Starting phenix.real_space_refine on Wed Jul 30 12:28:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vxy_43643/07_2025/8vxy_43643.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vxy_43643/07_2025/8vxy_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_2025/8vxy_43643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vxy_43643/07_2025/8vxy_43643.map" model { file = "/net/cci-nas-00/data/ceres_data/8vxy_43643/07_2025/8vxy_43643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vxy_43643/07_2025/8vxy_43643.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.35, per 1000 atoms: 0.60 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: 3.00 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 4.14 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: 5.78 Time building geometry restraints manager: 3.56 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 - 0.090: 1853 0.090 - 0.180: 86 0.180 - 0.270: 0 0.270 - 0.360: 3 0.360 - 0.450: 28 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 2.35 -2.80 -0.45 2.00e-01 2.50e+01 5.05e+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 2.35 -2.77 -0.43 2.00e-01 2.50e+01 4.56e+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 2.35 -2.76 -0.41 2.00e-01 2.50e+01 4.22e+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: 0.820 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 34.220 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 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= 0.176 Angle : 0.807 18.565 17491 Z= 0.416 Chirality : 0.062 0.450 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (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 TRP 0.011 0.001 TRP B 35 HIS 0.003 0.001 HIS B 260 PHE 0.019 0.001 PHE B 256 TYR 0.013 0.001 TYR B 58 ARG 0.003 0.000 ARG B 841 Details of bonding type rmsd hydrogen bonds : bond 0.21320 ( 594) hydrogen bonds : angle 7.23033 ( 1686) covalent geometry : bond 0.00281 (12691) covalent geometry : angle 0.80715 (17491) *********************** 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 : 1.106 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: 0.7339 (t0) REVERT: A 19 TYR cc_start: 0.5912 (t80) cc_final: 0.5592 (t80) 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: 0.5628 (tp) REVERT: A 152 GLU cc_start: 0.7561 (pt0) cc_final: 0.7232 (pp20) REVERT: A 215 GLU cc_start: 0.7001 (tt0) cc_final: 0.6721 (tp30) REVERT: B 23 ARG cc_start: 0.7310 (mtm-85) cc_final: 0.6442 (mtp85) REVERT: B 525 TRP cc_start: 0.7287 (p90) cc_final: 0.6675 (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: 0.6196 (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: 0.3053 time to fit residues: 107.1054 Evaluate side-chains 153 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 4.9990 chunk 110 optimal weight: 0.0010 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 130 GLN ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 ASN B 502 GLN ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 HIS B 959 GLN B 989 ASN B1026 GLN B1068 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.225901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.188726 restraints weight = 18233.325| |-----------------------------------------------------------------------------| r_work (start): 0.4524 rms_B_bonded: 2.29 r_work: 0.4357 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 12691 Z= 0.175 Angle : 0.664 10.382 17491 Z= 0.352 Chirality : 0.043 0.198 1970 Planarity : 0.005 0.039 2057 Dihedral : 19.213 88.630 2319 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.94 % Allowed : 8.48 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.22), residues: 1400 helix: 0.62 (0.19), residues: 726 sheet: -1.02 (0.43), residues: 147 loop : -1.40 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 797 HIS 0.020 0.002 HIS B1068 PHE 0.028 0.002 PHE B 199 TYR 0.018 0.002 TYR B 58 ARG 0.007 0.001 ARG B 514 Details of bonding type rmsd hydrogen bonds : bond 0.04919 ( 594) hydrogen bonds : angle 5.36037 ( 1686) covalent geometry : bond 0.00396 (12691) covalent geometry : angle 0.66385 (17491) *********************** 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: 11 poor density : 194 time to evaluate : 1.267 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: 0.2179 (tpp) cc_final: 0.0525 (ptt) REVERT: A 14 ASN cc_start: 0.7941 (p0) cc_final: 0.7668 (t0) REVERT: A 217 MET cc_start: 0.7226 (ptp) cc_final: 