Starting phenix.real_space_refine on Thu Jul 2 15:57:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u0w_41790/07_2026/8u0w_41790.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u0w_41790/07_2026/8u0w_41790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u0w_41790/07_2026/8u0w_41790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u0w_41790/07_2026/8u0w_41790.map" model { file = "/net/cci-nas-00/data/ceres_data/8u0w_41790/07_2026/8u0w_41790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u0w_41790/07_2026/8u0w_41790.cif" } resolution = 2.99 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= 0.011 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 23 5.16 5 C 5726 2.51 5 N 1565 2.21 5 O 1760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 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: 9086 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8845 Classifications: {'peptide': 1099} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 1066} Chain breaks: 6 Chain: "C" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 241 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Time building chain proxies: 1.43, per 1000 atoms: 0.16 Number of scatterers: 9086 At special positions: 0 Unit cell: (84.9864, 98.3176, 134.145, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 12 15.00 O 1760 8.00 N 1565 7.00 C 5726 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: 0.78 Conformation dependent library (CDL) restraints added in 285.5 milliseconds 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 10 sheets defined 56.7% alpha, 9.8% beta 0 base pairs and 9 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 20 through 38 removed outlier: 3.697A pdb=" N VAL A 25 " --> pdb=" O PRO A 21 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 78 removed outlier: 3.686A pdb=" N PHE A 62 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 112 Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.549A pdb=" N GLN A 131 " --> pdb=" O TYR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 146 through 157 Processing helix chain 'A' and resid 158 through 161 removed outlier: 3.825A pdb=" N ALA A 161 " --> pdb=" O ASN A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 158 through 161' Processing helix chain 'A' and resid 162 through 179 removed outlier: 4.227A pdb=" N HIS A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 209 Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 227 through 235 removed outlier: 4.139A pdb=" N LYS A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 276 through 286 removed outlier: 3.588A pdb=" N VAL A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 299 Processing helix chain 'A' and resid 324 through 336 Processing helix chain 'A' and resid 402 through 428 Processing helix chain 'A' and resid 445 through 457 removed outlier: 3.609A pdb=" N LEU A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 462 removed outlier: 3.821A pdb=" N GLN A 462 " --> pdb=" O PHE A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 474 removed outlier: 3.869A pdb=" N SER A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 removed outlier: 3.752A pdb=" N HIS A 496 " --> pdb=" O SER A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 558 through 565 Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'A' and resid 588 through 593 removed outlier: 3.796A pdb=" N ASN A 592 " --> pdb=" O ASN A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 616 removed outlier: 3.673A pdb=" N LEU A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 633 through 656 removed outlier: 4.482A pdb=" N ALA A 638 " --> pdb=" O GLU A 634 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N PHE A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 675 through 694 Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.520A pdb=" N SER A 717 " --> pdb=" O TYR A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 752 removed outlier: 3.696A pdb=" N GLY A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 807 removed outlier: 3.909A pdb=" N LEU A 795 " --> pdb=" O THR A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 824 Processing helix chain 'A' and resid 828 through 836 removed outlier: 3.629A pdb=" N GLN A 833 " --> pdb=" O GLU A 829 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN A 834 " --> pdb=" O ARG A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 853 removed outlier: 3.545A pdb=" N VAL A 853 " --> pdb=" O ILE A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 879 Processing helix chain 'A' and resid 889 through 902 removed outlier: 4.068A pdb=" N ALA A 902 " --> pdb=" O LYS A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 939 removed outlier: 3.924A pdb=" N ARG A 913 