Starting phenix.real_space_refine on Sat Jul 20 22:32:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxy_43643/07_2024/8vxy_43643.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxy_43643/07_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_43643/07_2024/8vxy_43643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxy_43643/07_2024/8vxy_43643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxy_43643/07_2024/8vxy_43643.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxy_43643/07_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-5388/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: 7.07, per 1000 atoms: 0.57 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: 5.26 Conformation dependent library (CDL) restraints added in 2.0 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: 4.33 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: 5.43 Time building geometry restraints manager: 5.74 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 2.440 nonbonded pdb=" O GLU B 367 " pdb=" OG SER B 371 " model vdw 2.224 2.440 nonbonded pdb=" O ARG B 317 " pdb=" NH2 ARG B 462 " model vdw 2.232 2.520 nonbonded pdb=" OG1 THR B 357 " pdb=" OG SER B 363 " model vdw 2.234 2.440 nonbonded pdb=" O ASN B 773 " pdb=" OH TYR B 861 " model vdw 2.239 2.440 ... (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 ========== 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: 0.770 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: 0.100 Set scattering table: 0.120 Process input model: 39.870 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.190 ------------------------------------------------------------------------------- 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 : 1.257 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: 0.3096 time to fit residues: 108.4239 Evaluate side-chains 153 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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: 3.9990 chunk 110 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 85 optimal weight: 0.1980 chunk 132 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS A 130 GLN A 231 GLN A 241 HIS ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 ASN B 494 ASN B 502 GLN B 684 HIS B 772 ASN B 836 GLN B 959 GLN B1026 GLN B1068 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12691 Z= 0.203 Angle : 0.616 10.048 17491 Z= 0.327 Chirality : 0.041 0.174 1970 Planarity : 0.004 0.040 2057 Dihedral : 19.150 88.538 2319 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.03 % Allowed : 8.13 % Favored : 90.84 % 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: -0.30 (0.23), residues: 1400 helix: 0.81 (0.20), residues: 723 sheet: -1.06 (0.43), residues: 156 loop : -1.28 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 797 HIS 0.020 0.002 HIS B1068 PHE 0.021 0.002 PHE B 199 TYR 0.018 0.001 TYR B 445 ARG 0.006 0.000 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 202 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 190 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2313 (tpp) cc_final: 0.0827 (ptt) REVERT: A 14 ASN cc_start: 0.7873 (p0) cc_final: 0.7331 (t0) REVERT: A 86 PHE cc_start: 0.5660 (m-80) cc_final: 0.5435 (m-80) REVERT: A 152 GLU cc_start: 0.7656 (pt0) cc_final: 0.7251 (pp20) REVERT: A 215 GLU cc_start: 0.7159 (tt0) cc_final: 0.6636 (tp30) REVERT: B 23 ARG cc_start: 0.7355 (mtm-85) cc_final: 0.6489 (mtp85) REVERT: B 335 LYS cc_start: 0.7442 (mttm) cc_final: 0.7199 (mtmt) REVERT: B 457 ASP cc_start: 0.7410 (p0) cc_final: 0.7034 (p0) REVERT: B 755 MET cc_start: 0.5011 (ptm) cc_final: 0.4733 (ptp) REVERT: B 827 ASP cc_start: 0.8669 (m-30) cc_final: 0.8396 (m-30) REVERT: B 840 GLN cc_start: 0.6534 (mm-40) cc_final: 0.6213 (pp30) REVERT: B 860 ARG cc_start: 0.6951 (mmt180) cc_final: 0.6684 (mtp-110) REVERT: B 1083 LEU cc_start: 0.5190 (tp) cc_final: 0.4505 (tp) REVERT: B 1102 MET cc_start: 0.7000 (mmt) cc_final: 0.6550 (mmm) REVERT: B 1160 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8129 (ttp-110) outliers start: 12 outliers final: 2 residues processed: 197 average time/residue: 0.2806 time to fit residues: 77.4851 Evaluate side-chains 150 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 