Starting phenix.real_space_refine on Thu Feb 13 16:55:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u0w_41790/02_2025/8u0w_41790.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u0w_41790/02_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_41790/02_2025/8u0w_41790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u0w_41790/02_2025/8u0w_41790.map" model { file = "/net/cci-nas-00/data/ceres_data/8u0w_41790/02_2025/8u0w_41790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u0w_41790/02_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-5592/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: 6.06, per 1000 atoms: 0.67 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: 2.24 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 3.20 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: 3.62 Time building geometry restraints manager: 2.65 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: 3.130 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.130 Find NCS groups from input model: 0.100 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:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.470 ------------------------------------------------------------------------------- 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= 0.449 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 *********************** 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 : 1.020 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: 1.4336 time to fit residues: 175.2232 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 : 0.973 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.076884 restraints weight = 16887.947| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.28 r_work: 0.2907 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 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= 0.210 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 *********************** 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 : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6657 (tm) REVERT: A 573 ARG cc_start: 0.7829 (tpp80) cc_final: 0.7480 (tpm-80) REVERT: A 706 ASP cc_start: 0.7946 (m-30) cc_final: 0.7322 (t0) REVERT: A 1071 PHE cc_start: 0.8882 (m-80) cc_final: 0.8595 (m-80) REVERT: A 1078 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8239 (t0) REVERT: A 1184 ILE cc_start: 0.9104 (mt) cc_final: 0.8877 (pp) outliers start: 16 outliers final: 5 residues processed: 100 average time/residue: 1.0791 time to fit residues: 117.6095 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 : 1.124 ------------------------------------------------------------------------------- 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: 6.9990 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 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: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.112487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.073700 restraints weight = 17438.748| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.32 r_work: 0.2858 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2567 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= 0.281 Angle : 0.578 8.501 12603 Z= 0.304 Chirality : 0.042 0.208 1403 Planarity : 0.004 0.036 1592 Dihedral : 11.225 79.681 1316 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.95 % Favored : 96.87 % Rotamer: Outliers : 1.95 % Allowed : 10.19 % Favored : 87.86 % 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: 0.86 (0.26), residues: 1085 helix: 1.88 (0.22), residues: 531 sheet: -0.51 (0.47), residues: 131 loop : -0.76 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 643 HIS 0.016 0.001 HIS A1188 PHE 0.028 0.001 PHE A 362 TYR 0.023 0.001 TYR A 662 ARG 0.004 0.000 ARG A1087 *********************** 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 94 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6540 (tm) REVERT: A 573 ARG cc_start: 0.7869 (tpp80) cc_final: 0.7502 (tpm-80) REVERT: A 706 ASP cc_start: 0.7926 (m-30) cc_final: 0.7274 (t0) REVERT: A 1078 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.8130 (t0) REVERT: A 1118 LYS cc_start: 0.8328 (mttt) cc_final: 0.7630 (mtpp) REVERT: A 1184 ILE cc_start: 0.9133 (mt) cc_final: 0.8845 (pp) outliers start: 19 outliers final: 7 residues processed: 84 average time/residue: 1.0181 time to fit residues: 93.9798 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 : 0.990 ------------------------------------------------------------------------------- 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 363 THR Chi-restraints excluded: chain A residue 402 LEU 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 1187 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 105 optimal weight: 0.0980 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: 0.8980 chunk 104 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** A 584 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.112815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.074147 restraints weight = 17101.048| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.30 r_work: 0.2866 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2917 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= 0.243 Angle : 0.540 8.775 12603 Z= 0.284 Chirality : 0.041 0.195 1403 Planarity : 0.003 0.039 1592 Dihedral : 11.452 81.259 1316 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.58 % Favored : 97.24 % Rotamer: Outliers : 2.06 % Allowed : 10.91 % 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: 1.18 (0.26), residues: 1085 helix: 2.15 (0.22), residues: 533 sheet: -0.44 (0.47), residues: 131 loop : -0.58 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 643 HIS 0.007 0.001 HIS A 836 PHE 0.026 0.001 PHE A 362 TYR 0.019 0.001 TYR A 662 ARG 0.003 0.000 ARG A1087 *********************** 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 96 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 1.049 Fit