Starting phenix.real_space_refine on Mon Apr 8 03:03:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxy_43643/04_2024/8vxy_43643_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxy_43643/04_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_43643/04_2024/8vxy_43643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxy_43643/04_2024/8vxy_43643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxy_43643/04_2024/8vxy_43643_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxy_43643/04_2024/8vxy_43643_updated.pdb" } 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-5288/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: 6.90, per 1000 atoms: 0.56 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: 5.34 Conformation dependent library (CDL) restraints added in 2.2 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... running ksdssp... Secondary structure from input PDB file: 64 helices and 6 sheets defined 49.7% alpha, 6.3% beta 27 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 6.57 Creating SS restraints... Processing helix chain 'A' and resid 29 through 40 removed outlier: 4.664A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LEU A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 58 removed outlier: 3.506A pdb=" N LEU A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 77 through 94 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) Processing helix chain 'A' and resid 147 through 162 removed outlier: 5.274A pdb=" N GLU A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLN A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 179 Processing helix chain 'A' and resid 182 through 193 Processing helix chain 'A' and resid 199 through 201 No H-bonds generated for 'chain 'A' and resid 199 through 201' Processing helix chain 'A' and resid 214 through 223 Processing helix chain 'A' and resid 241 through 244 No H-bonds generated for 'chain 'A' and resid 241 through 244' Processing helix chain 'B' and resid 5 through 15 Processing helix chain 'B' and resid 24 through 33 Processing helix chain 'B' and resid 49 through 71 removed outlier: 4.204A pdb=" N SER B 52 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 70 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 94 Processing helix chain 'B' and resid 104 through 117 Processing helix chain 'B' and resid 121 through 130 removed outlier: 3.593A pdb=" N MET B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 148 Processing helix chain 'B' and resid 152 through 165 Processing helix chain 'B' and resid 170 through 181 Processing helix chain 'B' and resid 195 through 223 removed outlier: 3.905A pdb=" N ASP B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 246 Processing helix chain 'B' and resid 249 through 268 removed outlier: 4.060A pdb=" N HIS B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 273 No H-bonds generated for 'chain 'B' and resid 270 through 273' Processing helix chain 'B' and resid 286 through 298 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 312 through 318 removed outlier: 4.261A pdb=" N GLY B 316 " --> pdb=" O ARG B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 349 Processing helix chain 'B' and resid 360 through 374 removed outlier: 3.573A pdb=" N THR B 373 " --> pdb=" O THR B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 3.848A pdb=" N ARG B 399 " --> pdb=" O GLU B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 417 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 422 removed outlier: 3.573A pdb=" N ILE B 422 " --> pdb=" O PRO B 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 419 through 422' Processing helix chain 'B' and resid 440 through 454 removed outlier: 3.557A pdb=" N TYR B 445 " --> pdb=" O ARG B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 460 No H-bonds generated for 'chain 'B' and resid 458 through 460' Processing helix chain 'B' and resid 474 through 483 removed outlier: 3.594A pdb=" N PHE B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 567 removed outlier: 3.561A pdb=" N ALA B 562 " --> pdb=" O CYS B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 583 through 595 removed outlier: 3.552A pdb=" N GLU B 587 " --> pdb=" O PRO B 584 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 589 " --> pdb=" O ALA B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 608 No H-bonds generated for 'chain 'B' and resid 606 through 608' Processing