Starting phenix.real_space_refine on Fri Jul 3 10:48:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w7v_65734/07_2026/9w7v_65734.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w7v_65734/07_2026/9w7v_65734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w7v_65734/07_2026/9w7v_65734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w7v_65734/07_2026/9w7v_65734.map" model { file = "/net/cci-nas-00/data/ceres_data/9w7v_65734/07_2026/9w7v_65734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w7v_65734/07_2026/9w7v_65734.cif" } resolution = 3.81 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 133 5.49 5 S 22 5.16 5 C 8038 2.51 5 N 2375 2.21 5 O 2885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 13453 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1296, 10591 Classifications: {'peptide': 1296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 1262} Chain breaks: 1 Chain: "B" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 598 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} 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: 1959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1959 Classifications: {'RNA': 92} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 44, 'rna3p_pyr': 37} Link IDs: {'rna2p': 11, 'rna3p': 80} Time building chain proxies: 2.93, per 1000 atoms: 0.22 Number of scatterers: 13453 At special positions: 0 Unit cell: (134.75, 104.566, 145.53, 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 133 15.00 O 2885 8.00 N 2375 7.00 C 8038 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: 1.23 Conformation dependent library (CDL) restraints added in 513.7 milliseconds 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2464 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 8 sheets defined 57.1% alpha, 9.0% beta 49 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.877A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.575A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.520A pdb=" N ILE A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.692A pdb=" N GLN A 228 " --> pdb=" O ASN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 246 Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 286 through 307 Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 346 through 353 removed outlier: 3.740A 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: 4.046A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.341A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.807A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP A 435 " --> pdb=" O PRO A 431 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 430 through 436' Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 477 through 482 removed outlier: 3.766A pdb=" N VAL A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 496 removed outlier: 4.173A pdb=" N MET A 495 " --> pdb=" O PHE A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 526 removed outlier: 4.090A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 553 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 removed outlier: 3.587A pdb=" N ILE A 632 " --> pdb=" O ASP A 628 " (cutoff:3.500A) 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 652 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 702 through 712 removed outlier: 4.346A pdb=" N GLU A 706 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 726 Processing helix chain 'A' and resid 730 through 752 removed outlier: 3.532A pdb=" N LYS A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A 752 " --> pdb=" O VAL A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 792 Processing helix chain 'A' and resid 794 through 799 removed outlier: 4.190A pdb=" N GLU A 798 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N HIS A 799 " --> pdb=" O ILE A 795 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 794 through 799' Processing helix chain 'A' and resid 802 through 808 Processing helix chain 'A' and resid 808 through 817 removed outlier: 3.664A pdb=" N TYR A 812 " --> pdb=" O ASN A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 836 removed outlier: 3.779A pdb=" N ASP A 835 " --> pdb=" O ASN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 866 removed outlier: 3.769A pdb=" N LYS A 866 " --> pdb=" O LYS A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 890 removed outlier: 4.136A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 906 Processing helix chain 'A' and resid 909 through 922 Processing helix chain 'A' and resid 926 through 940 removed outlier: 3.515A pdb=" N HIS A 930 " --> pdb=" O GLN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.918A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.463A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1088 removed outlier: 4.006A pdb=" N ALA A1081 " --> pdb=" O GLY A1077 " (cutoff:3.500A) 