Starting phenix.real_space_refine on Mon Aug 5 04:09:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxy_43643/08_2024/8vxy_43643.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxy_43643/08_2024/8vxy_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxy_43643/08_2024/8vxy_43643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxy_43643/08_2024/8vxy_43643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxy_43643/08_2024/8vxy_43643.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxy_43643/08_2024/8vxy_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 Residue "B PHE 1029": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 7.14, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 5.30 Conformation dependent library (CDL) restraints added in 1.9 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: 4.16 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: 5.16 Time building geometry restraints manager: 5.78 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: 99.70 - 106.94: 717 106.94 - 114.18: 7309 114.18 - 121.42: 6243 121.42 - 128.66: 3059 128.66 - 135.90: 163 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: 0.890 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 39.480 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.210 ------------------------------------------------------------------------------- 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 1.308 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: 0.3036 time to fit residues: 106.3091 Evaluate side-chains 153 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 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= 0.258 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 *********************** 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 fitting. rotamer outliers: 11 poor density : 194 time to evaluate : 1.096 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: 0.2375 (tpp) cc_final: 0.0872 (ptt) REVERT: A 14 ASN cc_start: 0.7879 (p0) cc_final: 0.7349 (t0) REVERT: A 86 PHE cc_start: 0.5597 (m-80) cc_final: 0.5382 (m-80) REVERT: A 108 LYS cc_start: 0.7412 (tptp) cc_final: 0.7110 (tmtt) REVERT: A 217 MET cc_start: 0.7434 (ptp) cc_final: 0.7142 (ptt) REVERT: B 23 ARG cc_start: 0.7416 (mtm-85) cc_final: 0.6532 (mtp85) REVERT: B 144 LEU cc_start: 0.7121 (tp) cc_final: 0.6873 (tp) REVERT: B 335 LYS cc_start: 0.7545 (mttm) cc_final: 0.7238 (mtmt) REVERT: B 474 GLU cc_start: 0.6813 (pp20) cc_final: 0.6578 (pp20) REVERT: B 840 GLN cc_start: 0.6614 (mm-40) cc_final: 0.6289 (pp30) REVERT: B 860 ARG cc_start: 0.6981 (mmt180) cc_final: 0.6681 (mtp85) REVERT: B 900 ASP cc_start: 0.6697 (t70) cc_final: 0.6116 (t0) REVERT: B 1083 LEU cc_start: 0.5390 (tp) cc_final: 0.4628 (tp) REVERT: B 1102 MET cc_start: 0.7044 (mmt) cc_final: 0.6583 (mmm) REVERT: B 1160 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7892 (ttp-110) outliers start: 11 outliers final: 4 residues processed: 200 average time/residue: 0.2922 time to fit residues: 80.4208 Evaluate side-chains 154 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 1160 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN B 245 GLN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12691 Z= 0.277 Angle : 0.659 10.231 17491 Z= 0.350 Chirality : 0.043 0.224 1970 Planarity : 0.005 0.047 2057 Dihedral : 19.215 92.413 2319 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.71 % Allowed : 11.99 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.81 (0.22), residues: 1400 helix: 0.46 (0.19), residues: 729 sheet: -1.61 (0.40), residues: 156 loop : -1.54 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B1105 HIS 0.006 0.001 HIS B 119 PHE 0.018 0.002 PHE B 718 TYR 0.021 0.002 TYR B 58 ARG 0.007 0.001 ARG B 696 *********************** 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 195 