helix chain 'B' and resid 610 through 617 Processing helix chain 'B' and resid 625 through 632 Processing helix chain 'B' and resid 643 through 654 removed outlier: 3.796A pdb=" N GLU B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 removed outlier: 4.090A pdb=" N GLY B 670 " --> pdb=" O LEU B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 701 Processing helix chain 'B' and resid 721 through 732 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) Processing helix chain 'B' and resid 743 through 758 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 764 through 771 removed outlier: 4.134A pdb=" N THR B 767 " --> pdb=" O LYS B 764 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 770 " --> pdb=" O THR B 767 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR B 771 " --> pdb=" O GLU B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 811 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 822 through 829 Processing helix chain 'B' and resid 834 through 841 removed outlier: 3.607A pdb=" N ARG B 841 " --> pdb=" O ARG B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 865 removed outlier: 3.941A pdb=" N LEU B 850 " --> pdb=" O ASN B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 877 Processing helix chain 'B' and resid 881 through 902 removed outlier: 3.854A pdb=" N ILE B 890 " --> pdb=" O ARG B 886 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA B 891 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ALA B 892 " --> pdb=" O ASP B 888 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LYS B 893 " --> pdb=" O ALA B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 924 Processing helix chain 'B' and resid 928 through 930 No H-bonds generated for 'chain 'B' and resid 928 through 930' Processing helix chain 'B' and resid 938 through 941 No H-bonds generated for 'chain 'B' and resid 938 through 941' Processing helix chain 'B' and resid 943 through 947 removed outlier: 3.858A pdb=" N LEU B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 943 through 947' Processing helix chain 'B' and resid 962 through 965 No H-bonds generated for 'chain 'B' and resid 962 through 965' Processing helix chain 'B' and resid 967 through 970 No H-bonds generated for 'chain 'B' and resid 967 through 970' Processing helix chain 'B' and resid 975 through 989 removed outlier: 3.686A pdb=" N THR B 987 " --> pdb=" O ARG B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1012 removed outlier: 3.824A pdb=" N ALA B1008 " --> pdb=" O LEU B1005 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL B1009 " --> pdb=" O GLY B1006 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA B1010 " --> pdb=" O PHE B1007 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B1012 " --> pdb=" O VAL B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1026 Processing helix chain 'B' and resid 1034 through 1039 Processing helix chain 'B' and resid 1049 through 1057 Processing helix chain 'B' and resid 1060 through 1066 Processing helix chain 'B' and resid 1075 through 1078 No H-bonds generated for 'chain 'B' and resid 1075 through 1078' Processing sheet with id= A, 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) Processing sheet with id= B, first strand: chain 'A' and resid 120 through 126 Processing sheet with id= C, first strand: chain 'B' and resid 326 through 328 removed outlier: 7.842A pdb=" N VAL B 327 " --> pdb=" O ILE B 463 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N CYS B 465 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL B 354 " --> pdb=" O ILE B 429 " (cutoff:3.500A) 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) Processing sheet with id= D, first strand: chain 'B' and resid 524 through 526 removed outlier: 4.498A pdb=" N ALA B 524 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL B 713 " --> pdb=" O GLY B 504 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL B 506 " --> pdb=" O VAL B 713 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR B 715 " --> pdb=" O VAL B 506 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N TRP B 508 " --> pdb=" O TYR B 715 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE B 717 " --> pdb=" O TRP B 508 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 1099 through 1102 removed outlier: 3.770A pdb=" N GLU B1153 " --> pdb=" O MET B1162 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 1117 through 1121 removed outlier: 4.029A