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 960 Processing helix chain 'A' and resid 970 through 972 No H-bonds generated for 'chain 'A' and resid 970 through 972' Processing helix chain 'A' and resid 992 through 996 removed outlier: 3.514A pdb=" N SER A 995 " --> pdb=" O ASP A 992 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE A 996 " --> pdb=" O PRO A 993 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 992 through 996' Processing helix chain 'A' and resid 1009 through 1013 Processing helix chain 'A' and resid 1014 through 1019 Processing helix chain 'A' and resid 1023 through 1032 removed outlier: 3.503A pdb=" N TRP A1027 " --> pdb=" O TYR A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1052 Processing helix chain 'A' and resid 1052 through 1068 Processing helix chain 'A' and resid 1077 through 1081 removed outlier: 3.703A pdb=" N TYR A1081 " --> pdb=" O ASN A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1127 Processing helix chain 'A' and resid 1155 through 1159 Processing helix chain 'A' and resid 1176 through 1189 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 44 removed outlier: 5.749A pdb=" N ALA A 43 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLY A 541 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 269 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ILE A 542 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE A 271 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR A 89 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ASP A 272 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL A 91 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 251 through 252 Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 292 removed outlier: 3.506A pdb=" N VAL A 354 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 595 through 601 removed outlier: 6.009A pdb=" N ILE A 774 " --> pdb=" O PHE A 869 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ASP A 871 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU A 776 " --> pdb=" O ASP A 871 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LYS A 698 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N PHE A 730 " --> pdb=" O LYS A 698 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N PHE A 700 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N THR A 732 " --> pdb=" O PHE A 700 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 744 through 745 Processing sheet with id=AA7, first strand: chain 'A' and resid 755 through 757 Processing sheet with id=AA8, first strand: chain 'A' and resid 962 through 963 removed outlier: 3.519A pdb=" N ASN A1042 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 983 through 985 Processing sheet with id=AB1, first strand: chain 'A' and resid 1071 through 1074 removed outlier: 3.699A pdb=" N ASN A1086 " --> pdb=" O LEU A1099 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A1088 " --> pdb=" O ILE A1097 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE A1097 " --> pdb=" O VAL A1088 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 9 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 1.03 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: 2171 1.33 - 1.45: 1939 1.45 - 1.57: 5115 1.57 - 1.69: 23 1.69 - 1.81: 36 Bond restraints: 9284 Sorted by residual: bond pdb=" C3' DT C 11 " pdb=" O3' DT C 11 " ideal model delta sigma weight residual 1.435 1.400 0.035 1.30e-02 5.92e+03 7.41e+00 bond pdb=" C3' DT C 17 " pdb=" C2' DT C 17 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.37e+00 bond pdb=" O4' DA C 12 " pdb=" C1' DA C 12 " ideal model delta sigma weight residual 1.420 1.391 0.029 1.10e-02 8.26e+03 6.75e+00 bond pdb=" C3' DT C 16 " pdb=" O3' DT C 16 " ideal model delta sigma weight residual 1.435 1.404 0.031 1.30e-02 5.92e+03 5.72e+00 bond pdb=" C4' DT C 16 " pdb=" C3' DT C 16 " ideal model delta sigma weight residual 1.529 1.506 0.023 1.00e-02 1.00e+04 5.35e+00 ... (remaining 9279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 12100 1.76 - 3.51: 438 3.51 - 5.27: 50 5.27 - 7.03: 11 7.03 - 8.78: 4 Bond angle restraints: 12603 Sorted by residual: angle pdb=" C SER A 361 " pdb=" N PHE A 362 " pdb=" CA PHE A 362 " ideal model delta sigma weight residual 121.54 129.77 -8.23 1.91e+00 2.74e-01 1.86e+01 angle pdb=" N3 DT C 18 " pdb=" C4 DT C 18 " pdb=" O4 DT C 18 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT C 17 " pdb=" C4 DT C 17 " pdb=" O4 DT C 17 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT C 19 " pdb=" C4 DT C 19 " pdb=" O4 DT C 19 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT C 11 " pdb=" C4 DT C 11 " pdb=" O4 DT C 11 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 ... (remaining 12598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 