Starting phenix.real_space_refine on Fri Jul 3 08:02:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w7u_65733/07_2026/9w7u_65733.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w7u_65733/07_2026/9w7u_65733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w7u_65733/07_2026/9w7u_65733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w7u_65733/07_2026/9w7u_65733.map" model { file = "/net/cci-nas-00/data/ceres_data/9w7u_65733/07_2026/9w7u_65733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w7u_65733/07_2026/9w7u_65733.cif" } resolution = 3.83 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 144 5.49 5 S 22 5.16 5 C 7549 2.51 5 N 2263 2.21 5 O 2771 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12749 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9657 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1176, 9646 Classifications: {'peptide': 1176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 1145} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1176, 9646 Classifications: {'peptide': 1176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 1145} Chain breaks: 2 bond proxies already assigned to first conformer: 9803 Chain: "B" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 698 Classifications: {'DNA': 34} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 33} Chain: "C" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 305 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "D" Number of atoms: 2089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2089 Classifications: {'RNA': 98} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 48, 'rna3p_pyr': 38} Link IDs: {'rna2p': 11, 'rna3p': 86} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 783 " occ=0.83 ... (20 atoms not shown) pdb=" NH2BARG A 783 " occ=0.17 Time building chain proxies: 4.27, per 1000 atoms: 0.33 Number of scatterers: 12749 At special positions: 0 Unit cell: (119.658, 103.488, 139.062, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 144 15.00 O 2771 8.00 N 2263 7.00 C 7549 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=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 900.5 milliseconds 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2238 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 8 sheets defined 56.1% alpha, 10.5% beta 51 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.873A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.534A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 295 through 306 Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 346 through 353 removed outlier: 3.548A pdb=" N ASP A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 382 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.672A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.290A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.726A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 477 through 482 removed outlier: 3.665A pdb=" N VAL A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 512 through 526 removed outlier: 4.160A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 644 through 654 removed outlier: 3.681A pdb=" N ARG A 653 " --> pdb=" O LYS A 649 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 654 " --> pdb=" O GLN A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 703 through 712 Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 730 through 751 Processing helix chain 'A' and resid 769 through 778 Processing helix chain 'A' and resid 779 through 792 removed outlier: 3.541A pdb=" N AARG A 783 " --> pdb=" O GLU A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 802 through 807 Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 829 through 833 removed outlier: 3.780A pdb=" N LEU A 833 " --> pdb=" O ILE A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 866 Processing helix chain 'A' and resid 872 through 890 removed outlier: 4.825A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N TYR A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 901 through 906 Processing helix chain 'A' and resid 909 through 914 removed outlier: 3.652A pdb=" N ALA A 914 " --> pdb=" O GLU A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 925 removed outlier: 4.189A pdb=" N LEU A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 925 " --> pdb=" O LEU A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 940 Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 980 through 999 removed outlier: 4.406A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 removed outlier: 3.534A pdb=" N VAL A1233 " --> pdb=" O PRO A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1264 through 1281 removed outlier: 3.556A pdb=" N GLU A1268 " --> pdb=" O HIS A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1313 Processing helix chain 'A' and resid 1314 through 1316 No H-bonds generated for 