pdb=" N HIS B1125 " --> pdb=" O ILE B1138 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B1127 " --> pdb=" O GLY B1136 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY B1136 " --> pdb=" O VAL B1127 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1242 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: 5.77 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: 1609 2.75 - 3.29: 12886 3.29 - 3.83: 22600 3.83 - 4.36: 26386 4.36 - 4.90: 42161 Nonbonded interactions: 105642 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 105637 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: 1.480 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: 4.170 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 40.890 Find NCS groups from input model: 0.320 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.060 ------------------------------------------------------------------------------- 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= 0.179 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 : 1.203 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: 0.3252 time to fit residues: 114.0391 Evaluate side-chains 153 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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: 1.9990 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 0.0040 chunk 74 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- 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 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 HIS B 836 GLN B 959 GLN B1026 GLN B1068 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 moved from start: 0.2192 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= 0.212 Angle : 0.616 10.255 17491 Z= 0.326 Chirality : 0.041 0.182 1970 Planarity : 0.005 0.042 2057 Dihedral : 19.147 88.572 2319 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.03 % Allowed : 8.56 % Favored : 90.41 % 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: -0.46 (0.22), residues: 1400 helix: 0.64 (0.20), residues: 693 sheet: -1.11 (0.43), residues: 145 loop : -1.22 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 797 HIS 0.021 0.002 HIS B1068 PHE 0.026 0.002 PHE B 199 TYR 0.019 0.001 TYR B 445 ARG 0.006 0.001 ARG B 983 *********************** 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 199 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 187 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2331 (tpp) cc_final: 0.0838 (ptt) REVERT: A 14 ASN cc_start: 0.7933 (p0) cc_final: 0.7353 (t0) REVERT: A 86 PHE cc_start: 0.5685 (m-80) cc_final: 0.5483 (m-80) REVERT: A 152 GLU cc_start: 0.7794 (pt0) cc_final: 0.7399 (pp20) REVERT: A 215 GLU cc_start: 0.7137 (tt0) cc_final: 0.6578 (tp30) REVERT: A 217 MET cc_start: 0.7434 (ptp) cc_final: 0.7141 (ptt) REVERT: B 23 ARG cc_start: 0.7347 (mtm-85) cc_final: 0.6478 (mtp85) REVERT: B 335 LYS cc_start: 0.7401 (mttm) cc_final: 0.7193 (mtmt) REVERT: B 840 GLN cc_start: 0.6808 (mm-40) cc_final: 0.6151 (pp30) REVERT: B 860 ARG cc_start: 0.6952 (mmt180) cc_final: 0.6686 (mtp-110) REVERT: B 900 ASP cc_start: 0.6939 (t70) cc_final: 0.6204 (t0) REVERT: B 1083 LEU cc_start: 0.5249 (tp) cc_final: 0.4525 (tp) REVERT: B 1102 MET cc_start: 0.7030 (mmt) cc_final: 0.6579 (mmm) REVERT: B 1160 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8131 (ttp-110) outliers start: 12 outliers final: 3 residues processed: 195 average time/residue: 0.2777 time to fit residues: 75.7721 Evaluate side-chains 155 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 151 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 926 THR 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: 0.9980 chunk 41 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 132 optimal weight: 0.0270 chunk 143 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 131 optimal weight: 0.0970 chunk 45 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 overall best weight: 0.5436 ------------------------------------------------------------------------------- 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 423 ASN B 989 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12691 Z= 0.179 Angle : 0.570 9.144 17491 Z= 0.304 Chirality : 0.040 0.149 1970 Planarity : 0.004 0.041 2057 Dihedral : 19.088 88.244 2319 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.28 % Allowed : 11.64 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.23), residues: 1400 helix: 