Starting phenix.real_space_refine on Thu Aug 6 12:43:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h4j_51861/08_2026/9h4j_51861.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h4j_51861/08_2026/9h4j_51861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9h4j_51861/08_2026/9h4j_51861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h4j_51861/08_2026/9h4j_51861.map" model { file = "/net/cci-nas-00/data/ceres_data/9h4j_51861/08_2026/9h4j_51861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h4j_51861/08_2026/9h4j_51861.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 187 5.49 5 S 22 5.16 5 C 8756 2.51 5 N 2611 2.21 5 O 3243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14819 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10887 Classifications: {'peptide': 1334} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 35, 'TRANS': 1298} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 2129 Classifications: {'RNA': 99} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 56, 'rna3p_pyr': 31} Link IDs: {'rna2p': 11, 'rna3p': 87} Chain breaks: 2 Chain: "C" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 904 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain breaks: 1 Chain: "D" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 899 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain breaks: 1 Time building chain proxies: 2.57, per 1000 atoms: 0.17 Number of scatterers: 14819 At special positions: 0 Unit cell: (114.4, 132, 134.2, 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 22 16.00 P 187 15.00 O 3243 8.00 N 2611 7.00 C 8756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 452.7 milliseconds 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2536 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 10 sheets defined 49.8% alpha, 7.0% beta 46 base pairs and 102 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 59 through 91 removed outlier: 4.635A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.578A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 209 through 214 removed outlier: 3.626A pdb=" N SER A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 236 through 247 removed outlier: 3.516A pdb=" N ASN A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 282 removed outlier: 3.772A pdb=" N ASP A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 286 through 304 removed outlier: 4.096A pdb=" N ASP A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 346 through 353 removed outlier: 3.545A pdb=" N ASP A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.231A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.705A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 526 removed outlier: 4.450A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 Processing helix chain 'A' and resid 561 through 572 removed outlier: 4.239A pdb=" N LYS A 565 " --> pdb=" O VAL A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 602 removed outlier: 3.624A pdb=" N HIS A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 600 " --> pdb=" O ASP A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 630 through 637 removed outlier: 3.947A pdb=" N GLU A 634 " --> pdb=" O GLU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 644 through 652 removed outlier: 3.609A pdb=" N MET A 648 " --> pdb=" O ASP A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 694 through 699 removed outlier: 3.622A pdb=" N HIS A 698 " --> pdb=" O MET A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 715 Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 730 through 750 removed outlier: 4.226A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS A 749 " --> pdb=" O ASP A 745 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 750 " --> pdb=" O GLU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 792 Processing helix chain 'A' and resid 794 through 799 removed outlier: 4.119A pdb=" N GLU A 798 " --> pdb=" O GLN A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 807 Processing helix chain 'A' and resid 808 through 817 removed outlier: 3.975A pdb=" N LEU A 813 " --> pdb=" O GLU A 809 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 814 " --> pdb=" O LYS A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 889 removed outlier: 4.165A pdb=" N VAL A 876 " --> pdb=" O SER A 872 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N TYR A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 901 through 906 removed outlier: 3.831A pdb=" N ARG A 905 " --> pdb=" O THR A 901 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY A 906 " --> pdb=" O LYS A 902 