Starting phenix.real_space_refine on Fri Jul 3 17:31:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h4j_51861/07_2026/9h4j_51861.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h4j_51861/07_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_51861/07_2026/9h4j_51861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h4j_51861/07_2026/9h4j_51861.map" model { file = "/net/cci-nas-00/data/ceres_data/9h4j_51861/07_2026/9h4j_51861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h4j_51861/07_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-dev-6108/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: 3.23, per 1000 atoms: 0.22 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: 1.23 Conformation dependent library (CDL) restraints added in 579.7 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: 1.83 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: 3.56 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.57: 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 1.50e-02 4.44e+03 8.38e+03 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: 21674 6.37 - 12.74: 27 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 1.50e+00 4.44e-01 4.20e+02 angle pdb=" C3' DA D -35 " pdb=" O3' DA D -35 " pdb=" P DG D -34 " ideal model delta sigma weight residual 120.20 138.58 -18.38 1.50e+00 4.44e-01 1.50e+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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.130 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.850 ------------------------------------------------------------------------------- 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= 0.804 Angle : 0.908 31.846 21711 Z= 0.591 Chirality : 0.060 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 0.01171 / 0.80 (15485) covalent geometry : angle 0.90771 / 0.59 (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 : 0.471 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: 0.1327 time to fit residues: 11.8026 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 : 0.462 ------------------------------------------------------------------------------- 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: 6.9990 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 = 0.125988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.072794 restraints weight = 30269.620| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.62 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: 0.8528 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15485 Z= 0.240 Angle : 0.728 27.259 21711 Z= 0.378 Chirality : 0.070 1.947 2489 Planarity : 0.004 0.055 2096 Dihedral : 21.784 153.457 3911 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.85 % Allowed : 23.39 % 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: -0.21 (0.23), residues: 1328 helix: 0.96 (0.21), residues: 614 sheet: -0.15 (0.52), residues: 97 loop : -1.28 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 925 TYR 0.016 0.002 TYR A 155 PHE 0.030 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 0.00517 / 0.24 (15485) covalent geometry : angle 0.72817 / 0.38 (21711) hydrogen bonds : bond 0.06230 / 4.27 ( 553) hydrogen bonds : angle 4.56311 / 3.26 ( 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 87 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 53 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 562 LYS cc_start: 0.8789 (pptt) cc_final: 0.8424 (tmtt) REVERT: A 566 GLU cc_start: 0.7406 (mt-10) cc_final: 0.6777 (mt-10) outliers start: 34 outliers final: 14 residues processed: 81 average time/residue: 0.1075 time to fit residues: 13.7591 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 : 0.482 ------------------------------------------------------------------------------- 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: 7.9990 chunk 125 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 10 optimal weight: 0.0570 chunk 108 optimal weight: 0.9980 chunk 139 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 overall best weight: 1.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4070 r_free = 0.4070 target = 0.127232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.074308 restraints weight = 30496.213| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.58 r_work: 0.2968 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15485 Z= 0.143 Angle : 0.640 26.731 21711 Z= 0.333 Chirality : 0.069 2.023 2489 Planarity : 0.003 0.058 2096 Dihedral : 21.669 152.513 3911 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % 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: -0.01 (0.23), residues: 1328 helix: 1.20 (0.21), residues: 600 sheet: 0.12 (0.53), residues: 97 loop : -1.23 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 307 TYR 0.011 0.001 TYR A 594 PHE 0.014 0.001 PHE A 916 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 0.00278 / 0.14 (15485) covalent geometry : angle 0.63998 / 0.33 (21711) hydrogen bonds : bond 0.05266 / 3.65 ( 553) hydrogen bonds : angle 4.24294 / 3.01 ( 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 86 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 354 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8148 (mp10) REVERT: A 562 LYS cc_start: 0.8779 (pptt) cc_final: 0.8555 (pptt) REVERT: A 763 MET cc_start: 0.8156 (mtp) cc_final: 0.7954 (mtp) REVERT: A 959 LYS cc_start: 0.8513 (ttpp) cc_final: 0.8268 (mttt) outliers start: 29 outliers final: 11 residues processed: 84 average time/residue: 0.1297 time to fit residues: 16.2892 Evaluate side-chains 64 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 