0.71 (0.21), residues: 687 sheet: -1.08 (0.44), residues: 145 loop : -1.19 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B1105 HIS 0.006 0.001 HIS B1064 PHE 0.015 0.002 PHE B1171 TYR 0.016 0.001 TYR B 445 ARG 0.007 0.000 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 177 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 162 time to evaluate : 1.305 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: 0.2421 (tpp) cc_final: 0.0902 (ptt) REVERT: A 14 ASN cc_start: 0.7840 (p0) cc_final: 0.7348 (t0) REVERT: A 86 PHE cc_start: 0.5786 (m-80) cc_final: 0.5458 (m-80) REVERT: B 23 ARG cc_start: 0.7411 (mtm-85) cc_final: 0.6519 (mtp85) REVERT: B 140 ILE cc_start: 0.6857 (mt) cc_final: 0.6420 (tt) REVERT: B 234 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6606 (pp20) REVERT: B 335 LYS cc_start: 0.7583 (mttm) cc_final: 0.7278 (mtmt) REVERT: B 383 MET cc_start: 0.8665 (ptm) cc_final: 0.8463 (ptm) REVERT: B 583 GLU cc_start: 0.6878 (tm-30) cc_final: 0.6623 (mm-30) REVERT: B 790 ARG cc_start: 0.7198 (tmm-80) cc_final: 0.6959 (tmm-80) REVERT: B 800 GLN cc_start: 0.6702 (mt0) cc_final: 0.6340 (pt0) REVERT: B 840 GLN cc_start: 0.6670 (mm-40) cc_final: 0.6225 (pp30) REVERT: B 860 ARG cc_start: 0.6976 (mmt180) cc_final: 0.6716 (mtp-110) REVERT: B 922 GLU cc_start: 0.7651 (mt-10) cc_final: 0.6900 (tp30) REVERT: B 1083 LEU cc_start: 0.5471 (tp) cc_final: 0.5017 (mp) REVERT: B 1102 MET cc_start: 0.7264 (mmt) cc_final: 0.6787 (mmm) REVERT: B 1160 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8189 (ttp-110) outliers start: 15 outliers final: 8 residues processed: 174 average time/residue: 0.2837 time to fit residues: 69.2726 Evaluate side-chains 155 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 844 ASP Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 1021 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: 0.7980 chunk 99 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 14 optimal weight: 20.0000 chunk 63 optimal weight: 0.0980 chunk 89 optimal weight: 0.4980 chunk 133 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 126 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12691 Z= 0.171 Angle : 0.553 7.695 17491 Z= 0.294 Chirality : 0.040 0.153 1970 Planarity : 0.004 0.039 2057 Dihedral : 19.023 87.992 2319 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.46 % Allowed : 12.67 % Favored : 85.87 % 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: -0.37 (0.23), residues: 1400 helix: 0.71 (0.21), residues: 699 sheet: -1.05 (0.41), residues: 156 loop : -1.19 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B1105 HIS 0.005 0.001 HIS B1064 PHE 0.013 0.001 PHE B 718 TYR 0.021 0.001 TYR A 19 ARG 0.005 0.000 ARG B 231 *********************** 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 185 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 1.160 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: 0.2354 (tpp) cc_final: 0.0883 (ptt) REVERT: A 14 ASN cc_start: 0.7825 (p0) cc_final: 0.7372 (t0) REVERT: A 86 PHE cc_start: 0.5760 (m-80) cc_final: 0.5452 (m-80) REVERT: B 23 ARG cc_start: 0.7354 (mtm-85) cc_final: 0.6413 (mtp85) REVERT: B 140 ILE cc_start: 0.6754 (mt) cc_final: 0.6316 (mm) REVERT: B 234 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6428 (pp20) REVERT: B 335 LYS cc_start: 0.7492 (mttm) cc_final: 0.7182 (mtmt) REVERT: B 417 ASN cc_start: 0.6945 (m-40) cc_final: 0.6503 (m-40) REVERT: B 583 GLU cc_start: 0.6824 (tm-30) cc_final: 0.6618 (mm-30) REVERT: B 645 TYR cc_start: 0.7277 (t80) cc_final: 0.6875 (t80) REVERT: B 696 ARG cc_start: 0.7391 (mmm-85) cc_final: 0.7119 (mmm-85) REVERT: B 790 ARG cc_start: 0.7382 (tmm-80) cc_final: 0.6987 (tmm-80) REVERT: B 840 GLN cc_start: 0.6722 (mm-40) cc_final: 0.6272 (pp30) REVERT: B 860 ARG cc_start: 0.6966 (mmt180) cc_final: 0.6747 (mtp-110) REVERT: B 922 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7109 (tp30) REVERT: B 983 ARG cc_start: 0.8182 (ttp80) cc_final: 0.7890 (ttp-170) REVERT: B 1102 MET cc_start: 0.7137 (mmt) cc_final: 0.6660 (mmm) REVERT: B 1160 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8312 (ttp-110) outliers start: 17 outliers final: 12 residues processed: 181 average time/residue: 0.2578 time to fit residues: 64.6486 Evaluate side-chains 160 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 214 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 297 LEU 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 