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 901 through 906' Processing helix chain 'A' and resid 909 through 920 removed outlier: 3.892A pdb=" N GLN A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 940 Processing helix chain 'A' and resid 959 through 971 removed outlier: 4.171A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1001 removed outlier: 4.057A pdb=" N ALA A 987 " --> pdb=" O HIS A 983 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 998 " --> pdb=" O GLY A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1005 removed outlier: 3.602A pdb=" N GLU A1005 " --> pdb=" O PRO A1002 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1002 through 1005' Processing helix chain 'A' and resid 1079 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1168 through 1177 removed outlier: 4.704A pdb=" N SER A1172 " --> pdb=" O ILE A1168 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N SER A1173 " --> pdb=" O MET A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1264 through 1281 Processing helix chain 'A' and resid 1284 through 1297 Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 3.569A pdb=" N HIS A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A1312 " --> pdb=" O ASN A1308 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 6.263A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 528 through 529 removed outlier: 3.731A pdb=" N TYR A 529 " --> pdb=" O ALA A 538 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA A 538 " --> pdb=" O TYR A 529 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 837 through 840 removed outlier: 4.108A pdb=" N ASP A 837 " --> pdb=" O THR A 858 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A 858 " --> pdb=" O ASP A 837 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP A 839 " --> pdb=" O VAL A 856 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA6, first strand: chain 'A' and resid 1063 through 1065 Processing sheet with id=AA7, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA8, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 6.088A pdb=" N LYS A1156 " --> pdb=" O GLU A1150 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU A1150 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LYS A1158 " --> pdb=" O LYS A1148 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS A1148 " --> pdb=" O LYS A1158 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A1160 " --> pdb=" O VAL A1146 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL A1146 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU A1162 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU A1144 " --> pdb=" O GLU A1162 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU A1164 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N SER A1142 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE A1166 " --> pdb=" O ALA A1140 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1219 through 1222 removed outlier: 6.090A pdb=" N GLU A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1324 through 1325 441 hydrogen bonds defined for protein. 1293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 112 hydrogen bonds 216 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 102 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.57: 15075 1.57 - 1.92: 409 1.92 - 2.27: 0 2.27 - 2.63: 0 2.63 - 2.98: 1 Bond restraints: 15485 Sorted by residual: bond pdb=" O3' DA D -35 " pdb=" P DG D -34 " ideal model delta sigma weight residual 1.607 2.980 -1.373 1.20e-02 6.94e+03 1.31e+04 bond pdb=" C3' DC C 37 " pdb=" O3' DC C 37 " ideal model delta sigma weight residual 1.435 1.383 0.052 1.30e-02 5.92e+03 1.62e+01 bond pdb=" C3' DA C 41 " pdb=" C2' DA C 41 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.50e+01 bond pdb=" C1' DC D -31 " pdb=" N1 DC D -31 " ideal model delta sigma weight residual 1.468 1.522 -0.054 1.40e-02 5.10e+03 1.46e+01 bond pdb=" C3' DC D -27 " pdb=" C2' DC D -27 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.28e+01 ... (remaining 15480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.37: 21673 6.37 - 12.74: 28 12.74 - 19.11: 1 19.11 - 25.48: 4 25.48 - 31.85: 5 Bond angle restraints: 21711 Sorted by residual: angle pdb=" O3' DA D -35 " pdb=" P DG D -34 " pdb=" O5' DG D -34 " ideal model delta sigma weight residual 104.00 73.26 30.74 1.90e+00 2.77e-01 2.62e+02 angle pdb=" C3' DA D -35 " pdb=" O3' DA D -35 " pdb=" P DG D -34 " ideal model delta sigma weight residual 119.70 138.58 -18.88 1.20e+00 6.94e-01 2.48e+02 angle pdb=" O3' DT C 39 " pdb=" P DT C 40 " pdb=" OP2 DT C 40 " ideal model delta sigma weight residual 108.00 76.15 31.85 3.00e+00 1.11e-01 1.13e+02 