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: 3.530A 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: 3.565A pdb=" N GLU A1268 " --> pdb=" O HIS A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 removed outlier: 3.539A pdb=" N LYS A1296 " --> pdb=" O SER A1292 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 3.668A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) 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 1340 through 1344 removed outlier: 4.008A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 4.117A pdb=" N ASN A 758 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 762 " --> pdb=" O LEU A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 10.452A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 4.075A 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: 3.638A pdb=" N LYS A 528 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 839 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: 3.836A 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: 3.836A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1324 through 1326 removed outlier: 3.581A pdb=" N PHE A1324 " --> pdb=" O ILE A1331 " (cutoff:3.500A) 530 hydrogen bonds defined for protein. 1548 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 124 hydrogen bonds 240 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 3.36 Time building geometry restraints manager: 1.63 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: 2869 1.33 - 1.45: 3586 1.45 - 1.57: 7219 1.57 - 1.69: 266 1.69 - 1.81: 42 Bond restraints: 13982 Sorted by residual: bond pdb=" C3' DT C 9 " pdb=" C2' DT C 9 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DA C 13 " pdb=" C2' DA C 13 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.96e+00 bond pdb=" C3' DG B 11 " pdb=" C2' DG B 11 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.60e+00 bond pdb=" C3' DC B 14 " pdb=" C2' DC B 14 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.37e+00 bond pdb=" C3' DT C 12 " pdb=" C2' DT C 12 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.62e+00 ... (remaining 13977 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 18337 1.26 - 2.51: 949 2.51 - 3.77: 144 3.77 - 5.02: 20 5.02 - 6.28: 6 Bond angle restraints: 19456 Sorted by residual: angle pdb=" O4' DG B 18 " pdb=" C4' DG B 18 " pdb=" C3' DG B 18 " ideal model delta sigma weight residual 106.00 102.64 3.36 6.00e-01 2.78e+00 3.13e+01 angle pdb=" O4' DT B 19 " pdb=" C4' DT B 19 " pdb=" C3' DT B 19 " ideal model delta sigma weight residual 106.00 103.22 2.78 6.00e-01 2.78e+00 2.15e+01 angle pdb=" N3 DT B 4 " pdb=" C4 DT B 4 " pdb=" O4 DT B 4 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT C 9 " pdb=" C4 DT C 9 " pdb=" O4 DT C 9 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT B 19 " pdb=" C4 DT B 19 " pdb=" O4 DT B 19 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 ... (remaining 19451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 8155 35.29 - 70.58: 323 70.58 - 105.87: 28 105.87 - 141.16: 0 141.16 - 176.45: 2 Dihedral angle restraints: 8508 sinusoidal: 4700 harmonic: 3808 Sorted by residual: 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 43.55 176.45 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA ILE A 305 " pdb=" C ILE A 305 " pdb=" N LEU A 306 " pdb=" CA LEU A 306 " ideal model delta harmonic sigma weight residual -180.00 -160.44 -19.56 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" C4' DG B 28 " pdb=" C3' DG B 28 " pdb=" O3' DG B 28 " pdb=" P DC B 29 " ideal model delta sinusoidal sigma weight residual 220.00 65.65 154.35 1 3.50e+01 8.16e-04 1.49e+01 ... (remaining 8505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1580 0.038 - 0.076: 471 0.076 - 0.113: 147 0.113 - 0.151: 23 0.151 - 0.189: 4 Chirality restraints: 2225 Sorted by residual: chirality pdb=" P DC B 29 " pdb=" OP1 DC B 29 " pdb=" OP2 DC B 29 " pdb=" O5' DC B 29 " both_signs ideal model delta sigma weight residual True 2.34 -2.52 -0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CG LEU A 158 " pdb=" CB LEU A 158 " pdb=" CD1 LEU A 158 " pdb=" CD2 LEU A 158 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.66e-01 chirality pdb=" CA ILE A 956 " pdb=" N ILE A 956 " pdb=" C ILE A 956 " pdb=" CB ILE A 956 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.29e-01 ... (remaining 2222 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A D 42 " 0.027 2.00e-02 2.50e+03 1.24e-02 4.24e+00 pdb=" N9 A D 42 " -0.029 2.00e-02 2.50e+03 pdb=" C8 A D 42 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A D 42 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A D 42 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A D 42 " 0.000 2.00e-02 2.50e+03 pdb=" N6 A D 42 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A D 42 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A