Starting phenix.real_space_refine on Wed Aug 5 23:44:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vxy_43643/08_2026/8vxy_43643.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vxy_43643/08_2026/8vxy_43643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vxy_43643/08_2026/8vxy_43643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vxy_43643/08_2026/8vxy_43643.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vxy_43643/08_2026/8vxy_43643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vxy_43643/08_2026/8vxy_43643.map" } resolution = 3.19 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= 0.001 sd= 0.034 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 64 5.49 5 S 38 5.16 5 C 7570 2.51 5 N 2186 2.21 5 O 2466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 12324 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 617 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Chain: "D" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 651 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "A" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1919 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 7, 'TRANS': 237} Chain: "B" Number of atoms: 9106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1161, 9106 Classifications: {'peptide': 1161} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 46, 'TRANS': 1111} Chain breaks: 1 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.83, per 1000 atoms: 0.23 Number of scatterers: 12324 At special positions: 0 Unit cell: (116.328, 117.376, 145.672, 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 38 16.00 P 64 15.00 O 2466 8.00 N 2186 7.00 C 7570 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: 1.03 Conformation dependent library (CDL) restraints added in 588.6 milliseconds 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2612 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 6 sheets defined 57.2% alpha, 7.3% beta 27 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 28 through 38 Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 47 through 57 Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 76 through 95 removed outlier: 5.601A pdb=" N GLY A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLU A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 159 removed outlier: 3.646A pdb=" N VAL A 150 " --> pdb=" O THR A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 165 through 180 Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 213 through 224 removed outlier: 4.438A pdb=" N MET A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 245 removed outlier: 3.756A pdb=" N ILE A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 16 Processing helix chain 'B' and resid 23 through 34 Processing helix chain 'B' and resid 50 through 72 Processing helix chain 'B' and resid 77 through 95 Processing helix chain 'B' and resid 103 through 118 Processing helix chain 'B' and resid 120 through 129 Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 151 through 166 Processing helix chain 'B' and resid 169 through 182 Processing helix chain 'B' and resid 194 through 224 removed outlier: 3.905A pdb=" N ASP B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 247 removed outlier: 4.155A pdb=" N LEU B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 269 removed outlier: 4.060A pdb=" N HIS B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 285 through 299 removed outlier: 3.949A pdb=" N GLU B 291 " --> pdb=" O PRO B 287 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 removed outlier: 4.664A pdb=" N GLU B 313 " --> pdb=" O PRO B 309 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ALA B 314 " --> pdb=" O SER B 310 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 315 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY B 316 " --> pdb=" O ARG B 312 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL B 319 " --> pdb=" O ALA B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 349 removed outlier: 3.651A pdb=" N ALA B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 375 removed outlier: 3.573A pdb=" N THR B 373 " --> pdb=" O THR B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 401 removed outlier: 3.554A pdb=" N ALA B 397 " --> pdb=" O MET B 393 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG B 399 " --> pdb=" O GLU B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 418 removed outlier: 3.732A pdb=" N ALA B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 423 removed outlier: 3.573A pdb=" N ILE B 422 " --> pdb=" O PRO B 419 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN B 423 " --> pdb=" O SER B 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 419 through 423' Processing helix chain 'B' and resid 439 through 455 removed outlier: 3.557A pdb=" N TYR B 445 " --> pdb=" O ARG B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 461 Processing helix chain 'B' and resid 473 through 484 removed outlier: 3.594A pdb=" N PHE B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 568 removed outlier: 3.561A pdb=" N