'chain 'A' and resid 1314 through 1316' Processing helix chain 'A' and resid 1339 through 1344 removed outlier: 3.523A pdb=" N VAL A1342 " --> pdb=" O THR A1339 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 959 removed outlier: 3.551A pdb=" N MET A 763 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASN A 758 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU A 762 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ILE A 11 " --> pdb=" O GLU A 762 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A1095 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 10.040A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539 removed outlier: 3.562A pdb=" N LYS A 528 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 837 through 840 Processing sheet with id=AA5, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.791A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.791A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1324 through 1326 removed outlier: 3.858A pdb=" N PHE A1324 " --> pdb=" O ILE A1331 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1384 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 129 hydrogen bonds 246 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 3.55 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3119 1.33 - 1.45: 3186 1.45 - 1.57: 6655 1.57 - 1.69: 288 1.69 - 1.81: 42 Bond restraints: 13290 Sorted by residual: bond pdb=" C3' DA B 8 " pdb=" C2' DA B 8 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.32e+01 bond pdb=" C3' DG B 7 " pdb=" C2' DG B 7 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DC B 3 " pdb=" C2' DC B 3 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DA C 11 " pdb=" C2' DA C 11 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.67e+00 bond pdb=" C3' DT C 9 " pdb=" C2' DT C 9 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.76e+00 ... (remaining 13285 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 17677 1.23 - 2.46: 760 2.46 - 3.69: 112 3.69 - 4.93: 16 4.93 - 6.16: 4 Bond angle restraints: 18569 Sorted by residual: angle pdb=" O4' DA B 22 " pdb=" C4' DA B 22 " pdb=" C3' DA B 22 " ideal model delta sigma weight residual 106.00 102.84 3.16 6.00e-01 2.78e+00 2.78e+01 angle pdb=" O4' DG B 23 " pdb=" C4' DG B 23 " pdb=" C3' DG B 23 " ideal model delta sigma weight residual 106.00 103.12 2.88 6.00e-01 2.78e+00 2.31e+01 angle pdb=" O4' DA B 24 " pdb=" C4' DA B 24 " pdb=" C3' DA B 24 " ideal model delta sigma weight residual 106.00 103.38 2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT B 10 " pdb=" C4 DT B 10 " pdb=" O4 DT B 10 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" O4' DT B 17 " pdb=" C4' DT B 17 " pdb=" C3' DT B 17 " ideal model delta sigma weight residual 106.00 103.42 2.58 6.00e-01 2.78e+00 1.85e+01 ... (remaining 18564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.48: 7638 31.48 - 62.97: 381 62.97 - 94.45: 54 94.45 - 125.94: 0 125.94 - 157.42: 1 Dihedral angle restraints: 8074 sinusoidal: 4615 harmonic: 3459 Sorted by residual: dihedral pdb=" CA ARG A 925 " pdb=" C ARG A 925 " pdb=" N GLN A 926 " pdb=" CA GLN A 926 " ideal model delta harmonic sigma weight residual -180.00 -132.85 -47.15 0 5.00e+00 4.00e-02 8.89e+01 dihedral pdb=" CA LEU A 625 " pdb=" C LEU A 625 " pdb=" N PHE A 626 " pdb=" CA PHE A 626 " ideal model delta harmonic sigma weight residual -180.00 -159.81 -20.19 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" C4' DG B 7 " pdb=" C3' DG B 7 " pdb=" O3' DG B 7 " pdb=" P DA B 8 " ideal model delta sinusoidal sigma weight residual 220.00 62.58 157.42 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 8071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1409 0.030 - 0.059: 454 0.059 - 0.089: 170 0.089 - 0.119: 85 0.119 - 0.149: 11 Chirality restraints: 2129 Sorted by residual: chirality pdb=" P DA B 8 " pdb=" OP1 DA B 8 " pdb=" OP2 DA B 8 " pdb=" O5' DA B 8 " both_signs ideal model delta sigma weight residual True 2.34 -2.48 -0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CB ILE A 795 " pdb=" CA ILE A 795 " pdb=" CG1 ILE A 795 " pdb=" CG2 ILE A 795 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" C3' DG B 7 " pdb=" C4' DG B 7 " pdb=" O3' DG B 7 " pdb=" C2' DG B 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 2126 not shown) Planarity restraints: 1839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U D 97 " 0.020 2.00e-02 2.50e+03 1.04e-02 2.42e+00 pdb=" N1 U D 97 " -0.022 2.00e-02 2.50e+03 pdb=" C2 U D 97 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U D 97 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U D 97 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U D 97 " 0.003 2.00e-02 2.50e+03 pdb=" O4 U D 97 " 0.005 2.00e-02 2.50e+03 pdb=" C5 U D 97 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U D 97 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A D 49 " 