Starting phenix.real_space_refine on Sat Oct 24 01:10:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mb7_63768/10_2026/9mb7_63768.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mb7_63768/10_2026/9mb7_63768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mb7_63768/10_2026/9mb7_63768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mb7_63768/10_2026/9mb7_63768.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mb7_63768/10_2026/9mb7_63768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mb7_63768/10_2026/9mb7_63768.map" } resolution = 2.88 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= 0.002 sd= 0.027 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 162 5.49 5 Mg 1 5.21 5 S 23 5.16 5 C 6784 2.51 5 N 2056 2.21 5 O 2596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11622 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 310 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "C" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 486 Unusual residues: {' AS': 2, ' GS': 2, ' SC': 3} Classifications: {'DNA': 17, 'undetermined': 7} Link IDs: {'rna3p': 16, None: 7} Not linked: pdbres=" SC C 13 " pdbres=" SC C 14 " Not linked: pdbres=" SC C 14 " pdbres=" AS C 15 " Not linked: pdbres=" AS C 15 " pdbres=" AS C 16 " Not linked: pdbres=" AS C 16 " pdbres=" GS C 17 " Not linked: pdbres=" GS C 17 " pdbres=" SC C 18 " ... (remaining 2 not shown) Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Chain: "D" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "D" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 346 Unusual residues: {' GS': 2} Classifications: {'DNA': 15, 'undetermined': 2} Link IDs: {'rna3p': 14, None: 2} Not linked: pdbres=" GS D -2 " pdbres=" GS D -1 " Not linked: pdbres=" GS D -1 " pdbres=" DC D 0 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "A" Number of atoms: 8198 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 986, 8190 Classifications: {'peptide': 986} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 961} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 986, 8190 Classifications: {'peptide': 986} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 961} Chain breaks: 3 bond proxies already assigned to first conformer: 8323 Chain: "B" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2092 Classifications: {'RNA': 98} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 5, 'rna3p_pur': 49, 'rna3p_pyr': 40} Link IDs: {'rna2p': 9, 'rna3p': 88} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.07, per 1000 atoms: 0.35 Number of scatterers: 11622 At special positions: 0 Unit cell: (92.8377, 129.119, 130.186, 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 23 16.00 P 162 15.00 Mg 1 11.99 O 2596 8.00 N 2056 7.00 C 6784 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 - 3.00 Amino acid : True - 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 825.5 milliseconds 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 8 sheets defined 50.5% alpha, 10.9% beta 58 base pairs and 85 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 40 through 74 removed outlier: 4.282A pdb=" N ASN A 44 " --> pdb=" O ASN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 101 through 115 removed outlier: 3.534A pdb=" N ARG A 115 " --> pdb=" O HIS A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 172 through 191 removed outlier: 4.449A pdb=" N ALA A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR A 190 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 207 Processing helix chain 'A' and resid 225 through 234 Processing helix chain 'A' and resid 250 through 265 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 326 through 336 removed outlier: 3.880A pdb=" N HIS A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 344 through 358 Processing helix chain 'A' and resid 360 through 370 removed outlier: 3.619A pdb=" N GLU A 366 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 384 Processing helix chain 'A' and resid 396 through 410 removed outlier: 3.588A pdb=" N ILE A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLU A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.998A pdb=" N ASP A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N PHE A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 469 Processing helix chain 'A' and resid 484 through 513 Processing helix chain 'A' and resid 517 through 530 removed outlier: 3.511A pdb=" N ILE