Starting phenix.real_space_refine on Sun Jun 8 02:23:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u0w_41790/06_2025/8u0w_41790.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u0w_41790/06_2025/8u0w_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_41790/06_2025/8u0w_41790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u0w_41790/06_2025/8u0w_41790.map" model { file = "/net/cci-nas-00/data/ceres_data/8u0w_41790/06_2025/8u0w_41790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u0w_41790/06_2025/8u0w_41790.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.00, per 1000 atoms: 0.66 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: 2.29 Conformation dependent library (CDL) restraints added in 998.5 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: 3.07 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: 3.56 Time building geometry restraints manager: 2.72 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=" CA PHE A 999 " pdb=" CB PHE A 999 " ideal model delta sigma weight residual 1.530 1.498 0.032 1.69e-02 3.50e+03 3.65e+00 bond pdb=" CG1 ILE A 771 " pdb=" CD1 ILE A 771 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.34e+00 bond pdb=" CB VAL A 91 " pdb=" CG2 VAL A 91 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.34e+00 bond pdb=" CG LEU A 782 " pdb=" CD1 LEU A 782 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.07e+00 bond pdb=" CB THR A 363 " pdb=" CG2 THR A 363 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.95e+00 ... (remaining 9279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 12135 1.76 - 3.51: 403 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=" C PHE A 998 " pdb=" N PHE A 999 " pdb=" CA PHE A 999 " ideal model delta sigma weight residual 121.54 128.99 -7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" N PHE A 362 " pdb=" CA PHE A 362 " pdb=" C PHE A 362 " ideal model delta sigma weight residual 110.80 117.18 -6.38 2.13e+00 2.20e-01 8.97e+00 angle pdb=" N PHE A 459 " pdb=" CA PHE A 459 " pdb=" C PHE A 459 " ideal model delta sigma weight residual 111.28 114.53 -3.25 1.09e+00 8.42e-01 8.90e+00 angle pdb=" C GLY A 565 " pdb=" N ASN A 566 " pdb=" CA ASN A 566 " ideal model delta sigma weight residual 122.73 117.99 4.74 1.61e+00 3.86e-01 8.65e+00 ... (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: 1077 0.051 - 0.102: 269 0.102 - 0.152: 49 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: 3.750 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.900 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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= 0.291 Angle : 0.761 8.784 12603 Z= 0.437 Chirality : 0.046 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.002 TRP A 643 HIS 0.020 0.002 HIS A 836 PHE 0.040 0.002 PHE A 416 TYR 0.052 0.002 TYR A 662 ARG 0.010 0.001 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.16434 ( 455) hydrogen bonds : angle 7.35985 ( 1293) covalent geometry : bond 0.00694 ( 9284) covalent geometry : angle 0.76134 (12603) *********************** 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 : 1.657 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: 1.4418 time to fit residues: 176.6313 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 : 1.133 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** A 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 GLN A 800 GLN A 940 GLN A1022 GLN A1135 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.115368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.076889 restraints weight = 16887.947| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.28 r_work: 0.2910 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9284 Z= 0.146 Angle : 0.606 10.445 12603 Z= 0.323 Chirality : 0.042 0.208 1403 Planarity : 0.004 0.039 1592 Dihedral : 11.425 86.260 1318 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.04 % Favored : 96.77 % Rotamer: Outliers : 1.65 % Allowed : 7.20 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1085 helix: 1.38 (0.22), residues: 530 sheet: -0.48 (0.46), residues: 131 loop : -0.84 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 643 HIS 0.010 0.001 HIS A 836 PHE 0.030 0.001 PHE A 362 TYR 0.031 0.001 TYR A 662 ARG 0.005 0.001 ARG A1177 Details of bonding type rmsd hydrogen bonds : bond 0.04124 ( 455) hydrogen bonds : angle 4.93097 ( 1293) covalent geometry : bond 0.00325 ( 9284) covalent geometry : angle 0.60583 (12603) *********************** 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 109 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6664 (tm) REVERT: A 573 ARG cc_start: 0.7836 (tpp80) cc_final: 0.7490 (tpm-80) REVERT: A 706 ASP cc_start: 0.7953 (m-30) cc_final: 0.7328 (t0) REVERT: A 1071 PHE cc_start: 0.8887 (m-80) cc_final: 0.8598 (m-80) REVERT: A 1078 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8241 (t0) REVERT: A 1184 ILE cc_start: 0.9106 (mt) cc_final: 0.8878 (pp) outliers start: 16 outliers final: 5 residues processed: 100 average time/residue: 1.1277 time to fit residues: 123.1097 Evaluate side-chains 72 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1078 ASN Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1187 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 0.0170 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3693 r_free = 0.3693 target = 0.113184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.074545 restraints weight = 17396.616| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.31 r_work: 0.2871 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9284 Z= 0.165 Angle : 0.566 8.701 12603 Z= 0.298 Chirality : 0.042 0.197 1403 Planarity : 0.004 0.036 1592 Dihedral : 11.203 79.665 1316 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.95 % Favored : 96.87 % Rotamer: Outliers : 1.95 % Allowed : 10.08 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1085 helix: 1.92 (0.22), residues: 531 sheet: -0.49 (0.47), residues: 131 loop : -0.74 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 643 HIS 0.017 0.001 HIS A1188 PHE 0.027 0.001 PHE A 362 TYR 0.022 0.001 TYR A 662 ARG 0.004 0.000 ARG A1087 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 455) hydrogen bonds : angle 4.60968 ( 1293) covalent geometry : bond 0.00382 ( 9284) covalent geometry : angle 0.56630 (12603) *********************** 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 95 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6527 (tm) REVERT: A 416 PHE cc_start: 0.6239 (t80) cc_final: 0.6032 (t80) REVERT: A 573 ARG cc_start: 0.7854 (tpp80) cc_final: 0.7494 (tpm-80) REVERT: A 706 ASP cc_start: 0.7926 (m-30) cc_final: 0.7273 (t0) REVERT: A 1078 ASN cc_start: 0.8355 (OUTLIER) cc_final: 0.8149 (t0) REVERT: A 1118 LYS cc_start: 0.8309 (mttt) cc_final: 0.7642 (mtpp) REVERT: A 1184 ILE cc_start: 0.9136 (mt) cc_final: 0.8846 (pp) outliers start: 19 outliers final: 8 residues processed: 85 average time/residue: 0.9868 time to fit residues: 92.1407 Evaluate side-chains 81 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU 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 420 MET Chi-restraints excluded: chain A residue 826 MET Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1078 ASN Chi-restraints excluded: chain A residue 1101 SER 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 78 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 105 optimal weight: 0.0870 chunk 55 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 584 HIS A 938 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.111192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.073072 restraints weight = 17221.323| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.25 r_work: 0.2838 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9284 Z= 0.211 Angle : 0.583 8.705 12603 Z= 0.307 Chirality : 0.042 0.201 1403 Planarity : 0.004 0.040 1592 Dihedral : 11.506 81.393 1316 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.95 % Favored : 96.87 % Rotamer: Outliers : 2.57 % Allowed : 10.39 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1085 helix: 2.07 (0.22), residues: 532 sheet: -0.50 (0.47), residues: 131 loop : -0.64 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 643 HIS 0.007 0.001 HIS A1188 PHE 0.029 0.001 PHE A 362 TYR 0.021 0.001 TYR A 662 ARG 0.003 0.000 ARG A1087 Details of bonding type rmsd hydrogen bonds : bond 0.03961 ( 455) hydrogen bonds : angle 4.53701 ( 1293) covalent geometry : bond 0.00496 ( 9284) covalent geometry : angle 0.58252 (12603) *********************** 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 98 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 416 PHE cc_start: 0.6267 (t80) cc_final: 0.6047 (t80) REVERT: A 573 ARG cc_start: 0.7970 (tpp80) cc_final: 0.7587 (tpm-80) REVERT: A 706 ASP cc_start: 0.7927 (m-30) cc_final: 0.7303 (t0) REVERT: A 1083 ARG cc_start: 0.8378 (mmt180) cc_final: 0.8147 (mmm160) REVERT: A 1085 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7811 (p0) REVERT: A 1095 GLN cc_start: 0.6153 (OUTLIER) cc_final: 0.5937 (tp-100) REVERT: A 1118 LYS cc_start: 0.8441 (mttt) cc_final: 0.7752 (mtpp) REVERT: A 1121 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8847 (pp) outliers start: 25 outliers final: 14 residues processed: 87 average time/residue: 1.0533 time to fit residues: 