Starting phenix.real_space_refine on Fri Mar 15 10:22:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oma_16972/03_2024/8oma_16972_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oma_16972/03_2024/8oma_16972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oma_16972/03_2024/8oma_16972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oma_16972/03_2024/8oma_16972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oma_16972/03_2024/8oma_16972_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oma_16972/03_2024/8oma_16972_updated.pdb" } resolution = 3.29 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= 0.024 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: 6 Type Number sf(0) Gaussians P 40 5.49 5 Mg 1 5.21 5 S 52 5.16 5 C 7099 2.51 5 N 1952 2.21 5 O 2235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 188": "OE1" <-> "OE2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A GLU 590": "OE1" <-> "OE2" Residue "A GLU 643": "OE1" <-> "OE2" Residue "A GLU 698": "OE1" <-> "OE2" Residue "A GLU 728": "OE1" <-> "OE2" Residue "A GLU 852": "OE1" <-> "OE2" Residue "A GLU 902": "OE1" <-> "OE2" Residue "B GLU 651": "OE1" <-> "OE2" Residue "B GLU 732": "OE1" <-> "OE2" Residue "B GLU 812": "OE1" <-> "OE2" Residue "B GLU 926": "OE1" <-> "OE2" Residue "B GLU 1124": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11379 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 351 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "D" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 346 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 5990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 5990 Classifications: {'peptide': 760} Link IDs: {'PTRANS': 21, 'TRANS': 738} Chain breaks: 4 Chain: "B" Number of atoms: 4629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4629 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 17, 'TRANS': 559} Chain breaks: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.67, per 1000 atoms: 0.59 Number of scatterers: 11379 At special positions: 0 Unit cell: (94.1626, 107.876, 173.698, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 52 16.00 P 40 15.00 Mg 1 11.99 O 2235 8.00 N 1952 7.00 C 7099 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.51 Conformation dependent library (CDL) restraints added in 2.4 seconds 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2530 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 11 sheets defined 51.2% alpha, 7.2% beta 17 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 6.04 Creating SS restraints... Processing helix chain 'A' and resid 185 through 192 Processing helix chain 'A' and resid 208 through 219 removed outlier: 4.023A pdb=" N LYS A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 237 through 244 Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 264 through 276 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 326 through 330 Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 353 through 368 Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 401 through 423 Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 430 through 456 Proline residue: A 439 - end of helix removed outlier: 4.778A pdb=" N LYS A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 464 Processing helix chain 'A' and resid 476 through 503 Processing helix chain 'A' and resid 554 through 614 removed outlier: 4.769A pdb=" N GLU A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASN A 583 " --> pdb=" O LYS A 579 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLU A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) Proline residue: A 591 - end of helix Processing helix chain 'A' and resid 675 through 691 Processing helix chain 'A' and resid 724 through 738 Processing helix chain 'A' and resid 757 through 772 Processing helix chain 'A' and resid 787 through 792 Processing helix chain 'A' and resid 827 through 833 Processing helix chain 'A' and resid 838 through 850 Processing helix chain 'A' and resid 879 through 893 Processing helix chain 'A' and resid 901 through 918 Processing helix chain 'A' and resid 921 through 929 removed outlier: 3.716A pdb=" N ILE A 926 " --> pdb=" O PHE A 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 560 through 564 Processing helix chain 'B' and resid 570 through 580 Processing helix chain 'B' and resid 587 through 601 Processing helix chain 'B' and resid 607 through 616 Processing helix chain 'B' and resid 623 through 629 Processing helix chain 'B' and resid 635 through 662 Proline residue: B 657 - end of helix Processing helix chain 'B' and resid 666 through 678 removed outlier: 3.954A pdb=" N ILE B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Proline residue: B 676 - end of helix Processing helix chain 'B' and resid 680 through 687 removed outlier: 3.858A pdb=" N GLU B 683 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N HIS B 684 " --> pdb=" O PRO B 681 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 686 " --> pdb=" O GLU B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 696 Processing helix chain 'B' and resid 706 through 708 No H-bonds generated for 'chain 'B' and resid 706 through 708' Processing helix chain 'B' and resid 710 through 737 removed outlier: 3.707A pdb=" N ARG B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN B 731 " --> pdb=" O ARG B 727 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU B 732 " --> pdb=" O MET B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 761 No H-bonds generated for 'chain 'B' and resid 759 through 761' Processing helix chain 'B' and resid 783 through 843 removed outlier: 4.049A pdb=" N HIS B 817 " --> pdb=" O LYS B 813 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N HIS B 819 " --> pdb=" O SER B 815 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N SER B 820 " --> pdb=" O GLU B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 870 Processing helix chain 'B' and resid 902 through 918 Processing helix chain 'B' and resid 945 through 947 No H-bonds generated for 'chain 'B' and resid 945 through 947' Processing helix chain 'B' and resid 951 through 965 Processing helix chain 'B' and resid 983 through 999 Processing helix