ALA B 562 " --> pdb=" O CYS B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 582 Processing helix chain 'B' and resid 583 through 596 removed outlier: 3.910A pdb=" N GLU B 587 " --> pdb=" O GLU B 583 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 608 Processing helix chain 'B' and resid 609 through 618 removed outlier: 3.576A pdb=" N GLU B 618 " --> pdb=" O SER B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 631 removed outlier: 3.644A pdb=" N ALA B 628 " --> pdb=" O SER B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 655 removed outlier: 3.796A pdb=" N GLU B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 671 removed outlier: 4.192A pdb=" N LEU B 671 " --> pdb=" O LEU B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 702 Processing helix chain 'B' and resid 720 through 733 removed outlier: 3.687A pdb=" N THR B 726 " --> pdb=" O ASN B 722 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN B 727 " --> pdb=" O LYS B 723 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER B 733 " --> pdb=" O HIS B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 759 removed outlier: 3.586A pdb=" N LEU B 751 " --> pdb=" O LEU B 747 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG B 758 " --> pdb=" O ARG B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 772 removed outlier: 3.840A pdb=" N TYR B 769 " --> pdb=" O ALA B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 812 removed outlier: 3.796A pdb=" N ARG B 790 " --> pdb=" O SER B 786 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP B 791 " --> pdb=" O PRO B 787 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE B 792 " --> pdb=" O GLN B 788 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 810 " --> pdb=" O THR B 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 830 Processing helix chain 'B' and resid 833 through 842 removed outlier: 3.607A pdb=" N ARG B 841 " --> pdb=" O ARG B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 866 removed outlier: 3.582A pdb=" N ARG B 848 " --> pdb=" O ASP B 844 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 850 " --> pdb=" O ASN B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 878 Processing helix chain 'B' and resid 880 through 890 removed outlier: 3.854A pdb=" N ILE B 890 " --> pdb=" O ARG B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 903 Processing helix chain 'B' and resid 909 through 925 Processing helix chain 'B' and resid 927 through 931 removed outlier: 3.607A pdb=" N ILE B 931 " --> pdb=" O TYR B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 942 removed outlier: 3.969A pdb=" N GLY B 941 " --> pdb=" O GLY B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 948 removed outlier: 3.732A pdb=" N TRP B 946 " --> pdb=" O ILE B 942 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 966 Processing helix chain 'B' and resid 966 through 971 Processing helix chain 'B' and resid 974 through 990 removed outlier: 3.686A pdb=" N THR B 987 " --> pdb=" O ARG B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1006 removed outlier: 4.073A pdb=" N GLY B1006 " --> pdb=" O TYR B1003 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1003 through 1006' Processing helix chain 'B' and resid 1007 through 1013 removed outlier: 3.912A pdb=" N VAL B1012 " --> pdb=" O ALA B1008 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU B1013 " --> pdb=" O VAL B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1021 through 1028 removed outlier: 3.509A pdb=" N ILE B1025 " --> pdb=" O SER B1021 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY B1028 " --> pdb=" O LEU B1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1040 removed outlier: 4.281A pdb=" N THR B1040 " --> pdb=" O ILE B1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1056 removed outlier: 3.845A pdb=" N ARG B1054 " --> pdb=" O GLN B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1059 through 1067 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 11 removed outlier: 3.676A pdb=" N ASP A 9 " --> pdb=" O THR A 24 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 24 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN A 21 " --> pdb=" O CYS A 235 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ARG A 237 " --> pdb=" O GLN A 21 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE A 23 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ARG A 203 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE A 134 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU A 205 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LYS A 136 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N PHE A 207 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA A 138 " --> pdb=" O PHE A 207 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU A 209 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 381 through 383 removed outlier: 3.776A pdb=" N SER B 382 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 405 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL B 326 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 524 