0.018 2.00e-02 2.50e+03 8.49e-03 1.98e+00 pdb=" N9 A D 49 " -0.019 2.00e-02 2.50e+03 pdb=" C8 A D 49 " -0.000 2.00e-02 2.50e+03 pdb=" N7 A D 49 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A D 49 " -0.006 2.00e-02 2.50e+03 pdb=" C6 A D 49 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A D 49 " 0.006 2.00e-02 2.50e+03 pdb=" N1 A D 49 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A D 49 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A D 49 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A D 49 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A D 42 " 0.019 2.00e-02 2.50e+03 8.37e-03 1.93e+00 pdb=" N9 A D 42 " -0.019 2.00e-02 2.50e+03 pdb=" C8 A D 42 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A D 42 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A D 42 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A D 42 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A D 42 " 0.005 2.00e-02 2.50e+03 pdb=" N1 A D 42 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A D 42 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A D 42 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A D 42 " -0.005 2.00e-02 2.50e+03 ... (remaining 1836 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 2 2.02 - 2.74: 1187 2.74 - 3.46: 17770 3.46 - 4.18: 32376 4.18 - 4.90: 51869 Nonbonded interactions: 103204 Sorted by model distance: nonbonded pdb=" ND2 ASN A 77 " pdb=" O2 U D 59 " model vdw 1.299 3.120 nonbonded pdb=" NH1 ARG A 71 " pdb=" C5 C D 18 " model vdw 1.431 3.420 nonbonded pdb=" O ARG A 925 " pdb=" N ILE A 927 " model vdw 2.125 3.120 nonbonded pdb=" N2 DG B 9 " pdb=" O2 DC C 8 " model vdw 2.164 2.496 nonbonded pdb=" OD1 ASN A 14 " pdb=" OG SER A 55 " model vdw 2.188 3.040 ... (remaining 103199 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=0.17 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.430 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.470 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 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 : 0.004 0.039 13290 Z= 0.281 Angle : 0.581 6.157 18569 Z= 0.437 Chirality : 0.038 0.149 2129 Planarity : 0.004 0.034 1839 Dihedral : 16.464 157.423 5836 Min Nonbonded Distance : 1.299 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.79 % Favored : 98.03 % Rotamer: Outliers : 0.09 % Allowed : 0.00 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.61 (0.24), residues: 1173 helix: 1.83 (0.21), residues: 595 sheet: 1.15 (0.56), residues: 100 loop : 0.16 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 780 TYR 0.017 0.001 TYR A 882 PHE 0.014 0.001 PHE A 462 TRP 0.019 0.002 TRP A1126 HIS 0.008 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.28 (13290) covalent geometry : angle 0.58101 / 0.44 (18569) hydrogen bonds : bond 0.16378 / 10.49 ( 594) hydrogen bonds : angle 6.07783 / 4.41 ( 1630) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 LEU cc_start: 0.9320 (tp) cc_final: 0.8964 (tt) REVERT: A 504 ASN cc_start: 0.9337 (m-40) cc_final: 0.8713 (p0) REVERT: A 623 LEU cc_start: 0.9553 (mt) cc_final: 0.9155 (tt) REVERT: A 740 THR cc_start: 0.9600 (m) cc_final: 0.9394 (p) REVERT: A 815 TYR cc_start: 0.9165 (m-80) cc_final: 0.8614 (m-80) REVERT: A 895 ARG cc_start: 0.9093 (tpt90) cc_final: 0.8830 (tpm170) REVERT: A 930 HIS cc_start: 0.8666 (m170) cc_final: 0.8407 (m-70) REVERT: A 989 LEU cc_start: 0.9753 (mt) cc_final: 0.9427 (tt) REVERT: A 1182 LEU cc_start: 0.9715 (mt) cc_final: 0.9491 (pp) REVERT: A 1236 LEU cc_start: 0.9795 (mt) cc_final: 0.9593 (pp) REVERT: A 1313 PHE cc_start: 0.9213 (m-80) cc_final: 0.8967 (m-10) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1338 time to fit residues: 39.8669 Evaluate side-chains 125 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 0.3980 chunk 55 optimal weight: 0.0980 chunk 129 optimal weight: 30.0000 overall best weight: 4.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 309 ASN A 712 GLN A1091 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.052142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.035998 restraints weight = 137391.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.037844 restraints weight = 56975.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.039022 restraints weight = 34897.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.039816 restraints weight = 25804.