0.6999 (ptt) REVERT: B 23 ARG cc_start: 0.7552 (mtm-85) cc_final: 0.7041 (mtp85) REVERT: B 144 LEU cc_start: 0.6828 (tp) cc_final: 0.6526 (tp) REVERT: B 680 MET cc_start: 0.7473 (mmm) cc_final: 0.7092 (mmt) REVERT: B 900 ASP cc_start: 0.6506 (t70) cc_final: 0.6024 (t0) REVERT: B 1083 LEU cc_start: 0.6003 (tp) cc_final: 0.5351 (tp) REVERT: B 1102 MET cc_start: 0.6794 (mmt) cc_final: 0.6471 (mmm) outliers start: 11 outliers final: 4 residues processed: 200 average time/residue: 0.3050 time to fit residues: 84.1834 Evaluate side-chains 148 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 1012 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 85 optimal weight: 0.9980 chunk 24 optimal weight: 0.0270 chunk 119 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 0.0470 chunk 68 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN A 241 HIS B 245 GLN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 772 ASN ** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.230010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.189568 restraints weight = 18564.351| |-----------------------------------------------------------------------------| r_work (start): 0.4514 rms_B_bonded: 2.41 r_work: 0.4378 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.2999 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= 0.137 Angle : 0.597 9.069 17491 Z= 0.320 Chirality : 0.041 0.196 1970 Planarity : 0.004 0.042 2057 Dihedral : 19.142 88.227 2319 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.94 % Allowed : 11.99 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.23), residues: 1400 helix: 0.73 (0.20), residues: 720 sheet: -1.38 (0.41), residues: 156 loop : -1.41 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B1105 HIS 0.005 0.001 HIS B1064 PHE 0.032 0.002 PHE A 86 TYR 0.014 0.001 TYR B 445 ARG 0.006 0.001 ARG B 696 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 594) hydrogen bonds : angle 5.05373 ( 1686) covalent geometry : bond 0.00296 (12691) covalent geometry : angle 0.59699 (17491) *********************** 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 185 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2228 (tpp) cc_final: 0.0587 (ptt) REVERT: A 14 ASN cc_start: 0.7961 (p0) cc_final: 0.7723 (t0) REVERT: B 23 ARG cc_start: 0.7519 (mtm-85) cc_final: 0.7110 (mtp180) REVERT: B 680 MET cc_start: 0.7348 (mmm) cc_final: 0.6992 (mmt) REVERT: B 712 LEU cc_start: 0.7663 (tp) cc_final: 0.7327 (mt) REVERT: B 755 MET cc_start: 0.4887 (ptm) cc_final: 0.4544 (ptp) REVERT: B 900 ASP cc_start: 0.6538 (t70) cc_final: 0.6335 (t0) REVERT: B 979 MET cc_start: 0.5803 (ptp) cc_final: 0.5594 (ptp) REVERT: B 1070 TRP cc_start: 0.5628 (t60) cc_final: 0.5350 (t60) REVERT: B 1083 LEU cc_start: 0.6056 (tp) cc_final: 0.5488 (mp) REVERT: B 1102 MET cc_start: 0.6816 (mmt) cc_final: 0.6397 (mmm) outliers start: 11 outliers final: 5 residues processed: 183 average time/residue: 0.2833 time to fit residues: 72.8560 Evaluate side-chains 153 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 148 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 1137 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 1 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1067 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.220201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.182714 restraints weight = 18312.604| |-----------------------------------------------------------------------------| r_work (start): 0.4463 rms_B_bonded: 2.27 r_work: 0.4301 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12691 Z= 0.220 Angle : 0.692 10.475 17491 Z= 0.363 Chirality : 0.045 0.248 1970 Planarity : 0.005 0.048 2057 Dihedral : 19.222 89.774 2319 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.48 % Allowed : 13.01 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.22), residues: 1400 helix: 0.29 (0.19), residues: 732 sheet: -1.66 (0.40), residues: 147 loop : -1.62 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B1105 HIS 0.007 0.002 HIS B1068 PHE 0.020 0.002 PHE B 718 TYR 0.022 0.002 TYR B 445 ARG 0.013 0.001 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.04527 ( 594) hydrogen bonds : angle 5.24633 ( 1686) covalent geometry : bond 0.00507 (12691) covalent geometry : angle 0.69215 (17491) *********************** 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 199 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2440 (tpp) cc_final: 0.0710 (ptt) REVERT: A 14 ASN cc_start: 0.7988 (p0) cc_final: 0.7755 (t0) REVERT: A 78 ARG cc_start: 0.5781 (mmt-90) cc_final: 0.4846 (mmt180) REVERT: B 102 ARG cc_start: 0.7722 (mmm-85) cc_final: 0.7430 (ttm-80) REVERT: B 140 ILE cc_start: 0.7378 (mt) cc_final: 0.7072 (mt) REVERT: B 234 GLU cc_start: 0.6676 (pp20) cc_final: 0.6312 (pp20) REVERT: B 383 MET cc_start: 0.7955 (ptm) cc_final: 0.7521 (ptm) REVERT: B 417 ASN cc_start: 0.6428 (m-40) cc_final: 0.6197 (m110) REVERT: B 597 LEU cc_start: 0.5024 (OUTLIER) cc_final: 0.4469 (pp) REVERT: B 1021 SER cc_start: 0.6118 (OUTLIER) cc_final: 0.5671 (m) REVERT: B 1082 PHE cc_start: 0.6694 (t80) cc_final: 0.6048 (t80) REVERT: B 1102 MET cc_start: 0.7053 (mmt) cc_final: 0.6545 (mmm) outliers start: 29 outliers final: 15 residues processed: 194 average time/residue: 0.2874 time to fit residues: 77.1543 Evaluate side-chains 154 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 214 ILE 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 597 LEU Chi-restraints excluded: chain B residue 609 LEU 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 883 THR Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1104 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 92 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 110 optimal weight: 0.0980 chunk 97 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 ASN B1026 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4892 r_free = 0.4892 target = 0.225448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.188616 restraints weight = 18400.604| |-----------------------------------------------------------------------------| r_work (start): 0.4531 rms_B_bonded: 2.22 r_work: 0.4372 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.4074 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= 0.137 Angle : 0.608 8.523 17491 Z= 0.323 Chirality : 0.041 0.230 1970 Planarity : 0.004 0.042 2057 Dihedral : 19.094 87.326 2319 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.71 % Allowed : 15.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.22), residues: 1400 helix: 0.53 (0.20), residues: 726 sheet: -1.89 (0.39), residues: 156 loop : -1.45 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B1105 HIS 0.004 0.001 HIS B 638 PHE 0.015 0.001 PHE B 718 TYR 0.013 0.001 TYR B 58 ARG 0.009 0.001 ARG B 500 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 594) hydrogen bonds : angle 4.97125 ( 1686) covalent geometry : bond 0.00302 (12691) covalent geometry : angle 0.60765 (17491) *********************** 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 185 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2566 (tpp) cc_final: 0.0851 (ptt) REVERT: A 78 ARG cc_start: 0.5733 (mmt-90) cc_final: 0.4897 (mpt180) REVERT: A 230 ASN cc_start: 0.7224 (OUTLIER) cc_final: 0.5839 (t0) REVERT: B 58 TYR cc_start: 0.7367 (t80) cc_final: 0.7139 (t80) REVERT: B 140 ILE cc_start: 0.7126 (mt) cc_final: 0.6750 (mp) REVERT: B 383 MET cc_start: 0.7797 (ptm) cc_final: 0.7475 (ptm) REVERT: B 417 ASN cc_start: 0.6088 (m-40) cc_final: 0.5884 (m110) REVERT: B 680 MET cc_start: 0.7366 (mmm) cc_final: 0.6949 (mmt) REVERT: B 1083 LEU cc_start: 0.6461 (tp) cc_final: 0.5887 (mt) REVERT: B 1102 MET cc_start: 0.7049 (mmt) cc_final: 0.6507 (mmm) outliers start: 20 outliers final: 12 residues processed: 180 average time/residue: 0.3036 time to fit residues: 76.5012 Evaluate side-chains 149 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 72 LEU 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 609 LEU Chi-restraints excluded: chain B residue 672 ASN 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 55 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 13 optimal weight: 0.0030 chunk 9 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1026 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.224844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.188180 restraints weight = 18641.205| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 2.24 r_work: 0.4372 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.4242 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= 0.142 Angle : 0.612 10.299 17491 Z= 0.322 Chirality : 0.041 0.245 1970 Planarity : 0.004 0.041 2057 Dihedral : 19.031 87.137 2319 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.05 % Allowed : 15.