side-chains REVERT: A 416 PHE cc_start: 0.6303 (t80) cc_final: 0.6102 (t80) REVERT: A 573 ARG cc_start: 0.7897 (tpp80) cc_final: 0.7536 (tpm-80) REVERT: A 706 ASP cc_start: 0.7928 (m-30) cc_final: 0.7291 (t0) REVERT: A 1085 ASP cc_start: 0.8090 (m-30) cc_final: 0.7678 (p0) REVERT: A 1095 GLN cc_start: 0.6128 (OUTLIER) cc_final: 0.5914 (tp-100) REVERT: A 1101 SER cc_start: 0.6928 (OUTLIER) cc_final: 0.6680 (p) REVERT: A 1118 LYS cc_start: 0.8438 (mttt) cc_final: 0.7779 (mtpp) REVERT: A 1185 LYS cc_start: 0.8752 (tmmm) cc_final: 0.8306 (tppt) REVERT: A 1188 HIS cc_start: 0.8399 (m90) cc_final: 0.7903 (m90) outliers start: 20 outliers final: 9 residues processed: 87 average time/residue: 0.9373 time to fit residues: 89.9565 Evaluate side-chains 79 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 285 LEU 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 Chi-restraints excluded: chain A residue 1095 GLN Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain A residue 1101 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.110711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.072545 restraints weight = 17422.942| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.27 r_work: 0.2828 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 9284 Z= 0.361 Angle : 0.611 9.233 12603 Z= 0.316 Chirality : 0.043 0.201 1403 Planarity : 0.004 0.042 1592 Dihedral : 11.528 83.829 1316 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.76 % Favored : 97.05 % Rotamer: Outliers : 2.26 % Allowed : 11.73 % Favored : 86.01 % 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: 1.21 (0.26), residues: 1085 helix: 2.17 (0.22), residues: 534 sheet: -0.45 (0.47), residues: 131 loop : -0.57 (0.30), residues: 420 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 0.028 0.001 PHE A 362 TYR 0.017 0.001 TYR A 662 ARG 0.002 0.000 ARG A 846 *********************** 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: 22 poor density : 71 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 706 ASP cc_start: 0.7953 (m-30) cc_final: 0.7328 (t0) REVERT: A 1085 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7859 (p0) REVERT: A 1095 GLN cc_start: 0.6084 (OUTLIER) cc_final: 0.5839 (tp-100) REVERT: A 1118 LYS cc_start: 0.8421 (mttt) cc_final: 0.7811 (mtpp) outliers start: 22 outliers final: 12 residues processed: 85 average time/residue: 0.9612 time to fit residues: 89.7006 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 : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER 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 520 PHE 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 84 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.112858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.074810 restraints weight = 17131.568| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.27 r_work: 0.2874 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3305 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= 0.218 Angle : 0.556 8.538 12603 Z= 0.288 Chirality : 0.041 0.199 1403 Planarity : 0.003 0.042 1592 Dihedral : 11.447 89.437 1316 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.67 % Favored : 97.14 % Rotamer: Outliers : 1.75 % Allowed : 13.37 % 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: 1.38 (0.26), residues: 1085 helix: 2.37 (0.22), residues: 534 sheet: -0.54 (0.46), residues: 134 loop : -0.50 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 643 HIS 0.006 0.001 HIS A 836 PHE 0.024 0.001 PHE A 362 TYR 0.021 0.001 TYR A 788 ARG 0.004 0.000 ARG A 573 *********************** 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: 17 poor density : 69 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 573 ARG cc_start: 0.7971 (tpp80) cc_final: 0.7577 (tpm-80) REVERT: A 706 ASP cc_start: 0.7941 (m-30) cc_final: 0.7318 (t0) REVERT: A 1085 ASP cc_start: 0.8070 (m-30) cc_final: 0.7768 (p0) REVERT: A 1118 LYS cc_start: 0.8479 (mttt) cc_final: 0.7866 (mtpp) outliers start: 17 outliers final: 9 residues processed: 80 average time/residue: 0.9178 time to fit residues: 81.4002 Evaluate side-chains 75 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 5.9990 chunk 1 optimal weight: 0.0770 chunk 96 optimal weight: 0.2980 chunk 13 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 101 optimal weight: 0.0570 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 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 = 0.3745 r_free = 0.3745 target = 0.115726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.077369 restraints weight = 17239.714| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.25 r_work: 0.2938 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9284 Z= 0.161 Angle : 0.528 9.736 12603 Z= 0.274 Chirality : 0.039 0.197 1403 Planarity : 0.003 0.042 1592 Dihedral : 11.401 87.042 1316 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.49 % Favored : 97.33 % Rotamer: Outliers : 1.23 % Allowed : 14.20 % 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: 1.57 (0.26), residues: 1085 helix: 2.56 (0.22), residues: 534 sheet: -0.49 (0.46), residues: 135 loop : -0.43 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 643 HIS 0.004 0.001 HIS A 836 PHE 0.023 0.001 PHE A 362 TYR 0.006 0.001 TYR A 629 ARG 0.003 0.000 ARG A 573 *********************** 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 84 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 573 ARG cc_start: 0.7815 (tpp80) cc_final: 0.7430 (tpm170) REVERT: A 1085 ASP cc_start: 0.7985 (m-30) cc_final: 0.7782 (p0) REVERT: A 1118 LYS cc_start: 0.8440 (mttt) cc_final: 0.7877 (mtpp) outliers start: 12 outliers final: 7 residues processed: 80 average time/residue: 0.9219 time to fit residues: 81.5553 Evaluate side-chains 75 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER 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 514 VAL Chi-restraints excluded: chain A residue 965 PHE 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: 