through 531 removed outlier: 8.639A pdb=" N VAL B 526 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N LEU B 517 " --> pdb=" O VAL B 526 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ARG B 528 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU B 515 " --> pdb=" O ARG B 528 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLY B 504 " --> pdb=" O TYR B 715 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE B 717 " --> pdb=" O GLY B 504 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL B 506 " --> pdb=" O ILE B 717 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 572 through 573 removed outlier: 6.870A pdb=" N VAL B 572 " --> pdb=" O THR B 661 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1095 through 1096 Processing sheet with id=AA6, first strand: chain 'B' and resid 1099 through 1102 removed outlier: 3.770A pdb=" N GLU B1153 " --> pdb=" O MET B1162 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B1152 " --> pdb=" O LEU B1116 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N HIS B1125 " --> pdb=" O SER B1137 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER B1137 " --> pdb=" O HIS B1125 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL B1127 " --> pdb=" O LEU B1135 " (cutoff:3.500A) 540 hydrogen bonds defined for protein. 1578 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3222 1.33 - 1.45: 2517 1.45 - 1.57: 6762 1.57 - 1.69: 126 1.69 - 1.81: 64 Bond restraints: 12691 Sorted by residual: bond pdb=" C4 ATP B1201 " pdb=" C5 ATP B1201 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.66e+01 bond pdb=" C5 ATP B1201 " pdb=" C6 ATP B1201 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.07e+01 bond pdb=" C4 ATP B1201 " pdb=" N9 ATP B1201 " ideal model delta sigma weight residual 1.374 1.325 0.049 1.00e-02 1.00e+04 2.44e+01 bond pdb=" C5 ATP B1201 " pdb=" N7 ATP B1201 " ideal model delta sigma weight residual 1.387 1.340 0.047 1.00e-02 1.00e+04 2.22e+01 bond pdb=" C8 ATP B1201 " pdb=" N7 ATP B1201 " ideal model delta sigma weight residual 1.310 1.353 -0.043 1.00e-02 1.00e+04 1.87e+01 ... (remaining 12686 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.71: 17391 3.71 - 7.43: 39 7.43 - 11.14: 58 11.14 - 14.85: 1 14.85 - 18.56: 2 Bond angle restraints: 17491 Sorted by residual: angle pdb=" PA ATP B1201 " pdb=" O3A ATP B1201 " pdb=" PB ATP B1201 " ideal model delta sigma weight residual 136.83 118.27 18.56 1.00e+00 1.00e+00 3.45e+02 angle pdb=" PB ATP B1201 " pdb=" O3B ATP B1201 " pdb=" PG ATP B1201 " ideal model delta sigma weight residual 139.87 122.96 16.91 1.00e+00 1.00e+00 2.86e+02 angle pdb=" C5 ATP B1201 " pdb=" C4 ATP B1201 " pdb=" N3 ATP B1201 " ideal model delta sigma weight residual 126.80 119.42 7.38 1.00e+00 1.00e+00 5.45e+01 angle pdb=" N3 ATP B1201 " pdb=" C4 ATP B1201 " pdb=" N9 ATP B1201 " ideal model delta sigma weight residual 127.04 134.58 -7.54 1.15e+00 7.59e-01 4.31e+01 angle pdb=" N1 ATP B1201 " pdb=" C2 ATP B1201 " pdb=" N3 ATP B1201 " ideal model delta sigma weight residual 128.69 123.49 5.20 1.00e+00 1.00e+00 2.70e+01 ... (remaining 17486 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 6676 17.73 - 35.45: 551 35.45 - 53.18: 243 53.18 - 70.90: 62 70.90 - 88.63: 6 Dihedral angle restraints: 7538 sinusoidal: 3493 harmonic: 4045 Sorted by residual: dihedral pdb=" CA HIS B 638 " pdb=" C HIS B 638 " pdb=" N GLY B 639 " pdb=" CA GLY B 639 " ideal model delta harmonic sigma weight residual 180.00 161.25 18.75 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA PHE B 966 " pdb=" C PHE B 966 " pdb=" N VAL B 967 " pdb=" CA VAL B 967 " ideal model delta harmonic sigma weight residual -180.00 -163.38 -16.62 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ILE B 94 " pdb=" C ILE B 94 " pdb=" N ALA B 95 " pdb=" CA ALA B 95 " ideal model delta harmonic sigma weight residual -180.00 -163.89 -16.11 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 7535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1856 0.092 - 0.184: 83 0.184 - 0.276: 0 0.276 - 0.368: 2 0.368 - 0.460: 29 Chirality restraints: 1970 Sorted by residual: chirality pdb=" P DA D 11 " pdb=" OP1 DA D 11 " pdb=" OP2 DA D 11 " pdb=" O5' DA D 11 " both_signs ideal model delta sigma weight residual True 2.34 -2.80 -0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" P DA D 21 " pdb=" OP1 DA D 21 " pdb=" OP2 DA D 21 " pdb=" O5' DA D 21 " both_signs ideal model delta sigma weight residual True 2.34 -2.77 -0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" P DA D 20 " pdb=" OP1 DA D 20 " pdb=" OP2 DA D 20 " pdb=" O5' DA D 20 " both_signs ideal model delta sigma weight residual True 2.34 -2.76 -0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 1967 not shown) Planarity restraints: 2057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT C 12 " -0.029 2.00e-02 2.50e+03 1.30e-02 4.20e+00 pdb=" N1 DT C 12 " 0.024 2.00e-02 2.50e+03 pdb=" C2 DT C 12 " 0.004 2.00e-02 2.50e+03 pdb=" O2 DT C 12 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DT C 12 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DT C 12 " -0.002 