A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 549 Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 577 through 584 Processing helix chain 'A' and resid 587 through 593 Processing helix chain 'A' and resid 600 through 613 Processing helix chain 'A' and resid 619 through 627 Processing helix chain 'A' and resid 635 through 640 removed outlier: 4.228A pdb=" N LYS A 639 " --> pdb=" O PHE A 635 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP A 640 " --> pdb=" O SER A 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 635 through 640' Processing helix chain 'A' and resid 649 through 668 Processing helix chain 'A' and resid 677 through 688 removed outlier: 3.907A pdb=" N THR A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 717 removed outlier: 4.032A pdb=" N ALA A 702 " --> pdb=" O TYR A 698 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 707 " --> pdb=" O GLU A 703 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASP A 712 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N PHE A 713 " --> pdb=" O ALA A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 766 Processing helix chain 'A' and resid 814 through 823 Processing helix chain 'A' and resid 824 through 826 No H-bonds generated for 'chain 'A' and resid 824 through 826' Processing helix chain 'A' and resid 827 through 833 removed outlier: 4.071A pdb=" N HIS A 831 " --> pdb=" O LEU A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 847 removed outlier: 3.896A pdb=" N ILE A 843 " --> pdb=" O LYS A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 862 removed outlier: 3.620A pdb=" N LYS A 856 " --> pdb=" O ASN A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 897 Processing helix chain 'A' and resid 943 through 954 Processing helix chain 'A' and resid 1000 through 1009 Processing sheet with id=AA1, first strand: chain 'A' and resid 672 through 673 removed outlier: 4.110A pdb=" N ASP A 473 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL A 16 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL A 33 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR A 18 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA A 31 " --> pdb=" O TYR A 18 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE A 20 " --> pdb=" O ILE A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267 Processing sheet with id=AA3, first strand: chain 'A' and resid 314 through 315 removed outlier: 4.245A pdb=" N ARG A 314 " --> pdb=" O GLU A 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 553 through 557 Processing sheet with id=AA5, first strand: chain 'A' and resid 880 through 886 removed outlier: 4.890A pdb=" N ILE A 801 " --> pdb=" O GLY A 884 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LYS A 886 " --> pdb=" O THR A 799 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N THR A 799 " --> pdb=" O LYS A 886 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N SER A 790 " --> pdb=" O VAL A 802 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 922 through 929 removed outlier: 6.488A pdb=" N PHE A 914 " --> pdb=" O SER A 965 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER A 965 " --> pdb=" O PHE A 914 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 916 " --> pdb=" O ILE A 963 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 933 through 935 Processing sheet with id=AA8, first strand: chain 'A' and resid 1016 through 1019 removed outlier: 4.220A pdb=" N ILE A1016 " --> pdb=" O VAL A 994 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ALA A 991 " --> pdb=" O VAL A 984 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL A 984 " --> pdb=" O ALA A 991 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLU A 993 " --> pdb=" O ILE A 982 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 971 " --> pdb=" O TYR A1030 " (cutoff:3.500A) 375 hydrogen bonds defined for protein. 