D 42 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A D 42 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A D 42 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 71 " -0.122 9.50e-02 1.11e+02 5.49e-02 1.89e+00 pdb=" NE ARG A 71 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 71 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 71 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 71 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A1228 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.79e+00 pdb=" N PRO A1229 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A1229 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A1229 " -0.019 5.00e-02 4.00e+02 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 2 2.02 - 2.74: 1287 2.74 - 3.46: 18691 3.46 - 4.18: 33506 4.18 - 4.90: 54217 Nonbonded interactions: 107703 Sorted by model distance: nonbonded pdb=" ND2 ASN A 77 " pdb=" O2 U D 59 " model vdw 1.298 3.120 nonbonded pdb=" NH1 ARG A 71 " pdb=" C5 C D 18 " model vdw 1.432 3.420 nonbonded pdb=" OG SER A 851 " pdb=" OD1 ASP A 853 " model vdw 2.108 3.040 nonbonded pdb=" OD1 ASN A 14 " pdb=" OG SER A 55 " model vdw 2.119 3.040 nonbonded pdb=" O GLN A 817 " pdb=" OH TYR A 882 " model vdw 2.160 3.040 ... (remaining 107698 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=1.00 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.170 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 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 0.036 13982 Z= 0.289 Angle : 0.639 6.280 19456 Z= 0.464 Chirality : 0.040 0.189 2225 Planarity : 0.004 0.055 1998 Dihedral : 16.396 176.451 6044 Min Nonbonded Distance : 1.298 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.23), residues: 1292 helix: 1.41 (0.20), residues: 662 sheet: 1.29 (0.56), residues: 94 loop : 0.28 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 457 TYR 0.016 0.002 TYR A 450 PHE 0.015 0.002 PHE A 97 TRP 0.019 0.002 TRP A 464 HIS 0.006 0.002 HIS A 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.29 (13982) covalent geometry : angle 0.63898 / 0.46 (19456) hydrogen bonds : bond 0.16475 / 10.48 ( 643) hydrogen bonds : angle 5.90693 / 4.27 ( 1788) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.446 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 271 TYR cc_start: 0.9160 (t80) cc_final: 0.8596 (t80) REVERT: A 398 LEU cc_start: 0.9296 (tp) cc_final: 0.9044 (tp) REVERT: A 419 LEU cc_start: 0.9341 (tp) cc_final: 0.9115 (tp) REVERT: A 534 MET cc_start: 0.3063 (mtt) cc_final: 0.1983 (ttm) REVERT: A 648 MET cc_start: 0.8741 (mmm) cc_final: 0.8488 (mmm) REVERT: A 727 LEU cc_start: 0.8850 (mt) cc_final: 0.8598 (mp) REVERT: A 1164 LEU cc_start: 0.8865 (tp) cc_final: 0.8661 (tt) REVERT: A 1226 LEU cc_start: 0.8869 (tp) cc_final: 0.8303 (tp) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1203 time to fit residues: 32.0003 Evaluate side-chains 98 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 30.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 HIS ** A 844 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 = 0.3191 r_free = 0.3191 target = 0.052291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.033235 restraints weight = 87995.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.034603 restraints weight = 42077.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.035427 restraints weight = 26943.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.035871 restraints weight = 20834.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.036219 restraints weight = 18007.405| |-----------------------------------------------------------------------------| r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13982 Z= 0.244 Angle : 0.672 8.127 19456 Z= 0.379 Chirality : 0.042 0.224 2225 Planarity : 0.005 0.053 1998 Dihedral : 18.656 178.894 3285 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.48 % Favored : 97.45 % Rotamer: Outliers : 1.63 % Allowed : 6.87 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.23), residues: 1292 helix: 1.16 (0.20), residues: 675 sheet: 1.74 (0.56), residues: 86 loop : 0.13 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 71 TYR 0.023 0.002 TYR A 656 PHE 0.013 0.002 PHE A1258 TRP 0.008 0.001 TRP A1074 HIS 0.006 0.002 HIS A 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.24 (13982) covalent geometry : angle 0.67229 / 0.38 (19456) hydrogen bonds : bond 0.06508 / 4.36 ( 643) hydrogen bonds : angle 5.09784 / 3.70 ( 1788) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8926 (pm20) REVERT: A 161 MET cc_start: 0.9305 (OUTLIER) cc_final: 0.8917 (mmm) REVERT: A 271 TYR cc_start: 0.9393 (t80) cc_final: 0.8592 (t80) REVERT: A 321 MET cc_start: 0.9556 (mmp) cc_final: 0.9326 (mmp) REVERT: A 493 GLU cc_start: 0.9446 (mt-10) cc_final: 0.9021 (tp30) REVERT: A 495 MET cc_start: 