147 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 844 ASP 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: 0.8980 chunk 41 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12691 Z= 0.210 Angle : 0.589 8.641 17491 Z= 0.316 Chirality : 0.041 0.202 1970 Planarity : 0.004 0.043 2057 Dihedral : 19.110 88.353 2319 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.46 % Allowed : 11.39 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.41 (0.23), residues: 1400 helix: 0.78 (0.20), residues: 726 sheet: -1.32 (0.41), residues: 156 loop : -1.37 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B1105 HIS 0.006 0.001 HIS B1064 PHE 0.018 0.002 PHE B1171 TYR 0.018 0.001 TYR B 445 ARG 0.004 0.000 ARG B 871 *********************** 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: 17 poor density : 178 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2427 (tpp) cc_final: 0.0910 (ptt) REVERT: A 14 ASN cc_start: 0.7839 (p0) cc_final: 0.7337 (t0) REVERT: A 86 PHE cc_start: 0.5631 (m-80) cc_final: 0.5407 (m-80) REVERT: B 23 ARG cc_start: 0.7451 (mtm-85) cc_final: 0.6537 (mtp85) REVERT: B 102 ARG cc_start: 0.7481 (mtp180) cc_final: 0.7167 (ttm-80) REVERT: B 140 ILE cc_start: 0.6680 (mt) cc_final: 0.6223 (mm) REVERT: B 335 LYS cc_start: 0.7484 (mttm) cc_final: 0.7143 (mtmt) REVERT: B 790 ARG cc_start: 0.7198 (tmm-80) cc_final: 0.6965 (tmm-80) REVERT: B 800 GLN cc_start: 0.6701 (mt0) cc_final: 0.6340 (pt0) REVERT: B 840 GLN cc_start: 0.6521 (mm-40) cc_final: 0.6167 (pp30) REVERT: B 860 ARG cc_start: 0.6908 (mmt180) cc_final: 0.6707 (mtp-110) REVERT: B 900 ASP cc_start: 0.7215 (t0) cc_final: 0.6679 (t0) REVERT: B 922 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: B 979 MET cc_start: 0.5546 (ptp) cc_final: 0.5176 (ptp) REVERT: B 1083 LEU cc_start: 0.5594 (tp) cc_final: 0.5133 (mp) REVERT: B 1102 MET cc_start: 0.6919 (mmt) cc_final: 0.6408 (mmm) REVERT: B 1160 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8191 (ttp-110) outliers start: 17 outliers final: 8 residues processed: 191 average time/residue: 0.2728 time to fit residues: 72.6531 Evaluate side-chains 161 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 151 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 126 SER Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 844 ASP Chi-restraints excluded: chain B residue 922 GLU 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: 3.9990 chunk 99 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 63 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 133 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 423 ASN B 502 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.3212 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= 0.202 Angle : 0.577 8.139 17491 Z= 0.308 Chirality : 0.040 0.215 1970 Planarity : 0.004 0.042 2057 Dihedral : 19.054 88.079 2319 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.88 % Allowed : 13.27 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.41 (0.23), residues: 1400 helix: 0.80 (0.20), residues: 721 sheet: -1.36 (0.40), residues: 157 loop : -1.38 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B1105 HIS 0.004 0.001 HIS B1064 PHE 0.014 0.001 PHE B 718 TYR 0.017 0.001 TYR A 19 ARG 0.010 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 188 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2384 (tpp) cc_final: 0.0889 (ptt) REVERT: A 14 ASN cc_start: 0.7836 (p0) cc_final: 0.7369 (t0) REVERT: A 86 PHE cc_start: 0.5674 (m-80) cc_final: 0.5401 (m-80) REVERT: B 23 ARG cc_start: 0.7526 (mtm-85) cc_final: 0.6509 (mtp85) REVERT: B 102 ARG cc_start: 0.7392 (mtp180) cc_final: 0.7092 (ttm-80) REVERT: B 234 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6424 (pp20) REVERT: B 335 LYS cc_start: 0.7481 (mttm) cc_final: 0.7150 (mtmt) REVERT: B 790 ARG cc_start: 0.7349 (tmm-80) cc_final: 0.6954 (tmm-80) REVERT: B 840 GLN cc_start: 0.6378 (mm-40) cc_final: 0.6116 (pp30) REVERT: B 860 ARG cc_start: 0.6990 (mmt180) cc_final: 0.6770 (mtp-110) REVERT: B 900 ASP cc_start: 0.7352 (t0) cc_final: 0.6986 (t70) REVERT: B 922 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: B 1102 MET cc_start: 0.6965 (mmt) cc_final: 0.6448 (mmm) REVERT: B 1160 