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.22), residues: 1400 helix: 0.63 (0.19), residues: 723 sheet: -1.87 (0.38), residues: 156 loop : -1.37 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B1105 HIS 0.003 0.001 HIS B 638 PHE 0.015 0.002 PHE B 602 TYR 0.015 0.001 TYR B 58 ARG 0.007 0.000 ARG B 500 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 594) hydrogen bonds : angle 4.90484 ( 1686) covalent geometry : bond 0.00318 (12691) covalent geometry : angle 0.61216 (17491) *********************** 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 166 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2581 (tpp) cc_final: 0.0874 (ptt) REVERT: A 78 ARG cc_start: 0.5783 (mmt-90) cc_final: 0.5032 (mmt180) REVERT: A 217 MET cc_start: 0.6988 (ptt) cc_final: 0.6736 (ptt) REVERT: A 230 ASN cc_start: 0.7323 (OUTLIER) cc_final: 0.5820 (t0) REVERT: B 140 ILE cc_start: 0.7087 (mt) cc_final: 0.6684 (mp) REVERT: B 383 MET cc_start: 0.7786 (ptm) cc_final: 0.7434 (ptm) REVERT: B 613 ILE cc_start: 0.7942 (pt) cc_final: 0.7732 (mt) REVERT: B 680 MET cc_start: 0.7312 (mmm) cc_final: 0.6742 (mmt) REVERT: B 1102 MET cc_start: 0.6890 (mmt) cc_final: 0.6347 (mmm) outliers start: 24 outliers final: 13 residues processed: 159 average time/residue: 0.2868 time to fit residues: 63.7180 Evaluate side-chains 144 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 72 LEU 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 609 LEU Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 900 ASP Chi-restraints excluded: chain B residue 1104 ASP Chi-restraints excluded: chain B residue 1108 THR Chi-restraints excluded: chain B residue 1137 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 156 ASN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.219138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.181203 restraints weight = 18428.511| |-----------------------------------------------------------------------------| r_work (start): 0.4454 rms_B_bonded: 2.25 r_work: 0.4304 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12691 Z= 0.250 Angle : 0.718 11.348 17491 Z= 0.374 Chirality : 0.047 0.295 1970 Planarity : 0.005 0.055 2057 Dihedral : 19.099 89.191 2319 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.23 % Allowed : 16.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.22), residues: 1400 helix: 0.21 (0.19), residues: 728 sheet: -2.03 (0.38), residues: 158 loop : -1.62 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP B1105 HIS 0.009 0.002 HIS B 260 PHE 0.018 0.002 PHE B1082 TYR 0.027 0.002 TYR B 58 ARG 0.011 0.001 ARG B 70 Details of bonding type rmsd hydrogen bonds : bond 0.04376 ( 594) hydrogen bonds : angle 5.18736 ( 1686) covalent geometry : bond 0.00585 (12691) covalent geometry : angle 0.71769 (17491) *********************** 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: 26 poor density : 136 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2561 (tpp) cc_final: 0.0658 (ptp) REVERT: A 78 ARG cc_start: 0.5828 (mmt-90) cc_final: 0.5058 (mmt180) REVERT: A 231 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.5819 (mp-120) REVERT: B 234 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6357 (pp20) REVERT: B 383 MET cc_start: 0.7850 (ptm) cc_final: 0.7521 (ptm) REVERT: B 680 MET cc_start: 0.7521 (mmm) cc_final: 0.6902 (mmt) REVERT: B 922 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7137 (mp0) REVERT: B 1102 MET cc_start: 0.6816 (mmt) cc_final: 0.6286 (mmm) REVERT: B 1104 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7250 (p0) outliers start: 26 outliers final: 18 residues processed: 154 average time/residue: 0.2892 time to fit residues: 62.9098 Evaluate side-chains 150 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 GLN Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 211 MET 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 381 ILE 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 641 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 900 ASP Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1104 ASP Chi-restraints excluded: chain B residue 1108 THR Chi-restraints excluded: chain B residue 1137 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 106 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1026 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.223897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.186840 restraints weight = 