0.9114 (mtp) cc_final: 0.8544 (ttm) REVERT: A 534 MET cc_start: 0.4026 (mtt) cc_final: 0.2815 (ttm) REVERT: A 648 MET cc_start: 0.9184 (mmm) cc_final: 0.8713 (mmm) REVERT: A 727 LEU cc_start: 0.9101 (mt) cc_final: 0.8641 (mp) REVERT: A 822 MET cc_start: 0.8323 (tmm) cc_final: 0.7652 (ptm) REVERT: A 908 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7965 (pp) REVERT: A 986 ASP cc_start: 0.9166 (m-30) cc_final: 0.8949 (p0) REVERT: A 1164 LEU cc_start: 0.9308 (tp) cc_final: 0.8978 (tt) REVERT: A 1169 MET cc_start: 0.9452 (tpp) cc_final: 0.9244 (mmm) outliers start: 19 outliers final: 11 residues processed: 109 average time/residue: 0.1090 time to fit residues: 17.2784 Evaluate side-chains 96 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1236 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 77 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 139 optimal weight: 30.0000 chunk 44 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 20 optimal weight: 50.0000 chunk 116 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 GLN ** A 844 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 = 0.3197 r_free = 0.3197 target = 0.052102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.033029 restraints weight = 86649.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.034393 restraints weight = 41241.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.035250 restraints weight = 26466.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.035745 restraints weight = 20258.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.036093 restraints weight = 17328.035| |-----------------------------------------------------------------------------| r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13982 Z= 0.169 Angle : 0.574 9.405 19456 Z= 0.325 Chirality : 0.039 0.234 2225 Planarity : 0.004 0.034 1998 Dihedral : 18.672 179.419 3285 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.63 % Favored : 97.29 % Rotamer: Outliers : 1.80 % Allowed : 6.70 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.23), residues: 1292 helix: 1.27 (0.20), residues: 675 sheet: 1.59 (0.55), residues: 86 loop : 0.06 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 71 TYR 0.012 0.001 TYR A 656 PHE 0.011 0.001 PHE A1276 TRP 0.007 0.001 TRP A1074 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.17 (13982) covalent geometry : angle 0.57381 / 0.33 (19456) hydrogen bonds : bond 0.05484 / 3.72 ( 643) hydrogen bonds : angle 4.70211 / 3.40 ( 1788) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8824 (mp0) REVERT: A 90 MET cc_start: 0.9304 (tpp) cc_final: 0.8941 (tpp) REVERT: A 161 MET cc_start: 0.9388 (OUTLIER) cc_final: 0.8977 (mmm) REVERT: A 271 TYR cc_start: 0.9362 (t80) cc_final: 0.8712 (t80) REVERT: A 303 SER cc_start: 0.9391 (t) cc_final: 0.9151 (p) REVERT: A 321 MET cc_start: 0.9513 (mmp) cc_final: 0.9272 (mmp) REVERT: A 419 LEU cc_start: 0.9796 (tp) cc_final: 0.9510 (tp) REVERT: A 495 MET cc_start: 0.9027 (mtp) cc_final: 0.8398 (ttm) REVERT: A 534 MET cc_start: 0.3939 (mtt) cc_final: 0.2757 (ttm) REVERT: A 648 MET cc_start: 0.9176 (mmm) cc_final: 0.8700 (mmm) REVERT: A 727 LEU cc_start: 0.9023 (mt) cc_final: 0.8530 (mp) REVERT: A 822 MET cc_start: 0.8251 (tmm) cc_final: 0.7633 (ptm) REVERT: A 908 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8033 (pp) REVERT: A 939 MET cc_start: 0.9452 (mmm) cc_final: 0.8513 (tpp) REVERT: A 1087 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9258 (pp) REVERT: A 1164 LEU cc_start: 0.9333 (tp) cc_final: 0.9009 (tt) REVERT: A 1169 MET cc_start: 0.9459 (tpp) cc_final: 0.9249 (mmm) outliers start: 21 outliers final: 9 residues processed: 106 average time/residue: 0.1123 time to fit residues: 17.6132 Evaluate side-chains 90 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1236 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 26 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 112 optimal weight: 8.9990 chunk 131 optimal weight: 20.0000 chunk 73 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1262 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.050627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.031914 restraints weight = 89628.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.033221 restraints weight = 42879.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.034049 restraints weight = 27697.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.034546 restraints weight = 21242.