chain 'B' and resid 1017 through 1020 No H-bonds generated for 'chain 'B' and resid 1017 through 1020' Processing helix chain 'B' and resid 1069 through 1075 Processing helix chain 'B' and resid 1080 through 1110 Processing helix chain 'B' and resid 1116 through 1123 Processing sheet with id= A, first strand: chain 'A' and resid 223 through 227 removed outlier: 3.746A pdb=" N LEU A 201 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N MET A 152 " --> pdb=" O PRO A 202 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL A 147 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 166 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A 160 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 513 through 516 Processing sheet with id= C, first strand: chain 'A' and resid 539 through 541 Processing sheet with id= D, first strand: chain 'A' and resid 632 through 635 removed outlier: 3.698A pdb=" N SER A 699 " --> pdb=" O LYS A 635 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 797 through 800 removed outlier: 6.701A pdb=" N PHE A 664 " --> pdb=" O ASN A 798 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU A 800 " --> pdb=" O PHE A 664 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE A 666 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N CYS A 778 " --> pdb=" O HIS A 665 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE A 667 " --> pdb=" O CYS A 778 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE A 780 " --> pdb=" O ILE A 667 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N CYS A 707 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE A 746 " --> pdb=" O CYS A 707 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU A 709 " --> pdb=" O ILE A 746 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 804 through 807 Processing sheet with id= G, first strand: chain 'B' and resid 754 through 756 Processing sheet with id= H, first strand: chain 'B' and resid 857 through 860 Processing sheet with id= I, first strand: chain 'B' and resid 891 through 896 Processing sheet with id= J, first strand: chain 'B' and resid 935 through 937 removed outlier: 6.313A pdb=" N LEU B 971 " --> pdb=" O PHE B 936 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU B1004 " --> pdb=" O VAL B 972 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 1032 through 1034 removed outlier: 3.749A pdb=" N THR B1054 " --> pdb=" O LEU B1033 " (cutoff:3.500A) 503 hydrogen bonds defined for protein. 1476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 4.65 Time building geometry restraints manager: 5.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3522 1.34 - 1.48: 2877 1.48 - 1.61: 5153 1.61 - 1.75: 2 1.75 - 1.88: 84 Bond restraints: 11638 Sorted by residual: bond pdb=" CA SER A 637 " pdb=" CB SER A 637 " ideal model delta sigma weight residual 1.529 1.460 0.069 1.66e-02 3.63e+03 1.73e+01 bond pdb=" CE1 HIS B 864 " pdb=" NE2 HIS B 864 " ideal model delta sigma weight residual 1.321 1.354 -0.033 1.00e-02 1.00e+04 1.09e+01 bond pdb=" CA SER B 920 " pdb=" CB SER B 920 " ideal model delta sigma weight residual 1.528 1.480 0.048 1.48e-02 4.57e+03 1.07e+01 bond pdb=" CG MET B 953 " pdb=" SD MET B 953 " ideal model delta sigma weight residual 1.803 1.884 -0.081 2.50e-02 1.60e+03 1.04e+01 bond pdb=" CD ARG B 938 " pdb=" NE ARG B 938 " ideal model delta sigma weight residual 1.458 1.419 0.039 1.40e-02 5.10e+03 7.95e+00 ... (remaining 11633 not shown) Histogram of bond angle deviations from ideal: 98.17 - 106.10: 411 106.10 - 114.04: 6493 114.04 - 121.97: 6403 121.97 - 129.91: 2482 129.91 - 137.84: 67 Bond angle restraints: 15856 Sorted by residual: angle pdb=" C5' ATP B2000 " pdb=" O5' ATP B2000 " pdb=" PA ATP B2000 " ideal model delta sigma weight residual 121.27 113.20 8.07 1.00e+00 1.00e+00 6.50e+01 angle pdb=" N THR B 951 " pdb=" CA THR B 951 " pdb=" CB THR B 951 " ideal model delta sigma weight residual 109.72 117.37 -7.65 1.70e+00 3.46e-01 2.02e+01 angle pdb=" C ARG A 711 " pdb=" CA ARG A 711 " pdb=" CB ARG A 711 " ideal model delta sigma weight residual 111.70 117.20 -5.50 1.31e+00 5.83e-01 1.77e+01 angle pdb=" C PRO A 652 " pdb=" CA PRO A 652 " pdb=" CB PRO A 652 " ideal model delta sigma weight residual 111.23 106.06 5.17 1.28e+00 6.10e-01 1.63e+01 angle pdb=" N GLY A 692 " pdb=" CA GLY A 692 " pdb=" C GLY A 692 " ideal model delta sigma weight residual 114.95 109.31 5.64 1.41e+00 5.03e-01 1.60e+01 ... (remaining 15851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5764 17.96 - 35.92: 869 35.92 - 53.88: 323 53.88 - 71.85: 66 71.85 - 89.81: 18 Dihedral angle restraints: 7040 sinusoidal: 3145 harmonic: 3895 Sorted by residual: dihedral pdb=" CA GLY A 504 " pdb=" C GLY A 504 " pdb=" N LEU A 505 " pdb=" CA LEU A 505 " ideal model delta harmonic sigma weight residual 180.00 -152.34 -27.66 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA MET B 728 " pdb=" C MET B 728 " pdb=" N HIS B 729 " pdb=" CA HIS B 729 " ideal model delta harmonic sigma weight residual 180.00 155.28 24.72 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA SER B1067 " pdb=" C SER B1067 " pdb=" N TYR B1068 " pdb=" CA TYR B1068 " ideal model delta harmonic sigma weight residual -180.00 -155.91 -24.09 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 7037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1034 0.076 - 0.152: 625 0.152 - 0.228: 128 0.228 - 0.304: 25 0.304 - 0.380: 7 Chirality restraints: 1819 Sorted by residual: chirality pdb=" CA ARG A 171 " pdb=" N ARG A 171 " pdb=" C ARG A 171 " pdb=" CB ARG A 171 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CG LEU B 640 " pdb=" CB LEU B 640 " pdb=" CD1 LEU B 640 " pdb=" CD2 LEU B 640 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CB THR B 951 " pdb=" CA THR B 951 " pdb=" OG1 THR B 951 " pdb=" CG2 THR B 951 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.36 2.00e-01 2.50e+01 3.15e+00 ... (remaining 1816 not shown) Planarity restraints: 1897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 938 " 0.406 9.50e-02 1.11e+02 1.82e-01 2.25e+01 pdb=" NE ARG B 938 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG B 938 " 0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG B 938 