Starting phenix.real_space_refine on Fri Jul 3 05:35:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vxy_43643/07_2026/8vxy_43643.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vxy_43643/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vxy_43643/07_2026/8vxy_43643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vxy_43643/07_2026/8vxy_43643.map" model { file = "/net/cci-nas-00/data/ceres_data/8vxy_43643/07_2026/8vxy_43643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vxy_43643/07_2026/8vxy_43643.cif" } 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-dev-6108/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: 2.54, per 1000 atoms: 0.21 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: 0.93 Conformation dependent library (CDL) restraints added in 528.9 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: 1.13 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: 2.32 Time building geometry restraints manager: 1.19 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: 1.060 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.870 Find NCS groups from input model: 0.140 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.370 ------------------------------------------------------------------------------- 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 : 0.844 18.565 17491 Z= 0.522 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 0.84414 / 0.52 (17491) hydrogen bonds : bond 0.21320 / 22.41 ( 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 : 0.290 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: 0.1287 time to fit residues: 45.3502 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 : 0.423 ------------------------------------------------------------------------------- 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 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 HIS ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 ASN B 502 GLN B 684 HIS B 772 ASN B 959 GLN B1026 GLN B1068 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.228939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.192779 restraints weight = 18286.535| |-----------------------------------------------------------------------------| r_work (start): 0.4568 rms_B_bonded: 2.27 r_work: 0.4415 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12691 Z= 0.155 Angle : 0.679 9.196 17491 Z= 0.364 Chirality : 0.044 0.209 1970 Planarity : 0.005 0.044 2057 Dihedral : 19.382 89.135 2319 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.20 % Allowed : 7.79 % Favored : 91.01 % 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: -0.42 (0.22), residues: 1400 helix: 0.72 (0.20), residues: 719 sheet: -1.08 (0.45), residues: 136 loop : -1.36 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 106 TYR 0.019 0.002 TYR A 19 PHE 0.020 0.002 PHE B 199 TRP 0.032 0.002 TRP B 797 HIS 0.021 0.002 HIS B1068 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 (12691) covalent geometry : angle 0.67905 / 0.36 (17491) hydrogen bonds : bond 0.05401 / 5.57 ( 594) hydrogen bonds : angle 5.50760 / 7.16 ( 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 205 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2206 (tpp) cc_final: 0.0578 (ptt) REVERT: A 14 ASN cc_start: 0.7948 (p0) cc_final: 0.7633 (t0) REVERT: B 23 ARG cc_start: 0.7402 (mtm-85) cc_final: 0.6970 (mtp85) REVERT: B 238 ILE cc_start: 0.5965 (mt) cc_final: 0.5743 (mt) REVERT: B 755 MET cc_start: 0.4880 (ptm) cc_final: 0.4585 (ptp) REVERT: B 827 ASP cc_start: 0.8257 (m-30) cc_final: 0.7954 (m-30) REVERT: B 1102 MET cc_start: 0.6693 (mmt) cc_final: 0.6421 (mmm) outliers start: 14 outliers final: 2 residues processed: 198 average time/residue: 0.0981 time to fit residues: 28.1109 Evaluate side-chains 144 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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: 0.9990 chunk 45 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 chunk 143 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.227225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.190381 restraints weight = 18560.977| |-----------------------------------------------------------------------------| r_work (start): 0.4535 rms_B_bonded: 2.29 r_work: 0.4394 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12691 Z= 0.152 Angle : 0.641 11.122 17491 Z= 0.344 Chirality : 0.043 0.206 1970 Planarity : 0.004 0.041 2057 Dihedral : 19.349 88.750 2319 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.03 % Allowed : 10.53 % Favored : 88.44 % 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: 0.66 (0.20), residues: 715 sheet: -1.29 (0.43), residues: 146 loop : -1.36 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 595 TYR 0.017 0.002 TYR B 445 PHE 0.025 0.002 PHE A 86 TRP 0.041 0.002 TRP B1105 HIS 0.003 0.001 HIS B 