926 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 2 optimal weight: 20.0000 chunk 105 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 chunk 35 optimal weight: 0.4980 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 502 GLN B1026 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12691 Z= 0.184 Angle : 0.562 7.344 17491 Z= 0.298 Chirality : 0.040 0.149 1970 Planarity : 0.004 0.038 2057 Dihedral : 18.974 87.905 2319 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.05 % Allowed : 13.36 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.23), residues: 1400 helix: 0.62 (0.20), residues: 703 sheet: -1.07 (0.41), residues: 156 loop : -1.28 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B1105 HIS 0.003 0.001 HIS B 119 PHE 0.014 0.001 PHE B 718 TYR 0.018 0.001 TYR B 445 ARG 0.006 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 188 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 164 time to evaluate : 1.202 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: 0.2535 (tpp) cc_final: 0.0945 (ptt) REVERT: A 14 ASN cc_start: 0.7764 (p0) cc_final: 0.7320 (t0) REVERT: A 217 MET cc_start: 0.7205 (ptt) cc_final: 0.6894 (pmm) REVERT: A 236 LEU cc_start: 0.6110 (tt) cc_final: 0.5857 (mp) REVERT: B 23 ARG cc_start: 0.7521 (mtm-85) cc_final: 0.6532 (mtp85) REVERT: B 140 ILE cc_start: 0.6927 (mt) cc_final: 0.6454 (mm) REVERT: B 234 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6552 (pp20) REVERT: B 335 LYS cc_start: 0.7369 (mttm) cc_final: 0.7002 (mtmt) REVERT: B 381 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8024 (mt) REVERT: B 417 ASN cc_start: 0.6791 (m-40) cc_final: 0.6468 (m110) REVERT: B 645 TYR cc_start: 0.7232 (t80) cc_final: 0.6814 (t80) REVERT: B 696 ARG cc_start: 0.7408 (mmm-85) cc_final: 0.7126 (mmm-85) REVERT: B 712 LEU cc_start: 0.7951 (tp) cc_final: 0.7673 (mt) REVERT: B 790 ARG cc_start: 0.7328 (tmm-80) cc_final: 0.6981 (tmm-80) REVERT: B 840 GLN cc_start: 0.6651 (mm-40) cc_final: 0.6216 (pp30) REVERT: B 922 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7103 (tp30) REVERT: B 983 ARG cc_start: 0.8283 (ttp80) cc_final: 0.8036 (ttt-90) REVERT: B 1102 MET cc_start: 0.6968 (mmt) cc_final: 0.6356 (mmm) REVERT: B 1160 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8327 (ttp-110) outliers start: 24 outliers final: 16 residues processed: 182 average time/residue: 0.2830 time to fit residues: 71.7451 Evaluate side-chains 167 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 214 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 381 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 694 GLU Chi-restraints excluded: chain B residue 844 ASP Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1104 ASP Chi-restraints excluded: chain B residue 1108 THR Chi-restraints excluded: chain B residue 1137 SER 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: 6.9990 chunk 127 optimal weight: 0.0050 chunk 27 optimal weight: 20.0000 chunk 82 optimal weight: 4.9990 chunk 34 optimal weight: 0.0030 chunk 141 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.6008 ------------------------------------------------------------------------------- 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** B1067 ASN B1097 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12691 Z= 0.283 Angle : 0.640 8.386 17491 Z= 0.337 Chirality : 0.043 0.175 1970 Planarity : 0.005 0.039 2057 Dihedral : 18.998 88.209 2319 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.74 % Allowed : 14.81 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.22), residues: 1400 helix: 0.40 (0.20), residues: 706 sheet: -1.24 (0.41), residues: 155 loop : -1.53 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B1105 HIS 0.012 0.002 HIS B 756 PHE 0.035 0.002 PHE A 86 TYR 0.022 0.002 TYR B 445 ARG 0.008 0.001 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 195 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 163 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2747 (tpp) cc_final: 0.1150 (ptt) REVERT: A 14 ASN cc_start: 0.7773 (p0) cc_final: 0.7327 (t0) REVERT: A 78 ARG cc_start: 0.5896 (mmt-90) cc_final: 0.5158 (mmt180) REVERT: A 81 ASP cc_start: 0.6070 (m-30) cc_final: 0.5779 (t0) REVERT: A 217 MET cc_start: 0.7055 (ptt) cc_final: 0.6853 (ptt) REVERT: B 23 ARG cc_start: 0.7593 (mtm-85) cc_final: 0.7220 (mtm180) REVERT: B 72 LEU cc_start: 0.6338 (mt) cc_final: 0.5792 (pp) REVERT: B 140 ILE cc_start: 0.7134 (mt) cc_final: 0.6686 (mp) REVERT: B 234 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6528 (pp20) REVERT: B 417 ASN cc_start: 0.6929 (m-40) cc_final: 0.6463 (m110) REVERT: B 696 ARG cc_start: 0.7368 (mmm-85) cc_final: 0.7060 (mmm-85) REVERT: B 790 ARG cc_start: 0.7161 (tmm-80) cc_final: 0.6815 (tmm-80) REVERT: B 840 GLN cc_start: 0.6804 (mm-40) cc_final: 0.6435 (pp30) REVERT: B 922 GLU cc_start: 0.7608 (mt-10) cc_final: 0.6946 (tp30) REVERT: B 1036 ILE cc_start: 0.4975 (OUTLIER) cc_final: 0.4437 (mm) REVERT: B 1080 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7473 (mm) REVERT: B 1102 MET cc_start: 0.7255 (mmt) cc_final: 0.6571 (mmm) REVERT: B 1160 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8289 (ttp-110) outliers start: 32 outliers final: 15 residues processed: 186 average time/residue: 0.3166 time to fit residues: 83.2015 Evaluate side-chains 162 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 214 ILE 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 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 694 GLU Chi-restraints excluded: chain B residue 844 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 80 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.6381 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12691 Z= 0.190 Angle : 0.595 10.281 17491 Z= 0.309 Chirality : 0.041 0.237 1970 Planarity : 0.004 0.036 2057 Dihedral : 18.871 86.767 2319 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.37 % Allowed : 17.04 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.55 (0.20), residues: 701 sheet: -1.18 (0.41), residues: 156 loop : -1.41 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B1105 HIS 0.008 0.001 HIS B 756 PHE 0.012 0.001 PHE B 718 TYR 0.015 0.001 TYR B 445 ARG 0.005 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 171 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2802 (tpp) cc_final: 0.1155 (ptt) REVERT: A 14 ASN cc_start: 0.7713 (p0) cc_final: 0.7308 (t0) REVERT: A 78 ARG cc_start: 0.5971 (mmt-90) cc_final: 0.5198 (mmt180) REVERT: A 170 MET cc_start: 0.5128 (mmm) cc_final: 0.4788 (mmm) REVERT: B 140 ILE cc_start: 0.7001 (mt) cc_final: 0.6544 (mp) REVERT: B 234 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6593 (pp20) REVERT: B 381 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8069 (mt) REVERT: B 417 ASN cc_start: 0.6749 (m-40) cc_final: 0.6500 (m-40) REVERT: B 525 TRP cc_start: 0.7178 (p90) cc_final: 0.6718 (p90) REVERT: B 645 TYR cc_start: 0.7341 (t80) cc_final: 0.6836 (t80) REVERT: B 696 ARG cc_start: 0.7357 (mmm-85) cc_final: 0.7070 (mmm-85) REVERT: B 790 ARG cc_start: 0.7152 (tmm-80) cc_final: 0.6861 (tmm-80) REVERT: B 840 GLN cc_start: 0.6727 (mm-40) cc_final: 0.6379 (pp30) REVERT: B 922 GLU cc_start: 0.7467 (mt-10) cc_final: 0.6820 (tp30) REVERT: B 1021 SER cc_start: 0.6141 (OUTLIER) cc_final: 0.5863 (m) REVERT: B 1102 MET cc_start: 0.6954 (mmt) cc_final: 0.6281 (mmm) REVERT: B 1160 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8272 (ttp-110) outliers start: 16 outliers final: 7 residues processed: 165 average time/residue: 0.3051 time to fit residues: 70.4370 Evaluate side-chains 155 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 381 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 844 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 89 optimal weight: 0.0970 chunk 95 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 13 optimal weight: 0.0470 chunk 110 optimal weight: 0.4980 chunk 128 optimal weight: 5.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 156 ASN A 230 ASN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1026 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12691 Z= 0.170 Angle : 0.568 10.088 17491 Z= 0.298 Chirality : 0.040 0.201 1970 Planarity : 0.004 0.038 2057 Dihedral : 18.796 86.309 2319 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.54 % Allowed : 17.12 % 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: -0.43 (0.22), residues: 1400 helix: 0.69 (0.20), residues: 694 sheet: -1.00 (0.41), residues: 156 loop : -1.27 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B1105 HIS 0.008 0.001 HIS B 756 PHE 0.013 0.001 PHE B 602 TYR 0.013 0.001 TYR B 445 ARG 0.007 0.000 ARG B 231 *********************** 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 173 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 155 