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.040315 restraints weight = 21303.970| |-----------------------------------------------------------------------------| r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13290 Z= 0.209 Angle : 0.701 10.328 18569 Z= 0.386 Chirality : 0.046 0.398 2129 Planarity : 0.005 0.070 1839 Dihedral : 18.556 162.814 3302 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.56 % Favored : 97.26 % Rotamer: Outliers : 1.69 % Allowed : 9.13 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.33 (0.24), residues: 1173 helix: 1.51 (0.21), residues: 612 sheet: 1.75 (0.59), residues: 83 loop : -0.01 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 71 TYR 0.019 0.002 TYR A1187 PHE 0.028 0.002 PHE A1258 TRP 0.020 0.002 TRP A 659 HIS 0.009 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.21 (13290) covalent geometry : angle 0.70094 / 0.39 (18569) hydrogen bonds : bond 0.06141 / 4.03 ( 594) hydrogen bonds : angle 5.19434 / 3.74 ( 1630) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.327 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: A 54 ASP cc_start: 0.9515 (t0) cc_final: 0.9214 (p0) REVERT: A 71 ARG cc_start: 0.9720 (mtm180) cc_final: 0.9391 (mtp85) REVERT: A 90 MET cc_start: 0.9411 (tpt) cc_final: 0.9049 (tpt) REVERT: A 153 LEU cc_start: 0.9888 (mp) cc_final: 0.9622 (pp) REVERT: A 504 ASN cc_start: 0.9448 (m-40) cc_final: 0.8769 (p0) REVERT: A 606 PHE cc_start: 0.9311 (t80) cc_final: 0.8704 (t80) REVERT: A 623 LEU cc_start: 0.9802 (mt) cc_final: 0.9208 (tt) REVERT: A 737 ILE cc_start: 0.9850 (mt) cc_final: 0.9636 (mm) REVERT: A 811 LEU cc_start: 0.9251 (tp) cc_final: 0.8854 (tp) REVERT: A 815 TYR cc_start: 0.9410 (m-80) cc_final: 0.8956 (m-80) REVERT: A 930 HIS cc_start: 0.9009 (m170) cc_final: 0.8775 (m90) REVERT: A 963 VAL cc_start: 0.9694 (t) cc_final: 0.9494 (p) REVERT: A 989 LEU cc_start: 0.9826 (mt) cc_final: 0.9567 (tt) outliers start: 17 outliers final: 10 residues processed: 134 average time/residue: 0.1202 time to fit residues: 23.1524 Evaluate side-chains 118 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 840 HIS Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1139 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 556 ASN A 698 HIS A1091 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.048979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.033310 restraints weight = 174749.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.035079 restraints weight = 66296.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.036248 restraints weight = 39447.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.037010 restraints weight = 28626.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.037458 restraints weight = 23445.102| |-----------------------------------------------------------------------------| r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (14 function evaluations) r_final: 0.2653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13290 Z= 0.301 Angle : 0.740 12.783 18569 Z= 0.409 Chirality : 0.045 0.326 2129 Planarity : 0.005 0.054 1839 Dihedral : 18.766 160.684 3302 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.74 % Favored : 97.09 % Rotamer: Outliers : 1.69 % Allowed : 9.78 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.65 (0.23), residues: 1173 helix: 0.91 (0.20), residues: 612 sheet: 1.27 (0.57), residues: 83 loop : -0.23 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 71 TYR 0.021 0.002 TYR A1356 PHE 0.024 0.002 PHE A 970 TRP 0.013 0.002 TRP A 659 HIS 0.009 0.002 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.30 (13290) covalent geometry : angle 0.73990 / 0.41 (18569) hydrogen bonds : bond 0.06190 / 4.16 ( 594) hydrogen bonds : angle 5.35799 / 3.84 ( 1630) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.9715 (mtm180) cc_final: 0.9324 (mtp85) REVERT: A 90 MET cc_start: 0.9446 (tpt) cc_final: 0.9043 (tpt) REVERT: A 153 LEU cc_start: 0.9909 (mp) cc_final: 0.9652 (pp) REVERT: A 495 MET cc_start: 0.9072 (mpp) cc_final: 0.8818 (mpp) REVERT: A 504 ASN cc_start: 0.9422 (m-40) cc_final: 0.8774 (p0) REVERT: A 811 LEU cc_start: 0.9254 (tp) cc_final: 0.9005 (tp) REVERT: A 815 TYR cc_start: 0.9432 (m-80) cc_final: 0.9138 (m-80) REVERT: A 930 HIS cc_start: 0.9070 (m170) cc_final: 0.8723 (m90) REVERT: A 939 MET cc_start: 0.9400 (mmm) cc_final: 0.9072 (mmm) REVERT: A 963 VAL cc_start: 0.9746 (t) cc_final: 0.9507 (p) REVERT: A 989 LEU cc_start: 0.9833 (mt) cc_final: 0.9554 (tt) REVERT: A 1089 MET cc_start: 0.9171 (mmm) cc_final: 0.8962 (mmm) REVERT: A 1108 GLU cc_start: 0.9280 (mt-10) cc_final: 0.9039 (mt-10) REVERT: A 1228 LEU cc_start: 0.9326 (tp) cc_final: 0.9061 (tt) outliers start: 17 outliers final: 13 residues processed: 118 average time/residue: 0.1198 time to fit residues: 20.4288 Evaluate side-chains 108 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 840 HIS Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS A 739 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.050681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.034670 restraints weight = 157754.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.036533 restraints weight = 60582.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.037744 restraints weight = 36116.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.038545 restraints weight = 26249.