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 938 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 991 " -0.032 2.00e-02 2.50e+03 1.72e-02 5.92e+00 pdb=" CG TYR B 991 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR B 991 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 991 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR B 991 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 991 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 991 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR B 991 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B1007 " 0.027 2.00e-02 2.50e+03 1.78e-02 5.55e+00 pdb=" CG PHE B1007 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE B1007 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE B1007 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE B1007 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B1007 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B1007 " 0.023 2.00e-02 2.50e+03 ... (remaining 1894 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 88 2.48 - 3.09: 8264 3.09 - 3.69: 19511 3.69 - 4.30: 27317 4.30 - 4.90: 42566 Nonbonded interactions: 97746 Sorted by model distance: nonbonded pdb=" O2G ATP B2000 " pdb="MG MG B2001 " model vdw 1.878 2.170 nonbonded pdb=" OG SER B 903 " pdb="MG MG B2001 " model vdw 2.000 2.170 nonbonded pdb=" OG1 THR A 335 " pdb=" OD2 ASP A 603 " model vdw 2.112 2.440 nonbonded pdb=" O LYS A 565 " pdb=" OG1 THR A 568 " model vdw 2.174 2.440 nonbonded pdb=" OD1 ASN A 186 " pdb=" NE2 GLN A 348 " model vdw 2.178 2.520 ... (remaining 97741 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=0.03 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: 3.260 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: 7.290 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 40.440 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 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 : 0.008 0.081 11638 Z= 0.494 Angle : 1.304 8.981 15856 Z= 0.857 Chirality : 0.094 0.380 1819 Planarity : 0.007 0.182 1897 Dihedral : 19.919 89.807 4510 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 28.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 2.97 % Allowed : 22.71 % Favored : 74.32 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.22), residues: 1321 helix: 0.08 (0.18), residues: 716 sheet: -2.00 (0.41), residues: 145 loop : -2.34 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.005 TRP A 764 HIS 0.016 0.003 HIS B 647 PHE 0.027 0.005 PHE B1007 TYR 0.032 0.005 TYR B 991 ARG 0.025 0.002 ARG B 938 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 217 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LYS cc_start: 0.6314 (OUTLIER) cc_final: 0.5035 (ttpp) REVERT: A 245 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7459 (tm) REVERT: A 253 MET cc_start: 0.8246 (tpp) cc_final: 0.5575 (tpp) REVERT: A 324 GLN cc_start: 0.8416 (mp10) cc_final: 0.8190 (mp10) REVERT: A 348 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.6843 (pt0) REVERT: A 466 HIS cc_start: 0.7335 (p90) cc_final: 0.7118 (p-80) REVERT: A 572 GLU cc_start: 0.9114 (pt0) cc_final: 0.8822 (pp20) REVERT: A 594 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8454 (t) REVERT: A 631 ARG cc_start: 0.8460 (ttp-170) cc_final: 0.8260 (ttp80) REVERT: A 638 ARG cc_start: 0.5886 (ptm-80) cc_final: 0.5583 (ptm-80) REVERT: A 729 MET cc_start: 0.5867 (OUTLIER) cc_final: 0.5528 (ttt) REVERT: A 743 SER cc_start: 0.7606 (t) cc_final: 0.7318 (t) REVERT: A 786 GLU cc_start: 0.7791 (tt0) cc_final: 0.7491 (tm-30) REVERT: A 815 TYR cc_start: 0.7436 (m-10) cc_final: 0.7129 (m-10) REVERT: B 549 GLN cc_start: 0.8411 (pt0) cc_final: 0.7890 (pt0) REVERT: B 557 LYS cc_start: 0.8175 (tptm) cc_final: 0.6044 (ptmm) REVERT: B 617 LYS cc_start: 0.8716 (tptp) cc_final: 0.7859 (mmtm) REVERT: B 781 HIS cc_start: 0.8721 (t70) cc_final: 0.8307 (t70) REVERT: B 796 ARG cc_start: 0.7896 (ptm-80) cc_final: 0.7559 (ptm-80) REVERT: B 892 MET cc_start: 0.8939 (ttm) cc_final: 0.8609 (ttm) outliers start: 35 outliers final: 17 residues processed: 236 average time/residue: 0.3053 time to fit residues: 95.6868 Evaluate side-chains 214 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 192 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 1027 ASN Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.3980 chunk 102 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 54 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 chunk 40 optimal weight: 0.0870 chunk 64 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN A 518 GLN A 566 ASN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN B 551 GLN B 647 HIS B 729 HIS ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1120 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11638 Z= 0.211 Angle : 0.634 9.874 15856 Z= 0.339 Chirality : 0.042 0.209 1819 Planarity : 0.004 0.073 1897 Dihedral : 18.012 87.836 1900 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 22.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.64 % Allowed : 21.86 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.97 (0.23), residues: 1321 helix: 0.46 (0.19), residues: 723 sheet: -1.98 (0.40), residues: 169 loop : -1.88 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 764 HIS 0.008 0.001 HIS B 729 PHE 0.039 0.002 PHE A 286 TYR 0.013 0.001 TYR B 877 ARG 0.003 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 203 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LYS cc_start: 0.6296 (OUTLIER) cc_final: 0.5327 (ttpp) REVERT: A 324 GLN cc_start: 0.8375 (mp10) cc_final: 0.8174 (mp10) REVERT: A 386 ASP cc_start: 0.6893 (t0) cc_final: 0.6683 (t0) REVERT: A 446 ASP cc_start: 0.8061 (m-30) cc_final: 0.7835 (m-30) REVERT: A 572 GLU cc_start: 0.9087 (pt0) cc_final: 0.8800 (pp20) REVERT: A 603 ASP cc_start: 0.6833 (t0) cc_final: 0.6608 (t0) REVERT: A 631 ARG cc_start: 0.8420 (ttp-170) cc_final: 0.8136 (ptm160) REVERT: A 786 GLU cc_start: 0.7621 (tt0) cc_final: 0.7200 (tm-30) REVERT: A 813 MET cc_start: 0.7743 (mmp) cc_final: 0.7474 (mmp) REVERT: A 815 TYR cc_start: 0.7088 (m-10) cc_final: 0.6473 (m-10) REVERT: B 549 GLN cc_start: 0.8216 (pt0) cc_final: 0.7684 (pt0) REVERT: B 578 LYS cc_start: 