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 175 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2488 (tpp) cc_final: 0.0904 (ptt) REVERT: A 14 ASN cc_start: 0.7883 (p0) cc_final: 0.7422 (t0) REVERT: A 86 PHE cc_start: 0.5618 (m-80) cc_final: 0.5360 (m-80) REVERT: A 126 ASP cc_start: 0.7436 (m-30) cc_final: 0.7201 (m-30) REVERT: B 234 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6507 (pp20) REVERT: B 335 LYS cc_start: 0.7545 (mttm) cc_final: 0.7255 (mmtt) REVERT: B 474 GLU cc_start: 0.7237 (pp20) cc_final: 0.6426 (pp20) REVERT: B 583 GLU cc_start: 0.7067 (tm-30) cc_final: 0.6819 (mm-30) REVERT: B 597 LEU cc_start: 0.4911 (OUTLIER) cc_final: 0.4354 (pp) REVERT: B 609 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7618 (mm) REVERT: B 840 GLN cc_start: 0.6432 (mm-40) cc_final: 0.6222 (pp30) REVERT: B 860 ARG cc_start: 0.7066 (mmt180) cc_final: 0.6863 (mtm180) REVERT: B 1021 SER cc_start: 0.5817 (OUTLIER) cc_final: 0.5500 (m) REVERT: B 1079 TRP cc_start: 0.6260 (t-100) cc_final: 0.4831 (t60) REVERT: B 1102 MET cc_start: 0.7175 (mmt) cc_final: 0.6566 (mmm) REVERT: B 1160 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8214 (mtm110) outliers start: 20 outliers final: 9 residues processed: 190 average time/residue: 0.2865 time to fit residues: 76.1424 Evaluate side-chains 156 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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 234 GLU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 407 THR 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 1021 SER Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1160 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 0.0570 chunk 99 optimal weight: 7.9990 chunk 68 optimal weight: 0.0010 chunk 14 optimal weight: 20.0000 chunk 63 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 overall best weight: 0.5104 ------------------------------------------------------------------------------- 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 502 GLN B1026 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12691 Z= 0.191 Angle : 0.594 8.959 17491 Z= 0.317 Chirality : 0.041 0.227 1970 Planarity : 0.004 0.041 2057 Dihedral : 19.119 87.527 2319 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.80 % Allowed : 13.27 % Favored : 84.93 % 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: -0.67 (0.22), residues: 1400 helix: 0.57 (0.19), residues: 738 sheet: -1.70 (0.40), residues: 156 loop : -1.45 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B1105 HIS 0.003 0.001 HIS B 638 PHE 0.015 0.001 PHE B 718 TYR 0.019 0.001 TYR A 19 ARG 0.008 0.000 ARG B 595 *********************** 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 193 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 172 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2682 (tpp) cc_final: 0.1163 (ptt) REVERT: A 14 ASN cc_start: 0.7834 (p0) cc_final: 0.7427 (t0) REVERT: A 78 ARG cc_start: 0.5840 (mmt-90) cc_final: 0.4922 (mmt180) REVERT: A 86 PHE cc_start: 0.5626 (m-80) cc_final: 0.5384 (m-80) REVERT: A 230 ASN cc_start: 0.6765 (OUTLIER) cc_final: 0.5100 (t0) REVERT: B 102 ARG cc_start: 0.7514 (mmm-85) cc_final: 0.7148 (ttm-80) REVERT: B 234 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6473 (pp20) REVERT: B 696 ARG cc_start: 0.7314 (mmm-85) cc_final: 0.7051 (mmm-85) REVERT: B 827 ASP cc_start: 0.8682 (m-30) cc_final: 0.8420 (m-30) REVERT: B 860 ARG cc_start: 0.7088 (mmt180) cc_final: 0.6824 (mtm180) REVERT: B 912 GLU cc_start: 0.6587 (tm-30) cc_final: 0.6385 (tm-30) REVERT: B 922 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6798 (tp30) REVERT: B 1083 LEU cc_start: 0.5579 (mt) cc_final: 0.5174 (mt) REVERT: B 1102 MET cc_start: 0.7061 (mmt) cc_final: 0.6476 (mmm) REVERT: B 1160 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7924 (ttp-110) outliers