angle pdb=" O3' DT C 39 " pdb=" P DT C 40 " pdb=" OP1 DT C 40 " ideal model delta sigma weight residual 108.00 77.34 30.66 3.00e+00 1.11e-01 1.04e+02 angle pdb=" O3' DA D -35 " pdb=" P DG D -34 " pdb=" OP1 DG D -34 " ideal model delta sigma weight residual 108.00 134.94 -26.94 3.00e+00 1.11e-01 8.06e+01 ... (remaining 21706 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.93: 8250 29.93 - 59.85: 878 59.85 - 89.78: 137 89.78 - 119.70: 2 119.70 - 149.63: 2 Dihedral angle restraints: 9269 sinusoidal: 5349 harmonic: 3920 Sorted by residual: dihedral pdb=" O4' C B 72 " pdb=" C1' C B 72 " pdb=" N1 C B 72 " pdb=" C2 C B 72 " ideal model delta sinusoidal sigma weight residual 200.00 55.86 144.14 1 1.50e+01 4.44e-03 7.72e+01 dihedral pdb=" CA ARG A 671 " pdb=" C ARG A 671 " pdb=" N ASP A 672 " pdb=" CA ASP A 672 " ideal model delta harmonic sigma weight residual 180.00 157.25 22.75 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA ASP A 576 " pdb=" C ASP A 576 " pdb=" N SER A 577 " pdb=" CA SER A 577 " ideal model delta harmonic sigma weight residual 180.00 157.37 22.63 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 9266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.380: 2486 0.380 - 0.761: 2 0.761 - 1.141: 0 1.141 - 1.522: 0 1.522 - 1.902: 1 Chirality restraints: 2489 Sorted by residual: chirality pdb=" P DT C 30 " pdb=" OP1 DT C 30 " pdb=" OP2 DT C 30 " pdb=" O5' DT C 30 " both_signs ideal model delta sigma weight residual True 2.34 0.43 1.90 2.00e-01 2.50e+01 9.05e+01 chirality pdb=" C3' DT C 39 " pdb=" C4' DT C 39 " pdb=" O3' DT C 39 " pdb=" C2' DT C 39 " both_signs ideal model delta sigma weight residual False -2.73 -2.32 -0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" C3' A B 9 " pdb=" C4' A B 9 " pdb=" O3' A B 9 " pdb=" C2' A B 9 " both_signs ideal model delta sigma weight residual False -2.48 -2.09 -0.39 2.00e-01 2.50e+01 3.80e+00 ... (remaining 2486 not shown) Planarity restraints: 2096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT C 39 " 0.051 2.00e-02 2.50e+03 3.02e-02 2.28e+01 pdb=" N1 DT C 39 " -0.079 2.00e-02 2.50e+03 pdb=" C2 DT C 39 " 0.009 2.00e-02 2.50e+03 pdb=" O2 DT C 39 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DT C 39 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT C 39 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT C 39 " 0.012 2.00e-02 2.50e+03 pdb=" C5 DT C 39 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT C 39 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DT C 39 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 8 " -0.038 2.00e-02 2.50e+03 2.65e-02 2.11e+01 pdb=" N9 G B 8 " 0.077 2.00e-02 2.50e+03 pdb=" C8 G B 8 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G B 8 " -0.005 2.00e-02 2.50e+03 pdb=" C5 G B 8 " -0.007 2.00e-02 2.50e+03 pdb=" C6 G B 8 " -0.008 2.00e-02 2.50e+03 pdb=" O6 G B 8 " 0.002 2.00e-02 2.50e+03 pdb=" N1 G B 8 " -0.000 2.00e-02 2.50e+03 pdb=" C2 G B 8 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G B 8 " 0.006 2.00e-02 2.50e+03 pdb=" N3 G B 8 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G B 8 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 573 " -0.022 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C GLU A 573 " 0.077 2.00e-02 2.50e+03 pdb=" O GLU A 573 " -0.029 2.00e-02 2.50e+03 pdb=" N CYS A 574 " -0.025 2.00e-02 2.50e+03 ... (remaining 2093 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 220 2.62 - 3.19: 12714 3.19 - 3.76: 24931 3.76 - 4.33: 33036 4.33 - 4.90: 50203 Nonbonded interactions: 121104 Sorted by model distance: nonbonded pdb=" NE2 GLN A 695 " pdb=" OP1 DT C 38 " model vdw 2.045 3.120 nonbonded pdb=" OG1 THR A 893 " pdb=" O2' A B 10 " model vdw 2.059 3.040 nonbonded pdb=" OG1 THR A 404 " pdb=" OD1 ASP A 406 " model vdw 2.068 3.040 nonbonded pdb=" OD1 ASN A 588 " pdb=" O2' C B 7 " model vdw 2.070 3.040 nonbonded pdb=" OD1 ASN A 240 " pdb=" OG1 THR A 249 " model vdw 2.110 3.040 ... (remaining 121099 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=0.00 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: 0.730 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.930 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 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 : 0.012 1.373 15485 Z= 0.977 Angle : 0.950 31.846 21711 Z= 0.631 Chirality : 0.065 1.902 2489 Planarity : 0.004 0.044 2096 Dihedral : 21.753 149.630 6733 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.17 % Allowed : 27.49 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.24), residues: 1328 helix: 1.48 (0.22), residues: 598 sheet: -0.31 (0.52), residues: 95 loop : -1.12 