100.8025 Evaluate side-chains 83 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 294 ILE 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 826 MET Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 968 GLU Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1095 GLN Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain A residue 1121 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 0.0870 chunk 94 optimal weight: 0.0170 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 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 = 0.3701 r_free = 0.3701 target = 0.113526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.074488 restraints weight = 17169.259| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.41 r_work: 0.2893 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3174 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= 0.116 Angle : 0.538 9.162 12603 Z= 0.280 Chirality : 0.039 0.194 1403 Planarity : 0.003 0.041 1592 Dihedral : 11.338 86.974 1316 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.49 % Favored : 97.33 % Rotamer: Outliers : 1.85 % Allowed : 12.35 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.26), residues: 1085 helix: 2.32 (0.22), residues: 534 sheet: -0.44 (0.46), residues: 134 loop : -0.54 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 643 HIS 0.006 0.001 HIS A 836 PHE 0.022 0.001 PHE A 362 TYR 0.014 0.001 TYR A 662 ARG 0.002 0.000 ARG A 969 Details of bonding type rmsd hydrogen bonds : bond 0.03294 ( 455) hydrogen bonds : angle 4.31519 ( 1293) covalent geometry : bond 0.00258 ( 9284) covalent geometry : angle 0.53805 (12603) *********************** 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 91 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: A 53 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8506 (tp) REVERT: A 162 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6447 (mp0) REVERT: A 573 ARG cc_start: 0.7850 (tpp80) cc_final: 0.7479 (tpm-80) REVERT: A 706 ASP cc_start: 0.7872 (m-30) cc_final: 0.7249 (t0) REVERT: A 1085 ASP cc_start: 0.8106 (m-30) cc_final: 0.7724 (p0) REVERT: A 1118 LYS cc_start: 0.8413 (mttt) cc_final: 0.7763 (mtpp) outliers start: 18 outliers final: 9 residues processed: 87 average time/residue: 0.9562 time to fit residues: 91.2387 Evaluate side-chains 77 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 294 ILE 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 965 PHE Chi-restraints excluded: chain A residue 968 GLU Chi-restraints excluded: chain A residue 999 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 84 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 966 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.111352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.072807 restraints weight = 17226.041| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.30 r_work: 0.2840 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9284 Z= 0.200 Angle : 0.582 9.448 12603 Z= 0.301 Chirality : 0.042 0.198 1403 Planarity : 0.003 0.042 1592 Dihedral : 11.472 88.655 1316 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.95 % Favored : 96.87 % Rotamer: Outliers : 2.06 % Allowed : 13.37 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.26), residues: 1085 helix: 2.36 (0.22), residues: 533 sheet: -0.52 (0.46), residues: 134 loop : -0.48 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 643 HIS 0.006 0.001 HIS A 836 PHE 0.028 0.001 PHE A 362 TYR 0.014 0.001 TYR A 662 ARG 0.002 0.000 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 455) hydrogen bonds : angle 4.42832 ( 1293) covalent geometry : bond 0.00469 ( 9284) covalent geometry : angle 0.58172 (12603) *********************** 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 88 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 53 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8567 (tp) REVERT: A 162 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6388 (mp0) REVERT: A 573 ARG cc_start: 0.7984 (tpp80) cc_final: 0.7634 (tpm-80) REVERT: A 706 ASP cc_start: 0.7926 (m-30) cc_final: 0.7303 (t0) REVERT: A 1085 ASP cc_start: 0.8222 (m-30) cc_final: 0.7835 (p0) REVERT: A 1118 LYS cc_start: 0.8464 (mttt) cc_final: 0.7838 (mtpp) outliers start: 20 outliers final: 11 residues processed: 81 average time/residue: 0.9669 time to fit residues: 86.4821 Evaluate side-chains 80 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 294 ILE 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 519 SER Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 968 GLU Chi-restraints excluded: chain A residue 999 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 96 