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.034806 restraints weight = 18139.630| |-----------------------------------------------------------------------------| r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13982 Z= 0.221 Angle : 0.598 8.639 19456 Z= 0.339 Chirality : 0.040 0.255 2225 Planarity : 0.004 0.040 1998 Dihedral : 18.729 178.195 3285 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.94 % Favored : 96.98 % Rotamer: Outliers : 1.80 % Allowed : 7.82 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.23), residues: 1292 helix: 1.24 (0.20), residues: 675 sheet: 1.42 (0.55), residues: 86 loop : -0.03 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 220 TYR 0.022 0.002 TYR A 656 PHE 0.016 0.001 PHE A 252 TRP 0.006 0.001 TRP A1074 HIS 0.007 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.22 (13982) covalent geometry : angle 0.59804 / 0.34 (19456) hydrogen bonds : bond 0.05632 / 3.89 ( 643) hydrogen bonds : angle 4.73829 / 3.43 ( 1788) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8750 (mp0) REVERT: A 90 MET cc_start: 0.9340 (tpp) cc_final: 0.8952 (tpp) REVERT: A 161 MET cc_start: 0.9443 (OUTLIER) cc_final: 0.9038 (mmm) REVERT: A 271 TYR cc_start: 0.9416 (t80) cc_final: 0.8804 (t80) REVERT: A 303 SER cc_start: 0.9407 (t) cc_final: 0.9163 (p) REVERT: A 321 MET cc_start: 0.9514 (mmp) cc_final: 0.9294 (mmp) REVERT: A 419 LEU cc_start: 0.9812 (tp) cc_final: 0.9497 (tt) REVERT: A 495 MET cc_start: 0.8882 (mtp) cc_final: 0.8313 (ttm) REVERT: A 510 LYS cc_start: 0.9531 (tttt) cc_final: 0.9318 (ptmt) REVERT: A 534 MET cc_start: 0.3880 (mtt) cc_final: 0.2927 (ttm) REVERT: A 648 MET cc_start: 0.9255 (mmm) cc_final: 0.8732 (mmm) REVERT: A 727 LEU cc_start: 0.9099 (mt) cc_final: 0.8575 (mp) REVERT: A 822 MET cc_start: 0.8189 (tmm) cc_final: 0.7705 (ttp) REVERT: A 908 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8071 (pp) REVERT: A 986 ASP cc_start: 0.9196 (m-30) cc_final: 0.8943 (p0) REVERT: A 1169 MET cc_start: 0.9439 (tpp) cc_final: 0.9219 (mmm) REVERT: A 1228 LEU cc_start: 0.9536 (tp) cc_final: 0.9267 (tp) outliers start: 21 outliers final: 12 residues processed: 91 average time/residue: 0.1066 time to fit residues: 14.8033 Evaluate side-chains 87 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1350 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 24 optimal weight: 30.0000 chunk 105 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 82 optimal weight: 30.0000 chunk 21 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.050298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.031681 restraints weight = 89714.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.032990 restraints weight = 42529.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.033799 restraints weight = 27278.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.034283 restraints weight = 20948.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.034540 restraints weight = 17922.072| |-----------------------------------------------------------------------------| r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13982 Z= 0.195 Angle : 0.564 9.968 19456 Z= 0.321 Chirality : 0.039 0.267 2225 Planarity : 0.004 0.040 1998 Dihedral : 18.777 178.466 3285 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.86 % Favored : 97.06 % Rotamer: Outliers : 1.98 % Allowed : 8.76 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.23), residues: 1292 helix: 1.38 (0.20), residues: 675 sheet: 1.42 (0.55), residues: 86 loop : -0.05 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 635 TYR 0.009 0.001 TYR A 656 PHE 0.011 0.001 PHE A 970 TRP 0.005 0.001 TRP A1074 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.20 (13982) covalent geometry : angle 0.56390 / 0.32 (19456) hydrogen bonds : bond 0.05174 / 3.56 ( 643) hydrogen bonds : angle 4.64369 / 3.35 ( 1788) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8730 (mp0) REVERT: A 90 MET cc_start: 0.9362 (tpp) cc_final: 0.8966 (tpp) REVERT: A 161 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.9058 (mmm) REVERT: A 271 TYR cc_start: 0.9415 (t80) cc_final: 0.8859 (t80) REVERT: A 300 ILE cc_start: 0.9235 (pt) cc_final: 0.8952 (pt) REVERT: A 303 SER cc_start: 0.9412 (t) cc_final: 0.9169 (p) REVERT: A 321 MET cc_start: 0.9512 (mmp) cc_final: 0.9291 (mmp) REVERT: A 399 LEU cc_start: 0.9705 (mp) cc_final: 0.9221 (mp) REVERT: A 419 LEU cc_start: 0.9815 (tp) cc_final: 0.9410 (tt) REVERT: A 495 MET cc_start: 0.8809 (mtp) cc_final: 0.8207 (ttm) REVERT: A 510 LYS cc_start: 0.9517 (tttt) cc_final: 0.9300 (ptmt) REVERT: A 534 MET cc_start: 0.3965 (mtt) cc_final: 0.2857 (ttt) REVERT: A 648 MET cc_start: 0.9280 (mmm) cc_final: 0.8849 (mmm) REVERT: A 727 LEU cc_start: 0.9087 (mt) cc_final: 0.8582 (mp) REVERT: A 806 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7117 (mm) REVERT: A 822 MET cc_start: 0.8128 (tmm) cc_final: 0.7587 (ttp) REVERT: A 908 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.7985 (pp) REVERT: A 1089 MET cc_start: 0.9243 (tpp) cc_final: 0.9011 (tpp) REVERT: A 1169 MET cc_start: 0.9428 (tpp) cc_final: 0.9201 (mmm) outliers start: 23 outliers final: 11 residues processed: 92 average time/residue: 0.1134 time to fit residues: 15.8038 Evaluate side-chains 85 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1236 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 77 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 139 optimal weight: 30.0000 chunk 40 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 17 optimal weight: 0.6980 chunk 4 optimal weight: 20.