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 307 TYR 0.019 0.001 TYR A 529 PHE 0.010 0.001 PHE A 643 TRP 0.008 0.002 TRP A 476 HIS 0.004 0.001 HIS A 982 Details of bonding type rmsd/Z covalent geometry : bond 0.01173 / 0.98 (15485) covalent geometry : angle 0.94976 / 0.63 (21711) hydrogen bonds : bond 0.15626 / 10.54 ( 553) hydrogen bonds : angle 5.48641 / 3.99 ( 1509) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 307 ARG cc_start: 0.7819 (mmp80) cc_final: 0.7494 (mmm160) REVERT: A 562 LYS cc_start: 0.8797 (pptt) cc_final: 0.8489 (tmtt) outliers start: 2 outliers final: 0 residues processed: 59 average time/residue: 0.1244 time to fit residues: 10.9389 Evaluate side-chains 52 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.0770 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 50.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 overall best weight: 3.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 501 ASN ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 GLN ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.126006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.072705 restraints weight = 30310.880| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.60 r_work: 0.2925 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15485 Z= 0.239 Angle : 0.766 32.738 21711 Z= 0.387 Chirality : 0.062 1.877 2489 Planarity : 0.004 0.056 2096 Dihedral : 21.736 152.840 3911 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.93 % Allowed : 23.30 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.23), residues: 1328 helix: 0.93 (0.21), residues: 614 sheet: -0.16 (0.52), residues: 97 loop : -1.29 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 925 TYR 0.017 0.002 TYR A 155 PHE 0.032 0.002 PHE A 916 TRP 0.010 0.002 TRP A 476 HIS 0.009 0.002 HIS A 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.24 (15485) covalent geometry : angle 0.76635 / 0.39 (21711) hydrogen bonds : bond 0.06292 / 4.32 ( 553) hydrogen bonds : angle 4.55753 / 3.25 ( 1509) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 53 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 562 LYS cc_start: 0.8790 (pptt) cc_final: 0.8422 (tmtt) REVERT: A 566 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6799 (mt-10) outliers start: 35 outliers final: 14 residues processed: 82 average time/residue: 0.0972 time to fit residues: 12.6733 Evaluate side-chains 65 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1291 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 76 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 10 optimal weight: 0.0670 chunk 108 optimal weight: 0.8980 chunk 139 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.128159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.075371 restraints weight = 30517.427| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.58 r_work: 0.2988 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15485 Z= 0.126 Angle : 0.626 26.095 21711 Z= 0.327 Chirality : 0.068 2.042 2489 Planarity : 0.003 0.057 2096 Dihedral : 21.576 151.444 3911 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.18 % Allowed : 23.64 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.23), residues: 1328 helix: 1.19 (0.21), residues: 607 sheet: 0.21 (0.53), residues: 97 loop : -1.25 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 653 TYR 0.011 0.001 TYR A 594 PHE 0.019 0.001 PHE A 916 TRP 0.005 0.001 TRP A 476 HIS 0.004 0.001 HIS A 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.13 (15485) covalent geometry : angle 0.62615 / 0.33 (21711) hydrogen bonds : bond 0.05135 / 3.59 ( 553) hydrogen bonds : angle 4.20499 / 2.99 ( 1509) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 57 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 354 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8159 (mp10) REVERT: A 562 LYS cc_start: 0.8778 (pptt) cc_final: 0.8542 (pptt) outliers start: 26 outliers final: 10 residues processed: 82 average time/residue: 0.0999 time to fit residues: 12.4786 Evaluate side-chains 61 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1149 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 2 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 GLN A 854 ASN ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.124811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.071417 restraints weight = 30577.853| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.61 r_work: 0.2895 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 15485 Z= 0.254 Angle : 0.723 26.072 21711 Z= 0.372 Chirality : 0.070 2.007 2489 Planarity : 0.004 0.061 2096 Dihedral : 21.554 