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2625 (tpp) cc_final: 0.1097 (ptt) REVERT: A 14 ASN cc_start: 0.7764 (p0) cc_final: 0.7367 (t0) REVERT: A 78 ARG cc_start: 0.5988 (mmt-90) cc_final: 0.5251 (mmt180) REVERT: A 81 ASP cc_start: 0.5934 (m-30) cc_final: 0.5563 (t0) REVERT: A 170 MET cc_start: 0.5112 (mmm) cc_final: 0.4778 (mmm) REVERT: B 72 LEU cc_start: 0.6242 (mt) cc_final: 0.5747 (pp) REVERT: B 140 ILE cc_start: 0.6861 (mt) cc_final: 0.6422 (mp) REVERT: B 234 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6632 (pp20) REVERT: B 381 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8024 (mt) REVERT: B 417 ASN cc_start: 0.6658 (m-40) cc_final: 0.6407 (m-40) REVERT: B 525 TRP cc_start: 0.7079 (p90) cc_final: 0.6692 (p90) REVERT: B 645 TYR cc_start: 0.7256 (t80) cc_final: 0.6727 (t80) REVERT: B 696 ARG cc_start: 0.7466 (mmm-85) cc_final: 0.7167 (mmm-85) REVERT: B 840 GLN cc_start: 0.6617 (mm-40) cc_final: 0.6291 (pp30) REVERT: B 922 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6810 (tp30) REVERT: B 1021 SER cc_start: 0.6079 (OUTLIER) cc_final: 0.5844 (m) REVERT: B 1036 ILE cc_start: 0.4719 (OUTLIER) cc_final: 0.4378 (mm) REVERT: B 1102 MET cc_start: 0.6955 (mmt) cc_final: 0.6323 (mmm) REVERT: B 1160 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8181 (ttp-110) outliers start: 18 outliers final: 8 residues processed: 168 average time/residue: 0.2874 time to fit residues: 67.2249 Evaluate side-chains 160 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain B residue 234 GLU 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 526 VAL Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 844 ASP Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1036 ILE Chi-restraints excluded: chain B residue 1104 ASP Chi-restraints excluded: chain B residue 1160 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 156 ASN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12691 Z= 0.217 Angle : 0.604 9.088 17491 Z= 0.313 Chirality : 0.041 0.206 1970 Planarity : 0.004 0.036 2057 Dihedral : 18.813 86.438 2319 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.20 % Allowed : 17.38 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.22), residues: 1400 helix: 0.62 (0.20), residues: 689 sheet: -1.08 (0.42), residues: 156 loop : -1.28 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 482 HIS 0.011 0.001 HIS A 18 PHE 0.019 0.002 PHE B 602 TYR 0.019 0.001 TYR B 445 ARG 0.007 0.000 ARG B 231 *********************** 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: 14 poor density : 147 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2643 (tpp) cc_final: 0.1083 (ptt) REVERT: A 14 ASN cc_start: 0.7711 (p0) cc_final: 0.7302 (t0) REVERT: A 78 ARG cc_start: 0.5934 (mmt-90) cc_final: 0.5215 (mmt180) REVERT: A 81 ASP cc_start: 0.6010 (m-30) cc_final: 0.5768 (t0) REVERT: A 170 MET cc_start: 0.5343 (mmm) cc_final: 0.5009 (mmm) REVERT: A 207 PHE cc_start: 0.7235 (OUTLIER) cc_final: 0.6472 (m-80) REVERT: B 72 LEU cc_start: 0.6418 (mt) cc_final: 0.5930 (pp) REVERT: B 140 ILE cc_start: 0.6981 (mt) cc_final: 0.6527 (mp) REVERT: B 234 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6648 (pp20) REVERT: B 256 PHE cc_start: 0.6892 (t80) cc_final: 0.6549 (t80) REVERT: B 417 ASN cc_start: 0.6704 (m-40) cc_final: 0.6432 (m-40) REVERT: B 482 TRP cc_start: 0.8353 (t60) cc_final: 0.8151 (t60) REVERT: B 525 TRP cc_start: 0.7099 (p90) cc_final: 0.6712 (p90) REVERT: B 645 TYR cc_start: 0.7340 (t80) cc_final: 0.6822 (t80) REVERT: B 696 ARG cc_start: 0.7567 (mmm-85) cc_final: 0.7269 (mmm-85) REVERT: B 840 GLN cc_start: 0.6612 (mm-40) cc_final: 0.6288 (pp30) REVERT: B 922 GLU cc_start: 0.7455 (mt-10) cc_final: 0.6799 (tp30) REVERT: B 1021 SER cc_start: 0.6147 (OUTLIER) cc_final: 0.5865 (m) REVERT: B 1036 ILE cc_start: 0.4820 (OUTLIER) cc_final: 0.4332 (mm) REVERT: B 1102 MET cc_start: 0.6903 (mmt) cc_final: 0.6280 (mmm) REVERT: B 1160 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8206 (ttp-110) outliers start: 14 outliers final: 8 residues processed: 156 average time/residue: 0.2830 time to fit residues: 62.0867 Evaluate side-chains 156 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 143 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 207 PHE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 844 ASP Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1036 ILE Chi-restraints excluded: chain B residue 1104 ASP