2.00e-02 2.50e+03 pdb=" O4 DT C 12 " -0.011 2.00e-02 2.50e+03 pdb=" C5 DT C 12 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT C 12 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT C 12 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 817 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO B 818 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 818 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 818 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 28 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C ALA A 28 " 0.025 2.00e-02 2.50e+03 pdb=" O ALA A 28 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU A 29 " -0.009 2.00e-02 2.50e+03 ... (remaining 2054 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1587 2.75 - 3.29: 12809 3.29 - 3.83: 22503 3.83 - 4.36: 26272 4.36 - 4.90: 42139 Nonbonded interactions: 105310 Sorted by model distance: nonbonded pdb=" O ALA B 314 " pdb=" OG SER B 318 " model vdw 2.215 3.040 nonbonded pdb=" O GLU B 367 " pdb=" OG SER B 371 " model vdw 2.224 3.040 nonbonded pdb=" O ARG B 317 " pdb=" NH2 ARG B 462 " model vdw 2.232 3.120 nonbonded pdb=" OG1 THR B 357 " pdb=" OG SER B 363 " model vdw 2.234 3.040 nonbonded pdb=" O ASN B 773 " pdb=" OH TYR B 861 " model vdw 2.239 3.040 ... (remaining 105305 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.310 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 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 : 0.003 0.075 12691 Z= 0.282 Angle : 0.845 18.565 17491 Z= 0.524 Chirality : 0.064 0.460 1970 Planarity : 0.003 0.040 2057 Dihedral : 16.144 88.626 4926 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1400 helix: 1.01 (0.21), residues: 674 sheet: -0.88 (0.50), residues: 119 loop : -1.19 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 841 TYR 0.013 0.001 TYR B 58 PHE 0.019 0.001 PHE B 256 TRP 0.011 0.001 TRP B 35 HIS 0.003 0.001 HIS B 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.28 (12691) covalent geometry : angle 0.84532 / 0.52 (17491) hydrogen bonds : bond 0.21320 / 22.56 ( 594) hydrogen bonds : angle 7.23033 / 9.06 ( 1686) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2473 (tpp) cc_final: 0.0976 (ptt) REVERT: A 14 ASN cc_start: 0.7933 (p0) cc_final: 0.7342 (t0) REVERT: A 86 PHE cc_start: 0.5694 (m-80) cc_final: 0.5412 (m-80) REVERT: A 123 ILE cc_start: 0.6147 (tt) cc_final: 0.5631 (tp) REVERT: A 152 GLU cc_start: 0.7561 (pt0) cc_final: 0.7234 (pp20) REVERT: A 215 GLU cc_start: 0.7001 (tt0) cc_final: 0.6720 (tp30) REVERT: B 23 ARG cc_start: 0.7310 (mtm-85) cc_final: 0.6442 (mtp85) REVERT: B 238 ILE cc_start: 0.5845 (mt) cc_final: 0.5641 (mt) REVERT: B 525 TRP cc_start: 0.7287 (p90) cc_final: 0.6677 (p90) REVERT: B 624 SER cc_start: 0.8462 (t) cc_final: 0.8002 (p) REVERT: B 650 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6197 (tt0) REVERT: B 1083 LEU cc_start: 0.5640 (tp) cc_final: 0.5178 (tp) REVERT: B 1141 ARG cc_start: 0.7288 (mtp-110) cc_final: 0.7030 (mtp-110) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.1360 time to fit residues: 48.4382 Evaluate side-chains 152 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 0.0030 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 overall best weight: 0.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 230 ASN ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 HIS ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 ASN B 502 GLN ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 HIS B 772 ASN B 959 GLN B1026 GLN B1068 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.228873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.192953 restraints weight = 18299.895| |-----------------------------------------------------------------------------| r_work (start): 0.4567 rms_B_bonded: 2.28 r_work: 0.4407 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12691 Z= 0.162 Angle : 0.677 8.866 17491 Z= 0.365 Chirality : 0.044 0.224 1970 Planarity : 0.005 0.044 2057 Dihedral : 19.364 89.147 2319 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.11 % Allowed : 7.71 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -0.39 (0.22), residues: 1400 helix: 0.75 (0.20), residues: 718 sheet: -1.05 (0.45), residues: 136 loop : -1.37 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 106 TYR 0.018 0.002 TYR A 19 PHE 0.016 0.002 PHE B 199 TRP 0.029 0.002 TRP B 797 HIS 0.023 0.002 HIS B1068 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (12691) covalent geometry : angle 0.67684 / 0.37 (17491) hydrogen bonds : bond 0.05519 / 5.73 ( 594) hydrogen bonds : angle 5.53500 / 7.19 ( 1686) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2206 (tpp) cc_final: 0.0561 (ptt) REVERT: A 14 ASN cc_start: 0.7953 (p0) cc_final: 0.7640 (t0) REVERT: B 23 ARG cc_start: 0.7398 (mtm-85) cc_final: 0.6973 (mtp85) REVERT: B 238 ILE cc_start: 0.5964 (mt) cc_final: 0.5741 (mt) REVERT: B 755 MET cc_start: 0.4857 (ptm) cc_final: 0.4557 (ptp) REVERT: B 827 ASP cc_start: 0.8247 (m-30) cc_final: 0.7943 (m-30) REVERT: B 1102 MET cc_start: 0.6716 (mmt) cc_final: 0.6436 (mmm) outliers