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 101 optimal weight: 0.3980 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 ASN A 966 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.112575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.074121 restraints weight = 17138.840| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.37 r_work: 0.2887 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3466 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= 0.121 Angle : 0.524 8.782 12603 Z= 0.274 Chirality : 0.040 0.206 1403 Planarity : 0.003 0.042 1592 Dihedral : 11.424 87.715 1316 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.40 % Favored : 97.42 % Rotamer: Outliers : 1.44 % Allowed : 13.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.26), residues: 1085 helix: 2.52 (0.22), residues: 534 sheet: -0.52 (0.46), residues: 134 loop : -0.40 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 643 HIS 0.005 0.001 HIS A 836 PHE 0.023 0.001 PHE A 362 TYR 0.021 0.001 TYR A 788 ARG 0.002 0.000 ARG A 972 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 455) hydrogen bonds : angle 4.25102 ( 1293) covalent geometry : bond 0.00275 ( 9284) covalent geometry : angle 0.52397 (12603) *********************** 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 83 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 53 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8522 (tp) REVERT: A 162 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.6167 (mp0) REVERT: A 573 ARG cc_start: 0.7856 (tpp80) cc_final: 0.7522 (tpm-80) REVERT: A 1085 ASP cc_start: 0.7988 (m-30) cc_final: 0.7718 (p0) REVERT: A 1118 LYS cc_start: 0.8438 (mttt) cc_final: 0.7837 (mtpp) outliers start: 14 outliers final: 9 residues processed: 79 average time/residue: 0.9990 time to fit residues: 87.0526 Evaluate side-chains 76 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 519 SER Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 968 GLU Chi-restraints excluded: chain A residue 999 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 72 optimal weight: 0.0980 chunk 101 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN ** A 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.113420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.075402 restraints weight = 17458.865| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.31 r_work: 0.2879 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9284 Z= 0.132 Angle : 0.534 9.722 12603 Z= 0.279 Chirality : 0.040 0.199 1403 Planarity : 0.003 0.041 1592 Dihedral : 11.449 89.779 1316 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.49 % Favored : 97.33 % Rotamer: Outliers : 1.54 % Allowed : 14.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.26), residues: 1085 helix: 2.58 (0.22), residues: 534 sheet: -0.52 (0.46), residues: 134 loop : -0.37 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 643 HIS 0.005 0.001 HIS A 836 PHE 0.025 0.001 PHE A 362 TYR 0.008 0.001 TYR A1004 ARG 0.003 0.000 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 455) hydrogen bonds : angle 4.24097 ( 1293) covalent geometry : bond 0.00303 ( 9284) covalent geometry : angle 0.53410 (12603) *********************** 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 86 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: A 53 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8551 (tp) REVERT: A 162 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.6122 (mp0) REVERT: A 573 ARG cc_start: 0.7922 (tpp80) cc_final: 0.7583 (tpm-80) REVERT: A 1085 ASP cc_start: 0.8001 (m-30) cc_final: 0.7783 (p0) REVERT: A 1118 LYS cc_start: 0.8474 (mttt) cc_final: 0.7927 (mtpp) outliers start: 15 outliers final: 8 residues processed: 82 average time/residue: 1.1527 time to fit residues: 104.2695 Evaluate side-chains 77 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 519 SER Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 999 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 91 optimal weight: 0.0870 chunk 66 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 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 = 0.3727 r_free = 0.3727 target = 0.114760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.075948 restraints weight = 17174.231| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.26 r_work: 0.2906 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9284 Z= 0.133 Angle : 0.547 9.442 12603 Z= 0.282 Chirality : 0.040 0.207 1403 Planarity : 0.003 0.040 1592 Dihedral : 11.577 89.152 1316 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.49 % Favored : 97.33 % Rotamer: Outliers : 0.93 % Allowed : 15.53 