152.527 3911 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.27 % Allowed : 22.63 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.23), residues: 1328 helix: 0.96 (0.21), residues: 606 sheet: -0.08 (0.53), residues: 95 loop : -1.32 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 437 TYR 0.020 0.002 TYR A 155 PHE 0.016 0.002 PHE A1045 TRP 0.010 0.002 TRP A 476 HIS 0.007 0.002 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.25 (15485) covalent geometry : angle 0.72299 / 0.37 (21711) hydrogen bonds : bond 0.06170 / 4.20 ( 553) hydrogen bonds : angle 4.36528 / 3.07 ( 1509) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 53 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 354 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8131 (mp10) REVERT: A 437 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7912 (ptm-80) REVERT: A 1334 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7871 (tptt) outliers start: 39 outliers final: 23 residues processed: 90 average time/residue: 0.1047 time to fit residues: 14.0773 Evaluate side-chains 73 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 47 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1334 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 49 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 145 optimal weight: 20.0000 chunk 113 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 103 optimal weight: 0.4980 chunk 115 optimal weight: 1.9990 chunk 80 optimal weight: 30.0000 chunk 68 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 HIS ** 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 = 0.4067 r_free = 0.4067 target = 0.127195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.074308 restraints weight = 30464.599| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.57 r_work: 0.2966 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15485 Z= 0.128 Angle : 0.634 25.972 21711 Z= 0.329 Chirality : 0.068 2.017 2489 Planarity : 0.003 0.061 2096 Dihedral : 21.521 151.882 3911 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.84 % Allowed : 24.06 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.23), residues: 1328 helix: 1.16 (0.21), residues: 606 sheet: -0.04 (0.52), residues: 97 loop : -1.31 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 557 TYR 0.009 0.001 TYR A1036 PHE 0.015 0.001 PHE A 970 TRP 0.006 0.001 TRP A 476 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.13 (15485) covalent geometry : angle 0.63387 / 0.33 (21711) hydrogen bonds : bond 0.04886 / 3.40 ( 553) hydrogen bonds : angle 4.12684 / 2.91 ( 1509) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 354 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8230 (mp10) REVERT: A 575 PHE cc_start: 0.6975 (m-10) cc_final: 0.6685 (t80) outliers start: 22 outliers final: 15 residues processed: 72 average time/residue: 0.1005 time to fit residues: 11.3735 Evaluate side-chains 65 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.0570 chunk 43 optimal weight: 0.0370 chunk 122 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 136 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 22 optimal weight: 40.0000 chunk 108 optimal weight: 3.9990 overall best weight: 1.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 HIS ** 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 = 0.4060 r_free = 0.4060 target = 0.126673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.073853 restraints weight = 30251.181| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.56 r_work: 0.2955 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15485 Z= 0.144 Angle : 0.626 26.001 21711 Z= 0.324 Chirality : 0.068 2.034 2489 Planarity : 0.003 0.058 2096 Dihedral : 21.410 151.748 3911 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.18 % Allowed : 23.72 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.23), residues: 1328 helix: 1.22 (0.21), residues: 607 sheet: 0.03 (0.53), residues: 95 loop : -1.30 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 653 TYR 0.013 0.001 TYR A 155 PHE 0.017 0.001 PHE A 916 TRP 0.007 0.001 TRP A 476 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (15485) covalent geometry : angle 0.62600 / 0.32 (21711) hydrogen bonds : bond 0.04803 / 3.29 ( 553) hydrogen bonds : angle 4.05578 / 2.85 ( 1509) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 0.429 Fit side-chains REVERT: A 51 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8133 (tp) REVERT: A 354 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8240 (mp10) REVERT: A 575 PHE cc_start: 0.7169 (m-10) cc_final: 0.6869 (t80) REVERT: A 655 ARG cc_start: 0.8249 (tpp80) cc_final: 0.7827 (tpp80) REVERT: A 1334 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7961 (tptt) outliers start: 26 outliers final: 16 residues processed: 75 average time/residue: 0.0929 time to fit residues: 10.9972 Evaluate side-chains 68 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1334 LYS Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 127 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 142 optimal weight: 30.0000 chunk 112 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 723 HIS ** 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 = 0.4038 r_free = 0.4038 target = 0.125255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.072359 restraints weight = 30013.871| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.47 r_work: 0.2918 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15485 Z= 0.213 Angle : 0.672 26.157 21711 Z= 0.348 Chirality : 0.070 2.048 2489 Planarity : 0.004 0.061 2096 Dihedral : 21.431 152.633 3911 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.43 % Allowed : 23.47 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.23), residues: 1328 helix: 1.07 (0.21), residues: 605 sheet: -0.19 (0.57), residues: 81 loop : -1.30 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 653 TYR 0.018 0.001 TYR A 155 PHE 0.021 0.002 PHE A 897 TRP 0.009 0.002 TRP A 883 HIS 0.006 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 (15485) covalent geometry : angle 0.67220 / 0.35 (21711) hydrogen bonds : bond 0.05367 / 3.67 ( 553) hydrogen bonds : angle 4.19435 / 2.93 ( 1509) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 49 time to evaluate : 0.338 Fit side-chains REVERT: A 51 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8152 (tp) REVERT: A 354 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8208 (mp10) REVERT: A 383 MET cc_start: 0.8751 (mmm) cc_final: 0.8531 (mmm) REVERT: A 575 PHE cc_start: 0.7261 (m-10) cc_final: 0.6828 (t80) REVERT: A 1334 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7944 (tptt) outliers start: 29 outliers final: 22 residues processed: 76 average time/residue: 0.1045 time to fit residues: 12.2290 Evaluate side-chains 72 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 47 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1334 LYS Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 114 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 143 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** 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 = 0.4043 r_free = 0.4043 target = 0.125657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.075841 restraints weight = 30130.234| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.83 r_work: 0.2893 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15485 Z= 0.172 Angle : 0.639 26.075 21711 Z= 0.332 Chirality : 0.069 2.042 2489 Planarity : 0.004 0.060 2096 Dihedral : 21.434 152.404 3911 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.01 % Allowed : 24.06 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.23), residues: 1328 helix: 1.03 (0.21), residues: 611 sheet: -0.45 (0.49), residues: 105 loop : -1.28 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 653 TYR 0.013 0.001 TYR A 155 PHE 0.012 0.001 PHE A 970 TRP 0.016 0.001 TRP A 883 HIS 0.005 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (15485) covalent geometry : angle 0.63898 / 0.33 (21711) hydrogen bonds : bond 0.05059 / 3.48 ( 553) hydrogen bonds : angle 4.11813 / 2.88 ( 1509) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 0.427 Fit side-chains REVERT: A 51 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8125 (tp) REVERT: A 354 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8220 (mp10) REVERT: A 383 MET cc_start: 0.8762 (mmm) cc_final: 0.8559 (mmm) REVERT: A 655 ARG cc_start: 0.8250 (tpp80) cc_final: 0.7855 (tpp80) REVERT: A 1334 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7965 (tptt) outliers start: 24 outliers final: 19 residues processed: 73 average time/residue: 0.0967 time to fit residues: 11.2132 Evaluate side-chains 70 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1334 LYS Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 70 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 145 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** 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 = 0.4029 r_free = 0.4029 target = 0.124782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.071543 restraints weight = 30387.487| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.56 r_work: 0.2900 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15485 