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (12691) covalent geometry : angle 0.64079 / 0.34 (17491) hydrogen bonds : bond 0.04864 / 5.00 ( 594) hydrogen bonds : angle 5.22662 / 6.69 ( 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 167 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2241 (tpp) cc_final: 0.0624 (ptt) REVERT: A 14 ASN cc_start: 0.7967 (p0) cc_final: 0.7679 (t0) REVERT: B 23 ARG cc_start: 0.7451 (mtm-85) cc_final: 0.6982 (mtp85) REVERT: B 234 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.6069 (pp20) REVERT: B 238 ILE cc_start: 0.5920 (mt) cc_final: 0.5684 (mt) REVERT: B 712 LEU cc_start: 0.7619 (tp) cc_final: 0.7336 (mt) REVERT: B 755 MET cc_start: 0.5005 (ptm) cc_final: 0.4660 (ptp) REVERT: B 827 ASP cc_start: 0.8236 (m-30) cc_final: 0.7871 (m-30) REVERT: B 900 ASP cc_start: 0.7041 (t0) cc_final: 0.6841 (t0) REVERT: B 979 MET cc_start: 0.5796 (ptp) cc_final: 0.5472 (ptp) REVERT: B 1102 MET cc_start: 0.6842 (mmt) cc_final: 0.6498 (mmm) outliers start: 12 outliers final: 10 residues processed: 163 average time/residue: 0.0991 time to fit residues: 23.0676 Evaluate side-chains 155 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 407 THR 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: 0.9990 chunk 110 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 1 optimal weight: 20.0000 chunk 117 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 ASN ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN B 989 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.227457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.186330 restraints weight = 18435.686| |-----------------------------------------------------------------------------| r_work (start): 0.4490 rms_B_bonded: 2.37 r_work: 0.4351 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12691 Z= 0.181 Angle : 0.656 7.854 17491 Z= 0.351 Chirality : 0.044 0.195 1970 Planarity : 0.005 0.045 2057 Dihedral : 19.368 89.242 2319 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.88 % Allowed : 11.47 % Favored : 86.64 % 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: -0.75 (0.22), residues: 1400 helix: 0.52 (0.19), residues: 718 sheet: -1.43 (0.41), residues: 157 loop : -1.55 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 31 TYR 0.020 0.002 TYR A 19 PHE 0.027 0.002 PHE A 86 TRP 0.048 0.002 TRP B1105 HIS 0.010 0.002 HIS B1068 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (12691) covalent geometry : angle 0.65621 / 0.35 (17491) hydrogen bonds : bond 0.04445 / 4.54 ( 594) hydrogen bonds : angle 5.13772 / 6.55 ( 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 187 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2226 (tpp) cc_final: 0.0564 (ptt) REVERT: A 14 ASN cc_start: 0.7984 (p0) cc_final: 0.7699 (t0) REVERT: A 230 ASN cc_start: 0.7168 (OUTLIER) cc_final: 0.5613 (t0) REVERT: B 23 ARG cc_start: 0.7684 (mtm-85) cc_final: 0.7094 (mtp85) REVERT: B 597 LEU cc_start: 0.4624 (OUTLIER) cc_final: 0.4039 (pp) REVERT: B 900 ASP cc_start: 0.6909 (t0) cc_final: 0.6187 (t0) REVERT: B 1070 TRP cc_start: 0.5461 (t60) cc_final: 0.5039 (t60) REVERT: B 1102 MET cc_start: 0.6795 (mmt) cc_final: 0.6390 (mmm) outliers start: 22 outliers final: 12 residues processed: 182 average time/residue: 0.1120 time to fit residues: 28.6001 Evaluate side-chains 156 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 844 ASP Chi-restraints excluded: chain B residue 1108 THR Chi-restraints excluded: chain B residue 1137 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 118 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 124 optimal weight: 0.4980 chunk 57 optimal weight: 0.0980 chunk 134 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.227963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.187380 restraints weight = 18518.797| |-----------------------------------------------------------------------------| r_work (start): 0.4502 rms_B_bonded: 2.35 r_work: 0.4362 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.3489 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= 0.160 Angle : 0.634 7.832 17491 Z= 0.338 Chirality : 0.043 0.244 1970 Planarity : 0.004 0.043 2057 Dihedral : 19.346 90.440 2319 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.48 % Allowed : 12.93 % Favored : 84.59 % 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: -0.81 (0.22), residues: 1400 helix: 0.47 (0.19), residues: 726 sheet: -1.57 (0.39), residues: 157 loop : -1.57 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 106 TYR 0.018 0.002 TYR B 58 PHE 0.020 0.002 PHE B1082 TRP 0.058 0.002 TRP B1105 HIS 0.005 0.001 HIS B1097 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (12691) covalent geometry : angle 0.63405 / 0.34 (17491) hydrogen bonds : bond 0.04221 / 4.33 ( 594) hydrogen bonds : angle 5.06544 / 6.42 ( 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 