5013 17.85 - 35.70: 414 35.70 - 53.55: 108 53.55 - 71.40: 13 71.40 - 89.25: 12 Dihedral angle restraints: 5560 sinusoidal: 2330 harmonic: 3230 Sorted by residual: dihedral pdb=" CA GLU A 997 " pdb=" C GLU A 997 " pdb=" N PHE A 998 " pdb=" CA PHE A 998 " ideal model delta harmonic sigma weight residual 180.00 -151.77 -28.23 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA SER A 358 " pdb=" C SER A 358 " pdb=" N ASP A 359 " pdb=" CA ASP A 359 " ideal model delta harmonic sigma weight residual 180.00 151.79 28.21 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA HIS A 238 " pdb=" C HIS A 238 " pdb=" N VAL A 239 " pdb=" CA VAL A 239 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 5557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1070 0.051 - 0.102: 270 0.102 - 0.152: 55 0.152 - 0.203: 6 0.203 - 0.254: 2 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CB THR A 363 " pdb=" CA THR A 363 " pdb=" OG1 THR A 363 " pdb=" CG2 THR A 363 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA PHE A 362 " pdb=" N PHE A 362 " pdb=" C PHE A 362 " pdb=" CB PHE A 362 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB ILE A1047 " pdb=" CA ILE A1047 " pdb=" CG1 ILE A1047 " pdb=" CG2 ILE A1047 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.91e-01 ... (remaining 1400 not shown) Planarity restraints: 1592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 662 " 0.019 2.00e-02 2.50e+03 2.20e-02 9.67e+00 pdb=" CG TYR A 662 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 662 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 662 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 662 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 662 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 662 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 662 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 416 " -0.018 2.00e-02 2.50e+03 1.73e-02 5.26e+00 pdb=" CG PHE A 416 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 416 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 416 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 416 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 416 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 416 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 999 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.81e+00 pdb=" C PHE A 999 " -0.038 2.00e-02 2.50e+03 pdb=" O PHE A 999 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP A1000 " 0.013 2.00e-02 2.50e+03 ... (remaining 1589 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 132 2.65 - 3.21: 8521 3.21 - 3.78: 13652 3.78 - 4.34: 19827 4.34 - 4.90: 32863 Nonbonded interactions: 74995 Sorted by model distance: nonbonded pdb=" O LEU A 488 " pdb=" OG SER A 489 " model vdw 2.091 3.040 nonbonded pdb=" O PHE A 999 " pdb=" N ARG A1001 " model vdw 2.135 3.120 nonbonded pdb=" OE2 GLU A 331 " pdb=" ND2 ASN A 335 " model vdw 2.173 3.120 nonbonded pdb=" OG SER A 754 " pdb=" NH1 ARG A 863 " model vdw 2.203 3.120 nonbonded pdb=" OE1 GLN A 683 " pdb=" OG1 THR A 699 " model vdw 2.212 3.040 ... (remaining 74990 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: 3.400 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.890 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 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 0.071 9284 Z= 0.320 Angle : 0.774 8.784 12603 Z= 0.477 Chirality : 0.047 0.254 1403 Planarity : 0.004 0.048 1592 Dihedral : 14.845 89.249 3462 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.50 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.58 (0.24), residues: 1085 helix: 0.37 (0.22), residues: 524 sheet: -0.85 (0.42), residues: 147 loop : -1.06 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 547 TYR 0.052 0.002 TYR A 662 PHE 0.040 0.002 PHE A 416 TRP 0.024 0.002 TRP A 643 HIS 0.020 0.002 HIS A 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00700 / 0.32 ( 9284) covalent geometry : angle 0.77393 / 0.48 (12603) hydrogen bonds : bond 0.16434 / 10.23 ( 455) hydrogen bonds : angle 7.35985 / 5.36 ( 1293) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.8817 (mt) cc_final: 0.8510 (mm) REVERT: A 1097 ILE cc_start: 0.8888 (mt) cc_final: 0.8627 (mm) REVERT: A 1100 ASP cc_start: 0.7137 (t0) cc_final: 0.6675 (p0) REVERT: A 1118 LYS cc_start: 0.8339 (mttt) cc_final: 0.8063 (mttp) REVERT: A 1184 ILE cc_start: 0.9197 (mt) cc_final: 0.8458 (pp) outliers start: 0 outliers final: 1 residues processed: 115 average time/residue: 0.6179 time to fit residues: 75.4150 Evaluate side-chains 68 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.1980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 GLN A 637 GLN A 800 GLN A1022 GLN