start: 21 outliers final: 6 residues processed: 185 average time/residue: 0.3110 time to fit residues: 78.3762 Evaluate side-chains 152 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 143 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 234 GLU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 900 ASP Chi-restraints excluded: chain B residue 1104 ASP Chi-restraints excluded: chain B residue 1160 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 0.0980 chunk 126 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 B1097 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6366 moved from start: 0.3981 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= 0.207 Angle : 0.601 8.431 17491 Z= 0.319 Chirality : 0.041 0.242 1970 Planarity : 0.004 0.042 2057 Dihedral : 19.069 87.998 2319 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.63 % Allowed : 14.90 % Favored : 83.48 % 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: -0.66 (0.22), residues: 1400 helix: 0.57 (0.19), residues: 736 sheet: -1.73 (0.40), residues: 156 loop : -1.40 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B1105 HIS 0.004 0.001 HIS B1068 PHE 0.016 0.001 PHE B 718 TYR 0.018 0.002 TYR B 769 ARG 0.005 0.000 ARG B 231 *********************** 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 174 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 155 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2756 (tpp) cc_final: 0.1212 (ptt) REVERT: A 14 ASN cc_start: 0.7808 (p0) cc_final: 0.7431 (t0) REVERT: A 78 ARG cc_start: 0.5875 (mmt-90) cc_final: 0.4883 (mmt180) REVERT: A 86 PHE cc_start: 0.5630 (m-80) cc_final: 0.5393 (m-80) REVERT: B 72 LEU cc_start: 0.6318 (mt) cc_final: 0.5734 (pp) REVERT: B 102 ARG cc_start: 0.7585 (mmm-85) cc_final: 0.7187 (ttm-80) REVERT: B 234 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6591 (pp20) REVERT: B 241 SER cc_start: 0.6501 (p) cc_final: 0.6300 (p) REVERT: B 417 ASN cc_start: 0.6794 (m-40) cc_final: 0.6379 (m110) REVERT: B 696 ARG cc_start: 0.7353 (mmm-85) cc_final: 0.7055 (mmm-85) REVERT: B 827 ASP cc_start: 0.8707 (m-30) cc_final: 0.8431 (m-30) REVERT: B 843 ARG cc_start: 0.7818 (pmt170) cc_final: 0.7208 (mmt-90) REVERT: B 860 ARG cc_start: 0.7052 (mmt180) cc_final: 0.6784 (mtm180) REVERT: B 912 GLU cc_start: 0.6778 (tm-30) cc_final: 0.6433 (tm-30) REVERT: B 922 GLU cc_start: 0.7448 (mt-10) cc_final: 0.6792 (tp30) REVERT: B 1082 PHE cc_start: 0.6145 (t80) cc_final: 0.5367 (t80) REVERT: B 1102 MET cc_start: 0.7290 (mmt) cc_final: 0.6607 (mmm) REVERT: B 1160 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8057 (mtm110) outliers start: 19 outliers final: 10 residues processed: 167 average time/residue: 0.2902 time to fit residues: 67.1335 Evaluate side-chains 153 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 141 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 48 SER 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 449 ILE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 1104 ASP Chi-restraints excluded: chain B residue 1160 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 7.9990 chunk 127 optimal weight: 0.0970 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 34 optimal weight: 0.0370 chunk 141 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1026 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12691 Z= 0.290 Angle : 0.656 10.426 17491 Z= 0.344 Chirality : 0.043 0.251 1970 Planarity : 0.005 0.047 2057 Dihedral : 19.073 88.907 2319 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.23 % Allowed : 15.15 % Favored : 82.62 % 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: -0.91 (0.22), residues: 1400 helix: 0.38 (0.19), residues: 735 sheet: -1.90 (0.39), residues: 157 loop : -1.53 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B1105 HIS 0.015 0.002 HIS B 