start: 13 outliers final: 2 residues processed: 196 average time/residue: 0.1177 time to fit residues: 32.8772 Evaluate side-chains 146 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 144 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain B residue 926 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 0.5980 chunk 24 optimal weight: 0.0040 chunk 45 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 0.0040 chunk 72 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 chunk 34 optimal weight: 0.0040 chunk 116 optimal weight: 6.9990 chunk 105 optimal weight: 0.0170 overall best weight: 0.1254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 GLN B 245 GLN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN B 965 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.229487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.191243 restraints weight = 18541.209| |-----------------------------------------------------------------------------| r_work (start): 0.4550 rms_B_bonded: 2.33 r_work: 0.4420 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6366 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12691 Z= 0.139 Angle : 0.627 10.521 17491 Z= 0.337 Chirality : 0.042 0.179 1970 Planarity : 0.004 0.042 2057 Dihedral : 19.336 88.640 2319 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.94 % Allowed : 10.36 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -0.50 (0.22), residues: 1400 helix: 0.64 (0.20), residues: 724 sheet: -1.22 (0.42), residues: 156 loop : -1.34 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1160 TYR 0.015 0.002 TYR B 445 PHE 0.030 0.002 PHE A 86 TRP 0.036 0.002 TRP B1105 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (12691) covalent geometry : angle 0.62668 / 0.34 (17491) hydrogen bonds : bond 0.04779 / 4.98 ( 594) hydrogen bonds : angle 5.18816 / 6.60 ( 1686) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2215 (tpp) cc_final: 0.0652 (ptt) REVERT: A 14 ASN cc_start: 0.8046 (p0) cc_final: 0.7740 (t0) REVERT: B 23 ARG cc_start: 0.7356 (mtm-85) cc_final: 0.6924 (mtp85) REVERT: B 234 GLU cc_start: 0.6250 (OUTLIER) cc_final: 0.6004 (pp20) REVERT: B 238 ILE cc_start: 0.5909 (mt) cc_final: 0.5650 (mt) REVERT: B 712 LEU cc_start: 0.7562 (tp) cc_final: 0.7326 (mt) REVERT: B 755 MET cc_start: 0.4873 (ptm) cc_final: 0.4598 (ptp) REVERT: B 979 MET cc_start: 0.5778 (ptp) cc_final: 0.5465 (ptp) REVERT: B 1083 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6518 (mt) REVERT: B 1102 MET cc_start: 0.6810 (mmt) cc_final: 0.6473 (mmm) outliers start: 11 outliers final: 8 residues processed: 162 average time/residue: 0.1063 time to fit residues: 24.8032 Evaluate side-chains 143 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain B residue 844 ASP Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 1083 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 41 optimal weight: 0.8980 chunk 110 optimal weight: 0.0050 chunk 86 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 1 optimal weight: 30.0000 chunk 117 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 78 optimal weight: 0.0570 overall best weight: 0.7916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 ASN ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN B 725 GLN B 800 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.231290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.191975 restraints weight = 18330.504| |-----------------------------------------------------------------------------| r_work (start): 0.4544 rms_B_bonded: 2.28 r_work: 0.4409 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12691 Z= 0.147 Angle : 0.613 8.174 17491 Z= 0.330 Chirality : 0.042 0.182 1970 Planarity : 0.004 0.038 2057 Dihedral : 19.320 89.078 2319 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.71 % Allowed : 11.99 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -0.52 (0.22), residues: 1400 helix: 0.61 (0.20), residues: 729 sheet: -1.26 (0.41), residues: 156 loop : -1.35 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 231 TYR 0.020 0.002 TYR A 19 PHE 0.025 0.002 PHE A 86 TRP 0.049 0.002 TRP B1105 HIS 0.006 0.001 HIS B1068 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (12691) covalent geometry : angle 0.61341 / 0.33 (17491) hydrogen bonds : bond 0.04331 / 4.52 ( 594) hydrogen bonds : angle 5.02710 / 6.39 ( 1686) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2255 (tpp) cc_final: 0.0688 (ptt) REVERT: A 14 ASN cc_start: 0.8021 (p0) cc_final: 0.7721 (t0) REVERT: B 23 ARG cc_start: 0.7508 (mtm-85) cc_final: 0.6995 (mtp85) REVERT: B 238 ILE cc_start: 0.5985 (mt) cc_final: 0.5750 (mt) REVERT: B 712 LEU cc_start: 0.7699 (tp) cc_final: 0.7430 (mt) REVERT: B 860 ARG cc_start: 0.7406 (mtp180) cc_final: 0.7204 (mtm180) REVERT: B 900 ASP cc_start: 0.6911 (t0) cc_final: 0.6259 (t0) REVERT: B 979 MET cc_start: 0.5721 (ptp) cc_final: 0.5504 (ptp) REVERT: B 1070 TRP cc_start: 0.5359 (t60) cc_final: 0.4892 (t60) REVERT: B 1102 MET cc_start: 0.6744 (mmt) cc_final: 0.6364 (mmm) outliers start: 20 outliers final: 9 residues processed: 176 average