Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 6 05:13:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oma_16972/07_2023/8oma_16972_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oma_16972/07_2023/8oma_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_16972/07_2023/8oma_16972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oma_16972/07_2023/8oma_16972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oma_16972/07_2023/8oma_16972_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oma_16972/07_2023/8oma_16972_updated.pdb" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-5013/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: 6.14, per 1000 atoms: 0.54 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: 5.47 Conformation dependent library (CDL) restraints added in 1.7 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: 4.33 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: 4.11 Time building geometry restraints manager: 5.61 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: 5732 17.96 - 35.92: 838 35.92 - 53.88: 305 53.88 - 71.85: 51 71.85 - 89.81: 16 Dihedral angle restraints: 6942 sinusoidal: 3047 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 6939 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: 7.380 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: 0.000 Extract box with map and model: 5.650 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 36.280 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.610 ------------------------------------------------------------------------------- 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 : 19.392 89.807 4412 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 % 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 *********************** 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 : 1.175 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 outliers start: 35 outliers final: 17 residues processed: 236 average time/residue: 0.3047 time to fit residues: 95.4972 Evaluate side-chains 206 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 189 time to evaluate : 1.194 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1344 time to fit residues: 5.6150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.0970 chunk 102 optimal weight: 0.9990 chunk 56 optimal weight: 0.0870 chunk 34 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 54 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 40 optimal weight: 0.0870 chunk 64 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 overall best weight: 0.2934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.6795 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 11638 Z= 0.201 Angle : 0.642 10.615 15856 Z= 0.340 Chirality : 0.042 0.193 1819 Planarity : 0.004 0.073 1897 Dihedral : 16.457 61.588 1761 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 22.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer Outliers : 3.14 % 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: -0.85 (0.23), residues: 1321 helix: 0.55 (0.19), residues: 712 sheet: -2.02 (0.39), residues: 171 loop : -1.69 (0.30), residues: 438 *********************** 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: 37 poor density : 209 time to evaluate : 1.296 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 outliers start: 37 outliers final: 23 residues processed: 227 average time/residue: 0.3055 time to fit residues: 92.9958 Evaluate side-chains 210 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 187 time to evaluate : 1.310 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1463 time to fit residues: 7.5539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 102 optimal weight: 0.3980 chunk 83 optimal weight: 0.0980 chunk 33 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN ** A 348 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 11638 Z= 0.220 Angle : 0.625 8.044 15856 Z= 0.337 Chirality : 0.042 0.247 1819 Planarity : 0.004 0.079 1897 Dihedral : 16.386 61.037 1761 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 23.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer Outliers : 2.03 % 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: -0.67 (0.23), residues: 1321 helix: 0.66 (0.19), residues: 720 sheet: -1.75 (0.40), residues: 173 loop : -1.68 (0.30), residues: 428 *********************** 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 231 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 207 time to evaluate : 1.238 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 outliers start: 24 outliers final: 10 residues processed: 220 average time/residue: 0.2968 time to fit residues: 88.0460 Evaluate side-chains 188 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 178 time to evaluate : 1.223 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1447 time to fit residues: 4.1873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 3.9990 chunk 92 optimal weight: 0.0670 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 chunk 82 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 130 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 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** A 846 GLN B 549 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: 0.6831 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 11638 Z= 0.205 Angle : 0.626 11.818 15856 Z= 0.332 Chirality : 0.042 0.208 1819 Planarity : 0.004 0.079 1897 Dihedral : 16.350 61.119 1761 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 2.63 % 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: 0.68 (0.19), residues: 722 sheet: -1.48 (0.43), residues: 162 loop : -1.67 (0.30), residues: 437 *********************** 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 221 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 190 time to evaluate : 1.437 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 outliers start: 31 outliers final: 10 residues processed: 210 average time/residue: 0.3025 time to fit residues: 86.0467 Evaluate side-chains 189 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 179 time to evaluate : 1.276 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1151 time to fit residues: 3.9139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 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: 0.6897 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 11638 Z= 0.269 Angle : 0.669 10.589 15856 Z= 0.357 Chirality : 0.043 0.204 1819 Planarity : 0.005 0.080 1897 Dihedral : 16.364 61.324 1761 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 24.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer Outliers : 2.71 % 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: -0.75 (0.23), residues: 1321 helix: 0.58 (0.19), residues: 722 sheet: -1.66 (0.43), residues: 165 loop : -1.77 (0.29), residues: 434 *********************** 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 228 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 196 time to evaluate : 1.269 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 outliers start: 32 outliers final: 10 residues processed: 215 average time/residue: 0.2950 time to fit residues: 86.6697 Evaluate side-chains 196 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 186 time to evaluate : 1.289 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1617 time to fit residues: 4.3397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 GLN ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN B 647 HIS B 684 HIS ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 11638 Z= 0.329 Angle : 0.722 12.077 15856 Z= 0.384 Chirality : 0.046 0.350 1819 Planarity : 0.005 0.080 1897 Dihedral : 16.398 60.822 1761 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 26.