756 PHE 0.017 0.002 PHE B 718 TYR 0.022 0.002 TYR B 445 ARG 0.013 0.001 ARG B 70 *********************** 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 fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2501 (tpp) cc_final: 0.1007 (ptt) REVERT: A 14 ASN cc_start: 0.7834 (p0) cc_final: 0.7463 (t0) REVERT: A 17 ASP cc_start: 0.7695 (t0) cc_final: 0.7477 (t0) REVERT: A 78 ARG cc_start: 0.5897 (mmt-90) cc_final: 0.5142 (mmt180) REVERT: A 86 PHE cc_start: 0.5697 (m-80) cc_final: 0.5460 (m-80) REVERT: A 230 ASN cc_start: 0.6854 (OUTLIER) cc_final: 0.5338 (t0) REVERT: A 231 GLN cc_start: 0.6749 (OUTLIER) cc_final: 0.5605 (mp-120) REVERT: B 102 ARG cc_start: 0.7697 (mmm-85) cc_final: 0.7218 (ttm-80) REVERT: B 234 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6559 (pp20) REVERT: B 304 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7705 (mt-10) REVERT: B 417 ASN cc_start: 0.6752 (m-40) cc_final: 0.6297 (m110) REVERT: B 597 LEU cc_start: 0.4810 (OUTLIER) cc_final: 0.4330 (pp) REVERT: B 696 ARG cc_start: 0.7450 (mmm-85) cc_final: 0.7103 (mmm-85) REVERT: B 729 HIS cc_start: 0.6665 (m90) cc_final: 0.6421 (m90) REVERT: B 843 ARG cc_start: 0.7788 (pmt170) cc_final: 0.7196 (mmt-90) REVERT: B 860 ARG cc_start: 0.7001 (mmt180) cc_final: 0.6728 (mtm180) REVERT: B 912 GLU cc_start: 0.6982 (tm-30) cc_final: 0.6551 (tm-30) REVERT: B 922 GLU cc_start: 0.7559 (mt-10) cc_final: 0.6847 (tp30) REVERT: B 1021 SER cc_start: 0.6114 (OUTLIER) cc_final: 0.5786 (m) REVERT: B 1080 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7677 (mm) REVERT: B 1102 MET cc_start: 0.7453 (mmt) cc_final: 0.6717 (mmm) REVERT: B 1160 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7990 (mtm110) outliers start: 26 outliers final: 14 residues processed: 168 average time/residue: 0.3058 time to fit residues: 70.5963 Evaluate side-chains 154 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 1.248 ------------------------------------------------------------------------------- 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 48 SER 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 449 ILE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 946 TRP Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1080 LEU Chi-restraints excluded: chain B residue 1104 ASP Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1160 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 79 optimal weight: 0.0970 chunk 118 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.4576 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= 0.200 Angle : 0.606 10.090 17491 Z= 0.319 Chirality : 0.042 0.268 1970 Planarity : 0.004 0.044 2057 Dihedral : 18.952 86.372 2319 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.14 % Allowed : 16.52 % Favored : 81.34 % 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: -0.73 (0.22), residues: 1400 helix: 0.57 (0.19), residues: 728 sheet: -1.93 (0.39), residues: 159 loop : -1.44 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B1105 HIS 0.011 0.001 HIS B 756 PHE 0.012 0.001 PHE B 718 TYR 0.016 0.001 TYR B 58 ARG 0.010 0.001 ARG B 70 *********************** 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 174 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2644 (tpp) cc_final: 0.1189 (ptt) REVERT: A 14 ASN cc_start: 0.7810 (p0) cc_final: 0.7475 (t0) REVERT: A 17 ASP cc_start: 0.7674 (t0) cc_final: 0.7444 (t0) REVERT: A 78 ARG cc_start: 0.5891 (mmt-90) cc_final: 0.5136 (mmt180) REVERT: A 86 PHE cc_start: 0.5646 (m-80) cc_final: 0.5444 (m-80) REVERT: A 230 ASN cc_start: 0.6841 (OUTLIER) cc_final: 0.5148 (t0) REVERT: B 102 ARG cc_start: 0.7695 (mmm-85) cc_final: 0.7226 (ttm-80) REVERT: B 234 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6628 (pp20) REVERT: B 304 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7576 (mt-10) REVERT: B 417 