18642.186| |-----------------------------------------------------------------------------| r_work (start): 0.4508 rms_B_bonded: 2.28 r_work: 0.4365 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.4852 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= 0.142 Angle : 0.621 10.331 17491 Z= 0.325 Chirality : 0.042 0.262 1970 Planarity : 0.004 0.045 2057 Dihedral : 18.943 85.719 2319 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.63 % Allowed : 17.55 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.22), residues: 1400 helix: 0.52 (0.19), residues: 720 sheet: -2.03 (0.37), residues: 158 loop : -1.53 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B1105 HIS 0.004 0.001 HIS B 260 PHE 0.012 0.002 PHE B 718 TYR 0.019 0.001 TYR B 210 ARG 0.007 0.001 ARG B 500 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 594) hydrogen bonds : angle 4.95383 ( 1686) covalent geometry : bond 0.00321 (12691) covalent geometry : angle 0.62101 (17491) *********************** 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 168 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2610 (tpp) cc_final: 0.1002 (ptt) REVERT: A 31 MET cc_start: 0.5396 (mtt) cc_final: 0.5182 (ptp) REVERT: A 78 ARG cc_start: 0.5825 (mmt-90) cc_final: 0.5004 (mpt180) REVERT: A 230 ASN cc_start: 0.7316 (OUTLIER) cc_final: 0.5975 (t0) REVERT: A 231 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6122 (mp-120) REVERT: B 58 TYR cc_start: 0.7353 (t80) cc_final: 0.6999 (t80) REVERT: B 383 MET cc_start: 0.7812 (ptm) cc_final: 0.7511 (ptm) REVERT: B 680 MET cc_start: 0.7172 (mmm) cc_final: 0.6687 (mmt) REVERT: B 922 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: B 952 MET cc_start: 0.4621 (tpt) cc_final: 0.4320 (tpt) REVERT: B 1021 SER cc_start: 0.6339 (OUTLIER) cc_final: 0.5952 (m) REVERT: B 1083 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6716 (mt) REVERT: B 1102 MET cc_start: 0.6776 (mmt) cc_final: 0.6218 (mmm) outliers start: 19 outliers final: 8 residues processed: 163 average time/residue: 0.2902 time to fit residues: 66.3699 Evaluate side-chains 147 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 231 GLN Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1083 LEU 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 95 optimal weight: 0.6980 chunk 139 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 63 optimal weight: 0.0770 overall best weight: 1.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.225518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.188008 restraints weight = 18254.639| |-----------------------------------------------------------------------------| r_work (start): 0.4528 rms_B_bonded: 2.22 r_work: 0.4378 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12691 Z= 0.197 Angle : 0.676 9.612 17491 Z= 0.352 Chirality : 0.047 0.578 1970 Planarity : 0.005 0.049 2057 Dihedral : 18.956 86.512 2319 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.88 % Allowed : 17.72 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.22), residues: 1400 helix: 0.38 (0.19), residues: 720 sheet: -2.11 (0.37), residues: 157 loop : -1.56 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B1105 HIS 0.012 0.002 HIS B 756 PHE 0.015 0.002 PHE B 718 TYR 0.022 0.002 TYR B 445 ARG 0.008 0.001 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.04048 ( 594) hydrogen bonds : angle 5.07628 ( 1686) covalent geometry : bond 0.00460 (12691) covalent geometry : angle 0.67612 (17491) *********************** 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 162 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2686 (tpp) cc_final: 0.0738 (ptt) REVERT: A 78 ARG cc_start: 0.5817 (mmt-90) cc_final: 0.5008 (mpt180) REVERT: A 230 ASN cc_start: 0.7427 (OUTLIER) cc_final: 0.6033 (t0) REVERT: A 231 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.6254 (mp-120) REVERT: B 234 GLU cc_start: 0.6491 (pp20) cc_final: 0.6284 (pp20) REVERT: B 383 MET cc_start: 0.7806 (ptm) cc_final: 0.7519 (ptm) REVERT: B 680 MET cc_start: 0.7297 (mmm) cc_final: 0.6727 (mmp) REVERT: B 922 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: B 1036 ILE cc_start: 0.5223 (OUTLIER) cc_final: 0.4758 (mm) REVERT: B 1083 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6719 (mt) REVERT: B 1102 MET cc_start: 0.6830 (mmt) cc_final: 0.6276 (mmm) outliers start: 22 outliers final: 13 residues processed: 158 average time/residue: 0.2958 time to fit residues: 65.7387 Evaluate side-chains 149 