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8303 (ttp-110) outliers start: 22 outliers final: 13 residues processed: 180 average time/residue: 0.3096 time to fit residues: 77.9406 Evaluate side-chains 166 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 150 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 101 SER Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain B residue 844 ASP Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 1108 THR 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: 3.9990 chunk 80 optimal weight: 0.8980 chunk 2 optimal weight: 20.0000 chunk 105 optimal weight: 0.0570 chunk 58 optimal weight: 0.5980 chunk 120 optimal weight: 0.8980 chunk 97 optimal weight: 0.0050 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 overall best weight: 0.4512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 ASN B 729 HIS B 989 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 moved from start: 0.3485 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= 0.176 Angle : 0.565 7.260 17491 Z= 0.301 Chirality : 0.040 0.216 1970 Planarity : 0.004 0.041 2057 Dihedral : 18.992 87.753 2319 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.23 % Allowed : 13.96 % Favored : 83.82 % 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: -0.33 (0.23), residues: 1400 helix: 0.87 (0.20), residues: 730 sheet: -1.45 (0.40), residues: 156 loop : -1.33 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B1105 HIS 0.003 0.001 HIS B 260 PHE 0.013 0.001 PHE B 718 TYR 0.016 0.001 TYR B 445 ARG 0.005 0.000 ARG B 345 *********************** 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 198 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 172 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2558 (tpp) cc_final: 0.0999 (ptt) REVERT: A 14 ASN cc_start: 0.7772 (p0) cc_final: 0.7317 (t0) REVERT: A 78 ARG cc_start: 0.5924 (mmt-90) cc_final: 0.4919 (mmt180) REVERT: A 86 PHE cc_start: 0.5647 (m-80) cc_final: 0.5399 (m-80) REVERT: B 102 ARG cc_start: 0.7402 (mtp180) cc_final: 0.7086 (ttm-80) REVERT: B 231 ARG cc_start: 0.4411 (ttm110) cc_final: 0.4053 (ttm170) REVERT: B 234 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6531 (pp20) REVERT: B 417 ASN cc_start: 0.6744 (m-40) cc_final: 0.6334 (m110) REVERT: B 583 GLU cc_start: 0.6869 (tm-30) cc_final: 0.6665 (mm-30) REVERT: B 790 ARG cc_start: 0.7331 (tmm-80) cc_final: 0.6990 (tmm-80) REVERT: B 840 GLN cc_start: 0.6146 (mm-40) cc_final: 0.5870 (pp30) REVERT: B 918 THR cc_start: 0.6658 (t) cc_final: 0.6316 (t) REVERT: B 922 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7337 (mp0) REVERT: B 1021 SER cc_start: 0.5685 (OUTLIER) cc_final: 0.5391 (m) REVERT: B 1102 MET cc_start: 0.6996 (mmt) cc_final: 0.6406 (mmm) REVERT: B 1160 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8328 (ttp-110) outliers start: 26 outliers final: 15 residues processed: 190 average time/residue: 0.2823 time to fit residues: 74.8025 Evaluate side-chains 161 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 101 SER Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 211 MET 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 617 GLU Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 672 ASN Chi-restraints excluded: chain B residue 844 ASP Chi-restraints excluded: chain B residue 881 LEU 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 1160 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 8.9990 chunk 127 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 65 optimal weight: 0.0970 chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- 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 729 HIS B 756 HIS B1097 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12691 Z= 0.278 Angle : 0.629 10.515 17491 Z= 0.329 Chirality : 0.042 0.238 1970 Planarity : 0.004 0.045 2057 Dihedral : 19.022 88.095 2319 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.31 % Allowed : 15.15 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.58 (0.22), residues: 1400 helix: 0.65 (0.19), residues: 742 sheet: -1.54 (0.39), residues: 157 loop : -1.50 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B1105 HIS 0.013 0.002 HIS B 756 PHE 0.022 0.002 PHE B 602 TYR 0.022 0.002 TYR