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.039070 restraints weight = 21386.948| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13290 Z= 0.135 Angle : 0.671 13.106 18569 Z= 0.354 Chirality : 0.043 0.378 2129 Planarity : 0.004 0.047 1839 Dihedral : 18.709 160.725 3302 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.65 % Favored : 97.18 % Rotamer: Outliers : 1.51 % Allowed : 11.48 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.96 (0.24), residues: 1173 helix: 1.15 (0.21), residues: 617 sheet: 1.35 (0.56), residues: 83 loop : -0.07 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 71 TYR 0.025 0.001 TYR A1356 PHE 0.031 0.002 PHE A1105 TRP 0.015 0.002 TRP A 659 HIS 0.008 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (13290) covalent geometry : angle 0.67054 / 0.35 (18569) hydrogen bonds : bond 0.05105 / 3.33 ( 594) hydrogen bonds : angle 4.82749 / 3.47 ( 1630) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.422 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: A 60 GLU cc_start: 0.9523 (pm20) cc_final: 0.9123 (pm20) REVERT: A 71 ARG cc_start: 0.9710 (mtm180) cc_final: 0.9378 (mtp85) REVERT: A 90 MET cc_start: 0.9424 (tpt) cc_final: 0.9020 (tpt) REVERT: A 153 LEU cc_start: 0.9891 (mp) cc_final: 0.9659 (pp) REVERT: A 495 MET cc_start: 0.9002 (mpp) cc_final: 0.8790 (mpp) REVERT: A 504 ASN cc_start: 0.9443 (m-40) cc_final: 0.8865 (p0) REVERT: A 746 GLU cc_start: 0.9616 (tt0) cc_final: 0.9360 (tt0) REVERT: A 858 THR cc_start: 0.6162 (m) cc_final: 0.5933 (m) REVERT: A 895 ARG cc_start: 0.9243 (tpt90) cc_final: 0.8986 (tpm170) REVERT: A 930 HIS cc_start: 0.8950 (m170) cc_final: 0.8742 (m90) REVERT: A 939 MET cc_start: 0.9364 (mmm) cc_final: 0.9048 (mmm) REVERT: A 1089 MET cc_start: 0.9122 (mmm) cc_final: 0.8857 (mmm) REVERT: A 1108 GLU cc_start: 0.9275 (mt-10) cc_final: 0.9036 (mt-10) REVERT: A 1257 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9222 (pp) outliers start: 15 outliers final: 12 residues processed: 118 average time/residue: 0.1196 time to fit residues: 20.5241 Evaluate side-chains 113 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 840 HIS Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 95 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.048805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.033897 restraints weight = 113289.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.035452 restraints weight = 52787.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.036465 restraints weight = 34133.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.037123 restraints weight = 25984.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.037442 restraints weight = 21938.494| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13290 Z= 0.223 Angle : 0.665 13.709 18569 Z= 0.364 Chirality : 0.042 0.306 2129 Planarity : 0.004 0.044 1839 Dihedral : 18.797 163.643 3302 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.65 % Favored : 97.18 % Rotamer: Outliers : 1.69 % Allowed : 11.57 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.24), residues: 1173 helix: 1.00 (0.21), residues: 611 sheet: 1.10 (0.55), residues: 83 loop : -0.15 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 71 TYR 0.016 0.002 TYR A 882 PHE 0.023 0.002 PHE A1105 TRP 0.008 0.001 TRP A 659 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.22 (13290) covalent geometry : angle 0.66461 / 0.36 (18569) hydrogen bonds : bond 0.05494 / 3.64 ( 594) hydrogen bonds : angle 4.99647 / 3.58 ( 1630) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.429 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: A 60 GLU cc_start: 0.9611 (pm20) cc_final: 0.9208 (pm20) REVERT: A 71 ARG cc_start: 0.9718 (mtm180) cc_final: 0.9334 (mtp85) REVERT: A 90 MET cc_start: 0.9466 (tpt) cc_final: 0.9124 (tpt) REVERT: A 153 LEU cc_start: 0.9902 (mp) cc_final: 0.9665 (pp) REVERT: A 495 MET cc_start: 0.8969 (mpp) cc_final: 0.8742 (mpp) REVERT: A 504 ASN cc_start: 0.9416 (m-40) cc_final: 0.8778 (p0) REVERT: A 746 GLU cc_start: 0.9619 (tt0) cc_final: 0.9365 (tt0) REVERT: A 939 MET cc_start: 0.9432 (mmm) cc_final: 0.9117 (mmm) REVERT: A 1108 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8982 (mt-10) outliers start: 17 outliers final: 12 residues processed: 108 average time/residue: 0.1199 time to fit residues: 18.9947 Evaluate side-chains 103 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 840 HIS Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 15 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.048305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.032579 restraints weight = 160258.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.034296 restraints weight = 62600.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.035443 restraints weight = 37696.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.036172 restraints weight = 27702.