Chi-restraints excluded: chain B residue 1160 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 145 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 89 optimal weight: 0.0370 chunk 71 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 156 ASN A 230 ASN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1026 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6358 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12691 Z= 0.178 Angle : 0.581 9.234 17491 Z= 0.302 Chirality : 0.040 0.200 1970 Planarity : 0.004 0.032 2057 Dihedral : 18.772 85.851 2319 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.28 % Allowed : 17.55 % 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: -0.45 (0.22), residues: 1400 helix: 0.66 (0.20), residues: 689 sheet: -1.00 (0.42), residues: 154 loop : -1.24 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 482 HIS 0.016 0.001 HIS A 18 PHE 0.015 0.001 PHE B 602 TYR 0.014 0.001 TYR B 445 ARG 0.008 0.000 ARG B 231 ********************** 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 162 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 147 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2644 (tpp) cc_final: 0.1101 (ptt) REVERT: A 14 ASN cc_start: 0.7691 (p0) cc_final: 0.7374 (t0) REVERT: A 78 ARG cc_start: 0.5882 (mmt-90) cc_final: 0.5187 (mmt180) REVERT: A 81 ASP cc_start: 0.5976 (m-30) cc_final: 0.5676 (t0) REVERT: A 170 MET cc_start: 0.5331 (mmm) cc_final: 0.5013 (mmm) REVERT: A 207 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.6379 (m-80) REVERT: B 72 LEU cc_start: 0.6403 (mt) cc_final: 0.5934 (pp) REVERT: B 140 ILE cc_start: 0.6931 (mt) cc_final: 0.6485 (mp) REVERT: B 234 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6623 (pp20) REVERT: B 381 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8130 (mt) REVERT: B 417 ASN cc_start: 0.6652 (m-40) cc_final: 0.6350 (m-40) REVERT: B 525 TRP cc_start: 0.7158 (p90) cc_final: 0.6782 (p90) REVERT: B 555 LYS cc_start: 0.6616 (mtpp) cc_final: 0.6133 (mtpp) REVERT: B 645 TYR cc_start: 0.7264 (t80) cc_final: 0.6755 (t80) REVERT: B 696 ARG cc_start: 0.7573 (mmm-85) cc_final: 0.7285 (mmm-85) REVERT: B 840 GLN cc_start: 0.6598 (mm-40) cc_final: 0.6285 (pp30) REVERT: B 922 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6771 (tp30) REVERT: B 1021 SER cc_start: 0.6110 (OUTLIER) cc_final: 0.5844 (m) REVERT: B 1036 ILE cc_start: 0.4741 (OUTLIER) cc_final: 0.4311 (mm) REVERT: B 1102 MET cc_start: 0.6939 (mmt) cc_final: 0.6304 (mmm) REVERT: B 1157 GLU cc_start: 0.8198 (mp0) cc_final: 0.7976 (mm-30) REVERT: B 1160 ARG cc_start: 0.8495 (ptp90) cc_final: 0.8139 (ttp-110) outliers start: 15 outliers final: 6 residues processed: 158 average time/residue: 0.2897 time to fit residues: 64.3914 Evaluate side-chains 154 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 PHE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 844 ASP Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1036 ILE Chi-restraints excluded: chain B residue 1104 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 106 optimal weight: 0.0570 chunk 17 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 48 optimal weight: 0.1980 chunk 119 optimal weight: 0.2980 chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.4700 ------------------------------------------------------------------------------- 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 B1026 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.227699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.190997 restraints weight = 18249.694| |-----------------------------------------------------------------------------| r_work (start): 0.4556 rms_B_bonded: 2.33 r_work: 0.4409 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12691 Z= 0.171 Angle : 0.582 9.064 17491 Z= 0.303 Chirality : 0.040 0.197 1970 Planarity : 0.004 0.037 2057 Dihedral : 18.729 85.676 2319 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.20 % Allowed : 17.81 % 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: -0.38 (0.23), residues: 1400 helix: 0.71 (0.20), residues: 687 sheet: -0.97 (0.42), residues: 154 loop : -1.20 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 482 HIS 0.007 0.001 HIS B 756 PHE 0.017 0.001 PHE B 256 TYR 0.013 0.001 TYR B 445 ARG 0.007 0.000 ARG B 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2837.78 seconds wall clock time: 54 minutes 29.07 seconds (3269.07 seconds total)