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.109750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.075135 restraints weight = 22744.166| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.43 r_work: 0.2888 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13086 Z= 0.172 Angle : 0.510 9.298 18296 Z= 0.281 Chirality : 0.037 0.387 2074 Planarity : 0.004 0.040 1893 Dihedral : 19.819 152.197 3201 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.77 % Favored : 96.15 % Rotamer: Outliers : 1.02 % Allowed : 16.14 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.24), residues: 1246 helix: 2.26 (0.21), residues: 593 sheet: 0.10 (0.43), residues: 133 loop : -1.11 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1020 TYR 0.016 0.001 TYR A1002 PHE 0.010 0.001 PHE A 712 TRP 0.013 0.001 TRP A 30 HIS 0.005 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (13086) covalent geometry : angle 0.51029 / 0.28 (18296) hydrogen bonds : bond 0.05312 / 3.82 ( 570) hydrogen bonds : angle 3.73728 / 2.81 ( 1561) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.254 Fit side-chains REVERT: A 136 MET cc_start: 0.8969 (mmt) cc_final: 0.8614 (mmm) REVERT: A 322 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8312 (mp0) REVERT: A 625 ASP cc_start: 0.8573 (t0) cc_final: 0.8202 (t0) REVERT: A 953 LYS cc_start: 0.8479 (ttpt) cc_final: 0.8275 (tttp) REVERT: A 960 ARG cc_start: 0.7598 (ttp80) cc_final: 0.7081 (tpp80) REVERT: A 1006 MET cc_start: 0.8066 (tmm) cc_final: 0.7827 (tmm) REVERT: A 1038 TYR cc_start: 0.7842 (t80) cc_final: 0.7579 (t80) REVERT: A 1064 MET cc_start: 0.8505 (mmp) cc_final: 0.8224 (mpm) REVERT: A 1084 LEU cc_start: 0.7742 (mp) cc_final: 0.7210 (pp) REVERT: A 1135 GLU cc_start: 0.8642 (tp30) cc_final: 0.8390 (tp30) REVERT: A 1159 GLU cc_start: 0.8153 (tp30) cc_final: 0.7642 (pm20) outliers start: 10 outliers final: 6 residues processed: 61 average time/residue: 0.6385 time to fit residues: 42.0081 Evaluate side-chains 59 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 812 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.109850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.075209 restraints weight = 22750.741| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.44 r_work: 0.2891 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13086 Z= 0.161 Angle : 0.501 9.365 18296 Z= 0.278 Chirality : 0.037 0.385 2074 Planarity : 0.004 0.039 1893 Dihedral : 19.829 152.187 3201 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.77 % Favored : 96.15 % Rotamer: Outliers : 1.12 % Allowed : 15.93 % Favored : 82.94 % 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: 1.04 (0.24), residues: 1246 helix: 2.27 (0.21), residues: 594 sheet: 0.11 (0.43), residues: 133 loop : -1.09 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1020 TYR 0.017 0.001 TYR A1002 PHE 0.009 0.001 PHE A 712 TRP 0.014 0.001 TRP A 30 HIS 0.004 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (13086) covalent geometry : angle 0.50101 / 0.28 (18296) hydrogen bonds : bond 0.05266 / 3.79 ( 570) hydrogen bonds : angle 3.72645 / 2.81 ( 1561) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2851.45 seconds wall clock time: 49 minutes 28.79 seconds (2968.79 seconds total)