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 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 = 0.3168 r_free = 0.3168 target = 0.050452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.031782 restraints weight = 90628.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.033061 restraints weight = 42910.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.033866 restraints weight = 27821.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.034328 restraints weight = 21375.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.034537 restraints weight = 18414.367| |-----------------------------------------------------------------------------| r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13982 Z= 0.159 Angle : 0.544 11.957 19456 Z= 0.306 Chirality : 0.039 0.335 2225 Planarity : 0.003 0.034 1998 Dihedral : 18.782 177.900 3285 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.40 % Favored : 97.52 % Rotamer: Outliers : 1.63 % Allowed : 9.71 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.23), residues: 1292 helix: 1.49 (0.20), residues: 674 sheet: 1.34 (0.54), residues: 87 loop : -0.04 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 100 TYR 0.011 0.001 TYR A 973 PHE 0.016 0.001 PHE A1276 TRP 0.004 0.001 TRP A1074 HIS 0.005 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (13982) covalent geometry : angle 0.54422 / 0.31 (19456) hydrogen bonds : bond 0.04869 / 3.34 ( 643) hydrogen bonds : angle 4.52253 / 3.28 ( 1788) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9358 (tpp) cc_final: 0.8935 (tpp) REVERT: A 161 MET cc_start: 0.9422 (OUTLIER) cc_final: 0.9039 (mmm) REVERT: A 271 TYR cc_start: 0.9408 (t80) cc_final: 0.8904 (t80) REVERT: A 300 ILE cc_start: 0.9226 (pt) cc_final: 0.8935 (pt) REVERT: A 303 SER cc_start: 0.9428 (t) cc_final: 0.9181 (p) REVERT: A 419 LEU cc_start: 0.9824 (tp) cc_final: 0.9528 (tt) REVERT: A 495 MET cc_start: 0.8824 (mtp) cc_final: 0.8214 (ttm) REVERT: A 510 LYS cc_start: 0.9508 (tttt) cc_final: 0.9291 (ptmt) REVERT: A 534 MET cc_start: 0.3843 (mtt) cc_final: 0.2550 (ttt) REVERT: A 648 MET cc_start: 0.9290 (mmm) cc_final: 0.8859 (mmm) REVERT: A 727 LEU cc_start: 0.9036 (mt) cc_final: 0.8539 (mp) REVERT: A 781 MET cc_start: 0.5886 (ptp) cc_final: 0.5626 (ptm) REVERT: A 806 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.6974 (mm) REVERT: A 822 MET cc_start: 0.8156 (tmm) cc_final: 0.7549 (ttp) REVERT: A 833 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7668 (mm) REVERT: A 879 MET cc_start: -0.1271 (mmt) cc_final: -0.1664 (mmt) REVERT: A 908 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7857 (pp) REVERT: A 939 MET cc_start: 0.9382 (mmm) cc_final: 0.9032 (tpt) REVERT: A 986 ASP cc_start: 0.9163 (m-30) cc_final: 0.8894 (p0) REVERT: A 1108 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8901 (pt0) REVERT: A 1169 MET cc_start: 0.9447 (tpp) cc_final: 0.8886 (tpp) outliers start: 19 outliers final: 12 residues processed: 90 average time/residue: 0.1195 time to fit residues: 16.1260 Evaluate side-chains 82 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1236 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 134 optimal weight: 30.0000 chunk 23 optimal weight: 30.0000 chunk 87 optimal weight: 30.0000 chunk 30 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 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 = 0.3147 r_free = 0.3147 target = 0.049463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.031025 restraints weight = 91566.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.032296 restraints weight = 43394.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.033054 restraints weight = 28007.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.033477 restraints weight = 21760.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.033641 restraints weight = 18899.727| |-----------------------------------------------------------------------------| r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13982 Z= 0.224 Angle : 0.602 12.460 19456 Z= 0.333 Chirality : 0.039 0.306 2225 Planarity : 0.004 0.034 1998 Dihedral : 18.848 177.224 3285 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.25 % Favored : 96.67 % Rotamer: Outliers : 2.06 % Allowed : 10.40 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.23), residues: 1292 helix: 1.35 (0.20), residues: 674 sheet: 1.23 (0.54), residues: 84 loop : -0.19 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 152 TYR 0.011 0.002 TYR A 656 