B 445 ARG 0.006 0.000 ARG B 31 *********************** 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 177 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2640 (tpp) cc_final: 0.1044 (ptt) REVERT: A 14 ASN cc_start: 0.7787 (p0) cc_final: 0.7349 (t0) REVERT: A 78 ARG cc_start: 0.5961 (mmt-90) cc_final: 0.5002 (mmt180) REVERT: A 86 PHE cc_start: 0.5646 (m-80) cc_final: 0.5380 (m-80) REVERT: A 145 MET cc_start: 0.6740 (mtt) cc_final: 0.6469 (mtt) REVERT: B 72 LEU cc_start: 0.6421 (mt) cc_final: 0.6179 (mt) REVERT: B 102 ARG cc_start: 0.7471 (mtp180) cc_final: 0.7157 (ttm110) REVERT: B 234 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6538 (pp20) REVERT: B 417 ASN cc_start: 0.6856 (m-40) cc_final: 0.6439 (m110) REVERT: B 790 ARG cc_start: 0.7286 (tmm-80) cc_final: 0.6924 (tmm-80) REVERT: B 840 GLN cc_start: 0.6240 (mm-40) cc_final: 0.5899 (pp30) REVERT: B 912 GLU cc_start: 0.6748 (tm-30) cc_final: 0.6488 (tm-30) REVERT: B 922 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: B 1021 SER cc_start: 0.5864 (OUTLIER) cc_final: 0.5581 (m) REVERT: B 1102 MET cc_start: 0.7106 (mmt) cc_final: 0.6439 (mmm) REVERT: B 1160 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8287 (ttp-110) outliers start: 27 outliers final: 15 residues processed: 168 average time/residue: 0.2977 time to fit residues: 70.0127 Evaluate side-chains 152 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 211 MET 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 624 SER Chi-restraints excluded: chain B residue 844 ASP Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1108 THR 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: 0.0980 chunk 15 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 88 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 729 HIS B1026 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12691 Z= 0.186 Angle : 0.578 10.664 17491 Z= 0.305 Chirality : 0.041 0.220 1970 Planarity : 0.004 0.042 2057 Dihedral : 18.894 87.061 2319 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.54 % Allowed : 16.61 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.43 (0.23), residues: 1400 helix: 0.81 (0.20), residues: 737 sheet: -1.60 (0.39), residues: 157 loop : -1.42 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B1105 HIS 0.003 0.001 HIS B 260 PHE 0.013 0.001 PHE B 602 TYR 0.018 0.001 TYR A 19 ARG 0.004 0.000 ARG B 231 *********************** 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 166 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2632 (tpp) cc_final: 0.1060 (ptt) REVERT: A 14 ASN cc_start: 0.7711 (p0) cc_final: 0.7304 (t0) REVERT: A 78 ARG cc_start: 0.5941 (mmt-90) cc_final: 0.5191 (mmt180) REVERT: A 86 PHE cc_start: 0.5627 (m-80) cc_final: 0.5397 (m-80) REVERT: B 102 ARG cc_start: 0.7464 (mtp180) cc_final: 0.7152 (ttm110) REVERT: B 234 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6532 (pp20) REVERT: B 417 ASN cc_start: 0.6975 (m-40) cc_final: 0.6472 (m110) REVERT: B 583 GLU cc_start: 0.7009 (tm-30) cc_final: 0.6698 (mm-30) REVERT: B 680 MET cc_start: 0.7023 (mmp) cc_final: 0.6810 (mmp) REVERT: B 827 ASP cc_start: 0.8766 (m-30) cc_final: 0.8503 (m-30) REVERT: B 840 GLN cc_start: 0.6218 (mm-40) cc_final: 0.5934 (pp30) REVERT: B 912 GLU cc_start: 0.6663 (tm-30) cc_final: 0.6415 (tm-30) REVERT: B 922 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: B 1021 SER cc_start: 0.6010 (OUTLIER) cc_final: 0.5745 (m) REVERT: B 1102 MET cc_start: 0.6976 (mmt) cc_final: 0.6379 (mmm) REVERT: B 1160 ARG cc_start: 0.8618 (ptp90) cc_final: 0.8289 (ttp-110) outliers start: 18 outliers final: 13 residues processed: 159 average time/residue: 0.2858 time to fit residues: 63.7829 Evaluate side-chains 149 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 211 MET 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 519 VAL Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain B residue 844 ASP Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1108 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 110 optimal weight: 0.0070 chunk 128 optimal weight: 5.