0.0670 chunk 68 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 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 = 0.3735 r_free = 0.3735 target = 0.115059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.076165 restraints weight = 17464.550| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.28 r_work: 0.2914 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3642 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= 0.197 Angle : 0.545 9.256 12603 Z= 0.282 Chirality : 0.040 0.202 1403 Planarity : 0.003 0.041 1592 Dihedral : 11.468 89.735 1316 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.58 % Favored : 97.24 % Rotamer: Outliers : 1.23 % Allowed : 14.40 % Favored : 84.36 % 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: 1.69 (0.26), residues: 1085 helix: 2.66 (0.22), residues: 534 sheet: -0.47 (0.46), residues: 134 loop : -0.38 (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 458 PHE 0.025 0.001 PHE A 362 TYR 0.020 0.001 TYR A 788 ARG 0.004 0.000 ARG A 969 *********************** 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 85 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 177 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.7036 (mmp80) REVERT: A 573 ARG cc_start: 0.7876 (tpp80) cc_final: 0.7486 (tpm170) REVERT: A 1085 ASP cc_start: 0.8020 (m-30) cc_final: 0.7820 (p0) REVERT: A 1118 LYS cc_start: 0.8461 (mttt) cc_final: 0.7901 (mtpp) outliers start: 12 outliers final: 8 residues processed: 80 average time/residue: 0.9666 time to fit residues: 84.8513 Evaluate side-chains 77 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 294 ILE Chi-restraints excluded: chain A residue 328 ARG 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: 1.9990 chunk 66 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.109774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.069839 restraints weight = 17159.582| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.39 r_work: 0.2830 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9284 Z= 0.310 Angle : 0.592 9.562 12603 Z= 0.303 Chirality : 0.042 0.198 1403 Planarity : 0.003 0.041 1592 Dihedral : 11.685 87.924 1316 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.76 % Favored : 97.05 % Rotamer: Outliers : 1.34 % Allowed : 14.61 % Favored : 84.05 % 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: 1.56 (0.27), residues: 1085 helix: 2.54 (0.22), residues: 534 sheet: -0.55 (0.46), residues: 134 loop : -0.42 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 643 HIS 0.006 0.001 HIS A 458 PHE 0.027 0.001 PHE A 362 TYR 0.022 0.001 TYR A 788 ARG 0.003 0.000 ARG A 573 *********************** 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 82 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 177 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6966 (mmp80) REVERT: A 573 ARG cc_start: 0.7970 (tpp80) cc_final: 0.7598 (tpm-80) REVERT: A 706 ASP cc_start: 0.7828 (m-30) cc_final: 0.7283 (t0) REVERT: A 1118 LYS cc_start: 0.8466 (mttt) cc_final: 0.7963 (mppt) outliers start: 13 outliers final: 9 residues processed: 78 average time/residue: 0.9408 time to fit residues: 80.8665 Evaluate side-chains 74 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 514 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 826 MET 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: 3.9990 chunk 66 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 105 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.114835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.076683 restraints weight = 17389.005| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.22 r_work: 0.2922 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9284 Z= 0.179 Angle : 0.546 9.299 12603 Z= 0.280 Chirality : 0.040 0.217 1403 Planarity : 0.003 0.041 1592 Dihedral : 11.683 88.261 1316 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.49 % Favored : 97.33 % Rotamer: Outliers : 0.51 % Allowed : 15.95 % 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: 2.66 (0.22), residues: 534 sheet: -0.51 (0.46), residues: 134 loop : -0.38 (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 458 PHE 0.024 0.001 PHE A 362 TYR 0.021 0.001 TYR A 788 ARG 0.003 0.000 ARG A 573 ********************** 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 70 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: A 573 ARG cc_start: 0.7870 (tpp80) cc_final: 0.7499 (tpm170) REVERT: A 706 ASP cc_start: 0.7821 (m-30) cc_final: 0.7324 (t0) REVERT: A 1118 LYS cc_start: 0.8457 (mttt) cc_final: 0.7941 (mppt) outliers start: 5 outliers final: 3 residues processed: 69 average time/residue: 0.9442 time to fit residues: 72.3812 Evaluate side-chains 67 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER 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: 0.0020 chunk 35 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 105 optimal weight: 0.0030 chunk 48 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.115695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.077574 restraints weight = 17219.024| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.24 r_work: 0.2946 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9284 Z= 0.161 Angle : 0.534 10.185 12603 Z= 0.273 Chirality : 0.040 0.200 1403 Planarity : 0.003 0.040 1592 Dihedral : 11.617 88.123 1316 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.30 % Favored : 97.51 % Rotamer: Outliers : 0.62 % Allowed : 15.64 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (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: 1.77 (0.26), residues: 1085 helix: 2.77 (0.22), residues: 534 sheet: -0.57 (0.46), residues: 134 loop : -0.35 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 643 HIS 0.004 0.001 HIS A 458 PHE 0.024 0.001 PHE A 362 TYR 0.020 0.001 TYR A 788 ARG 0.003 0.000 ARG A 573 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5079.80 seconds wall clock time: 90 minutes 51.24 seconds (5451.24 seconds total)