183 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2433 (tpp) cc_final: 0.0746 (ptt) REVERT: A 14 ASN cc_start: 0.7974 (p0) cc_final: 0.7707 (t0) REVERT: A 230 ASN cc_start: 0.7181 (OUTLIER) cc_final: 0.5642 (t0) REVERT: B 23 ARG cc_start: 0.7652 (mtm-85) cc_final: 0.7181 (mtp180) REVERT: B 381 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8146 (mt) REVERT: B 555 LYS cc_start: 0.6600 (mtpp) cc_final: 0.6274 (mtpp) REVERT: B 1070 TRP cc_start: 0.5562 (t60) cc_final: 0.5299 (t60) REVERT: B 1102 MET cc_start: 0.6850 (mmt) cc_final: 0.6425 (mmm) outliers start: 29 outliers final: 14 residues processed: 176 average time/residue: 0.1047 time to fit residues: 26.3698 Evaluate side-chains 154 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain B residue 48 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 519 VAL Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 844 ASP Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 1104 ASP Chi-restraints excluded: chain B residue 1108 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 119 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 6 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 HIS A 231 GLN B 255 ASN ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4823 r_free = 0.4823 target = 0.222325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.180531 restraints weight = 18577.033| |-----------------------------------------------------------------------------| r_work (start): 0.4426 rms_B_bonded: 2.52 r_work: 0.4277 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 12691 Z= 0.285 Angle : 0.779 8.815 17491 Z= 0.410 Chirality : 0.049 0.228 1970 Planarity : 0.006 0.060 2057 Dihedral : 19.423 92.055 2319 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.65 % Allowed : 14.21 % Favored : 83.13 % 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: -1.35 (0.22), residues: 1400 helix: -0.03 (0.19), residues: 735 sheet: -1.86 (0.38), residues: 157 loop : -1.72 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 595 TYR 0.031 0.003 TYR B 445 PHE 0.028 0.003 PHE B1082 TRP 0.044 0.003 TRP B1105 HIS 0.009 0.002 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.29 (12691) covalent geometry : angle 0.77891 / 0.41 (17491) hydrogen bonds : bond 0.04894 / 4.96 ( 594) hydrogen bonds : angle 5.39545 / 6.83 ( 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 176 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2545 (tpp) cc_final: 0.0736 (ptt) REVERT: A 14 ASN cc_start: 0.7982 (p0) cc_final: 0.7709 (t0) REVERT: A 78 ARG cc_start: 0.5842 (mmt-90) cc_final: 0.4863 (mmt180) REVERT: A 231 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.5917 (mp-120) REVERT: B 234 GLU cc_start: 0.6739 (pp20) cc_final: 0.6374 (pp20) REVERT: B 241 SER cc_start: 0.6783 (p) cc_final: 0.6515 (p) REVERT: B 555 LYS cc_start: 0.6738 (mtpp) cc_final: 0.6380 (mtpp) REVERT: B 900 ASP cc_start: 0.7125 (t0) cc_final: 0.6723 (t0) REVERT: B 1021 SER cc_start: 0.6130 (OUTLIER) cc_final: 0.5674 (m) REVERT: B 1036 ILE cc_start: 0.5743 (OUTLIER) cc_final: 0.5411 (mm) REVERT: B 1102 MET cc_start: 0.6916 (mmt) cc_final: 0.6376 (mmm) outliers start: 31 outliers final: 18 residues processed: 167 average time/residue: 0.0999 time to fit residues: 23.8192 Evaluate side-chains 151 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 214 ILE Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 449 ILE 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 709 VAL Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1036 ILE 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: 4.9990 chunk 75 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 3 optimal weight: 50.0000 chunk 82 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1026 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.226754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.185128 restraints weight = 18452.825| |-----------------------------------------------------------------------------| r_work (start): 0.4480 rms_B_bonded: 2.36 r_work: 0.4345 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12691 Z= 0.152 Angle : 0.658 10.673 17491 Z= 0.349 Chirality : 0.043 0.185 1970 Planarity : 0.005 0.048 2057 Dihedral : 19.339 89.951 2319 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.71 % Allowed : 16.52 % Favored : 81.76 % 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: -1.03 (0.22), residues: 1400 helix: 0.30 (0.19), residues: 734 sheet: -1.84 (0.39), residues: 157 loop : -1.64 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 500 TYR 0.018 0.002 TYR B 58 PHE 0.017 0.002 PHE B 718 TRP 0.036 0.002 TRP B1105 HIS 0.005 0.001 HIS B 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (12691) covalent geometry : angle 0.65805 / 0.35 (17491) hydrogen bonds : bond 0.04101 / 4.21 ( 594) hydrogen bonds : angle 