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 729 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12691 Z= 0.240 Angle : 0.612 9.583 17491 Z= 0.320 Chirality : 0.042 0.233 1970 Planarity : 0.004 0.044 2057 Dihedral : 18.859 87.238 2319 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.63 % Allowed : 17.21 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.62 (0.22), residues: 1400 helix: 0.64 (0.19), residues: 738 sheet: -1.70 (0.39), residues: 157 loop : -1.47 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B1105 HIS 0.004 0.001 HIS A 167 PHE 0.033 0.002 PHE B 602 TYR 0.026 0.002 TYR B 769 ARG 0.007 0.000 ARG B 696 *********************** 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 163 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 1.299 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: 0.2892 (tpp) cc_final: 0.1226 (ptt) REVERT: A 14 ASN cc_start: 0.7691 (p0) cc_final: 0.7290 (t0) REVERT: A 78 ARG cc_start: 0.5999 (mmt-90) cc_final: 0.5280 (mmt180) REVERT: A 86 PHE cc_start: 0.5623 (m-80) cc_final: 0.5388 (m-80) REVERT: A 170 MET cc_start: 0.5334 (mmm) cc_final: 0.4986 (mmm) REVERT: B 102 ARG cc_start: 0.7547 (mtp180) cc_final: 0.7254 (ttm110) REVERT: B 234 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6609 (pp20) REVERT: B 417 ASN cc_start: 0.6887 (m-40) cc_final: 0.6500 (m110) REVERT: B 696 ARG cc_start: 0.7388 (mmm-85) cc_final: 0.7145 (mmm-85) REVERT: B 840 GLN cc_start: 0.6154 (mm-40) cc_final: 0.5875 (pp30) REVERT: B 912 GLU cc_start: 0.6794 (tm-30) cc_final: 0.6536 (tm-30) REVERT: B 922 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: B 1021 SER cc_start: 0.6078 (OUTLIER) cc_final: 0.5755 (m) REVERT: B 1080 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7484 (mm) REVERT: B 1102 MET cc_start: 0.7052 (mmt) cc_final: 0.6442 (mmm) REVERT: B 1160 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8296 (ttp-110) outliers start: 19 outliers final: 11 residues processed: 157 average time/residue: 0.3020 time to fit residues: 65.9885 Evaluate side-chains 154 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 138 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 211 MET 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 519 VAL Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain B residue 844 ASP Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1080 LEU Chi-restraints excluded: chain B residue 1108 THR 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: 0.0470 chunk 122 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 729 HIS B1026 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.4636 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= 0.192 Angle : 0.583 10.192 17491 Z= 0.306 Chirality : 0.041 0.231 1970 Planarity : 0.004 0.042 2057 Dihedral : 18.809 86.260 2319 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.37 % Allowed : 17.72 % Favored : 80.91 % 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: -0.48 (0.22), residues: 1400 helix: 0.76 (0.20), residues: 740 sheet: -1.68 (0.39), residues: 156 loop : -1.41 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B1105 HIS 0.004 0.001 HIS B 260 PHE 0.029 0.002 PHE B 602 TYR 0.020 0.001 TYR B 769 ARG 0.007 0.000 ARG B 696 *********************** 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 161 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2710 (tpp) cc_final: 0.1151 (ptt) REVERT: A 14 ASN cc_start: 0.7697 (p0) cc_final: 0.7318 (t0) REVERT: A 78 ARG cc_start: 0.6000 (mmt-90) cc_final: 0.5280 (mmt180) REVERT: A 170 MET cc_start: 0.5375 (mmm) cc_final: 0.5027 (mmm) REVERT: B 102 ARG cc_start: 0.7542 (mtp180) cc_final: 0.7253 (ttm110) REVERT: B 234 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6603 (pp20) REVERT: B 417 ASN cc_start: 0.6666 (m-40) cc_final: 0.6352 (m-40) REVERT: B 680 MET cc_start: 0.7057 (mmt) cc_final: 0.6664 (mmp) REVERT: B 696 ARG cc_start: 0.7316 (mmm-85) cc_final: 0.7070 (mmm-85) REVERT: B 840 GLN cc_start: 0.6106 (mm-40) cc_final: 0.5874 (pp30) REVERT: B 922 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: B 1021 SER cc_start: 0.6132 (OUTLIER) cc_final: 0.5857 (m) REVERT: B 1102 MET cc_start: 0.7047 (mmt) cc_final: 0.6432 (mmm) REVERT: B 1160 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8273 (ttp-110) outliers start: 16 outliers final: 8 residues processed: 156 average time/residue: 