Z= 0.206 Angle : 0.671 26.086 21711 Z= 0.348 Chirality : 0.070 2.051 2489 Planarity : 0.004 0.060 2096 Dihedral : 21.447 152.919 3911 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.60 % Allowed : 23.72 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.23), residues: 1328 helix: 0.92 (0.21), residues: 617 sheet: -0.36 (0.57), residues: 81 loop : -1.32 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 653 TYR 0.017 0.001 TYR A 155 PHE 0.020 0.002 PHE A 897 TRP 0.009 0.001 TRP A 476 HIS 0.005 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.21 (15485) covalent geometry : angle 0.67079 / 0.35 (21711) hydrogen bonds : bond 0.05440 / 3.71 ( 553) hydrogen bonds : angle 4.18702 / 2.92 ( 1509) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 45 time to evaluate : 0.340 Fit side-chains REVERT: A 51 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8124 (tp) REVERT: A 354 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8203 (mp10) REVERT: A 655 ARG cc_start: 0.8304 (tpp80) cc_final: 0.7925 (tpp80) REVERT: A 822 MET cc_start: 0.3145 (mmt) cc_final: 0.2876 (mmt) outliers start: 31 outliers final: 25 residues processed: 74 average time/residue: 0.1028 time to fit residues: 11.8902 Evaluate side-chains 72 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 45 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1337 THR Chi-restraints excluded: chain A residue 1344 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 21 optimal weight: 5.9990 chunk 113 optimal weight: 0.0980 chunk 77 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 146 optimal weight: 50.0000 chunk 96 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** 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 = 0.4053 r_free = 0.4053 target = 0.126343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.073560 restraints weight = 30078.765| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.55 r_work: 0.2947 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15485 Z= 0.135 Angle : 0.624 26.015 21711 Z= 0.325 Chirality : 0.068 2.039 2489 Planarity : 0.003 0.067 2096 Dihedral : 21.419 152.499 3911 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.84 % Allowed : 24.22 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.23), residues: 1328 helix: 1.08 (0.21), residues: 612 sheet: -0.38 (0.50), residues: 105 loop : -1.33 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 653 TYR 0.010 0.001 TYR A1036 PHE 0.012 0.001 PHE A 970 TRP 0.017 0.001 TRP A 883 HIS 0.004 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (15485) covalent geometry : angle 0.62405 / 0.32 (21711) hydrogen bonds : bond 0.04667 / 3.22 ( 553) hydrogen bonds : angle 4.06712 / 2.84 ( 1509) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.341 Fit side-chains REVERT: A 51 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8113 (tp) REVERT: A 354 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8258 (mp10) REVERT: A 655 ARG cc_start: 0.8420 (tpp80) cc_final: 0.8080 (tpp80) REVERT: A 695 GLN cc_start: 0.6842 (OUTLIER) cc_final: 0.6258 (mt0) REVERT: A 1043 MET cc_start: 0.8792 (mtt) cc_final: 0.8430 (mtp) outliers start: 22 outliers final: 18 residues processed: 70 average time/residue: 0.0965 time to fit residues: 10.9249 Evaluate side-chains 69 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 695 GLN Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 139 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** 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 = 0.4026 r_free = 0.4026 target = 0.124507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.071348 restraints weight = 30139.747| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.54 r_work: 0.2898 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15485 Z= 0.228 Angle : 0.683 26.179 21711 Z= 0.353 Chirality : 0.070 2.050 2489 Planarity : 0.004 0.068 2096 Dihedral : 21.424 153.217 3911 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.35 % Allowed : 24.06 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.23), residues: 1328 helix: 0.99 (0.21), residues: 610 sheet: -0.48 (0.56), residues: 81 loop : -1.31 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 653 TYR 0.019 0.001 TYR A 155 PHE 0.013 0.002 PHE A1045 TRP 0.017 0.002 TRP A 883 HIS 0.007 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.23 (15485) covalent geometry : angle 0.68277 / 0.35 (21711) hydrogen bonds : bond 0.05420 / 3.69 ( 553) hydrogen bonds : angle 4.18949 / 2.92 ( 1509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3007.31 seconds wall clock time: 52 minutes 17.65 seconds (3137.65 seconds total)