1094 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 139 hydrogen bonds 274 hydrogen bond angles 0 basepair planarities 58 basepair parallelities 85 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 4740 1.39 - 1.56: 7073 1.56 - 1.74: 316 1.74 - 1.91: 25 1.91 - 2.08: 9 Bond restraints: 12163 Sorted by residual: bond pdb=" OP1 SC C 14 " pdb=" P SC C 14 " ideal model delta sigma weight residual 1.600 1.497 0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" OP1 SC C 18 " pdb=" P SC C 18 " ideal model delta sigma weight residual 1.600 1.498 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" OP1 SC C 13 " pdb=" P SC C 13 " ideal model delta sigma weight residual 1.600 1.500 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" OP1 AS C 15 " pdb=" P AS C 15 " ideal model delta sigma weight residual 1.588 1.491 0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" OP1 AS C 16 " pdb=" P AS C 16 " ideal model delta sigma weight residual 1.588 1.499 0.089 2.00e-02 2.50e+03 1.97e+01 ... (remaining 12158 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 15755 2.88 - 5.75: 1247 5.75 - 8.63: 91 8.63 - 11.50: 7 11.50 - 14.38: 3 Bond angle restraints: 17103 Sorted by residual: angle pdb=" CA PHE A 444 " pdb=" CB PHE A 444 " pdb=" CG PHE A 444 " ideal model delta sigma weight residual 113.80 122.03 -8.23 1.00e+00 1.00e+00 6.77e+01 angle pdb=" CA ASP A 443 " pdb=" CB ASP A 443 " pdb=" CG ASP A 443 " ideal model delta sigma weight residual 112.60 120.47 -7.87 1.00e+00 1.00e+00 6.19e+01 angle pdb=" N PHE A 444 " pdb=" CA PHE A 444 " pdb=" CB PHE A 444 " ideal model delta sigma weight residual 110.19 121.65 -11.46 1.55e+00 4.16e-01 5.46e+01 angle pdb=" C PHE A 444 " pdb=" CA PHE A 444 " pdb=" CB PHE A 444 " ideal model delta sigma weight residual 110.56 97.05 13.51 1.83e+00 2.99e-01 5.45e+01 angle pdb=" O3' G B 19 " pdb=" P C B 20 " pdb=" O5' C B 20 " ideal model delta sigma weight residual 104.00 92.73 11.27 1.90e+00 2.77e-01 3.52e+01 ... (remaining 17098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 6267 17.48 - 34.95: 708 34.95 - 52.43: 295 52.43 - 69.90: 173 69.90 - 87.38: 32 Dihedral angle restraints: 7475 sinusoidal: 4542 harmonic: 2933 Sorted by residual: dihedral pdb=" O4' U B 89 " pdb=" C2' U B 89 " pdb=" C1' U B 89 " pdb=" C3' U B 89 " ideal model delta sinusoidal sigma weight residual 25.00 -12.61 37.61 1 8.00e+00 1.56e-02 3.12e+01 dihedral pdb=" C4' U B 89 " pdb=" O4' U B 89 " pdb=" C1' U B 89 " pdb=" C2' U B 89 " ideal model delta sinusoidal sigma weight residual 3.00 -33.23 36.23 1 8.00e+00 1.56e-02 2.90e+01 dihedral pdb=" CA PHE A 565 " pdb=" C PHE A 565 " pdb=" N ASP A 566 " pdb=" CA ASP A 566 " ideal model delta harmonic sigma weight residual 180.00 156.36 23.64 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 7472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1715 0.131 - 0.261: 231 0.261 - 0.392: 6 0.392 - 0.522: 0 0.522 - 0.652: 2 Chirality restraints: 1954 Sorted by residual: chirality pdb=" P DA D -24 " pdb=" OP1 DA D -24 " pdb=" OP2 DA D -24 " pdb=" O5' DA D -24 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" P G B 0 " pdb=" OP1 G B 0 " pdb=" OP2 G B 0 " pdb=" O5' G B 0 " both_signs ideal model delta sigma weight residual True 2.41 2.98 -0.57 2.00e-01 2.50e+01 8.05e+00 chirality pdb=" CA ARG A 686 " pdb=" N ARG A 686 " pdb=" C ARG A 686 " pdb=" CB ARG A 686 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 1951 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA C 21 " -0.061 2.00e-02 2.50e+03 2.50e-02 1.72e+01 pdb=" N9 DA C 21 " 0.030 2.00e-02 2.50e+03 pdb=" C8 DA C 21 " 0.013 2.00e-02 2.50e+03 pdb=" N7 DA C 21 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DA C 21 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DA C 21 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA C 21 " -0.029 2.00e-02 2.50e+03 pdb=" N1 DA C 21 " -0.017 2.00e-02 2.50e+03 pdb=" C2 DA C 21 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DA C 21 " 0.019 2.00e-02 2.50e+03 pdb=" C4 DA C 21 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD BARG A 66 " 0.256 9.50e-02 1.11e+02 1.16e-01 1.29e+01 pdb=" NE BARG A 66 " -0.029 2.00e-02 2.50e+03 pdb=" CZ BARG A 66 " 0.035 2.00e-02 2.50e+03 pdb=" NH1BARG A 66 " -0.014 2.00e-02 2.50e+03 pdb=" NH2BARG A 66 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 774 " 0.291 9.50e-02 1.11e+02 1.31e-01 1.15e+01 pdb=" NE ARG A 774 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 774 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG A 774 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 774 " 0.016 2.00e-02 2.50e+03 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 124 2.63 - 3.20: 9228 3.20 - 3.77: 19588 3.77 - 4.33: 27273 4.33 - 4.90: 40226 Nonbonded interactions: 96439 Sorted by model distance: nonbonded pdb=" OD1 ASP A 556 " pdb="MG MG A1101 " model vdw 2.065 2.170 nonbonded pdb=" O LYS A 582 " pdb=" NH2 ARG A 586 " model vdw 2.330 3.120 nonbonded pdb=" O GLU A1040 " pdb=" O2' U B 97 " model vdw 2.351 3.040 nonbonded pdb=" OD2 ASP A 