0.8042 (tttt) cc_final: 0.7666 (tmtt) REVERT: B 640 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6756 (mp) REVERT: B 767 ASP cc_start: 0.3662 (OUTLIER) cc_final: 0.3371 (m-30) REVERT: B 796 ARG cc_start: 0.7889 (ptm-80) cc_final: 0.7531 (ptm-80) REVERT: B 839 LYS cc_start: 0.7589 (mttt) cc_final: 0.6995 (tptp) REVERT: B 892 MET cc_start: 0.8945 (ttm) cc_final: 0.8611 (ttm) REVERT: B 925 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7653 (mm-30) REVERT: B 938 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7215 (tpm170) outliers start: 43 outliers final: 26 residues processed: 224 average time/residue: 0.2759 time to fit residues: 84.8430 Evaluate side-chains 220 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 190 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 827 HIS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1113 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.0470 chunk 38 optimal weight: 5.9990 chunk 102 optimal weight: 0.0870 chunk 83 optimal weight: 0.5980 chunk 33 optimal weight: 0.0470 chunk 122 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 121 optimal weight: 0.0970 chunk 41 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 overall best weight: 0.1752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 GLN ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 HIS ** A 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11638 Z= 0.173 Angle : 0.593 7.462 15856 Z= 0.319 Chirality : 0.041 0.225 1819 Planarity : 0.004 0.077 1897 Dihedral : 17.654 86.900 1873 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.39 % Allowed : 23.56 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.23), residues: 1321 helix: 0.76 (0.19), residues: 720 sheet: -1.58 (0.41), residues: 166 loop : -1.66 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 807 HIS 0.007 0.001 HIS B 647 PHE 0.036 0.001 PHE A 286 TYR 0.013 0.001 TYR B 877 ARG 0.005 0.000 ARG B 964 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 202 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8222 (mptt) cc_final: 0.7971 (mppt) REVERT: A 311 ASN cc_start: 0.7428 (m110) cc_final: 0.7021 (t0) REVERT: A 324 GLN cc_start: 0.8407 (mp10) cc_final: 0.8057 (mp10) REVERT: A 344 GLN cc_start: 0.7127 (tm-30) cc_final: 0.6905 (tm-30) REVERT: A 386 ASP cc_start: 0.6806 (t0) cc_final: 0.6573 (t0) REVERT: A 464 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: A 603 ASP cc_start: 0.6846 (t0) cc_final: 0.6578 (t0) REVERT: A 638 ARG cc_start: 0.5733 (ptm-80) cc_final: 0.5488 (ptm-80) REVERT: A 805 LEU cc_start: 0.6182 (OUTLIER) cc_final: 0.5897 (tt) REVERT: A 813 MET cc_start: 0.7798 (mmp) cc_final: 0.7534 (mmp) REVERT: A 846 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7950 (mm-40) REVERT: B 549 GLN cc_start: 0.8203 (pt0) cc_final: 0.7595 (pt0) REVERT: B 553 ASP cc_start: 0.9038 (m-30) cc_final: 0.8577 (m-30) REVERT: B 573 ARG cc_start: 0.8180 (ttt180) cc_final: 0.7932 (ttm-80) REVERT: B 578 LYS cc_start: 0.8011 (tttt) cc_final: 0.7685 (tmtt) REVERT: B 612 GLU cc_start: 0.8789 (tp30) cc_final: 0.8559 (tm-30) REVERT: B 617 LYS cc_start: 0.8681 (tptp) cc_final: 0.7866 (mmtm) REVERT: B 767 ASP cc_start: 0.3588 (OUTLIER) cc_final: 0.3343 (m-30) REVERT: B 796 ARG cc_start: 0.7897 (ptm-80) cc_final: 0.7541 (ptm-80) REVERT: B 839 LYS cc_start: 0.7543 (mttt) cc_final: 0.6709 (tptp) REVERT: B 925 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7546 (mm-30) REVERT: B 1094 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8604 (mt-10) outliers start: 40 outliers final: 24 residues processed: 225 average time/residue: 0.2697 time to fit residues: 83.0270 Evaluate side-chains 216 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 189 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 827 HIS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1034 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 2.9990 chunk 92 optimal weight: 0.0770 chunk 63 optimal weight: 0.8980 chunk 13 optimal weight: 0.0170 chunk 58 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11638 Z= 0.199 Angle : 0.585 6.839 15856 Z= 0.317 Chirality : 0.041 0.191 1819 Planarity : 0.004 0.078 1897 Dihedral : 17.445 86.021 1864 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.32 % Allowed : 23.56 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.39 (0.23), residues: 1321 helix: 0.82 (0.19), residues: 720 sheet: -1.23 (0.44), residues: 152 loop : -1.62 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 764 HIS 0.006 0.001 HIS B 647 PHE 0.029 0.002 PHE A 286 TYR 0.016 0.002 TYR B 789 ARG 0.002 0.000 ARG B 593 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 191 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8322 (mptt) cc_final: 0.8098 (mmtm) REVERT: A 188 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8476 (pt0) REVERT: A 324 GLN cc_start: 0.8422 (mp10) cc_final: 0.8027 (mp10) REVERT: A 380 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6198 (mt) REVERT: A 386 ASP cc_start: 0.6905 (t0) cc_final: 0.6672 (t0) REVERT: A 446 ASP cc_start: 0.7883 (m-30) cc_final: 0.7659 (m-30) REVERT: A 450 PHE cc_start: 0.5172 (t80) cc_final: 0.4834 (t80) REVERT: A 535 ASN cc_start: 0.7179 (OUTLIER) cc_final: 0.6093 (t0) REVERT: A 572 GLU cc_start: 0.8943 (pt0) cc_final: 0.8667 (pp20) REVERT: A 603 ASP cc_start: 0.6875 (t0) cc_final: 0.6517 (t0) REVERT: A 661 LYS cc_start: 0.8083 (ttmt) cc_final: 0.7785 (ptmm) REVERT: A 813 MET cc_start: 0.7796 (mmp) cc_final: 0.7513 (mmp) REVERT: A 846 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7961 (mm-40) REVERT: B 549 GLN cc_start: 0.8262 (pt0) cc_final: 0.7639 (pt0) REVERT: B 553 ASP cc_start: 0.9053 (m-30) cc_final: 0.8482 (m-30) REVERT: B 555 LYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6857 (mtmt) REVERT: B 612 GLU cc_start: 0.8806 (tp30) cc_final: 0.8560 (tm-30) REVERT: B 617 LYS cc_start: 0.8681 (tptp) cc_final: 0.7858 (mmtm) REVERT: B 640 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6875 (mm) REVERT: B 775 LYS cc_start: -0.0208 (OUTLIER) cc_final: -0.0490 (tptt) REVERT: B 839 LYS cc_start: 0.7547 (mttt) cc_final: 0.6748 (tptp) REVERT: B 892 MET cc_start: 0.8972 (ttm) cc_final: 0.8628 (ttm) REVERT: B 925 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7548 (mm-30) REVERT: B 1091 LYS cc_start: 0.8635 (tppt) cc_final: 0.8368 (tppt) REVERT: B 1094 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8687 (mt-10) outliers start: 51 outliers final: 28 residues processed: 226 average time/residue: 0.2561 time to fit residues: 80.5257 Evaluate side-chains 217 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 184 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 896 PHE Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 775 LYS Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 827 HIS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1034 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 0.5980 chunk 117 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1029 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11638 Z= 0.246 Angle : 0.629 10.823 15856 Z= 0.340 Chirality : 0.042 0.185 1819 Planarity : 0.004 0.080 1897 Dihedral : 17.381 88.934 1864 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.49 % Allowed : 23.56 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.23), residues: 1321 helix: 0.66 (0.19), residues: 726 sheet: -1.29 (0.46), residues: 146 loop : -1.72 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 764 HIS 0.011 0.001 HIS B1029 PHE 0.022 0.002 PHE A 436 TYR 0.019 0.002 TYR B 877 ARG 0.003 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 195 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8357 (mptt) cc_final: 0.7981 (mmtm) REVERT: A 188 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8449 (pt0) REVERT: A 253 MET cc_start: 0.7870 (tpp) cc_final: 0.5516 (tpp) REVERT: A 324 GLN cc_start: 0.8418 (mp10) cc_final: 0.8012 (mp10) REVERT: A 380 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6042 (mt) REVERT: A 386 ASP cc_start: 0.6995 (t0) cc_final: 0.6762 (t0) REVERT: A 409 GLN cc_start: 0.6245 (OUTLIER) cc_final: 0.5819 (tt0) REVERT: A 431 LEU cc_start: 0.7670 (tp) cc_final: 0.7433 (tp) REVERT: A 446 ASP cc_start: 0.7893 (m-30) cc_final: 0.7674 (m-30) REVERT: A 535 ASN cc_start: 0.7191 (OUTLIER) cc_final: 0.6044 (t0) REVERT: A 572 GLU cc_start: 0.8954 (pt0) cc_final: 0.8751 (pp20) REVERT: A 631 ARG cc_start: 0.8435 (ttp-170) cc_final: 0.8217 (ptm160) REVERT: A 659 LYS cc_start: 0.7650 (tptp) cc_final: 0.7310 (tptm) REVERT: A 660 ASP cc_start: 0.8018 (t0) cc_final: 0.7655 (t70) REVERT: A 661 LYS cc_start: 0.8073 (ttmt) cc_final: 0.7749 (ptmm) REVERT: A 786 GLU cc_start: 0.7602 (pt0) cc_final: 0.7129 (tm-30) REVERT: A 805 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.6090 (tt) REVERT: A 813 MET cc_start: 0.7689 (mmp) cc_final: 0.7401 (mmp) REVERT: A 846 GLN cc_start: 0.8255 (mm-40) cc_final: 0.7983 (mm-40) REVERT: A 914 GLU cc_start: 0.4353 (OUTLIER) cc_final: 0.4008 (pm20) REVERT: B 549 GLN cc_start: 0.8339 (pt0) cc_final: 0.8029 (pt0) REVERT: B 553 ASP cc_start: 0.9086 (m-30) cc_final: 0.8769 (m-30) REVERT: B 573 ARG cc_start: 0.8246 (ttt180) cc_final: 0.7991 (ttm-80) REVERT: B 617 LYS cc_start: 0.8689 (tptp) cc_final: 0.7870 (mmtm) REVERT: B 640 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6767 (mm) REVERT: B 679 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.6354 (mt) REVERT: B 796 ARG cc_start: 0.7920 (ptm-80) cc_final: 0.7503 (ptm-80) REVERT: B 839 LYS cc_start: 0.7585 (mttt) cc_final: 0.7070 (mttt) REVERT: B 892 MET cc_start: 0.9042 (ttm) cc_final: 0.8774 (ttm) REVERT: B 925 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7649 (mm-30) REVERT: B 1091 LYS cc_start: 0.8648 (tppt) cc_final: 0.8247 (tppt) REVERT: B 1094 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8509 (mt-10) outliers start: 53 outliers final: 29 residues processed: 230 average time/residue: 0.2767 time to fit residues: 86.4180 Evaluate side-chains 227 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 191 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 1027 ASN Chi-restraints excluded: chain B residue 1034 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.4980 chunk 117 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 76 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 68 optimal weight: 0.0270 chunk 125 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN B 647 HIS ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11638 Z= 0.211 Angle : 0.625 9.732 15856 Z= 0.335 Chirality : 0.042 0.212 1819 Planarity : 0.005 0.080 1897 Dihedral : 17.231 85.841 1862 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.32 % Allowed : 24.83 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.59 (0.23), residues: 1321 helix: 0.65 (0.19), residues: 735 sheet: -1.38 (0.45), residues: 146 loop : -1.76 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 807 HIS 0.004 0.001 HIS B 647 PHE 0.025 0.002 PHE A 286 TYR 0.015 0.002 TYR B 877 ARG 0.006 0.000 ARG B1103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 194 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8323 (mptt) cc_final: 0.7994 (mmtm) REVERT: A 188 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8549 (pt0) REVERT: A 279 LEU cc_start: 0.5663 (OUTLIER) cc_final: 0.5410 (mp) REVERT: A 324 GLN cc_start: 0.8419 (mp10) cc_final: 0.8011 (mp10) REVERT: A 380 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.5911 (mt) REVERT: A 386 ASP cc_start: 0.7013 (t0) cc_final: 0.6811 (t0) REVERT: A 409 GLN cc_start: 0.6203 (OUTLIER) cc_final: 0.5775 (tt0) REVERT: A 413 GLN cc_start: 0.6733 (OUTLIER) cc_final: 0.4628 (mm110) REVERT: A 431 LEU cc_start: 0.7656 (tp) cc_final: 0.7425 (tp) REVERT: A 446 ASP cc_start: 0.7908 (m-30) cc_final: 0.7674 (m-30) REVERT: A 450 PHE cc_start: 0.5021 (t80) cc_final: 0.4521 (t80) REVERT: A 535 ASN cc_start: 0.7193 (OUTLIER) cc_final: 0.5962 (t0) REVERT: A 572 GLU cc_start: 0.8950 (pt0) cc_final: 0.8739 (pp20) REVERT: A 603 ASP cc_start: 0.6971 (t0) cc_final: 0.6282 (t0) REVERT: A 631 ARG cc_start: 0.8387 (ttp-170) cc_final: 0.8091 (ptm-80) REVERT: A 653 ASN cc_start: 0.7500 (t0) cc_final: 0.7225 (t0) REVERT: A 659 LYS cc_start: 0.7550 (tptp) cc_final: 0.7213 (tptm) REVERT: A 660 ASP cc_start: 0.8012 (t0) cc_final: 0.7657 (t70) REVERT: A 661 LYS cc_start: 0.8080 (ttmt) cc_final: 0.7752 (ptmm) REVERT: A 805 LEU cc_start: 0.6289 (OUTLIER) cc_final: 0.5985 (tt) REVERT: A 813 MET cc_start: 0.7686 (mmp) cc_final: 0.7446 (mmp) REVERT: A 815 TYR cc_start: 0.7312 (m-10) cc_final: 0.7021 (m-10) REVERT: A 846 GLN cc_start: 0.8263 (mm-40) cc_final: 0.7976 (mm-40) REVERT: A 914 GLU cc_start: 0.4344 (OUTLIER) cc_final: 0.3998 (pm20) REVERT: B 549 GLN cc_start: 0.8387 (pt0) cc_final: 0.7980 (pt0) REVERT: B 553 ASP cc_start: 0.9081 (m-30) cc_final: 0.8766 (m-30) REVERT: B 573 ARG cc_start: 0.8235 (ttt180) cc_final: 0.7988 (ttm-80) REVERT: B 617 LYS cc_start: 0.8676 (tptp) cc_final: 0.7845 (mmtm) REVERT: B 640 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6854 (mm) REVERT: B 679 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6394 (mt) REVERT: B 753 MET cc_start: -0.0791 (ttm) cc_final: -0.1142 (tpt) REVERT: B 796 ARG cc_start: 0.7947 (ptm-80) cc_final: 0.7532 (ptm-80) REVERT: B 839 LYS cc_start: 0.7239 (mttt) cc_final: 0.6606 (tptp) REVERT: B 852 GLN cc_start: 0.8512 (mt0) cc_final: 0.8270 (mt0) REVERT: B 892 MET cc_start: 0.9001 (ttm) cc_final: 0.8701 (ttm) REVERT: B 925 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7565 (mm-30) REVERT: B 1030 MET cc_start: 0.8707 (tmm) cc_final: 0.8487 (tmm) REVERT: B 1091 LYS cc_start: 0.8585 (tppt) cc_final: 0.8160 (tppt) REVERT: B 1094 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8635 (mt-10) outliers start: 51 outliers final: 30 residues processed: 229 average time/residue: 0.2822 time to fit residues: 87.9313 Evaluate side-chains 227 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 188 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 524 ARG Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 881 ASN Chi-restraints excluded: chain B residue 1027 ASN Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 95 optimal weight: 0.0770 chunk 73 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN B 582 GLN B 647 HIS ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11638 Z= 0.237 Angle : 0.643 9.697 15856 Z= 0.346 Chirality : 0.043 0.350 1819 Planarity : 0.005 0.080 1897 Dihedral : 17.189 87.100 1862 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 23.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.66 % Allowed : 24.49 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.23), residues: 1321 helix: 0.64 (0.19), residues: 733 sheet: -1.44 (0.44), residues: 146 loop : -1.72 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 764 HIS 0.010 0.001 HIS B 781 PHE 0.025 0.002 PHE B 571 TYR 0.019 0.002 TYR A 299 ARG 0.010 0.001 ARG B1103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 193 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8376 (mptt) cc_final: 0.8048 (mmtm) REVERT: A 279 LEU cc_start: 0.5669 (OUTLIER) cc_final: 0.5423 (mp) REVERT: A 324 GLN cc_start: 0.8433 (mp10) cc_final: 0.8019 (mp10) REVERT: A 380 LEU cc_start: 0.6677 (OUTLIER) cc_final: 0.6052 (mt) REVERT: A 413 GLN cc_start: 0.6727 (OUTLIER) cc_final: 0.5283 (mm110) REVERT: A 431 LEU cc_start: 0.7677 (tp) cc_final: 0.7448 (tp) REVERT: A 446 ASP cc_start: 0.7781 (m-30) cc_final: 0.7536 (m-30) REVERT: A 450 PHE cc_start: 0.4939 (t80) cc_final: 0.4489 (t80) REVERT: A 535 ASN cc_start: 0.7286 (OUTLIER) cc_final: 0.6033 (t0) REVERT: A 631 ARG cc_start: 0.8393 (ttp-170) cc_final: 0.8096 (ptm-80) REVERT: A 653 ASN cc_start: 0.7552 (t0) cc_final: 0.7278 (t0) REVERT: A 659 LYS cc_start: 0.7645 (tptp) cc_final: 0.7278 (tptm) REVERT: A 660 ASP cc_start: 0.8108 (t0) cc_final: 0.7754 (t70) REVERT: A 661 LYS cc_start: 0.8076 (ttmt) cc_final: 0.7748 (ptmm) REVERT: A 805 LEU cc_start: 0.6317 (OUTLIER) cc_final: 0.6022 (tt) REVERT: A 813 MET cc_start: 0.7707 (mmp) cc_final: 0.7472 (mmp) REVERT: A 815 TYR cc_start: 0.7344 (m-10) cc_final: 0.6654 (m-80) REVERT: A 846 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7995 (mm-40) REVERT: A 914 GLU cc_start: 0.4228 (OUTLIER) cc_final: 0.3880 (pm20) REVERT: B 549 GLN cc_start: 0.8415 (pt0) cc_final: 0.8103 (pt0) REVERT: B 553 ASP cc_start: 0.9084 (m-30) cc_final: 0.8767 (m-30) REVERT: B 573 ARG cc_start: 0.8271 (ttt180) cc_final: 0.8034 (ttm-80) REVERT: B 617 LYS cc_start: 0.8626 (tptp) cc_final: 0.7807 (mmtm) REVERT: B 679 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6360 (mt) REVERT: B 704 LYS cc_start: 0.6625 (OUTLIER) cc_final: 0.5983 (mtpt) REVERT: B 779 ARG cc_start: 0.7437 (tpp80) cc_final: 0.7168 (tpt170) REVERT: B 796 ARG cc_start: 0.7954 (ptm-80) cc_final: 0.7579 (ptm-80) REVERT: B 839 LYS cc_start: 0.7292 (mttt) cc_final: 0.6634 (tptp) REVERT: B 852 GLN cc_start: 0.8563 (mt0) cc_final: 0.8317 (mt0) REVERT: B 925 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7551 (mm-30) REVERT: B 1030 MET cc_start: 0.8688 (tmm) cc_final: 0.8414 (tmm) REVERT: B 1091 LYS cc_start: 0.8585 (tppt) cc_final: 0.8153 (tppt) REVERT: B 1094 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8641 (mt-10) outliers start: 55 outliers final: 32 residues processed: 229 average time/residue: 0.2702 time to fit residues: 84.6689 Evaluate side-chains 225 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 185 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 827 HIS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 881 ASN Chi-restraints excluded: chain B residue 1027 ASN Chi-restraints excluded: chain B residue 1058 GLN Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.3980 chunk 77 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11638 Z= 0.244 Angle : 0.662 11.093 15856 Z= 0.353 Chirality : 0.044 0.274 1819 Planarity : 0.005 0.080 1897 Dihedral : 17.132 89.195 1861 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 24.