2 optimal weight: 0.0030 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 89 optimal weight: 0.3980 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: 0.9990 chunk 127 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 GLN A 854 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.126831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.073829 restraints weight = 30502.776| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.57 r_work: 0.2951 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1515 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= 0.160 Angle : 0.649 26.685 21711 Z= 0.335 Chirality : 0.068 2.018 2489 Planarity : 0.004 0.060 2096 Dihedral : 21.569 152.877 3911 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.51 % Allowed : 23.13 % Favored : 74.35 % 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: -0.04 (0.23), residues: 1328 helix: 1.15 (0.21), residues: 603 sheet: 0.09 (0.52), residues: 97 loop : -1.24 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 653 TYR 0.013 0.001 TYR A 155 PHE 0.015 0.001 PHE A 970 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 0.00325 / 0.16 (15485) covalent geometry : angle 0.64946 / 0.34 (21711) hydrogen bonds : bond 0.05050 / 3.46 ( 553) hydrogen bonds : angle 4.19177 / 2.96 ( 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 89 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 59 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 354 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8163 (mp10) REVERT: A 653 ARG cc_start: 0.8479 (mtp-110) cc_final: 0.8276 (mtp-110) REVERT: A 763 MET cc_start: 0.8159 (mtp) cc_final: 0.7954 (mtp) REVERT: A 1334 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7915 (tptt) outliers start: 30 outliers final: 18 residues processed: 86 average time/residue: 0.1255 time to fit residues: 16.3534 Evaluate side-chains 71 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 109 optimal weight: 0.0970 chunk 145 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 103 optimal weight: 0.0060 chunk 115 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 overall best weight: 2.0200 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.126168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.073181 restraints weight = 30524.297| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.58 r_work: 0.2939 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15485 Z= 0.172 Angle : 0.650 26.791 21711 Z= 0.337 Chirality : 0.069 2.038 2489 Planarity : 0.003 0.060 2096 Dihedral : 21.536 153.127 3911 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.60 % Allowed : 23.64 % 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: -0.03 (0.23), residues: 1328 helix: 1.20 (0.21), residues: 601 sheet: 0.03 (0.53), residues: 95 loop : -1.26 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 655 TYR 0.014 0.001 TYR A 155 PHE 0.015 0.001 PHE A 970 TRP 0.007 0.001 TRP A 476 HIS 0.004 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (15485) covalent geometry : angle 0.64973 / 0.34 (21711) hydrogen bonds : bond 0.05052 / 3.46 ( 553) hydrogen bonds : angle 4.16018 / 2.92 ( 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 81 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 50 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 354 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8236 (mp10) REVERT: A 437 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7794 (ptm-80) REVERT: A 575 PHE cc_start: 0.7230 (m-10) cc_final: 0.6819 (t80) REVERT: A 763 MET cc_start: 0.8178 (mtp) cc_final: 0.7962 (mtp) REVERT: A 1334 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7890 (tptt) outliers start: 31 outliers final: 22 residues processed: 80 average time/residue: 0.1210 time to fit residues: 14.9245 Evaluate side-chains 74 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 49 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 136 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 24 optimal weight: 20.0000 chunk 22 optimal weight: 40.0000 chunk 108 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 ASN ** 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 = 0.4054 r_free = 0.4054 target = 0.126348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.073398 restraints weight = 30267.347| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.58 r_work: 0.2944 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15485 Z= 0.156 Angle : 0.629 26.731 21711 Z= 0.327 Chirality : 0.069 2.058 2489 Planarity : 0.003 0.058 2096 Dihedral : 21.488 152.846 3911 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.68 % Allowed : 23.13 % 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: -0.05 (0.23), residues: 1328 helix: 1.17 (0.21), residues: 607 sheet: 0.03 (0.53), residues: 95 loop : -1.29 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 653 TYR 0.012 0.001 TYR A 155 PHE 0.014 0.001 PHE A 970 TRP 0.007 0.001 TRP A 476 HIS 0.004 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (15485) covalent geometry : angle 0.62902 / 0.33 (21711) hydrogen bonds : bond 0.04796 / 3.28 ( 553) hydrogen bonds : angle 4.07556 / 2.86 ( 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 83 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 51 time to evaluate : 0.406 Fit side-chains REVERT: A 51 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8121 (tp) REVERT: A 575 PHE cc_start: 0.7212 (m-10) cc_final: 0.6864 (t80) REVERT: A 655 ARG cc_start: 0.8310 (tpp80) cc_final: 0.7908 (tpp80) REVERT: A 763 MET cc_start: 0.8171 (mtp) cc_final: 0.7943 (mtp) REVERT: A 1334 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7952 (tptt) outliers start: 32 outliers final: 22 residues processed: 81 average time/residue: 0.1086 time to fit residues: 14.1472 Evaluate side-chains 73 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 49 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER 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 313 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 858 THR Chi-restraints excluded: chain A residue 930 HIS 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 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: 3.9990 chunk 10 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 142 optimal weight: 30.0000 chunk 112 optimal weight: 0.5980 chunk 14 optimal weight: 8.9990 chunk 50 optimal weight: 0.0270 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4060 r_free = 0.4060 target = 0.126772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.074088 restraints weight = 30052.397| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.54 r_work: 0.2958 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15485 Z= 0.137 Angle : 0.621 26.688 21711 Z= 0.322 Chirality : 0.068 2.057 2489 Planarity : 0.003 0.059 2096 Dihedral : 21.450 152.952 3911 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.26 % Allowed : 23.81 % 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: -0.05 (0.23), residues: 1328 helix: 1.18 (0.21), residues: 607 sheet: 0.03 (0.53), residues: 95 loop : -1.28 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 653 TYR 0.011 0.001 TYR A 155 PHE 0.015 0.001 PHE A 897 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 0.00268 / 0.14 (15485) covalent geometry : angle 0.62101 / 0.32 (21711) hydrogen bonds : bond 0.04585 / 3.14 ( 553) hydrogen bonds : angle 4.04509 / 2.84 ( 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 79 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 52 time to evaluate : 0.340 Fit side-chains REVERT: A 575 PHE cc_start: 0.7196 (m-10) cc_final: 0.6801 (t80) REVERT: A 763 MET cc_start: 0.8181 (mtp) cc_final: 0.7951 (mtp) REVERT: A 1334 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7937 (tptt) outliers start: 27 outliers final: 21 residues processed: 77 average time/residue: 0.0971 time to fit residues: 11.7896 Evaluate side-chains 72 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 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 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 1329 THR Chi-restraints excluded: chain A residue 1334 LYS Chi-restraints excluded: chain A residue 1337 THR Chi-restraints excluded: chain A residue 1344 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 114 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 84 optimal weight: 30.0000 chunk 85 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.124936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.071823 restraints weight = 30160.157| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.57 r_work: 0.2908 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15485 Z= 0.214 Angle : 0.664 26.800 21711 Z= 0.346 Chirality : 0.070 2.070 2489 Planarity : 0.004 0.064 2096 Dihedral : 21.458 153.663 3911 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.77 % Allowed : 23.22 % Favored : 74.02 % 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: -0.15 (0.23), residues: 1328 helix: 1.04 (0.21), residues: 610 sheet: 0.12 (0.61), residues: 71 loop : -1.26 (0.23), residues: 647 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 0.015 0.001 PHE A 970 TRP 0.008 0.001 TRP A 476 HIS 0.006 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.21 (15485) covalent geometry : angle 0.66424 / 0.35 (21711) hydrogen bonds : bond 0.05296 / 3.60 ( 553) hydrogen bonds : angle 4.16571 / 2.91 ( 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 82 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 49 time to evaluate : 0.570 Fit side-chains REVERT: A 51 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8089 (tp) REVERT: A 354 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8225 (mp10) REVERT: A 437 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7842 (ptm-80) REVERT: A 575 PHE cc_start: 0.7207 (m-10) cc_final: 0.6775 (t80) REVERT: A 655 ARG cc_start: 0.8260 (tpp80) cc_final: 0.7872 (tpp80) REVERT: A 763 MET cc_start: 0.8214 (mtp) cc_final: 0.7974 (mtp) REVERT: A 965 ASP cc_start: 0.8505 (t0) cc_final: 0.8205 (t0) REVERT: A 1334 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7915 (tptt) outliers start: 33 outliers final: 25 residues processed: 79 average time/residue: 0.1067 time to fit residues: 13.0597 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 : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER 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 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 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 858 THR 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 997 LEU 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 Chi-restraints excluded: chain A residue 1337 THR Chi-restraints excluded: chain A residue 1344 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 70 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 127 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 chunk 145 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.125728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.072538 restraints weight = 30334.850| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.59 r_work: 0.2926 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15485 