545 " pdb=" OH TYR A 553 " model vdw 2.383 3.040 nonbonded pdb=" O THR A 649 " pdb=" OG1 THR A 653 " model vdw 2.401 3.040 ... (remaining 96434 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 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: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.480 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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: 0.000 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 : 0.009 0.103 12173 Z= 0.600 Angle : 1.619 14.375 17103 Z= 1.057 Chirality : 0.085 0.652 1954 Planarity : 0.010 0.131 1597 Dihedral : 19.069 87.378 5585 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.76 % Allowed : 5.07 % Favored : 92.17 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.23), residues: 979 helix: -1.06 (0.21), residues: 448 sheet: -1.16 (0.51), residues: 80 loop : -1.51 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.003 ARG A 694 TYR 0.025 0.004 TYR A 358 PHE 0.033 0.004 PHE A 444 TRP 0.026 0.006 TRP A 688 HIS 0.008 0.002 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00916 / 0.59 (12163) covalent geometry : angle 1.61904 / 1.06 (17103) hydrogen bonds : bond 0.18118 / 18.51 ( 514) hydrogen bonds : angle 7.22706 / 8.97 ( 1368) Misc. bond : bond 0.04316 / 3.86 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.8254 (ptm) cc_final: 0.8036 (ptm) REVERT: A 281 PHE cc_start: 0.7949 (t80) cc_final: 0.7624 (t80) REVERT: A 291 LYS cc_start: 0.7537 (mmtm) cc_final: 0.7005 (mmmt) REVERT: A 395 LEU cc_start: 0.8809 (mt) cc_final: 0.8497 (mt) REVERT: A 443 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7087 (p0) REVERT: A 496 LYS cc_start: 0.7999 (tttt) cc_final: 0.7694 (ttmm) REVERT: A 577 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.7237 (tm130) REVERT: A 672 LYS cc_start: 0.8013 (mttt) cc_final: 0.7788 (mmpt) REVERT: A 687 LYS cc_start: 0.8122 (mmpt) cc_final: 0.7478 (tmtp) REVERT: A 760 ILE cc_start: 0.7710 (mm) cc_final: 0.7500 (mm) REVERT: A 858 TYR cc_start: 0.8094 (t80) cc_final: 0.7709 (t80) REVERT: A 955 LYS cc_start: 0.8406 (mttt) cc_final: 0.8080 (mmmt) outliers start: 25 outliers final: 2 residues processed: 214 average time/residue: 0.6465 time to fit residues: 147.8990 Evaluate side-chains 114 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 761 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [108, 49, 97, 53, 5, 33, 65, 62, 51, 100, 106] chunk 108 optimal weight: 50.0000 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN A 370 ASN A 382 GLN A 472 ASN A 831 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.178656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.141929 restraints weight = 19387.453| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.27 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12173 Z= 0.209 Angle : 0.675 7.848 17103 Z= 0.381 Chirality : 0.046 0.236 1954 Planarity : 0.005 0.035 1597 Dihedral : 19.858 76.971 3421 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.31 % Allowed : 13.78 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.26), residues: 979 helix: 1.15 (0.24), residues: 455 sheet: -0.87 (0.53), residues: 85 loop : -0.93 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 650 TYR 0.021 0.002 TYR A 897 PHE 0.016 0.002 PHE A 444 TRP 0.018 0.002 TRP A 229 HIS 0.011 0.002 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.21 (12163) covalent geometry : angle 0.67496 / 0.38 (17103) hydrogen bonds : bond 0.05866 / 5.93 ( 514) hydrogen bonds : angle 4.64109 / 5.56 ( 1368) Misc. bond : bond 0.00209 / 0.18 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7737 (mp0) cc_final: 0.7432 (mp0) REVERT: A 281 PHE cc_start: 0.8219 (t80) cc_final: 0.7996 (t80) REVERT: A 443 ASP cc_start: 0.7054 (OUTLIER) cc_final: 0.6636 (m-30) REVERT: A 529 MET cc_start: 0.7505 (mtp) cc_final: 0.7274 (mtp) REVERT: A 858 TYR cc_start: 0.8178 (t80) cc_final: 0.7911 (t80) outliers start: 30 outliers final: 13 residues processed: 136 average time/residue: 0.6813 time to fit residues: 99.1253 Evaluate side-chains 108 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 761 LYS Chi-restraints excluded: chain A residue 841 LYS Chi-restraints excluded: chain A residue 1022 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [91, 29, 25, 42, 61, 102, 81, 41, 22, 3, 96] chunk 91 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 61 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 96 optimal