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.27), residues: 1085 helix: 2.62 (0.22), residues: 534 sheet: -0.50 (0.46), residues: 134 loop : -0.34 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 643 HIS 0.005 0.001 HIS A 836 PHE 0.024 0.001 PHE A 362 TYR 0.021 0.001 TYR A 788 ARG 0.002 0.000 ARG A 969 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 455) hydrogen bonds : angle 4.22012 ( 1293) covalent geometry : bond 0.00307 ( 9284) covalent geometry : angle 0.54668 (12603) *********************** 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 79 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 1.059 Fit side-chains REVERT: A 53 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8471 (tp) REVERT: A 162 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.5970 (mp0) REVERT: A 573 ARG cc_start: 0.7868 (tpp80) cc_final: 0.7520 (tpm-80) REVERT: A 1118 LYS cc_start: 0.8438 (mttt) cc_final: 0.7915 (mtpt) outliers start: 9 outliers final: 6 residues processed: 77 average time/residue: 0.9095 time to fit residues: 77.9468 Evaluate side-chains 74 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 1.747 ------------------------------------------------------------------------------- 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 363 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 514 VAL 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 67 optimal weight: 0.0170 chunk 66 optimal weight: 0.5980 chunk 20 optimal weight: 0.1980 chunk 72 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 105 optimal weight: 0.1980 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN A 581 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.116227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.077872 restraints weight = 17435.189| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.28 r_work: 0.2946 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9284 Z= 0.103 Angle : 0.527 10.178 12603 Z= 0.270 Chirality : 0.039 0.188 1403 Planarity : 0.003 0.040 1592 Dihedral : 11.602 89.118 1316 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.21 % Favored : 97.60 % Rotamer: Outliers : 0.93 % Allowed : 15.53 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.27), residues: 1085 helix: 2.74 (0.22), residues: 533 sheet: -0.45 (0.46), residues: 134 loop : -0.27 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 643 HIS 0.005 0.001 HIS A 458 PHE 0.023 0.001 PHE A 362 TYR 0.022 0.001 TYR A 788 ARG 0.003 0.000 ARG A 969 Details of bonding type rmsd hydrogen bonds : bond 0.03009 ( 455) hydrogen bonds : angle 4.13468 ( 1293) covalent geometry : bond 0.00230 ( 9284) covalent geometry : angle 0.52655 (12603) ********************** 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 80 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 53 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8428 (tp) REVERT: A 573 ARG cc_start: 0.7830 (tpp80) cc_final: 0.7511 (tpm-80) REVERT: A 706 ASP cc_start: 0.7765 (m-30) cc_final: 0.7240 (t0) REVERT: A 1118 LYS cc_start: 0.8443 (mttt) cc_final: 0.7898 (mtpp) outliers start: 9 outliers final: 4 residues processed: 77 average time/residue: 1.0296 time to fit residues: 86.5967 Evaluate side-chains 72 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 402 LEU Chi-restraints excluded: chain A residue 514 VAL 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 8 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 105 optimal weight: 0.0370 chunk 48 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.113225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.074568 restraints weight = 17169.702| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.32 r_work: 0.2880 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9284 Z= 0.142 Angle : 0.553 10.611 12603 Z= 0.284 Chirality : 0.041 0.211 1403 Planarity : 0.003 0.040 1592 Dihedral : 11.650 88.195 1316 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.30 % Favored : 97.51 % Rotamer: Outliers : 0.82 % Allowed : 15.64 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.27), residues: 1085 helix: 2.74 (0.22), residues: 533 sheet: -0.51 (0.46), residues: 134 loop : -0.33 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 643 HIS 0.005 0.001 HIS A 458 PHE 0.025 0.001 PHE A 362 TYR 0.009 0.001 TYR A 662 ARG 0.002 0.000 ARG A 969 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 455) hydrogen bonds : angle 4.21934 ( 1293) covalent geometry : bond 0.00329 ( 9284) covalent geometry : angle 0.55261 (12603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6278.87 seconds wall clock time: 111 minutes 20.19 seconds (6680.19 seconds total)