time/residue: 0.1080 time to fit residues: 26.8492 Evaluate side-chains 153 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 844 ASP Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 1108 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 118 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 HIS ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 989 ASN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1067 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.222067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.180132 restraints weight = 18645.520| |-----------------------------------------------------------------------------| r_work (start): 0.4411 rms_B_bonded: 2.60 r_work: 0.4269 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 12691 Z= 0.298 Angle : 0.829 10.360 17491 Z= 0.434 Chirality : 0.051 0.278 1970 Planarity : 0.007 0.075 2057 Dihedral : 19.501 113.667 2319 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.74 % Allowed : 12.16 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -1.36 (0.21), residues: 1400 helix: -0.08 (0.19), residues: 726 sheet: -1.75 (0.40), residues: 145 loop : -1.70 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG B 595 TYR 0.034 0.003 TYR B 842 PHE 0.027 0.003 PHE B1082 TRP 0.048 0.003 TRP B1105 HIS 0.010 0.003 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.30 (12691) covalent geometry : angle 0.82922 / 0.43 (17491) hydrogen bonds : bond 0.05208 / 5.26 ( 594) hydrogen bonds : angle 5.46611 / 6.98 ( 1686) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2443 (tpp) cc_final: 0.0687 (ptt) REVERT: A 14 ASN cc_start: 0.7964 (p0) cc_final: 0.7740 (t0) REVERT: A 78 ARG cc_start: 0.5756 (mmt-90) cc_final: 0.4841 (mmt180) REVERT: A 231 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.5896 (mp-120) REVERT: B 23 ARG cc_start: 0.7928 (mtm-85) cc_final: 0.7660 (mtm180) REVERT: B 72 LEU cc_start: 0.6396 (mt) cc_final: 0.6172 (mt) REVERT: B 120 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7688 (mm) REVERT: B 729 HIS cc_start: 0.6551 (m-70) cc_final: 0.6166 (m90) REVERT: B 790 ARG cc_start: 0.7018 (tmm-80) cc_final: 0.6671 (tmm-80) REVERT: B 1102 MET cc_start: 0.6899 (mmt) cc_final: 0.6461 (mmm) outliers start: 32 outliers final: 17 residues processed: 183 average time/residue: 0.1269 time to fit residues: 32.7215 Evaluate side-chains 156 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 231 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 1108 THR Chi-restraints excluded: chain B residue 1121 VAL Chi-restraints excluded: chain B residue 1137 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 119 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 HIS B 255 ASN ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1026 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.225931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.184995 restraints weight = 18425.243| |-----------------------------------------------------------------------------| r_work (start): 0.4466 rms_B_bonded: 2.60 r_work: 0.4321 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12691 Z= 0.163 Angle : 0.669 8.606 17491 Z= 0.352 Chirality : 0.044 0.213 1970 Planarity : 0.005 0.048 2057 Dihedral : 19.429 113.550 2319 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.88 % Allowed : 15.58 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -1.10 (0.22), residues: 1400 helix: 0.20 (0.19), residues: 730 sheet: -1.83 (0.38), residues: 156 loop : -1.62 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 106 TYR 0.025 0.002 TYR B1099 PHE 0.018 0.002 PHE B 718 TRP 0.056 0.002 TRP B1105 HIS 0.014 0.002 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (12691) covalent geometry : angle 0.66926 / 0.35 (17491) hydrogen bonds : bond 0.04215 / 4.35 ( 594) hydrogen bonds : angle 5.19300 / 6.53 ( 1686) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2442 (tpp) cc_final: 0.0734 (ptt) REVERT: A 14 ASN cc_start: 0.8001 (p0) cc_final: 0.7738 (t0) REVERT: A 78 ARG cc_start: 0.5813 (mmt-90) cc_final: 0.4869 (mmt180) REVERT: B 241 SER cc_start: 0.6401 (p) cc_final: 0.6133 (p) REVERT: B 381 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8082 (mt) REVERT: B 1082 PHE cc_start: 0.6635 (t80) cc_final: 0.6380 (t80) REVERT: B 1102 MET cc_start: 0.6851 (mmt) cc_final: 0.6375 (mmm) outliers start: 22 outliers final: 16 residues processed: 166 average time/residue: 0.1334 time to fit residues: 31.0041 Evaluate side-chains 146 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 946 TRP Chi-restraints excluded: chain B residue 1104 ASP Chi-restraints excluded: chain B residue 1108 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 121 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 95 optimal weight: 0.2980 chunk 75 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 34 optimal weight: 0.0040 chunk 47 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 3 optimal weight: 50.0000 chunk 82 optimal weight: 2.