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.036579 restraints weight = 22972.672| |-----------------------------------------------------------------------------| r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.2641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13290 Z= 0.202 Angle : 0.651 10.942 18569 Z= 0.358 Chirality : 0.042 0.285 2129 Planarity : 0.004 0.042 1839 Dihedral : 18.863 164.713 3302 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.08 % Favored : 96.75 % Rotamer: Outliers : 2.07 % Allowed : 11.67 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.57 (0.24), residues: 1173 helix: 0.88 (0.21), residues: 623 sheet: 0.81 (0.54), residues: 83 loop : -0.27 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 535 TYR 0.022 0.002 TYR A 128 PHE 0.025 0.002 PHE A1105 TRP 0.009 0.002 TRP A 476 HIS 0.011 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.20 (13290) covalent geometry : angle 0.65092 / 0.36 (18569) hydrogen bonds : bond 0.05244 / 3.47 ( 594) hydrogen bonds : angle 4.95820 / 3.56 ( 1630) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.426 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: A 60 GLU cc_start: 0.9646 (pm20) cc_final: 0.9251 (pm20) REVERT: A 71 ARG cc_start: 0.9720 (mtm180) cc_final: 0.9243 (mtp85) REVERT: A 90 MET cc_start: 0.9456 (tpt) cc_final: 0.9146 (tpt) REVERT: A 153 LEU cc_start: 0.9903 (mp) cc_final: 0.9665 (pp) REVERT: A 495 MET cc_start: 0.8990 (mpp) cc_final: 0.8710 (mpp) REVERT: A 504 ASN cc_start: 0.9435 (m-40) cc_final: 0.8842 (p0) REVERT: A 746 GLU cc_start: 0.9654 (tt0) cc_final: 0.9313 (tt0) REVERT: A 939 MET cc_start: 0.9481 (mmm) cc_final: 0.9208 (mmm) REVERT: A 1108 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8971 (mt-10) outliers start: 21 outliers final: 13 residues processed: 110 average time/residue: 0.1208 time to fit residues: 19.3596 Evaluate side-chains 104 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 840 HIS Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 69 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 71 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 121 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.046862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.031374 restraints weight = 169241.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.033025 restraints weight = 65984.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.034122 restraints weight = 39785.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.034824 restraints weight = 29334.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.035264 restraints weight = 24297.294| |-----------------------------------------------------------------------------| r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13290 Z= 0.266 Angle : 0.705 15.736 18569 Z= 0.385 Chirality : 0.044 0.400 2129 Planarity : 0.005 0.041 1839 Dihedral : 19.011 167.796 3302 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.68 % Favored : 96.15 % Rotamer: Outliers : 1.69 % Allowed : 12.42 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.31 (0.24), residues: 1173 helix: 0.69 (0.20), residues: 615 sheet: 0.58 (0.54), residues: 83 loop : -0.38 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 820 TYR 0.033 0.002 TYR A 823 PHE 0.023 0.002 PHE A 970 TRP 0.012 0.002 TRP A 476 HIS 0.010 0.002 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.27 (13290) covalent geometry : angle 0.70464 / 0.39 (18569) hydrogen bonds : bond 0.05826 / 3.91 ( 594) hydrogen bonds : angle 5.16637 / 3.71 ( 1630) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.9676 (pm20) cc_final: 0.9360 (pm20) REVERT: A 71 ARG cc_start: 0.9702 (mtm180) cc_final: 0.9179 (mtp85) REVERT: A 90 MET cc_start: 0.9485 (tpt) cc_final: 0.9193 (tpt) REVERT: A 125 GLU cc_start: 0.9586 (OUTLIER) cc_final: 0.8790 (mm-30) REVERT: A 153 LEU cc_start: 0.9912 (mp) cc_final: 0.9668 (pp) REVERT: A 495 MET cc_start: 0.9004 (mpp) cc_final: 0.8717 (mpp) REVERT: A 504 ASN cc_start: 0.9426 (m-40) cc_final: 0.8858 (p0) REVERT: A 746 GLU cc_start: 0.9623 (tt0) cc_final: 0.9272 (tt0) REVERT: A 939 MET cc_start: 0.9526 (mmm) cc_final: 0.9184 (mmm) REVERT: A 1108 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8945 (mt-10) outliers start: 17 outliers final: 14 residues processed: 108 average time/residue: 0.1246 time to fit residues: 19.4887 Evaluate side-chains 107 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 840 HIS Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 105 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 119 optimal weight: 30.0000 chunk 118 optimal weight: 40.0000 chunk 58 optimal weight: 20.0000 chunk 94 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 128 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 803 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.046860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.031696 restraints weight = 152102.