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.24 % Allowed : 25.34 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.23), residues: 1321 helix: 0.65 (0.19), residues: 731 sheet: -1.58 (0.43), residues: 149 loop : -1.67 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 764 HIS 0.007 0.001 HIS B 729 PHE 0.020 0.002 PHE B 571 TYR 0.019 0.002 TYR A 299 ARG 0.013 0.000 ARG B1103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 187 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8375 (mptt) cc_final: 0.8056 (mmtm) REVERT: A 279 LEU cc_start: 0.5665 (OUTLIER) cc_final: 0.5420 (mp) REVERT: A 324 GLN cc_start: 0.8415 (mp10) cc_final: 0.8053 (mp10) REVERT: A 344 GLN cc_start: 0.7392 (tm-30) cc_final: 0.7154 (tm-30) REVERT: A 380 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.5998 (mt) REVERT: A 413 GLN cc_start: 0.6697 (OUTLIER) cc_final: 0.5282 (mm110) REVERT: A 431 LEU cc_start: 0.7686 (tp) cc_final: 0.7457 (tp) REVERT: A 446 ASP cc_start: 0.7812 (m-30) cc_final: 0.7573 (m-30) REVERT: A 535 ASN cc_start: 0.7401 (OUTLIER) cc_final: 0.6179 (t0) REVERT: A 603 ASP cc_start: 0.6983 (t0) cc_final: 0.6190 (t0) REVERT: A 631 ARG cc_start: 0.8409 (ttp-170) cc_final: 0.8111 (ptm-80) REVERT: A 653 ASN cc_start: 0.7578 (t0) cc_final: 0.7297 (t0) REVERT: A 659 LYS cc_start: 0.7638 (tptp) cc_final: 0.7273 (tptm) REVERT: A 660 ASP cc_start: 0.8138 (t0) cc_final: 0.7791 (t70) REVERT: A 661 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7749 (ptmm) REVERT: A 786 GLU cc_start: 0.7295 (pt0) cc_final: 0.6860 (tm-30) REVERT: A 805 LEU cc_start: 0.6326 (OUTLIER) cc_final: 0.6010 (tt) REVERT: A 813 MET cc_start: 0.7698 (mmp) cc_final: 0.7395 (mmp) REVERT: A 846 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7990 (mm-40) REVERT: A 914 GLU cc_start: 0.4204 (OUTLIER) cc_final: 0.3848 (pm20) REVERT: B 532 MET cc_start: 0.5446 (mpp) cc_final: 0.5187 (tpp) REVERT: B 543 ARG cc_start: 0.8261 (ptm-80) cc_final: 0.7984 (ptm-80) REVERT: B 549 GLN cc_start: 0.8448 (pt0) cc_final: 0.8243 (pt0) REVERT: B 553 ASP cc_start: 0.9085 (m-30) cc_final: 0.8768 (m-30) REVERT: B 573 ARG cc_start: 0.8272 (ttt180) cc_final: 0.8031 (ttm-80) REVERT: B 617 LYS cc_start: 0.8610 (tptp) cc_final: 0.7871 (mmtm) REVERT: B 679 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6439 (mm) REVERT: B 704 LYS cc_start: 0.6569 (OUTLIER) cc_final: 0.5961 (mtpt) REVERT: B 779 ARG cc_start: 0.7552 (tpp80) cc_final: 0.7317 (tpt170) REVERT: B 796 ARG cc_start: 0.7954 (ptm-80) cc_final: 0.7575 (ptm-80) REVERT: B 839 LYS cc_start: 0.7299 (mttt) cc_final: 0.6627 (tptp) REVERT: B 852 GLN cc_start: 0.8555 (mt0) cc_final: 0.8330 (mt0) REVERT: B 925 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7579 (mm-30) REVERT: B 1030 MET cc_start: 0.8701 (tmm) cc_final: 0.8462 (tmm) REVERT: B 1091 LYS cc_start: 0.8576 (tppt) cc_final: 0.8121 (tppt) REVERT: B 1094 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8628 (mt-10) outliers start: 50 outliers final: 33 residues processed: 221 average time/residue: 0.2742 time to fit residues: 82.8643 Evaluate side-chains 228 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 186 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 827 HIS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 881 ASN Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 1027 ASN Chi-restraints excluded: chain B residue 1058 GLN Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.0370 chunk 121 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 37 optimal weight: 50.0000 chunk 109 optimal weight: 0.4980 chunk 114 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN B 647 HIS ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11638 Z= 0.224 Angle : 0.664 14.666 15856 Z= 0.350 Chirality : 0.044 0.419 1819 Planarity : 0.004 0.081 1897 Dihedral : 17.064 89.454 1861 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 23.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.41 % Allowed : 25.59 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.23), residues: 1321 helix: 0.69 (0.19), residues: 728 sheet: -1.78 (0.42), residues: 152 loop : -1.69 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 764 HIS 0.010 0.001 HIS B 729 PHE 0.020 0.002 PHE B 571 TYR 0.020 0.002 TYR A 299 ARG 0.012 0.001 ARG B1103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 193 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8377 (mptt) cc_final: 0.8080 (mmtm) REVERT: A 279 LEU cc_start: 0.5674 (OUTLIER) cc_final: 0.5419 (mp) REVERT: A 324 GLN cc_start: 0.8471 (mp10) cc_final: 0.8094 (mp10) REVERT: A 344 GLN cc_start: 0.7273 (tm-30) cc_final: 0.7072 (tm-30) REVERT: A 364 GLU cc_start: 0.7576 (tt0) cc_final: 0.7249 (pp20) REVERT: A 380 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6016 (mt) REVERT: A 413 GLN cc_start: 0.6628 (OUTLIER) cc_final: 0.5614 (mm110) REVERT: A 431 LEU cc_start: 0.7685 (tp) cc_final: 0.7458 (tp) REVERT: A 446 ASP cc_start: 0.7857 (m-30) cc_final: 0.7602 (m-30) REVERT: A 535 ASN cc_start: 0.7425 (OUTLIER) cc_final: 0.6271 (t0) REVERT: A 563 TYR cc_start: 0.9091 (t80) cc_final: 0.8749 (t80) REVERT: A 603 ASP cc_start: 0.6988 (t0) cc_final: 0.6191 (t0) REVERT: A 631 ARG cc_start: 0.8389 (ttp-170) cc_final: 0.8097 (ptm-80) REVERT: A 653 ASN cc_start: 0.7596 (t0) cc_final: 0.7312 (t0) REVERT: A 659 LYS cc_start: 0.7432 (tptp) cc_final: 0.7123 (tptm) REVERT: A 660 ASP cc_start: 0.8118 (t0) cc_final: 0.7778 (t70) REVERT: A 661 LYS cc_start: 0.7983 (ttmt) cc_final: 0.7745 (ptmm) REVERT: A 707 CYS cc_start: 0.7703 (p) cc_final: 0.7501 (p) REVERT: A 786 GLU cc_start: 0.7205 (pt0) cc_final: 0.6822 (tm-30) REVERT: A 813 MET cc_start: 0.7738 (mmp) cc_final: 0.7463 (mmp) REVERT: A 815 TYR cc_start: 0.7334 (m-10) cc_final: 0.6422 (m-10) REVERT: A 846 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7981 (mm-40) REVERT: B 532 MET cc_start: 0.5546 (OUTLIER) cc_final: 0.5238 (tpp) REVERT: B 543 ARG cc_start: 0.8284 (ptm-80) cc_final: 0.7972 (ptm-80) REVERT: B 549 GLN cc_start: 0.8489 (pt0) cc_final: 0.8288 (pt0) REVERT: B 553 ASP cc_start: 0.9106 (m-30) cc_final: 0.8783 (m-30) REVERT: B 573 ARG cc_start: 0.8287 (ttt180) cc_final: 0.8045 (ttm-80) REVERT: B 617 LYS cc_start: 0.8609 (tptp) cc_final: 0.7889 (mmtm) REVERT: B 672 ILE cc_start: 0.2966 (OUTLIER) cc_final: 0.2109 (mt) REVERT: B 679 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6430 (mm) REVERT: B 704 LYS cc_start: 0.6528 (OUTLIER) cc_final: 0.5940 (mtpt) REVERT: B 753 MET cc_start: 0.2270 (ttt) cc_final: 0.1456 (ttm) REVERT: B 779 ARG cc_start: 0.7674 (tpp80) cc_final: 0.7408 (tpt-90) REVERT: B 796 ARG cc_start: 0.7962 (ptm-80) cc_final: 0.7577 (ptm-80) REVERT: B 839 LYS cc_start: 0.7244 (mttt) cc_final: 0.6574 (tptp) REVERT: B 852 GLN cc_start: 0.8546 (mt0) cc_final: 