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 HIS ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1026 GLN ** B1064 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 = 0.4871 r_free = 0.4871 target = 0.227659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.186427 restraints weight = 18414.636| |-----------------------------------------------------------------------------| r_work (start): 0.4492 rms_B_bonded: 2.37 r_work: 0.4357 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12691 Z= 0.141 Angle : 0.640 8.350 17491 Z= 0.338 Chirality : 0.044 0.309 1970 Planarity : 0.004 0.044 2057 Dihedral : 19.326 108.708 2319 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.71 % Allowed : 15.92 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -0.97 (0.22), residues: 1400 helix: 0.33 (0.19), residues: 738 sheet: -1.79 (0.39), residues: 158 loop : -1.61 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1141 TYR 0.021 0.002 TYR A 19 PHE 0.017 0.001 PHE B 718 TRP 0.046 0.002 TRP B1105 HIS 0.014 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (12691) covalent geometry : angle 0.63980 / 0.34 (17491) hydrogen bonds : bond 0.03949 / 4.10 ( 594) hydrogen bonds : angle 5.08446 / 6.31 ( 1686) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2570 (tpp) cc_final: 0.0842 (ptt) REVERT: A 14 ASN cc_start: 0.7975 (p0) cc_final: 0.7748 (t0) REVERT: A 78 ARG cc_start: 0.5725 (mmt-90) cc_final: 0.4807 (mmt180) REVERT: B 120 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7620 (mm) REVERT: B 613 ILE cc_start: 0.8150 (mt) cc_final: 0.7820 (pt) REVERT: B 922 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6976 (tp30) REVERT: B 1102 MET cc_start: 0.6872 (mmt) cc_final: 0.6351 (mmm) outliers start: 20 outliers final: 14 residues processed: 156 average time/residue: 0.1213 time to fit residues: 26.5927 Evaluate side-chains 141 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 946 TRP Chi-restraints excluded: chain B residue 1104 ASP Chi-restraints excluded: chain B residue 1108 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 34 optimal weight: 0.0010 chunk 127 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 130 optimal weight: 0.2980 chunk 48 optimal weight: 4.9990 chunk 129 optimal weight: 0.1980 chunk 121 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 63 optimal weight: 0.0570 chunk 76 optimal weight: 0.7980 overall best weight: 0.2704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1026 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1067 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4949 r_free = 0.4949 target = 0.230491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.193695 restraints weight = 18233.876| |-----------------------------------------------------------------------------| r_work (start): 0.4581 rms_B_bonded: 2.30 r_work: 0.4440 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12691 Z= 0.128 Angle : 0.630 8.266 17491 Z= 0.332 Chirality : 0.043 0.191 1970 Planarity : 0.004 0.042 2057 Dihedral : 19.227 106.148 2319 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.80 % Allowed : 16.10 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -0.74 (0.22), residues: 1400 helix: 0.55 (0.19), residues: 726 sheet: -1.73 (0.39), residues: 158 loop : -1.50 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1160 TYR 0.017 0.001 TYR A 19 PHE 0.015 0.001 PHE B 718 TRP 0.027 0.001 TRP B1105 HIS 0.005 0.001 HIS B1068 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (12691) covalent geometry : angle 0.62996 / 0.33 (17491) hydrogen bonds : bond 0.03753 / 3.90 ( 594) hydrogen bonds : angle 4.98141 / 6.16 ( 1686) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2622 (tpp) cc_final: 0.0898 (ptt) REVERT: A 14 ASN cc_start: 0.7967 (p0) cc_final: 0.7736 (t0) REVERT: A 78 ARG cc_start: 0.5687 (mmt-90) cc_final: 0.4873 (mpt180) REVERT: B 613 ILE cc_start: 0.7905 (mt) cc_final: 0.7703 (pt) REVERT: B 729 HIS cc_start: 0.6424 (m-70) cc_final: 0.5979 (m90) REVERT: B 1082 PHE cc_start: 0.6567 (t80) cc_final: 0.6364 (t80) REVERT: B 1102 MET cc_start: 0.6797 (mmt) cc_final: 0.6298 (mmm) outliers start: 21 outliers final: 15 residues processed: 158 average time/residue: 0.1251 time to fit residues: 28.2213 Evaluate side-chains 145 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 617 GLU Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 946 TRP Chi-restraints excluded: chain B residue 1104 ASP Chi-restraints excluded: chain B residue 1108 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 42 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 HIS B1026 GLN ** B1064 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 = 0.4927 r_free = 0.4927 target = 0.227961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.190613 restraints weight = 18124.654| |-----------------------------------------------------------------------------| r_work (start): 0.4552 rms_B_bonded: 2.18 r_work: 0.4405 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12691 Z= 0.166 Angle : 0.663 8.793 17491 Z= 0.346 Chirality : 0.044 0.252 1970 Planarity : 0.005 0.045 2057 Dihedral : 19.188 106.743 2319 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.54 % Allowed : 17.04 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -0.84 (0.22), residues: 1400 helix: 0.46 (0.19), residues: 735 sheet: -1.78 (0.39), residues: 158 loop : -1.56 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 231 TYR 0.039 0.002 TYR B 769 PHE 0.017 0.002 PHE B 718 TRP 0.036 0.002 TRP B1105 HIS 0.005 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (12691) covalent geometry : angle 0.66265 / 0.35 (17491) hydrogen bonds : bond 0.03949 / 4.06 ( 594) hydrogen bonds : angle 5.02811 / 6.23 ( 1686) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2571 (tpp) cc_final: 0.0894 (ptt) REVERT: A 21 GLN cc_start: 0.7238 (tt0) cc_final: 0.6620 (mt0) REVERT: A 78 ARG cc_start: 0.5783 (mmt-90) cc_final: 0.4841 (mmt180) REVERT: A 217 MET cc_start: 0.6780 (ptt) cc_final: 0.6535 (ptt) REVERT: B 241 SER cc_start: 0.6773 (p) cc_final: 0.6452 (p) REVERT: B 613 ILE cc_start: 0.7850 (mt) cc_final: 0.7644 (pt) REVERT: B 1021 SER cc_start: 0.6085 (OUTLIER) cc_final: 0.5673 (m) REVERT: B 1102 MET cc_start: 0.6872 (mmt) cc_final: 0.6371 (mmm) outliers start: 18 outliers final: 15 residues processed: 144 average time/residue: 0.1183 time to fit residues: 23.9443 Evaluate side-chains 143 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 617 GLU Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 1.9990 chunk 5 optimal weight: 40.0000 chunk 31 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 122 optimal weight: 0.0970 chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 HIS ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 HIS ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1026 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.227929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.190734 restraints weight = 18265.252| |-----------------------------------------------------------------------------| r_work (start): 0.4551 rms_B_bonded: 2.17 r_work: 0.4404 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12691 Z= 0.165 Angle : 0.674 9.959 17491 Z= 0.353 Chirality : 0.045 0.396 1970 Planarity : 0.005 0.046 2057 Dihedral : 19.161 105.743 2319 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.71 % Allowed : 17.21 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -0.84 (0.22), residues: 1400 helix: 0.46 (0.19), residues: 721 sheet: -1.83 (0.38), residues: 159 loop : -1.49 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 345 TYR 0.026 0.002 TYR B 769 PHE 0.016 0.002 PHE B 718 TRP 0.040 0.002 TRP B1105 HIS 0.030 0.002 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (12691) covalent geometry : angle 0.67447 / 0.35 (17491) hydrogen bonds : bond 0.03908 / 4.04 ( 594) hydrogen bonds : angle 5.02931 / 6.24 ( 1686) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2480 (tpp) cc_final: 0.0830 (ptt) REVERT: A 21 GLN cc_start: 0.7287 (tt0) cc_final: 0.6685 (mt0) REVERT: A 78 ARG cc_start: 0.5746 (mmt-90) cc_final: 0.4986 (mmt180) REVERT: A 217 MET cc_start: 0.6920 (ptt) cc_final: 0.6661 (ptt) REVERT: B 241 SER cc_start: 0.6855 (p) cc_final: 0.6530 (p) REVERT: B 613 ILE cc_start: 0.7935 (mt) cc_final: 0.7719 (pt) REVERT: B 729 HIS cc_start: 0.6418 (m-70) cc_final: 0.6077 (m90) REVERT: B 1021 SER cc_start: 0.6075 (OUTLIER) cc_final: 0.5639 (m) REVERT: B 1102 MET cc_start: 0.6773 (mmt) cc_final: 0.6270 (mmm) outliers start: 20 outliers final: 16 residues processed: 146 average time/residue: 0.1138 time to fit residues: 23.4589 Evaluate side-chains 143 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 617 GLU Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 756 HIS Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 946 TRP Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 109 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 ASN ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 HIS B1026 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4935 r_free = 0.4935 target = 0.228680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.191656 restraints weight = 18156.667| |-----------------------------------------------------------------------------| r_work (start): 0.4563 rms_B_bonded: 2.22 r_work: 0.4419 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12691 Z= 0.146 Angle : 0.658 9.466 17491 Z= 0.344 Chirality : 0.044 0.321 1970 Planarity : 0.005 0.044 2057 Dihedral : 19.133 104.214 2319 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.28 % Allowed : 17.29 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -0.84 (0.22), residues: 1400 helix: 0.48 (0.19), residues: 724 sheet: -1.85 (0.38), residues: 159 loop : -1.52 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 70 TYR 0.024 0.002 TYR B 769 PHE 0.015 0.002 PHE B 718 TRP 0.036 0.002 TRP B1105 HIS 0.021 0.002 HIS B 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (12691) covalent geometry : angle 0.65798 / 0.34 (17491) hydrogen bonds : bond 0.03852 / 3.98 ( 594) hydrogen bonds : angle 5.00609 / 6.21 ( 1686) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2932.26 seconds wall clock time: 51 minutes 3.75 seconds (3063.75 seconds total)