A1135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.114694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.075779 restraints weight = 17102.506| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.30 r_work: 0.2888 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9284 Z= 0.158 Angle : 0.664 11.377 12603 Z= 0.350 Chirality : 0.043 0.210 1403 Planarity : 0.005 0.039 1592 Dihedral : 11.414 81.672 1318 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.95 % Favored : 96.87 % Rotamer: Outliers : 1.65 % Allowed : 7.61 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.25), residues: 1085 helix: 1.25 (0.22), residues: 530 sheet: -0.52 (0.45), residues: 131 loop : -0.89 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1177 TYR 0.033 0.001 TYR A 662 PHE 0.035 0.002 PHE A 416 TRP 0.021 0.002 TRP A 643 HIS 0.010 0.001 HIS A 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 9284) covalent geometry : angle 0.66384 / 0.35 (12603) hydrogen bonds : bond 0.04661 / 3.09 ( 455) hydrogen bonds : angle 5.24215 / 3.78 ( 1293) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6776 (tm) REVERT: A 706 ASP cc_start: 0.7929 (m-30) cc_final: 0.7373 (t0) REVERT: A 1071 PHE cc_start: 0.8965 (m-80) cc_final: 0.8759 (m-80) REVERT: A 1080 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8579 (tp) REVERT: A 1118 LYS cc_start: 0.8170 (mttt) cc_final: 0.7863 (mttp) REVERT: A 1184 ILE cc_start: 0.9090 (mt) cc_final: 0.8845 (pt) outliers start: 16 outliers final: 6 residues processed: 91 average time/residue: 0.4439 time to fit residues: 44.0451 Evaluate side-chains 71 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1078 ASN Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1100 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 70 optimal weight: 0.0030 chunk 48 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 GLN ** A 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 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 = 0.3707 r_free = 0.3707 target = 0.114619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.075784 restraints weight = 17095.302| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.30 r_work: 0.2891 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9284 Z= 0.138 Angle : 0.570 7.708 12603 Z= 0.305 Chirality : 0.041 0.197 1403 Planarity : 0.004 0.035 1592 Dihedral : 11.308 81.398 1318 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.86 % Favored : 96.96 % Rotamer: Outliers : 1.85 % Allowed : 9.77 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.25), residues: 1085 helix: 1.74 (0.22), residues: 530 sheet: -0.49 (0.47), residues: 131 loop : -0.90 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1087 TYR 0.021 0.001 TYR A 662 PHE 0.027 0.001 PHE A 362 TRP 0.019 0.001 TRP A 643 HIS 0.017 0.001 HIS A1188 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 9284) covalent geometry : angle 0.56993 / 0.30 (12603) hydrogen bonds : bond 0.04028 / 2.67 ( 455) hydrogen bonds : angle 4.79590 / 3.45 ( 1293) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8137 (tpm170) REVERT: A 402 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6677 (tm) REVERT: A 573 ARG cc_start: 0.7867 (tpp80) cc_final: 0.7501 (tpm-80) REVERT: A 706 ASP cc_start: 0.7940 (m-30) cc_final: 0.7345 (t0) REVERT: A 1078 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.8121 (t0) REVERT: A 1080 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8568 (tp) REVERT: A 1085 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7544 (p0) REVERT: A 1184 ILE cc_start: 0.9119 (mt) cc_final: 0.8850 (pp) outliers start: 18 outliers final: 7 residues processed: 82 average time/residue: 0.4098 time to fit residues: 36.9802 Evaluate side-chains 72 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1078 ASN Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1187 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 6 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.112582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.074402 restraints weight = 17400.043| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.26 r_work: 0.2859 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9284 Z= 0.187 Angle : 0.575 8.107 12603 Z= 0.305 Chirality : 0.042 0.198 1403 Planarity : 0.004 0.036 1592 Dihedral : 11.177 77.631 1318 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.04 % Favored : 96.77 % Rotamer: Outliers : 2.57 % Allowed : 11.21 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.26), residues: 1085 helix: 1.96 (0.22), residues: 530 sheet: -0.46 (0.47), residues: 131 loop : -0.77 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 202 TYR 0.019 0.001 TYR A 662 PHE 0.027 0.001 PHE A 362 TRP 0.020 0.001 TRP A 643 HIS 0.008 0.001 HIS A1188 