ASN cc_start: 0.6627 (m-40) cc_final: 0.6167 (m110) REVERT: B 696 ARG cc_start: 0.7413 (mmm-85) cc_final: 0.7092 (mmm-85) REVERT: B 729 HIS cc_start: 0.6620 (m90) cc_final: 0.6344 (m90) REVERT: B 843 ARG cc_start: 0.7750 (pmt170) cc_final: 0.7187 (mmt-90) REVERT: B 860 ARG cc_start: 0.6973 (mmt180) cc_final: 0.6712 (mtm180) REVERT: B 922 GLU cc_start: 0.7452 (mt-10) cc_final: 0.6847 (tp30) REVERT: B 1021 SER cc_start: 0.6054 (OUTLIER) cc_final: 0.5755 (m) REVERT: B 1036 ILE cc_start: 0.5244 (OUTLIER) cc_final: 0.4792 (mm) REVERT: B 1080 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7610 (mm) REVERT: B 1102 MET cc_start: 0.7034 (mmt) cc_final: 0.6406 (mmm) REVERT: B 1158 ASN cc_start: 0.7766 (m-40) cc_final: 0.7122 (t0) REVERT: B 1160 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7917 (ttp-110) outliers start: 25 outliers final: 12 residues processed: 169 average time/residue: 0.2976 time to fit residues: 69.1352 Evaluate side-chains 157 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain B residue 48 SER 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 449 ILE Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 617 GLU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 946 TRP Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1036 ILE Chi-restraints excluded: chain B residue 1080 LEU Chi-restraints excluded: chain B residue 1104 ASP Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1160 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 95 optimal weight: 0.0770 chunk 69 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 110 optimal weight: 0.0070 chunk 128 optimal weight: 5.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 241 HIS ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1026 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.4780 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= 0.182 Angle : 0.598 9.886 17491 Z= 0.313 Chirality : 0.042 0.462 1970 Planarity : 0.004 0.044 2057 Dihedral : 18.847 85.955 2319 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.63 % Allowed : 17.29 % 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 (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: 0.65 (0.19), residues: 729 sheet: -1.90 (0.39), residues: 159 loop : -1.40 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B1105 HIS 0.009 0.001 HIS B 756 PHE 0.014 0.001 PHE A 207 TYR 0.014 0.001 TYR B 445 ARG 0.010 0.000 ARG B1141 *********************** 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 169 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 150 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2790 (tpp) cc_final: 0.1212 (ptp) REVERT: A 14 ASN cc_start: 0.7769 (p0) cc_final: 0.7485 (t0) REVERT: A 78 ARG cc_start: 0.5998 (mmt-90) cc_final: 0.5272 (mmt180) REVERT: A 86 PHE cc_start: 0.5744 (m-80) cc_final: 0.5461 (m-80) REVERT: A 230 ASN cc_start: 0.6839 (OUTLIER) cc_final: 0.5221 (t0) REVERT: B 102 ARG cc_start: 0.7739 (mmm-85) cc_final: 0.7255 (ttm-80) REVERT: B 234 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6568 (pp20) REVERT: B 304 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7472 (mt-10) REVERT: B 417 ASN cc_start: 0.7015 (m-40) cc_final: 0.6666 (m110) REVERT: B 533 ARG cc_start: 0.6257 (ptt180) cc_final: 0.5847 (ptt-90) REVERT: B 696 ARG cc_start: 0.7478 (mmm-85) cc_final: 0.7161 (mmm-85) REVERT: B 729 HIS cc_start: 0.6557 (m90) cc_final: 0.6260 (m90) REVERT: B 843 ARG cc_start: 0.7743 (pmt170) cc_final: 0.7166 (mmt-90) REVERT: B 860 ARG cc_start: 0.7045 (mmt180) cc_final: 0.6760 (mtm180) REVERT: B 922 GLU cc_start: 0.7443 (mt-10) cc_final: 0.6809 (tp30) REVERT: B 1021 SER cc_start: 0.6022 (OUTLIER) cc_final: 0.5707 (m) REVERT: B 1036 ILE cc_start: 0.5323 (OUTLIER) cc_final: 0.5017 (mm) REVERT: B 1080 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7594 (mm) REVERT: B 1102 MET cc_start: 0.7010 (mmt) cc_final: 0.6417 (mmm) REVERT: B 1158 ASN cc_start: 0.7717 (m-40) cc_final: 0.7005 (t0) REVERT: B 1160 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7819 (ttp-110) outliers start: 19 outliers final: 11 residues processed: 164 average time/residue: 0.2913 time to fit residues: 66.6022 Evaluate side-chains 152 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain B residue 48 SER 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 449 ILE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 617 GLU Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 946 TRP Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1036 ILE Chi-restraints excluded: chain B residue 1080 LEU Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1160 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 130 optimal weight: 0.0170 chunk 86 optimal weight: 0.6980 overall best weight: 0.7020 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.4920 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= 0.194 Angle : 0.616 10.805 17491 Z= 0.318 Chirality : 0.042 0.325 1970 Planarity : 0.004 0.043 2057 Dihedral : 18.796 85.826 2319 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.80 % Allowed : 16.87 % Favored : 81.34 % 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: -0.68 (0.22), residues: 1400 helix: 0.65 (0.19), residues: 729 sheet: -1.89 (0.38), residues: 159 loop : -1.50 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B1105 HIS 0.009 0.001 HIS B 756 PHE 0.013 0.001 PHE A 207 TYR 0.017 0.001 TYR B 445 ARG 0.008 0.000 ARG B1141 *********************** 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 175 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2812 (tpp) cc_final: 0.1405 (ptt) REVERT: A 14 ASN cc_start: 0.7775 (p0) cc_final: 0.7567 (t0) REVERT: A 78 ARG cc_start: 0.5976 (mmt-90) cc_final: 0.5252 (mmt180) REVERT: A 86 PHE cc_start: 0.5705 (m-80) cc_final: 0.5445 (m-80) REVERT: A 230 ASN cc_start: 0.6857 (OUTLIER) cc_final: 0.5352 (t0) REVERT: A 231 GLN cc_start: 0.6595 (OUTLIER) cc_final: 0.5606 (mp-120) REVERT: B 102 ARG cc_start: 0.7750 (mmm-85) cc_final: 0.7263 (ttm-80) REVERT: B 234 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6615 (pp20) REVERT: B 304 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7375 (mt-10) REVERT: B 417 ASN cc_start: 0.7009 (m-40) cc_final: 0.6660 (m110) REVERT: B 696 ARG cc_start: 0.7444 (mmm-85) cc_final: 0.7151 (mmm-85) REVERT: B 729 HIS cc_start: 0.6560 (m90) cc_final: 0.6257 (m90) REVERT: B 843 ARG cc_start: 0.7761 (pmt170) cc_final: 0.7185 (mmt-90) REVERT: B 860 ARG cc_start: 0.7064 (mmt180) cc_final: 0.6759 (mtm180) REVERT: B 922 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6848 (tp30) REVERT: B 1021 SER cc_start: 0.5996 (OUTLIER) cc_final: 0.5670 (m) REVERT: B 1036 ILE cc_start: 0.5118 (OUTLIER) cc_final: 0.4770 (mm) REVERT: B 1080 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7432 (mm) REVERT: B 1102 MET cc_start: 0.7060 (mmt) cc_final: 0.6427 (mmm) REVERT: B 1158 ASN cc_start: 0.7730 (m-40) cc_final: 0.6997 (t0) REVERT: B 1160 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7809 (ttp-110) outliers start: 21 outliers final: 12 residues processed: 166 average time/residue: 0.2838 time to fit residues: 66.4457 Evaluate side-chains 161 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 1.248 ------------------------------------------------------------------------------- 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 48 SER 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 449 ILE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 900 ASP Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1036 ILE Chi-restraints excluded: chain B residue 1080 LEU Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1160 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 133 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 71 optimal weight: 0.0170 chunk 92 optimal weight: 4.