5.13383 / 6.43 ( 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 162 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2480 (tpp) cc_final: 0.0717 (ptt) REVERT: A 31 MET cc_start: 0.5640 (mtt) cc_final: 0.5345 (ptp) REVERT: A 78 ARG cc_start: 0.5750 (mmt-90) cc_final: 0.4773 (mmt180) REVERT: A 217 MET cc_start: 0.6704 (ptt) cc_final: 0.6497 (ptt) REVERT: A 231 GLN cc_start: 0.6995 (mp10) cc_final: 0.6029 (mp10) REVERT: B 234 GLU cc_start: 0.6564 (pp20) cc_final: 0.6270 (pp20) REVERT: B 241 SER cc_start: 0.6755 (p) cc_final: 0.6453 (p) REVERT: B 900 ASP cc_start: 0.7268 (t0) cc_final: 0.6797 (t70) REVERT: B 1102 MET cc_start: 0.6914 (mmt) cc_final: 0.6340 (mmm) outliers start: 20 outliers final: 16 residues processed: 158 average time/residue: 0.1113 time to fit residues: 24.9454 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 : 0.402 ------------------------------------------------------------------------------- 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 214 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 357 THR 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 712 LEU Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain B residue 1072 THR 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: 0.0980 chunk 127 optimal weight: 3.9990 chunk 15 optimal weight: 0.0000 chunk 130 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 137 optimal weight: 0.0980 chunk 50 optimal weight: 7.9990 chunk 63 optimal weight: 0.0370 chunk 76 optimal weight: 0.9980 overall best weight: 0.2462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1026 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.231233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.195094 restraints weight = 18228.208| |-----------------------------------------------------------------------------| r_work (start): 0.4597 rms_B_bonded: 2.25 r_work: 0.4453 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12691 Z= 0.130 Angle : 0.642 10.139 17491 Z= 0.338 Chirality : 0.044 0.281 1970 Planarity : 0.005 0.048 2057 Dihedral : 19.207 89.754 2319 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.20 % Allowed : 16.95 % Favored : 81.85 % 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: -0.81 (0.22), residues: 1400 helix: 0.49 (0.19), residues: 729 sheet: -1.66 (0.39), residues: 159 loop : -1.59 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 500 TYR 0.014 0.001 TYR B 445 PHE 0.016 0.001 PHE B 718 TRP 0.039 0.002 TRP B1105 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (12691) covalent geometry : angle 0.64153 / 0.34 (17491) hydrogen bonds : bond 0.03885 / 4.00 ( 594) hydrogen bonds : angle 5.02995 / 6.23 ( 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 159 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2453 (tpp) cc_final: 0.0751 (ptt) REVERT: A 31 MET cc_start: 0.5586 (mtt) cc_final: 0.5311 (ptp) REVERT: A 78 ARG cc_start: 0.5740 (mmt-90) cc_final: 0.4958 (mmt180) REVERT: A 217 MET cc_start: 0.7065 (ptt) cc_final: 0.6789 (ptt) REVERT: B 729 HIS cc_start: 0.6351 (m-70) cc_final: 0.5916 (m90) REVERT: B 1102 MET cc_start: 0.6730 (mmt) cc_final: 0.6339 (mmm) outliers start: 14 outliers final: 13 residues processed: 154 average time/residue: 0.1254 time to fit residues: 27.3296 Evaluate side-chains 142 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 357 THR 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 567 GLU Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 946 TRP 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: 3.9990 chunk 134 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 HIS ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** 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 = 0.4906 r_free = 0.4906 target = 0.225253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.187820 restraints weight = 18161.122| |-----------------------------------------------------------------------------| r_work (start): 0.4528 rms_B_bonded: 2.13 r_work: 0.4374 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12691 Z= 0.214 Angle : 0.718 10.499 17491 Z= 0.376 Chirality : 0.046 0.280 1970 Planarity : 0.005 0.052 2057 Dihedral : 19.209 89.127 2319 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.88 % Allowed : 16.95 % Favored : 81.16 % 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: -1.08 (0.22), residues: 1400 helix: 0.26 (0.19), residues: 734 sheet: -1.79 (0.39), residues: 159 loop : -1.71 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 500 TYR 0.040 0.003 TYR B 769 PHE 0.018 0.002 PHE B1082 TRP 0.031 0.002 TRP B1105 HIS 0.008 0.002 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 (12691) covalent geometry : angle 0.71779 / 0.38 (17491) hydrogen bonds : bond 0.04307 / 4.41 ( 594) hydrogen bonds : angle 5.18039 / 6.47 ( 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 