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 231 GLN Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 756 HIS Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1036 ILE Chi-restraints excluded: chain B residue 1083 LEU 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 110 optimal weight: 0.0020 chunk 8 optimal weight: 5.9990 chunk 79 optimal weight: 0.3980 chunk 108 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 140 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 HIS B1026 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.229002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.192405 restraints weight = 18070.486| |-----------------------------------------------------------------------------| r_work (start): 0.4570 rms_B_bonded: 2.27 r_work: 0.4424 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12691 Z= 0.141 Angle : 0.632 9.970 17491 Z= 0.331 Chirality : 0.044 0.383 1970 Planarity : 0.004 0.044 2057 Dihedral : 18.862 85.077 2319 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.37 % Allowed : 18.07 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.22), residues: 1400 helix: 0.50 (0.19), residues: 719 sheet: -2.08 (0.37), residues: 157 loop : -1.53 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B1105 HIS 0.025 0.001 HIS B 756 PHE 0.012 0.002 PHE B 246 TYR 0.015 0.001 TYR B 58 ARG 0.009 0.001 ARG B 484 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 594) hydrogen bonds : angle 4.97495 ( 1686) covalent geometry : bond 0.00317 (12691) covalent geometry : angle 0.63164 (17491) ********************** 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 166 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 1.159 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: 0.2866 (tpp) cc_final: 0.0960 (ptt) REVERT: A 78 ARG cc_start: 0.5883 (mmt-90) cc_final: 0.5039 (mpt180) REVERT: A 230 ASN cc_start: 0.7346 (OUTLIER) cc_final: 0.5936 (t0) REVERT: A 231 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.6210 (mp-120) REVERT: B 58 TYR cc_start: 0.7288 (t80) cc_final: 0.6947 (t80) REVERT: B 234 GLU cc_start: 0.6462 (pp20) cc_final: 0.6254 (pp20) REVERT: B 383 MET cc_start: 0.7842 (ptm) cc_final: 0.7567 (ptm) REVERT: B 680 MET cc_start: 0.7265 (mmm) cc_final: 0.6855 (mmt) REVERT: B 922 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: B 1021 SER cc_start: 0.6300 (OUTLIER) cc_final: 0.5899 (m) REVERT: B 1036 ILE cc_start: 0.5315 (OUTLIER) cc_final: 0.4906 (mm) REVERT: B 1102 MET cc_start: 0.6724 (mmt) cc_final: 0.6179 (mmm) outliers start: 16 outliers final: 10 residues processed: 162 average time/residue: 0.2960 time to fit residues: 66.0721 Evaluate side-chains 150 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 231 GLN Chi-restraints excluded: chain B residue 101 SER 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 519 VAL Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 900 ASP Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1036 ILE 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 101 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 133 optimal weight: 0.0670 chunk 27 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1026 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.229028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.191786 restraints weight = 18131.913| |-----------------------------------------------------------------------------| r_work (start): 0.4561 rms_B_bonded: 2.34 r_work: 0.4416 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.5283 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= 0.143 Angle : 0.631 9.037 17491 Z= 0.331 Chirality : 0.043 0.341 1970 Planarity : 0.005 0.057 2057 Dihedral : 18.770 88.332 2319 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.20 % Allowed : 18.66 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.22), residues: 1400 helix: 0.51 (0.19), residues: 722 sheet: -2.06 (0.37), residues: 158 loop : -1.46 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B1105 HIS 0.003 0.001 HIS A 167 PHE 0.010 0.001 PHE B 718 TYR 0.015 0.001 TYR B 58 ARG 0.007 0.001 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 594) hydrogen bonds : angle 4.91555 ( 1686) covalent geometry : bond 0.00326 (12691) covalent geometry : angle 0.63074 (17491) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6411.51 seconds wall clock time: 111 minutes 3.93 seconds (6663.93 seconds total)