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.033265 restraints weight = 61295.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.034342 restraints weight = 37380.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.035018 restraints weight = 27645.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.035416 restraints weight = 22971.198| |-----------------------------------------------------------------------------| r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13290 Z= 0.214 Angle : 0.664 11.043 18569 Z= 0.364 Chirality : 0.042 0.267 2129 Planarity : 0.004 0.042 1839 Dihedral : 19.020 170.388 3302 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.33 % Favored : 96.50 % Rotamer: Outliers : 1.60 % Allowed : 12.98 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.38 (0.24), residues: 1173 helix: 0.76 (0.21), residues: 614 sheet: 0.58 (0.54), residues: 83 loop : -0.36 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 71 TYR 0.024 0.002 TYR A 823 PHE 0.020 0.002 PHE A 970 TRP 0.010 0.002 TRP A 476 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.21 (13290) covalent geometry : angle 0.66404 / 0.36 (18569) hydrogen bonds : bond 0.05307 / 3.54 ( 594) hydrogen bonds : angle 5.05487 / 3.64 ( 1630) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.9683 (pm20) cc_final: 0.9382 (pm20) REVERT: A 71 ARG cc_start: 0.9702 (mtm180) cc_final: 0.9145 (mtp85) REVERT: A 90 MET cc_start: 0.9439 (tpt) cc_final: 0.9174 (tpt) REVERT: A 125 GLU cc_start: 0.9594 (OUTLIER) cc_final: 0.8778 (mm-30) REVERT: A 153 LEU cc_start: 0.9900 (mp) cc_final: 0.9658 (pp) REVERT: A 495 MET cc_start: 0.9005 (mpp) cc_final: 0.8697 (mpp) REVERT: A 504 ASN cc_start: 0.9413 (m-40) cc_final: 0.8886 (p0) REVERT: A 746 GLU cc_start: 0.9630 (tt0) cc_final: 0.9298 (tt0) REVERT: A 895 ARG cc_start: 0.9302 (tpt90) cc_final: 0.9084 (tpm170) REVERT: A 939 MET cc_start: 0.9542 (mmm) cc_final: 0.9208 (mmm) REVERT: A 1108 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8937 (mt-10) outliers start: 16 outliers final: 15 residues processed: 104 average time/residue: 0.1237 time to fit residues: 18.6308 Evaluate side-chains 105 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 840 HIS Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 127 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.047298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.032402 restraints weight = 109598.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.033853 restraints weight = 51515.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.034814 restraints weight = 33551.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.035432 restraints weight = 25784.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.035779 restraints weight = 21856.021| |-----------------------------------------------------------------------------| r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13290 Z= 0.156 Angle : 0.631 11.212 18569 Z= 0.344 Chirality : 0.041 0.267 2129 Planarity : 0.004 0.042 1839 Dihedral : 18.997 172.654 3302 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.25 % Favored : 96.58 % Rotamer: Outliers : 1.22 % Allowed : 13.36 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.62 (0.24), residues: 1173 helix: 0.94 (0.21), residues: 605 sheet: 0.71 (0.52), residues: 93 loop : -0.22 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 71 TYR 0.026 0.001 TYR A 823 PHE 0.021 0.001 PHE A 606 TRP 0.008 0.002 TRP A 464 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 (13290) covalent geometry : angle 0.63111 / 0.34 (18569) hydrogen bonds : bond 0.04995 / 3.30 ( 594) hydrogen bonds : angle 4.87793 / 3.50 ( 1630) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.435 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: A 60 GLU cc_start: 0.9687 (pm20) cc_final: 0.9380 (pm20) REVERT: A 71 ARG cc_start: 0.9699 (mtm180) cc_final: 0.9111 (mtp85) REVERT: A 90 MET cc_start: 0.9435 (tpt) cc_final: 0.9169 (tpt) REVERT: A 125 GLU cc_start: 0.9603 (OUTLIER) cc_final: 0.8761 (mm-30) REVERT: A 153 LEU cc_start: 0.9894 (mp) cc_final: 0.9651 (pp) REVERT: A 321 MET cc_start: 0.9508 (mmm) cc_final: 0.9264 (mmm) REVERT: A 495 MET cc_start: 0.9008 (mpp) cc_final: 0.8690 (mpp) REVERT: A 504 ASN cc_start: 0.9436 (m-40) cc_final: 0.8912 (p0) REVERT: A 746 GLU cc_start: 0.9604 (tt0) cc_final: 0.9253 (tt0) REVERT: A 895 ARG cc_start: 0.9292 (tpt90) cc_final: 0.9081 (tpm170) REVERT: A 929 LYS cc_start: 0.9448 (ptmt) cc_final: 0.8911 (ptpp) REVERT: A 939 MET cc_start: 0.9542 (mmm) cc_final: 0.9250 (mmm) REVERT: A 1108 GLU cc_start: 0.9249 (mt-10) cc_final: 0.8963 (mt-10) outliers start: 12 outliers final: 9 residues processed: 98 average time/residue: 0.1274 time to fit residues: 18.1990 Evaluate side-chains 98 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 840 HIS Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 56 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 34 optimal weight: 0.0000 chunk 119 optimal weight: 30.0000 chunk 20 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 128 optimal weight: 30.0000 chunk 14 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.2997 r_free = 0.2997 target = 0.047308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.032075 restraints weight = 142807.