0.2801 time to fit residues: 61.1821 Evaluate side-chains 151 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 234 GLU 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 623 HIS Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1108 THR 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: 6.9990 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 133 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 89 optimal weight: 0.1980 chunk 71 optimal weight: 0.7980 chunk 92 optimal weight: 0.0070 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 729 HIS B1026 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12691 Z= 0.184 Angle : 0.579 9.951 17491 Z= 0.304 Chirality : 0.042 0.516 1970 Planarity : 0.004 0.040 2057 Dihedral : 18.751 86.001 2319 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.11 % Allowed : 17.89 % Favored : 80.99 % 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: -0.40 (0.23), residues: 1400 helix: 0.79 (0.20), residues: 729 sheet: -1.57 (0.40), residues: 156 loop : -1.30 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B1105 HIS 0.004 0.001 HIS B 260 PHE 0.026 0.001 PHE B 602 TYR 0.020 0.001 TYR B 769 ARG 0.007 0.000 ARG B 696 ********************** 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 160 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2648 (tpp) cc_final: 0.1097 (ptt) REVERT: A 14 ASN cc_start: 0.7681 (p0) cc_final: 0.7318 (t0) REVERT: A 78 ARG cc_start: 0.5967 (mmt-90) cc_final: 0.5278 (mmt180) REVERT: A 81 ASP cc_start: 0.6092 (m-30) cc_final: 0.5701 (t0) REVERT: A 170 MET cc_start: 0.5414 (mmm) cc_final: 0.5080 (mmm) REVERT: B 58 TYR cc_start: 0.7290 (t80) cc_final: 0.7062 (t80) REVERT: B 102 ARG cc_start: 0.7582 (mtp180) cc_final: 0.7249 (ttm110) REVERT: B 234 GLU cc_start: 0.6975 (pt0) cc_final: 0.6596 (pp20) REVERT: B 417 ASN cc_start: 0.6677 (m-40) cc_final: 0.6373 (m-40) REVERT: B 583 GLU cc_start: 0.7050 (tm-30) cc_final: 0.6689 (mm-30) REVERT: B 645 TYR cc_start: 0.7307 (t80) cc_final: 0.6887 (t80) REVERT: B 680 MET cc_start: 0.6983 (mmt) cc_final: 0.6398 (mmm) REVERT: B 696 ARG cc_start: 0.7435 (mmm-85) cc_final: 0.7197 (mmm-85) REVERT: B 840 GLN cc_start: 0.6121 (mm-40) cc_final: 0.5893 (pp30) REVERT: B 918 THR cc_start: 0.6805 (t) cc_final: 0.6388 (t) REVERT: B 922 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: B 1021 SER cc_start: 0.6146 (OUTLIER) cc_final: 0.5872 (m) REVERT: B 1102 MET cc_start: 0.7060 (mmt) cc_final: 0.6449 (mmm) REVERT: B 1160 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8261 (ttp-110) outliers start: 13 outliers final: 7 residues processed: 157 average time/residue: 0.2869 time to fit residues: 63.7149 Evaluate side-chains 151 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 141 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 519 VAL 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 1108 THR 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 123 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 119 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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** B 729 HIS B 836 GLN B1067 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.226078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.189370 restraints weight = 17966.552| |-----------------------------------------------------------------------------| r_work (start): 0.4545 rms_B_bonded: 2.23 r_work: 0.4398 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.4275 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12691 Z= 0.295 Angle : 0.665 12.340 17491 Z= 0.343 Chirality : 0.045 0.411 1970 Planarity : 0.005 0.048 2057 Dihedral : 18.834 86.611 2319 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.03 % Allowed : 18.15 % 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: -0.75 (0.22), residues: 1400 helix: 0.58 (0.19), residues: 725 sheet: -1.77 (0.39), residues: 150 loop : -1.57 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B1105 HIS 0.006 0.001 HIS A 167 PHE 0.032 0.002 PHE B 602 TYR 0.023 0.002 TYR B 445 ARG 0.006 0.001 ARG B 345 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3040.58 seconds wall clock time: 54 minutes 44.11 seconds (3284.11 seconds total)