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 ( 9284) covalent geometry : angle 0.57515 / 0.31 (12603) hydrogen bonds : bond 0.03923 / 2.62 ( 455) hydrogen bonds : angle 4.67121 / 3.36 ( 1293) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 573 ARG cc_start: 0.7919 (tpp80) cc_final: 0.7530 (tpm-80) REVERT: A 706 ASP cc_start: 0.7938 (m-30) cc_final: 0.7322 (t0) REVERT: A 969 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7489 (ttm110) REVERT: A 1078 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.8129 (t0) REVERT: A 1080 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8581 (tp) REVERT: A 1085 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7649 (p0) REVERT: A 1095 GLN cc_start: 0.6269 (OUTLIER) cc_final: 0.6059 (tp-100) REVERT: A 1118 LYS cc_start: 0.8344 (mttt) cc_final: 0.7677 (mtpp) REVERT: A 1184 ILE cc_start: 0.9090 (mt) cc_final: 0.8715 (tp) REVERT: A 1185 LYS cc_start: 0.8776 (tmmm) cc_final: 0.8205 (tppt) REVERT: A 1188 HIS cc_start: 0.8352 (m90) cc_final: 0.7605 (m90) outliers start: 25 outliers final: 10 residues processed: 84 average time/residue: 0.4007 time to fit residues: 36.9425 Evaluate side-chains 80 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 826 MET Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 969 ARG Chi-restraints excluded: chain A residue 1078 ASN Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1095 GLN Chi-restraints excluded: chain A residue 1187 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 GLN A 584 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.112108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.073529 restraints weight = 17261.132| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.29 r_work: 0.2852 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9284 Z= 0.188 Angle : 0.573 9.090 12603 Z= 0.301 Chirality : 0.042 0.199 1403 Planarity : 0.003 0.036 1592 Dihedral : 11.222 78.192 1316 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.95 % Favored : 96.87 % Rotamer: Outliers : 2.67 % Allowed : 11.93 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.26), residues: 1085 helix: 2.16 (0.22), residues: 529 sheet: -0.48 (0.47), residues: 131 loop : -0.65 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1087 TYR 0.016 0.001 TYR A 662 PHE 0.026 0.001 PHE A 362 TRP 0.020 0.001 TRP A 643 HIS 0.006 0.001 HIS A 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 ( 9284) covalent geometry : angle 0.57321 / 0.30 (12603) hydrogen bonds : bond 0.03858 / 2.58 ( 455) hydrogen bonds : angle 4.56167 / 3.29 ( 1293) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8562 (tp) REVERT: A 706 ASP cc_start: 0.7917 (m-30) cc_final: 0.7300 (t0) REVERT: A 1080 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8636 (tp) REVERT: A 1085 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7626 (p0) REVERT: A 1095 GLN cc_start: 0.6212 (OUTLIER) cc_final: 0.5986 (tp-100) REVERT: A 1184 ILE cc_start: 0.9101 (mt) cc_final: 0.8842 (pp) REVERT: A 1185 LYS cc_start: 0.8782 (tmmm) cc_final: 0.8254 (tppt) REVERT: A 1188 HIS cc_start: 0.8310 (m90) cc_final: 0.7719 (m90) outliers start: 26 outliers final: 10 residues processed: 86 average time/residue: 0.3486 time to fit residues: 33.0488 Evaluate side-chains 78 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 826 MET Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1095 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 21 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.113758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.074882 restraints weight = 17258.307| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.24 r_work: 0.2891 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9284 Z= 0.153 Angle : 0.551 8.408 12603 Z= 0.292 Chirality : 0.041 0.195 1403 Planarity : 0.003 0.035 1592 Dihedral : 11.232 78.047 1316 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.95 % Favored : 96.87 % Rotamer: Outliers : 2.06 % Allowed : 12.96 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.26), residues: 1085 helix: 2.31 (0.22), residues: 531 sheet: -0.55 (0.45), residues: 134 loop : -0.59 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 573 TYR 0.018 0.001 TYR A 788 PHE 0.034 0.001 PHE A 416 TRP 0.020 0.001 TRP A 643 HIS 0.006 0.001 HIS A 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 9284) covalent geometry : angle 0.55123 / 0.29 (12603) hydrogen bonds : bond 0.03675 / 2.46 ( 455) hydrogen bonds : angle 4.45053 / 3.20 ( 1293) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8525 (tp) REVERT: A 706 ASP cc_start: 0.7864 (m-30) cc_final: 0.7268 (t0) REVERT: A 1085 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7669 (p0) REVERT: A 1118 LYS cc_start: 0.8351 (mttt) cc_final: 0.7697 (mtpp) REVERT: A 1184 ILE cc_start: 0.9095 (mt) cc_final: 0.8801 (pp) REVERT: A 1185 LYS cc_start: 0.8791 (tmmm) cc_final: 0.8252 (tppt) REVERT: A 1188 HIS cc_start: 0.8312 (m90) cc_final: 0.7715 (m90) outliers start: 20 outliers final: 8 residues processed: 81 average time/residue: 0.3994 time to fit residues: 35.7853 Evaluate side-chains 75 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1085 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 30.0000 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 GLN A 966 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.112493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.073463 restraints weight = 17419.782| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.27 r_work: 0.2858 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9284 Z= 0.209 Angle : 0.577 8.634 12603 Z= 0.305 Chirality : 0.042 0.199 1403 Planarity : 0.004 0.036 1592 Dihedral : 11.289 77.676 1316 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.23 % Favored : 96.59 % Rotamer: Outliers : 1.65 % Allowed : 13.48 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.26), residues: 1085 helix: 2.33 (0.22), residues: 531 sheet: -0.60 (0.46), residues: 131 loop : -0.57 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 177 TYR 0.017 0.001 TYR A 788 PHE 0.036 0.001 PHE A 416 TRP 0.019 0.001 TRP A 643 HIS 0.006 0.001 HIS A 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 ( 9284) covalent geometry : angle 0.57696 / 0.30 (12603) hydrogen bonds : bond 0.03858 / 2.57 ( 455) hydrogen bonds : angle 4.48574 / 3.23 ( 1293) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8533 (tp) REVERT: A 706 ASP cc_start: 0.7848 (m-30) cc_final: 0.7210 (t0) REVERT: A 1080 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8645 (tp) REVERT: A 1085 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7660 (p0) REVERT: A 1118 LYS cc_start: 0.8337 (mttt) cc_final: 0.7741 (mtpp) REVERT: A 1184 ILE cc_start: 0.9094 (mt) cc_final: 0.8858 (pp) outliers start: 16 outliers final: 11 residues processed: 76 average time/residue: 0.3868 time to fit residues: 32.2822 Evaluate side-chains 79 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 826 MET Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1085 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 101 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 37 optimal weight: 30.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 966 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.113397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.074624 restraints weight = 17278.586| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.24 r_work: 0.2882 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9284 Z= 0.156 Angle : 0.566 9.199 12603 Z= 0.300 Chirality : 0.041 0.197 1403 Planarity : 0.003 0.035 1592 Dihedral : 11.334 78.124 1316 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.86 % Favored : 96.96 % Rotamer: Outliers : 1.44 % Allowed : 14.30 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.26), residues: 1085 helix: 2.36 (0.22), residues: 532 sheet: -0.63 (0.46), residues: 134 loop : -0.55 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 573 TYR 0.016 0.001 TYR A 788 PHE 0.038 0.001 PHE A 416 TRP 0.020 0.001 TRP A 643 HIS 0.007 0.001 HIS A1188 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 9284) covalent geometry : angle 0.56583 / 0.30 (12603) hydrogen bonds : bond 0.03662 / 2.45 ( 455) hydrogen bonds : angle 4.43428 / 3.19 ( 1293) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8530 (tp) REVERT: A 573 ARG cc_start: 0.7920 (tpp80) cc_final: 0.7468 (tpm-80) REVERT: A 706 ASP cc_start: 0.7861 (m-30) cc_final: 0.7268 (t0) REVERT: A 1080 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8617 (tp) REVERT: A 1085 ASP cc_start: 0.7914 (m-30) cc_final: 0.7645 (p0) REVERT: A 1118 LYS cc_start: 0.8362 (mttt) cc_final: 0.7755 (mtpp) REVERT: A 1184 ILE cc_start: 0.9090 (mt) cc_final: 0.8761 (OUTLIER) REVERT: A 1185 LYS cc_start: 0.8575 (ptmm) cc_final: 0.8118 (tppt) outliers start: 14 outliers final: 11 residues processed: 76 average time/residue: 0.4130 time to fit residues: 34.4448 Evaluate side-chains 79 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 826 MET Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1187 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 5 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 966 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.113529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.074753 restraints weight = 17234.694| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.23 r_work: 0.2888 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9284 Z= 0.150 Angle : 0.578 11.092 12603 Z= 0.306 