Z= 0.165 Angle : 0.636 26.719 21711 Z= 0.331 Chirality : 0.069 2.063 2489 Planarity : 0.003 0.061 2096 Dihedral : 21.466 153.580 3911 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.51 % Allowed : 23.47 % Favored : 74.02 % 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: -0.12 (0.23), residues: 1328 helix: 1.08 (0.21), residues: 610 sheet: -0.15 (0.53), residues: 95 loop : -1.26 (0.23), residues: 623 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 0.015 0.001 PHE A 916 TRP 0.016 0.001 TRP A 883 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (15485) covalent geometry : angle 0.63569 / 0.33 (21711) hydrogen bonds : bond 0.04858 / 3.32 ( 553) hydrogen bonds : angle 4.09245 / 2.86 ( 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 79 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 49 time to evaluate : 0.389 Fit side-chains REVERT: A 51 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8109 (tp) REVERT: A 354 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8234 (mp10) REVERT: A 437 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7861 (ptm-80) REVERT: A 655 ARG cc_start: 0.8293 (tpp80) cc_final: 0.7916 (tpp80) REVERT: A 695 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.6389 (mt0) REVERT: A 763 MET cc_start: 0.8205 (mtp) cc_final: 0.7954 (mtp) REVERT: A 1334 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7938 (tptt) outliers start: 30 outliers final: 24 residues processed: 77 average time/residue: 0.1079 time to fit residues: 12.9196 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 : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER 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 437 ARG Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 695 GLN 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 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 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: 7.9990 chunk 113 optimal weight: 0.9990 chunk 77 optimal weight: 30.0000 chunk 39 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 146 optimal weight: 50.0000 chunk 96 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4063 r_free = 0.4063 target = 0.127003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.074293 restraints weight = 30101.576| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.50 r_work: 0.2962 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15485 Z= 0.126 Angle : 0.618 26.629 21711 Z= 0.320 Chirality : 0.068 2.058 2489 Planarity : 0.003 0.059 2096 Dihedral : 21.416 153.140 3911 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.93 % Allowed : 23.97 % 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: -0.08 (0.23), residues: 1328 helix: 1.15 (0.21), residues: 613 sheet: -0.05 (0.53), residues: 95 loop : -1.31 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 653 TYR 0.009 0.001 TYR A 155 PHE 0.013 0.001 PHE A 970 TRP 0.016 0.001 TRP A 883 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.13 (15485) covalent geometry : angle 0.61824 / 0.32 (21711) hydrogen bonds : bond 0.04384 / 3.00 ( 553) hydrogen bonds : angle 4.00511 / 2.80 ( 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 77 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 54 time to evaluate : 0.448 Fit side-chains REVERT: A 51 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8137 (tp) REVERT: A 307 ARG cc_start: 0.8313 (mmp80) cc_final: 0.7691 (mmp-170) REVERT: A 354 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8256 (mp10) REVERT: A 437 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7705 (ptm-80) REVERT: A 655 ARG cc_start: 0.8380 (tpp80) cc_final: 0.8040 (tpp80) REVERT: A 695 GLN cc_start: 0.6918 (OUTLIER) cc_final: 0.6319 (mt0) REVERT: A 763 MET cc_start: 0.8225 (mtp) cc_final: 0.7974 (mtp) REVERT: A 1043 MET cc_start: 0.8810 (mtt) cc_final: 0.8431 (mtp) outliers start: 23 outliers final: 18 residues processed: 76 average time/residue: 0.1071 time to fit residues: 12.8929 Evaluate side-chains 74 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 52 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 437 ARG Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 599 LYS 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 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 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 139 optimal weight: 10.0000 chunk 50 optimal weight: 0.0270 chunk 57 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- 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 = 0.4031 r_free = 0.4031 target = 0.124815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.071636 restraints weight = 30131.667| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.56 r_work: 0.2907 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15485 Z= 0.229 Angle : 0.669 26.723 21711 Z= 0.348 Chirality : 0.070 2.067 2489 Planarity : 0.004 0.058 2096 Dihedral : 21.433 154.089 3911 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.43 % Allowed : 23.72 % Favored : 73.85 % 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: 610 sheet: -0.02 (0.60), residues: 71 loop : -1.30 (0.23), residues: 647 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 0.015 0.002 PHE A 970 TRP 0.016 0.002 TRP A 883 HIS 0.007 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.23 (15485) covalent geometry : angle 0.66928 / 0.35 (21711) hydrogen bonds : bond 0.05259 / 3.56 ( 553) hydrogen bonds : angle 4.14720 / 2.89 ( 1509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3603.45 seconds wall clock time: 62 minutes 34.25 seconds (3754.25 seconds total)