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer Outliers : 3.14 % 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: -1.07 (0.23), residues: 1321 helix: 0.32 (0.19), residues: 732 sheet: -1.80 (0.44), residues: 154 loop : -1.98 (0.28), residues: 435 *********************** 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 225 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 188 time to evaluate : 1.163 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 outliers start: 37 outliers final: 18 residues processed: 210 average time/residue: 0.2984 time to fit residues: 84.7221 Evaluate side-chains 200 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 182 time to evaluate : 1.253 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1393 time to fit residues: 6.0878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.8980 chunk 74 optimal weight: 0.0370 chunk 95 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 0.0070 chunk 72 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 79 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.4076 ------------------------------------------------------------------------------- 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 846 GLN B 647 HIS ** 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: 0.6877 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 11638 Z= 0.215 Angle : 0.696 13.943 15856 Z= 0.361 Chirality : 0.044 0.400 1819 Planarity : 0.004 0.081 1897 Dihedral : 16.327 61.303 1761 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 23.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer Outliers : 1.27 % 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: -0.80 (0.23), residues: 1321 helix: 0.53 (0.19), residues: 731 sheet: -1.65 (0.45), residues: 144 loop : -1.85 (0.28), residues: 446 *********************** 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 205 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 190 time to evaluate : 1.203 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 outliers start: 15 outliers final: 7 residues processed: 197 average time/residue: 0.2932 time to fit residues: 78.6004 Evaluate side-chains 189 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 182 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1550 time to fit residues: 3.5390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 39 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 0.0670 chunk 102 optimal weight: 0.7980 chunk 118 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 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 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 11638 Z= 0.241 Angle : 0.709 15.134 15856 Z= 0.367 Chirality : 0.044 0.427 1819 Planarity : 0.005 0.076 1897 Dihedral : 16.300 60.920 1761 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 24.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer Outliers : 1.36 % 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: -0.78 (0.23), residues: 1321 helix: 0.54 (0.19), residues: 729 sheet: -1.65 (0.45), residues: 143 loop : -1.82 (0.29), residues: 449 *********************** 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 200 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 184 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 194 average time/residue: 0.2846 time to fit residues: 76.2679 Evaluate side-chains 185 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 176 time to evaluate : 1.191 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1221 time to fit residues: 3.7135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.9990 chunk 121 optimal weight: 0.0570 chunk 124 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 109 optimal weight: 0.1980 chunk 114 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN A 846 GLN B 582 GLN B 647 HIS ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 11638 Z= 0.242 Angle : 0.732 15.352 15856 Z= 0.377 Chirality : 0.045 0.431 1819 Planarity : 0.005 0.075 1897 Dihedral : 16.260 60.796 1761 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 24.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer Outliers : 0.51 % 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: -0.79 (0.23), residues: 1321 helix: 0.51 (0.19), residues: 729 sheet: -1.62 (0.45), residues: 142 loop : -1.79 (0.29), residues: 450 *********************** 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 191 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 185 time to evaluate : 1.323 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 outliers start: 6 outliers final: 4 residues processed: 188 average time/residue: 0.3058 time to fit residues: 78.0050 Evaluate side-chains 179 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 175 time to evaluate : 1.309 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1388 time to fit residues: 2.8091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.0270 chunk 78 optimal weight: 0.0670 chunk 60 optimal weight: 0.2980 chunk 89 optimal weight: 0.8980 chunk 134 optimal weight: 0.0970 chunk 123 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 65 optimal weight: 0.1980 chunk 85 optimal weight: 0.9980 overall best weight: 0.1374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 11638 Z= 0.192 Angle : 0.728 14.421 15856 Z= 0.372 Chirality : 0.044 0.457 1819 Planarity : 0.005 0.074 1897 Dihedral : 16.169 60.997 1761 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer Outliers : 0.68 % 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: -0.55 (0.23), residues: 1321 helix: 0.65 (0.19), residues: 724 sheet: -1.30 (0.46), residues: 143 loop : -1.64 (0.29), residues: 454 ********************** 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 188 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 180 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 182 average time/residue: 0.2822 time to fit residues: 71.1109 Evaluate side-chains 183 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 179 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2556 time to fit residues: 3.2175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 110 optimal weight: 0.0000 chunk 13 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.218411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.186767 restraints weight = 18615.868| |-----------------------------------------------------------------------------| r_work (start): 0.4506 rms_B_bonded: 3.61 r_work: 0.4374 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4383 r_free = 0.4383 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4383 r_free = 0.4383 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5898 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 11638 Z= 0.248 Angle : 0.741 14.600 15856 Z= 0.382 Chirality : 0.045 0.430 1819 Planarity : 0.005 0.069 1897 Dihedral : 16.136 60.789 1761 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 24.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer Outliers : 0.42 % 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: -0.57 (0.24), residues: 1321 helix: 0.65 (0.19), residues: 723 sheet: -1.35 (0.46), residues: 143 loop : -1.67 (0.29), residues: 455 =============================================================================== Job complete usr+sys time: 3050.04 seconds wall clock time: 56 minutes 12.42 seconds (3372.42 seconds total)