Chirality : 0.041 0.196 1403 Planarity : 0.003 0.035 1592 Dihedral : 11.411 77.616 1316 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.04 % Favored : 96.77 % Rotamer: Outliers : 1.44 % Allowed : 14.30 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.26), residues: 1085 helix: 2.34 (0.22), residues: 533 sheet: -0.63 (0.46), residues: 134 loop : -0.55 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 573 TYR 0.015 0.001 TYR A 788 PHE 0.050 0.001 PHE A 416 TRP 0.020 0.001 TRP A 643 HIS 0.005 0.001 HIS A1188 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 9284) covalent geometry : angle 0.57827 / 0.31 (12603) hydrogen bonds : bond 0.03686 / 2.46 ( 455) hydrogen bonds : angle 4.46139 / 3.21 ( 1293) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 53 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8522 (tp) REVERT: A 162 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6081 (mp0) REVERT: A 706 ASP cc_start: 0.7867 (m-30) cc_final: 0.7259 (t0) REVERT: A 1085 ASP cc_start: 0.7926 (m-30) cc_final: 0.7671 (p0) REVERT: A 1118 LYS cc_start: 0.8359 (mttt) cc_final: 0.7769 (mtpp) REVERT: A 1184 ILE cc_start: 0.9119 (mt) cc_final: 0.8883 (tp) REVERT: A 1185 LYS cc_start: 0.8608 (ptmm) cc_final: 0.8129 (tppt) outliers start: 14 outliers final: 9 residues processed: 76 average time/residue: 0.3738 time to fit residues: 31.5289 Evaluate side-chains 75 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 826 MET Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 999 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 966 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.113659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.074967 restraints weight = 17333.810| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.24 r_work: 0.2887 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9284 Z= 0.151 Angle : 0.578 10.583 12603 Z= 0.306 Chirality : 0.042 0.218 1403 Planarity : 0.003 0.034 1592 Dihedral : 11.482 77.540 1316 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.95 % Favored : 96.87 % Rotamer: Outliers : 1.44 % Allowed : 14.61 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.26), residues: 1085 helix: 2.36 (0.22), residues: 533 sheet: -0.67 (0.46), residues: 134 loop : -0.50 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 573 TYR 0.015 0.001 TYR A 788 PHE 0.050 0.001 PHE A 416 TRP 0.020 0.001 TRP A 643 HIS 0.005 0.001 HIS A 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 9284) covalent geometry : angle 0.57837 / 0.31 (12603) hydrogen bonds : bond 0.03653 / 2.43 ( 455) hydrogen bonds : angle 4.45222 / 3.21 ( 1293) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 53 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8525 (tp) REVERT: A 162 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.6235 (mp0) REVERT: A 573 ARG cc_start: 0.7898 (tpp80) cc_final: 0.7510 (tpm-80) REVERT: A 706 ASP cc_start: 0.7865 (m-30) cc_final: 0.7261 (t0) REVERT: A 1085 ASP cc_start: 0.7953 (m-30) cc_final: 0.7666 (p0) REVERT: A 1118 LYS cc_start: 0.8429 (mttt) cc_final: 0.7844 (mtpp) REVERT: A 1184 ILE cc_start: 0.9124 (mt) cc_final: 0.8882 (tp) outliers start: 14 outliers final: 9 residues processed: 73 average time/residue: 0.3939 time to fit residues: 31.8694 Evaluate side-chains 74 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 826 MET Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 999 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 70 optimal weight: 0.0270 chunk 21 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 966 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.112630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.074006 restraints weight = 17145.162| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.20 r_work: 0.2870 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9284 Z= 0.199 Angle : 0.593 10.139 12603 Z= 0.311 Chirality : 0.043 0.205 1403 Planarity : 0.003 0.036 1592 Dihedral : 11.614 80.481 1316 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.13 % Favored : 96.68 % Rotamer: Outliers : 1.34 % Allowed : 15.02 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.26), residues: 1085 helix: 2.30 (0.22), residues: 534 sheet: -0.69 (0.46), residues: 134 loop : -0.50 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 573 TYR 0.016 0.001 TYR A 788 PHE 0.027 0.001 PHE A 362 TRP 0.019 0.001 TRP A 643 HIS 0.005 0.001 HIS A 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 ( 9284) covalent geometry : angle 0.59294 / 0.31 (12603) hydrogen bonds : bond 0.03814 / 2.54 ( 455) hydrogen bonds : angle 4.52382 / 3.26 ( 1293) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2282.79 seconds wall clock time: 39 minutes 54.26 seconds (2394.26 seconds total)