153 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2417 (tpp) cc_final: 0.0746 (ptt) REVERT: A 21 GLN cc_start: 0.7363 (tt0) cc_final: 0.6611 (mt0) REVERT: A 31 MET cc_start: 0.5618 (mtt) cc_final: 0.5342 (ptp) REVERT: A 78 ARG cc_start: 0.5827 (mmt-90) cc_final: 0.5059 (mmt180) REVERT: A 217 MET cc_start: 0.6935 (ptt) cc_final: 0.6734 (ptt) REVERT: B 1021 SER cc_start: 0.6146 (OUTLIER) cc_final: 0.5704 (m) REVERT: B 1102 MET cc_start: 0.6697 (mmt) cc_final: 0.6261 (mmm) outliers start: 22 outliers final: 13 residues processed: 147 average time/residue: 0.1048 time to fit residues: 22.0264 Evaluate side-chains 137 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain B residue 254 LEU 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 567 GLU 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 888 ASP 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 87 optimal weight: 0.8980 chunk 5 optimal weight: 30.0000 chunk 31 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 49 optimal weight: 0.0270 chunk 134 optimal weight: 0.5980 chunk 122 optimal weight: 0.0070 chunk 42 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 HIS ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4941 r_free = 0.4941 target = 0.229295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.192483 restraints weight = 18264.322| |-----------------------------------------------------------------------------| r_work (start): 0.4569 rms_B_bonded: 2.31 r_work: 0.4429 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12691 Z= 0.136 Angle : 0.658 10.472 17491 Z= 0.345 Chirality : 0.044 0.292 1970 Planarity : 0.005 0.051 2057 Dihedral : 19.157 89.892 2319 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.94 % Allowed : 17.81 % Favored : 81.25 % 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: -0.89 (0.22), residues: 1400 helix: 0.44 (0.20), residues: 727 sheet: -1.80 (0.38), residues: 159 loop : -1.59 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 484 TYR 0.025 0.002 TYR B 769 PHE 0.015 0.002 PHE B 718 TRP 0.053 0.002 TRP B1105 HIS 0.036 0.002 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (12691) covalent geometry : angle 0.65822 / 0.35 (17491) hydrogen bonds : bond 0.03896 / 4.01 ( 594) hydrogen bonds : angle 5.06441 / 6.30 ( 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 144 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2537 (tpp) cc_final: 0.0869 (ptt) REVERT: A 21 GLN cc_start: 0.7108 (tt0) cc_final: 0.6751 (mt0) REVERT: A 31 MET cc_start: 0.5735 (mtt) cc_final: 0.5484 (ptp) REVERT: A 78 ARG cc_start: 0.5764 (mmt-90) cc_final: 0.4968 (mmt180) REVERT: A 217 MET cc_start: 0.6880 (ptt) cc_final: 0.6669 (ptt) REVERT: B 234 GLU cc_start: 0.6458 (pp20) cc_final: 0.6117 (pp20) REVERT: B 1102 MET cc_start: 0.6558 (mmt) cc_final: 0.6157 (mmm) outliers start: 11 outliers final: 10 residues processed: 141 average time/residue: 0.0999 time to fit residues: 20.1249 Evaluate side-chains 136 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 357 THR 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 567 GLU Chi-restraints excluded: chain B residue 946 TRP 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: 2.9990 chunk 55 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 110 optimal weight: 0.0770 chunk 53 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 15 optimal weight: 0.0000 chunk 103 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 overall best weight: 0.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 HIS ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** 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 = 0.4943 r_free = 0.4943 target = 0.229593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.192914 restraints weight = 18171.231| |-----------------------------------------------------------------------------| r_work (start): 0.4574 rms_B_bonded: 2.31 r_work: 0.4434 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12691 Z= 0.135 Angle : 0.650 10.641 17491 Z= 0.340 Chirality : 0.043 0.233 1970 Planarity : 0.005 0.043 2057 Dihedral : 19.109 89.959 2319 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.94 % Allowed : 17.98 % 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: -0.86 (0.22), residues: 1400 helix: 0.46 (0.19), residues: 733 sheet: -1.84 (0.39), residues: 158 loop : -1.58 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 595 TYR 0.025 0.002 TYR B 769 PHE 0.014 0.001 PHE B 718 TRP 0.034 0.002 TRP B1105 HIS 0.039 0.002 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (12691) covalent geometry : angle 0.65006 / 0.34 (17491) hydrogen bonds : bond 0.03826 / 3.95 ( 594) hydrogen bonds : angle 5.00880 / 6.23 ( 1686) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2718.76 seconds wall clock time: 47 minutes 12.86 seconds (2832.86 seconds total)