weight: 0.0570 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 ASN A 701 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.179995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.144228 restraints weight = 18878.225| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.43 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12173 Z= 0.127 Angle : 0.557 7.321 17103 Z= 0.322 Chirality : 0.039 0.184 1954 Planarity : 0.004 0.037 1597 Dihedral : 19.636 76.106 3418 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.43 % Allowed : 15.99 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.26), residues: 979 helix: 1.65 (0.24), residues: 456 sheet: -0.48 (0.55), residues: 87 loop : -0.77 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 901 TYR 0.014 0.001 TYR A 897 PHE 0.010 0.001 PHE A 914 TRP 0.016 0.002 TRP A 229 HIS 0.005 0.001 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.13 (12163) covalent geometry : angle 0.55657 / 0.32 (17103) hydrogen bonds : bond 0.04389 / 4.40 ( 514) hydrogen bonds : angle 4.19023 / 5.09 ( 1368) Misc. bond : bond 0.00128 / 0.09 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7703 (mp0) cc_final: 0.7386 (mp0) REVERT: A 123 GLU cc_start: 0.5710 (OUTLIER) cc_final: 0.4947 (pt0) REVERT: A 281 PHE cc_start: 0.8239 (t80) cc_final: 0.7981 (t80) REVERT: A 561 ARG cc_start: 0.7501 (tpt170) cc_final: 0.7266 (tpt90) REVERT: A 687 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.6856 (tmtp) REVERT: A 858 TYR cc_start: 0.8139 (t80) cc_final: 0.7872 (t80) outliers start: 22 outliers final: 5 residues processed: 115 average time/residue: 0.6738 time to fit residues: 82.8397 Evaluate side-chains 101 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 687 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [21, 25, 100, 34, 33, 58, 94, 42, 87, 52, 92] chunk 21 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 100 optimal weight: 30.0000 chunk 34 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 ASN A 365 GLN A 472 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.177023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.141272 restraints weight = 15779.178| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.10 r_work: 0.2970 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12173 Z= 0.194 Angle : 0.610 7.234 17103 Z= 0.339 Chirality : 0.042 0.205 1954 Planarity : 0.004 0.035 1597 Dihedral : 19.579 75.819 3410 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.43 % Allowed : 17.53 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.26), residues: 979 helix: 1.64 (0.24), residues: 457 sheet: -0.42 (0.52), residues: 87 loop : -0.88 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 504 TYR 0.019 0.002 TYR A 897 PHE 0.019 0.002 PHE A 914 TRP 0.019 0.003 TRP A 229 HIS 0.007 0.001 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (12163) covalent geometry : angle 0.61013 / 0.34 (17103) hydrogen bonds : bond 0.04867 / 4.96 ( 514) hydrogen bonds : angle 4.22483 / 5.22 ( 1368) Misc. bond : bond 0.00080 / 0.10 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 25 THR cc_start: 0.8976 (p) cc_final: 0.8731 (t) REVERT: A 103 GLU cc_start: 0.8367 (mp0) cc_final: 0.8070 (mp0) REVERT: A 116 ARG cc_start: 0.9250 (OUTLIER) cc_final: 0.6919 (ptt-90) REVERT: A 239 TYR cc_start: 0.8637 (m-80) cc_final: 0.8402 (m-80) REVERT: A 311 LYS cc_start: 0.8064 (mptt) cc_final: 0.7727 (mppt) REVERT: A 435 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7701 (pt0) REVERT: A 624 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7770 (mt-10) REVERT: A 625 TYR cc_start: 0.8800 (m-10) cc_final: 0.8576 (m-10) REVERT: A 653 THR cc_start: 0.7758 (m) cc_final: 0.7265 (p) REVERT: A 856 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8353 (tmtm) REVERT: A 858 TYR cc_start: 0.8626 (t80) cc_final: 0.8335 (t80) outliers start: 22 outliers final: 9 residues processed: 122 average time/residue: 0.6706 time to fit residues: 87.8572 Evaluate side-chains 106 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 829 MET Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 1022 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [26, 44, 68, 39, 15, 79, 54, 88, 0, 85, 49] chunk 26 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 68 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 88 optimal weight: 0.8980 chunk 0 optimal weight: 50.0000 chunk 85 