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.033668 restraints weight = 58083.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.034749 restraints weight = 35738.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.035437 restraints weight = 26456.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.035891 restraints weight = 21986.866| |-----------------------------------------------------------------------------| r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13290 Z= 0.152 Angle : 0.619 11.170 18569 Z= 0.336 Chirality : 0.040 0.240 2129 Planarity : 0.004 0.041 1839 Dihedral : 18.972 174.311 3302 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.25 % Favored : 96.58 % Rotamer: Outliers : 1.13 % Allowed : 13.26 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.71 (0.24), residues: 1173 helix: 1.02 (0.21), residues: 605 sheet: 0.87 (0.51), residues: 92 loop : -0.20 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 71 TYR 0.023 0.001 TYR A 823 PHE 0.017 0.001 PHE A1258 TRP 0.008 0.001 TRP A1126 HIS 0.003 0.001 HIS A 799 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (13290) covalent geometry : angle 0.61860 / 0.34 (18569) hydrogen bonds : bond 0.04889 / 3.22 ( 594) hydrogen bonds : angle 4.80110 / 3.44 ( 1630) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.468 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: A 60 GLU cc_start: 0.9699 (pm20) cc_final: 0.9385 (pm20) REVERT: A 71 ARG cc_start: 0.9688 (mtm180) cc_final: 0.9090 (mtp85) REVERT: A 125 GLU cc_start: 0.9620 (OUTLIER) cc_final: 0.8796 (mm-30) REVERT: A 153 LEU cc_start: 0.9893 (mp) cc_final: 0.9656 (pp) REVERT: A 321 MET cc_start: 0.9505 (mmm) cc_final: 0.9121 (mmm) REVERT: A 495 MET cc_start: 0.8990 (mpp) cc_final: 0.8671 (mpp) REVERT: A 504 ASN cc_start: 0.9395 (m-40) cc_final: 0.8894 (p0) REVERT: A 746 GLU cc_start: 0.9595 (tt0) cc_final: 0.9245 (tt0) REVERT: A 895 ARG cc_start: 0.9295 (tpt90) cc_final: 0.9079 (tpm170) REVERT: A 929 LYS cc_start: 0.9436 (ptmt) cc_final: 0.8902 (ptpp) REVERT: A 939 MET cc_start: 0.9548 (mmm) cc_final: 0.9160 (mmm) REVERT: A 1108 GLU cc_start: 0.9272 (mt-10) cc_final: 0.9001 (mt-10) outliers start: 11 outliers final: 10 residues processed: 100 average time/residue: 0.1292 time to fit residues: 18.7461 Evaluate side-chains 101 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 840 HIS Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 108 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 8 optimal weight: 0.0270 chunk 93 optimal weight: 0.0670 chunk 62 optimal weight: 0.4980 chunk 119 optimal weight: 30.0000 chunk 86 optimal weight: 0.0870 chunk 73 optimal weight: 20.0000 chunk 129 optimal weight: 40.0000 chunk 87 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 overall best weight: 0.9356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 612 ASN ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.048383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.033243 restraints weight = 110006.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.034772 restraints weight = 50151.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.035787 restraints weight = 32198.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.036386 restraints weight = 24527.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.036829 restraints weight = 20940.313| |-----------------------------------------------------------------------------| r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13290 Z= 0.120 Angle : 0.630 12.272 18569 Z= 0.332 Chirality : 0.040 0.250 2129 Planarity : 0.003 0.041 1839 Dihedral : 18.933 175.875 3302 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.08 % Favored : 96.75 % Rotamer: Outliers : 0.94 % Allowed : 13.64 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.84 (0.24), residues: 1173 helix: 1.12 (0.21), residues: 606 sheet: 0.89 (0.55), residues: 82 loop : -0.11 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 71 TYR 0.017 0.001 TYR A 823 PHE 0.019 0.001 PHE A1258 TRP 0.013 0.002 TRP A 464 HIS 0.002 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 (13290) covalent geometry : angle 0.63020 / 0.33 (18569) hydrogen bonds : bond 0.04647 / 3.02 ( 594) hydrogen bonds : angle 4.62716 / 3.31 ( 1630) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2417.35 seconds wall clock time: 42 minutes 42.79 seconds (2562.79 seconds total)