PHE 0.018 0.002 PHE A 916 TRP 0.006 0.001 TRP A 659 HIS 0.007 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.22 (13982) covalent geometry : angle 0.60158 / 0.33 (19456) hydrogen bonds : bond 0.05180 / 3.56 ( 643) hydrogen bonds : angle 4.63340 / 3.34 ( 1788) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9385 (tpp) cc_final: 0.8994 (tpp) REVERT: A 125 GLU cc_start: 0.9392 (OUTLIER) cc_final: 0.8593 (mm-30) REVERT: A 161 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.9064 (mmm) REVERT: A 300 ILE cc_start: 0.9255 (pt) cc_final: 0.8954 (pt) REVERT: A 303 SER cc_start: 0.9445 (t) cc_final: 0.9206 (p) REVERT: A 419 LEU cc_start: 0.9823 (tp) cc_final: 0.9551 (tt) REVERT: A 495 MET cc_start: 0.8907 (mtp) cc_final: 0.8235 (ttm) REVERT: A 510 LYS cc_start: 0.9525 (tttt) cc_final: 0.9314 (ptmt) REVERT: A 517 TYR cc_start: 0.9291 (m-80) cc_final: 0.8951 (m-80) REVERT: A 534 MET cc_start: 0.3932 (mtt) cc_final: 0.2985 (ttm) REVERT: A 648 MET cc_start: 0.9372 (mmm) cc_final: 0.8917 (mmm) REVERT: A 727 LEU cc_start: 0.9106 (mt) cc_final: 0.8609 (mp) REVERT: A 822 MET cc_start: 0.8181 (tmm) cc_final: 0.7574 (ttp) REVERT: A 833 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7670 (mm) REVERT: A 879 MET cc_start: -0.1588 (mmt) cc_final: -0.1930 (mmt) REVERT: A 939 MET cc_start: 0.9459 (mmm) cc_final: 0.9079 (tpt) REVERT: A 1169 MET cc_start: 0.9440 (tpp) cc_final: 0.8862 (tpp) outliers start: 24 outliers final: 14 residues processed: 83 average time/residue: 0.1081 time to fit residues: 13.9584 Evaluate side-chains 81 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1236 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 39 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 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 = 0.3140 r_free = 0.3140 target = 0.049011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.030689 restraints weight = 91173.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.031938 restraints weight = 43123.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.032712 restraints weight = 27880.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.033138 restraints weight = 21476.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.033305 restraints weight = 18615.238| |-----------------------------------------------------------------------------| r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13982 Z= 0.212 Angle : 0.594 12.207 19456 Z= 0.329 Chirality : 0.040 0.336 2225 Planarity : 0.004 0.034 1998 Dihedral : 18.872 179.530 3285 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.02 % Favored : 96.90 % Rotamer: Outliers : 1.80 % Allowed : 10.40 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.23), residues: 1292 helix: 1.31 (0.20), residues: 677 sheet: 1.05 (0.54), residues: 84 loop : -0.22 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 586 TYR 0.014 0.001 TYR A 973 PHE 0.014 0.002 PHE A 970 TRP 0.004 0.001 TRP A 659 HIS 0.006 0.001 HIS A1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.21 (13982) covalent geometry : angle 0.59437 / 0.33 (19456) hydrogen bonds : bond 0.04969 / 3.40 ( 643) hydrogen bonds : angle 4.63333 / 3.33 ( 1788) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8160 (tmm) cc_final: 0.7841 (tmm) REVERT: A 90 MET cc_start: 0.9389 (tpp) cc_final: 0.8997 (tpp) REVERT: A 125 GLU cc_start: 0.9346 (OUTLIER) cc_final: 0.8525 (mm-30) REVERT: A 161 MET cc_start: 0.9404 (OUTLIER) cc_final: 0.9006 (mmm) REVERT: A 271 TYR cc_start: 0.9454 (t80) cc_final: 0.9065 (t80) REVERT: A 300 ILE cc_start: 0.9288 (pt) cc_final: 0.9025 (pt) REVERT: A 303 SER cc_start: 0.9455 (t) cc_final: 0.9199 (p) REVERT: A 398 LEU cc_start: 0.9587 (tp) cc_final: 0.9076 (mt) REVERT: A 419 LEU cc_start: 0.9828 (tp) cc_final: 0.9558 (tt) REVERT: A 495 MET cc_start: 0.8909 (mtp) cc_final: 0.8246 (ttm) REVERT: A 510 LYS cc_start: 0.9525 (tttt) cc_final: 0.9318 (ptmt) REVERT: A 517 TYR cc_start: 0.9395 (m-80) cc_final: 0.9018 (m-80) REVERT: A 534 MET cc_start: 0.3982 (mtt) cc_final: 0.3059 (ttm) REVERT: A 648 MET cc_start: 0.9407 (mmm) cc_final: 0.8974 (mmm) REVERT: A 781 MET cc_start: 0.5847 (ptp) cc_final: 0.5609 (ptm) REVERT: A 822 MET cc_start: 0.8256 (tmm) cc_final: 0.7658 (ttp) REVERT: A 833 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7630 (mm) REVERT: A 879 MET cc_start: -0.1676 (mmt) cc_final: -0.1957 (mmt) REVERT: A 908 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7673 (pp) REVERT: A 939 MET cc_start: 0.9445 (mmm) cc_final: 0.9089 (tpt) REVERT: A 1169 MET cc_start: 0.9437 (tpp) cc_final: 0.8865 (tpp) outliers start: 21 outliers final: 14 residues processed: 83 average time/residue: 0.1082 time to fit residues: 14.0244 Evaluate side-chains 81 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 TYR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1236 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 94 optimal weight: 0.0570 chunk 87 optimal weight: 50.0000 chunk 82 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 131 optimal weight: 30.0000 chunk 97 optimal weight: 0.0370 chunk 1 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 overall best weight: 4.