0.8336 (mt0) REVERT: B 893 ILE cc_start: 0.8456 (mt) cc_final: 0.8183 (mm) REVERT: B 925 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7507 (mm-30) REVERT: B 1030 MET cc_start: 0.8691 (tmm) cc_final: 0.8448 (tmm) REVERT: B 1091 LYS cc_start: 0.8535 (tppt) cc_final: 0.8111 (tppt) REVERT: B 1094 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8622 (mt-10) outliers start: 52 outliers final: 34 residues processed: 228 average time/residue: 0.3161 time to fit residues: 99.2791 Evaluate side-chains 226 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 184 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 881 ASN Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 1027 ASN Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 65 optimal weight: 0.0270 chunk 85 optimal weight: 0.7980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 GLN ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11638 Z= 0.230 Angle : 0.687 14.694 15856 Z= 0.366 Chirality : 0.045 0.406 1819 Planarity : 0.005 0.081 1897 Dihedral : 17.012 88.602 1861 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 23.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.98 % Allowed : 26.53 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.23), residues: 1321 helix: 0.67 (0.19), residues: 727 sheet: -1.49 (0.46), residues: 136 loop : -1.74 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 764 HIS 0.011 0.001 HIS B 729 PHE 0.020 0.002 PHE B 571 TYR 0.021 0.002 TYR A 299 ARG 0.016 0.001 ARG B1103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 194 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8356 (mptt) cc_final: 0.8066 (mmtm) REVERT: A 253 MET cc_start: 0.7810 (tpp) cc_final: 0.5465 (tpp) REVERT: A 279 LEU cc_start: 0.5645 (OUTLIER) cc_final: 0.5405 (mp) REVERT: A 324 GLN cc_start: 0.8471 (mp10) cc_final: 0.8194 (mp10) REVERT: A 364 GLU cc_start: 0.7574 (tt0) cc_final: 0.7251 (pp20) REVERT: A 380 LEU cc_start: 0.6613 (OUTLIER) cc_final: 0.5935 (mt) REVERT: A 413 GLN cc_start: 0.6664 (OUTLIER) cc_final: 0.4619 (tp-100) REVERT: A 431 LEU cc_start: 0.7716 (tp) cc_final: 0.7492 (tp) REVERT: A 462 GLN cc_start: 0.5447 (mp10) cc_final: 0.5033 (mp10) REVERT: A 535 ASN cc_start: 0.7443 (OUTLIER) cc_final: 0.6354 (t0) REVERT: A 563 TYR cc_start: 0.9097 (t80) cc_final: 0.8763 (t80) REVERT: A 603 ASP cc_start: 0.6991 (t0) cc_final: 0.6183 (t0) REVERT: A 631 ARG cc_start: 0.8378 (ttp-170) cc_final: 0.8070 (mtm110) REVERT: A 653 ASN cc_start: 0.7616 (t0) cc_final: 0.7328 (t0) REVERT: A 660 ASP cc_start: 0.8151 (t0) cc_final: 0.7899 (t70) REVERT: A 707 CYS cc_start: 0.7704 (p) cc_final: 0.7472 (p) REVERT: A 743 SER cc_start: 0.7507 (t) cc_final: 0.6938 (m) REVERT: A 786 GLU cc_start: 0.7268 (pt0) cc_final: 0.6915 (tm-30) REVERT: A 813 MET cc_start: 0.7730 (mmp) cc_final: 0.7417 (mmp) REVERT: A 846 GLN cc_start: 0.8311 (mm-40) cc_final: 0.8088 (mm-40) REVERT: A 850 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7102 (mm-30) REVERT: B 532 MET cc_start: 0.5629 (OUTLIER) cc_final: 0.5422 (tpp) REVERT: B 543 ARG cc_start: 0.8265 (ptm-80) cc_final: 0.7997 (ptm-80) REVERT: B 549 GLN cc_start: 0.8473 (pt0) cc_final: 0.8272 (pt0) REVERT: B 573 ARG cc_start: 0.8290 (ttt180) cc_final: 0.8054 (ttm-80) REVERT: B 617 LYS cc_start: 0.8561 (tptp) cc_final: 0.7851 (mmtm) REVERT: B 672 ILE cc_start: 0.2987 (OUTLIER) cc_final: 0.2109 (mt) REVERT: B 679 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6612 (mt) REVERT: B 704 LYS cc_start: 0.6522 (OUTLIER) cc_final: 0.5933 (mtpt) REVERT: B 753 MET cc_start: 0.1895 (ttt) cc_final: 0.1015 (ttm) REVERT: B 779 ARG cc_start: 0.7749 (tpp80) cc_final: 0.7478 (tpt-90) REVERT: B 796 ARG cc_start: 0.7959 (ptm-80) cc_final: 0.7575 (ptm-80) REVERT: B 839 LYS cc_start: 0.7218 (mttt) cc_final: 0.6533 (tptp) REVERT: B 852 GLN cc_start: 0.8524 (mt0) cc_final: 0.8319 (mt0) REVERT: B 893 ILE cc_start: 0.8509 (mt) cc_final: 0.8280 (mm) REVERT: B 908 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7080 (tt0) REVERT: B 925 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7500 (mm-30) REVERT: B 1000 ASP cc_start: 0.7781 (t0) cc_final: 0.7437 (t0) REVERT: B 1030 MET cc_start: 0.8695 (tmm) cc_final: 0.8461 (tmm) REVERT: B 1091 LYS cc_start: 0.8509 (tppt) cc_final: 0.8049 (tppt) REVERT: B 1094 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8618 (mt-10) outliers start: 47 outliers final: 35 residues processed: 224 average time/residue: 0.2714 time to fit residues: 83.7099 Evaluate side-chains 232 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 188 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 881 ASN Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 1027 ASN Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1103 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.6980 chunk 32 optimal weight: 0.2980 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 0.0770 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4892 r_free = 0.4892 target = 0.217234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.184561 restraints weight = 18158.511| |-----------------------------------------------------------------------------| r_work (start): 0.4498 rms_B_bonded: 3.60 r_work: 0.4361 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4359 r_free = 0.4359 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4359 r_free = 0.4359 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5941 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11638 Z= 0.229 Angle : 0.681 14.548 15856 Z= 0.361 Chirality : 0.045 0.427 1819 Planarity : 0.005 0.080 1897 Dihedral : 16.906 88.103 1861 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 23.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.32 % Allowed : 26.19 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.24), residues: 1321 helix: 0.72 (0.19), residues: 717 sheet: -1.47 (0.46), residues: 136 loop : -1.64 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 345 HIS 0.010 0.001 HIS B 729 PHE 0.019 0.002 PHE B 571 TYR 0.019 0.002 TYR A 299 ARG 0.015 0.001 ARG B1103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3157.21 seconds wall clock time: 57 minutes 27.43 seconds (3447.43 seconds total)