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.5092 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= 0.215 Angle : 0.640 11.120 17491 Z= 0.327 Chirality : 0.043 0.313 1970 Planarity : 0.004 0.043 2057 Dihedral : 18.752 85.754 2319 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.63 % Allowed : 17.72 % Favored : 80.65 % 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: -0.74 (0.22), residues: 1400 helix: 0.57 (0.19), residues: 735 sheet: -1.92 (0.38), residues: 159 loop : -1.50 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B1105 HIS 0.008 0.001 HIS B 756 PHE 0.017 0.001 PHE A 207 TYR 0.020 0.001 TYR B 445 ARG 0.008 0.001 ARG B1141 ********************** 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 165 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3098 (tpp) cc_final: 0.1466 (ptt) REVERT: A 14 ASN cc_start: 0.7748 (p0) cc_final: 0.7540 (t0) REVERT: A 78 ARG cc_start: 0.5970 (mmt-90) cc_final: 0.5178 (mpt180) REVERT: A 86 PHE cc_start: 0.5670 (m-80) cc_final: 0.5421 (m-80) REVERT: A 231 GLN cc_start: 0.6637 (OUTLIER) cc_final: 0.5191 (mp-120) REVERT: B 102 ARG cc_start: 0.7767 (mmm-85) cc_final: 0.7287 (ttm-80) REVERT: B 234 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6636 (pp20) REVERT: B 304 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7430 (mt-10) REVERT: B 417 ASN cc_start: 0.7024 (m-40) cc_final: 0.6682 (m110) REVERT: B 696 ARG cc_start: 0.7405 (mmm-85) cc_final: 0.7131 (mmm-85) REVERT: B 729 HIS cc_start: 0.6562 (m90) cc_final: 0.6309 (m90) REVERT: B 843 ARG cc_start: 0.7773 (pmt170) cc_final: 0.7177 (mmt-90) REVERT: B 912 GLU cc_start: 0.7223 (tm-30) cc_final: 0.6825 (tm-30) REVERT: B 922 GLU cc_start: 0.7465 (mt-10) cc_final: 0.6860 (tp30) REVERT: B 1036 ILE cc_start: 0.4841 (OUTLIER) cc_final: 0.4447 (mm) REVERT: B 1102 MET cc_start: 0.7037 (mmt) cc_final: 0.6400 (mmm) REVERT: B 1158 ASN cc_start: 0.7731 (m-40) cc_final: 0.6924 (t0) REVERT: B 1160 ARG cc_start: 0.8137 (ptp90) cc_final: 0.7592 (ttp-110) outliers start: 19 outliers final: 13 residues processed: 158 average time/residue: 0.2816 time to fit residues: 63.3556 Evaluate side-chains 158 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 GLN 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 449 ILE 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 641 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 900 ASP Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1036 ILE Chi-restraints excluded: chain B residue 1137 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 119 optimal weight: 0.1980 chunk 14 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4900 r_free = 0.4900 target = 0.225832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.188226 restraints weight = 18214.870| |-----------------------------------------------------------------------------| r_work (start): 0.4526 rms_B_bonded: 2.28 r_work: 0.4378 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.5202 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= 0.201 Angle : 0.628 10.602 17491 Z= 0.322 Chirality : 0.043 0.301 1970 Planarity : 0.004 0.043 2057 Dihedral : 18.718 85.332 2319 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.28 % Allowed : 17.89 % 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: -0.71 (0.22), residues: 1400 helix: 0.63 (0.19), residues: 728 sheet: -1.89 (0.38), residues: 158 loop : -1.52 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B1105 HIS 0.008 0.001 HIS B 756 PHE 0.011 0.001 PHE B 927 TYR 0.019 0.001 TYR B 445 ARG 0.008 0.001 ARG B1141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2720.38 seconds wall clock time: 50 minutes 34.61 seconds (3034.61 seconds total)