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.177242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.142149 restraints weight = 15545.109| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.97 r_work: 0.3002 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12173 Z= 0.171 Angle : 0.573 8.134 17103 Z= 0.323 Chirality : 0.040 0.190 1954 Planarity : 0.004 0.037 1597 Dihedral : 19.528 75.352 3410 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.09 % Allowed : 18.41 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.26), residues: 979 helix: 1.63 (0.24), residues: 458 sheet: -0.44 (0.51), residues: 94 loop : -0.84 (0.27), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 650 TYR 0.019 0.002 TYR A 897 PHE 0.015 0.002 PHE A 914 TRP 0.018 0.003 TRP A 688 HIS 0.006 0.001 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (12163) covalent geometry : angle 0.57302 / 0.32 (17103) hydrogen bonds : bond 0.04401 / 4.49 ( 514) hydrogen bonds : angle 4.15674 / 5.05 ( 1368) Misc. bond : bond 0.00084 / 0.10 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 25 THR cc_start: 0.8929 (p) cc_final: 0.8652 (t) REVERT: A 103 GLU cc_start: 0.8344 (mp0) cc_final: 0.8017 (mp0) REVERT: A 116 ARG cc_start: 0.9242 (OUTLIER) cc_final: 0.6864 (ptt-90) REVERT: A 239 TYR cc_start: 0.8641 (m-80) cc_final: 0.8402 (m-80) REVERT: A 338 ARG cc_start: 0.8083 (mtp180) cc_final: 0.7852 (mtm-85) REVERT: A 624 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: A 858 TYR cc_start: 0.8596 (t80) cc_final: 0.8270 (t80) outliers start: 19 outliers final: 8 residues processed: 117 average time/residue: 0.6586 time to fit residues: 82.6934 Evaluate side-chains 106 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 1022 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [16, 90, 43, 56, 81, 104, 46, 68, 26, 20, 100] chunk 16 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 104 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 100 optimal weight: 30.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 365 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.175022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.138463 restraints weight = 13635.356| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.86 r_work: 0.2991 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12173 Z= 0.199 Angle : 0.592 8.028 17103 Z= 0.329 Chirality : 0.041 0.197 1954 Planarity : 0.004 0.034 1597 Dihedral : 19.534 74.923 3410 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.09 % Allowed : 19.29 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.26), residues: 979 helix: 1.52 (0.24), residues: 460 sheet: -0.34 (0.51), residues: 94 loop : -0.84 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 901 TYR 0.019 0.002 TYR A 897 PHE 0.019 0.002 PHE A 914 TRP 0.020 0.003 TRP A 688 HIS 0.006 0.001 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (12163) covalent geometry : angle 0.59232 / 0.33 (17103) hydrogen bonds : bond 0.04705 / 4.85 ( 514) hydrogen bonds : angle 4.20421 / 5.16 ( 1368) Misc. bond : bond 0.00092 / 0.12 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 25 THR cc_start: 0.8948 (p) cc_final: 0.8675 (t) REVERT: A 30 ASP cc_start: 0.8140 (m-30) cc_final: 0.7588 (t0) REVERT: A 103 GLU cc_start: 0.8386 (mp0) cc_final: 0.8091 (mp0) REVERT: A 116 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.6894 (ptt-90) REVERT: A 168 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8452 (pp) REVERT: A 239 TYR cc_start: 0.8646 (m-80) cc_final: 0.8395 (m-80) REVERT: A 249 TYR cc_start: 0.8395 (m-80) cc_final: 0.7985 (m-80) REVERT: A 856 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8665 (tmtm) REVERT: A 858 TYR cc_start: 0.8667 (t80) cc_final: 0.8372 (t80) outliers start: 19 outliers final: 10 residues processed: 116 average time/residue: 0.6533 time to fit residues: 81.3623 Evaluate side-chains 106 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 1022 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [54, 68, 75, 78, 60, 59, 10, 89, 101, 61, 33] chunk 54 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.175537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.139189 restraints weight = 15626.053| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.99 r_work: 0.2986 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12173 Z= 0.180 Angle : 0.574 9.009 17103 Z= 0.322 Chirality : 0.040 0.188 1954 Planarity : 0.004 0.037 1597 Dihedral : 19.505 74.463 3410 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.98 % Allowed : 19.40 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.26), residues: 979 helix: 1.52 (0.24), residues: 460 sheet: -0.24 (0.50), residues: 94 loop : -0.81 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 497 TYR 0.018 0.002 TYR A 897 PHE 0.016 0.002 PHE A 914 TRP 0.015 0.002 TRP A 688 HIS 0.005 0.001 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (12163) covalent geometry : angle 0.57442 / 0.32 (17103) hydrogen bonds : bond 0.04409 / 4.51 ( 514) hydrogen bonds : angle 4.17518 / 5.11 ( 1368) Misc. bond : bond 0.00080 / 0.10 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 THR cc_start: 0.8929 (p) cc_final: 0.8664 (t) REVERT: A 30 ASP cc_start: 0.8164 (m-30) cc_final: 0.7625 (t0) REVERT: A 103 GLU cc_start: 0.8388 (mp0) cc_final: 0.8091 (mp0) REVERT: A 116 ARG cc_start: 0.9248 (OUTLIER) cc_final: 0.6849 (ptt-90) REVERT: A 168 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8492 (pp) REVERT: A 232 MET cc_start: 0.8497 (ptt) cc_final: 0.8151 (ptm) REVERT: A 239 TYR cc_start: 0.8607 (m-80) cc_final: 0.8333 (m-80) REVERT: A 249 TYR cc_start: 0.8385 (m-80) cc_final: 0.7986 (m-80) REVERT: A 338 ARG cc_start: 0.8115 (mtp180) cc_final: 0.7628 (mtm-85) REVERT: A 500 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8412 (mt0) REVERT: A 856 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8600 (tmtm) REVERT: A 858 TYR cc_start: 0.8657 (t80) cc_final: 0.8333 (t80) outliers start: 18 outliers final: 9 residues processed: 115 average time/residue: 0.6341 time to fit residues: 78.6244 Evaluate side-chains 108 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 856 LYS Chi-restraints excluded: chain A residue 1022 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [77, 60, 105, 73, 72, 52, 7, 42, 89, 43, 96] chunk 77 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 73 optimal weight: 0.6980 chunk 72 optimal weight: 0.0170 chunk 52 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 96 optimal weight: 0.2980 overall best weight: 1.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.179610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.143772 restraints weight = 18247.009| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.24 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12173 Z= 0.116 Angle : 0.510 9.387 17103 Z= 0.294 Chirality : 0.037 0.161 1954 Planarity : 0.003 0.036 1597 Dihedral : 19.407 74.765 3410 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.54 % Allowed : 19.96 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.26), residues: 979 helix: 1.72 (0.24), residues: 460 sheet: -0.16 (0.51), residues: 94 loop : -0.70 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 630 TYR 0.016 0.001 TYR A 329 PHE 0.010 0.001 PHE A 715 TRP 0.011 0.002 TRP A 229 HIS 0.004 0.001 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.12 (12163) covalent geometry : angle 0.50952 / 0.29 (17103) hydrogen bonds : bond 0.03751 / 3.75 ( 514) hydrogen bonds : angle 3.99606 / 4.85 ( 1368) Misc. bond : bond 0.00046 / 0.05 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7351 (m-30) cc_final: 0.7127 (t0) REVERT: A 103 GLU cc_start: 0.7734 (mp0) cc_final: 0.7467 (mp0) REVERT: A 116 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.6584 (ptt-90) REVERT: A 123 GLU cc_start: 0.5684 (OUTLIER) cc_final: 0.5061 (pt0) REVERT: A 232 MET cc_start: 0.7592 (ptt) cc_final: 0.7315 (ptm) REVERT: A 858 TYR cc_start: 0.8168 (t80) cc_final: 0.7912 (t80) outliers start: 14 outliers final: 8 residues processed: 104 average time/residue: 0.6884 time to fit residues: 76.7112 Evaluate side-chains 100 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 1022 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [79, 31, 105, 86, 4, 3, 13, 7, 93, 43, 37] chunk 79 optimal weight: 4.9990 chunk 31 optimal weight: 0.0980 chunk 105 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.179371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.144294 restraints weight = 15269.003| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.99 r_work: 0.3044 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.154 12173 Z= 0.165 Angle : 0.761 59.160 17103 Z= 0.461 Chirality : 0.039 0.533 1954 Planarity : 0.004 0.085 1597 Dihedral : 19.406 74.670 3410 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.32 % Allowed : 20.07 % Favored : 78.61 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.26), residues: 979 helix: 1.72 (0.24), residues: 460 sheet: -0.16 (0.51), residues: 94 loop : -0.69 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 630 TYR 0.014 0.001 TYR A 256 PHE 0.010 0.001 PHE A 914 TRP 0.011 0.002 TRP A 229 HIS 0.007 0.001 HIS A 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 (12163) covalent geometry : angle 0.76108 / 0.46 (17103) hydrogen bonds : bond 0.03781 / 3.80 ( 514) hydrogen bonds : angle 3.99771 / 4.85 ( 1368) Misc. bond : bond 0.00056 / 0.07 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.8078 (m-30) cc_final: 0.7605 (t0) REVERT: A 103 GLU cc_start: 0.8366 (mp0) cc_final: 0.8062 (mp0) REVERT: A 116 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.6880 (ptt-90) REVERT: A 123 GLU cc_start: 0.6248 (OUTLIER) cc_final: 0.5618 (pt0) REVERT: A 232 MET cc_start: 0.8473 (ptt) cc_final: 0.8118 (ptm) REVERT: A 858 TYR cc_start: 0.8591 (t80) cc_final: 0.8295 (t80) outliers start: 12 outliers final: 8 residues processed: 99 average time/residue: 0.6932 time to fit residues: 73.4285 Evaluate side-chains 98 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1022 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [61, 13, 93, 20, 8, 4, 18, 38, 68, 35, 6] chunk 61 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN A 920 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.179412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.144678 restraints weight = 14221.556| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.93 r_work: 0.3055 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.154 12173 Z= 0.165 Angle : 0.761 59.160 17103 Z= 0.461 Chirality : 0.039 0.533 1954 Planarity : 0.004 0.085 1597 Dihedral : 19.406 74.670 3410 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.21 % Allowed : 20.29 % Favored : 78.50 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.26), residues: 979 helix: 1.72 (0.24), residues: 460 sheet: -0.16 (0.51), residues: 94 loop : -0.69 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 630 TYR 0.014 0.001 TYR A 256 PHE 0.010 0.001 PHE A 914 TRP 0.011 0.002 TRP A 229 HIS 0.007 0.001 HIS A 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 (12163) covalent geometry : angle 0.76108 / 0.46 (17103) hydrogen bonds : bond 0.03781 / 3.80 ( 514) hydrogen bonds : angle 3.99771 / 4.85 ( 1368) Misc. bond : bond 0.00056 / 0.07 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.8058 (m-30) cc_final: 0.7591 (t0) REVERT: A 103 GLU cc_start: 0.8364 (mp0) cc_final: 0.8066 (mp0) REVERT: A 116 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.6881 (ptt-90) REVERT: A 123 GLU cc_start: 0.6240 (OUTLIER) cc_final: 0.5599 (pt0) REVERT: A 232 MET cc_start: 0.8468 (ptt) cc_final: 0.8112 (ptm) REVERT: A 858 TYR cc_start: 0.8592 (t80) cc_final: 0.8298 (t80) outliers start: 11 outliers final: 8 residues processed: 98 average time/residue: 0.6916 time to fit residues: 72.4225 Evaluate side-chains 98 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1022 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [19, 74, 20, 100, 15, 45, 91, 4, 39, 40, 86] chunk 19 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 39 optimal weight: 40.0000 chunk 40 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN A 920 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.179412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.143838 restraints weight = 18369.462| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.24 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.154 12173 Z= 0.165 Angle : 0.761 59.160 17103 Z= 0.461 Chirality : 0.039 0.533 1954 Planarity : 0.004 0.085 1597 Dihedral : 19.406 74.670 3410 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.21 % Allowed : 20.29 % Favored : 78.50 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.26), residues: 979 helix: 1.72 (0.24), residues: 460 sheet: -0.16 (0.51), residues: 94 loop : -0.69 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 630 TYR 0.014 0.001 TYR A 256 PHE 0.010 0.001 PHE A 914 TRP 0.011 0.002 TRP A 229 HIS 0.007 0.001 HIS A 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 (12163) covalent geometry : angle 0.76108 / 0.46 (17103) hydrogen bonds : bond 0.03781 / 3.80 ( 514) hydrogen bonds : angle 3.99771 / 4.85 ( 1368) Misc. bond : bond 0.00056 / 0.07 ( 10) =============================================================================== Job complete usr+sys time: 3285.21 seconds wall clock time: 56 minutes 53.09 seconds (3413.09 seconds total)