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1350 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.049284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.030881 restraints weight = 89251.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.032100 restraints weight = 43151.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.032860 restraints weight = 28153.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.033311 restraints weight = 21830.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.033504 restraints weight = 18940.159| |-----------------------------------------------------------------------------| r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 13982 Z= 0.174 Angle : 0.579 13.273 19456 Z= 0.317 Chirality : 0.040 0.325 2225 Planarity : 0.003 0.034 1998 Dihedral : 18.865 179.599 3285 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.10 % Favored : 96.83 % Rotamer: Outliers : 1.63 % Allowed : 10.91 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.23), residues: 1292 helix: 1.45 (0.20), residues: 670 sheet: 1.12 (0.53), residues: 85 loop : -0.15 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 783 TYR 0.008 0.001 TYR A 812 PHE 0.011 0.001 PHE A 970 TRP 0.005 0.001 TRP A 883 HIS 0.005 0.001 HIS A1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (13982) covalent geometry : angle 0.57930 / 0.32 (19456) hydrogen bonds : bond 0.04742 / 3.23 ( 643) hydrogen bonds : angle 4.59597 / 3.31 ( 1788) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9392 (tpp) cc_final: 0.9005 (tpp) REVERT: A 125 GLU cc_start: 0.9350 (OUTLIER) cc_final: 0.8562 (mm-30) REVERT: A 161 MET cc_start: 0.9363 (OUTLIER) cc_final: 0.8951 (mmm) REVERT: A 300 ILE cc_start: 0.9339 (pt) cc_final: 0.9041 (pt) REVERT: A 303 SER cc_start: 0.9465 (t) cc_final: 0.9208 (p) REVERT: A 398 LEU cc_start: 0.9581 (tp) cc_final: 0.9025 (mt) REVERT: A 419 LEU cc_start: 0.9820 (tp) cc_final: 0.9550 (tt) REVERT: A 495 MET cc_start: 0.8885 (mtp) cc_final: 0.8187 (ttm) REVERT: A 510 LYS cc_start: 0.9532 (tttt) cc_final: 0.9320 (ptmt) REVERT: A 517 TYR cc_start: 0.9419 (m-80) cc_final: 0.9015 (m-80) REVERT: A 534 MET cc_start: 0.3991 (mtt) cc_final: 0.2988 (ttm) REVERT: A 648 MET cc_start: 0.9416 (mmm) cc_final: 0.8977 (mmm) REVERT: A 781 MET cc_start: 0.5892 (ptp) cc_final: 0.5652 (ptm) REVERT: A 822 MET cc_start: 0.8217 (tmm) cc_final: 0.7700 (ttp) REVERT: A 833 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7577 (mm) REVERT: A 879 MET cc_start: -0.1923 (mmt) cc_final: -0.2170 (mmt) REVERT: A 908 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7661 (pp) REVERT: A 939 MET cc_start: 0.9446 (mmm) cc_final: 0.9100 (tpt) REVERT: A 1108 GLU cc_start: 0.9311 (mt-10) cc_final: 0.8962 (pt0) REVERT: A 1169 MET cc_start: 0.9440 (tpp) cc_final: 0.8844 (tpp) outliers start: 19 outliers final: 13 residues processed: 80 average time/residue: 0.1084 time to fit residues: 13.5964 Evaluate side-chains 81 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 161 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1236 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 94 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 19 optimal weight: 30.0000 chunk 110 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 2 optimal weight: 0.0870 chunk 33 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 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 = 0.3162 r_free = 0.3162 target = 0.049508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.031212 restraints weight = 88590.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.032425 restraints weight = 42280.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.033185 restraints weight = 27499.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.033571 restraints weight = 21265.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.033875 restraints weight = 18615.303| |-----------------------------------------------------------------------------| r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13982 Z= 0.155 Angle : 0.574 14.486 19456 Z= 0.311 Chirality : 0.040 0.406 2225 Planarity : 0.003 0.034 1998 Dihedral : 18.834 179.374 3285 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.94 % Favored : 96.98 % Rotamer: Outliers : 1.29 % Allowed : 11.34 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.24), residues: 1292 helix: 1.49 (0.20), residues: 669 sheet: 1.09 (0.53), residues: 85 loop : -0.12 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 165 TYR 0.009 0.001 TYR A 973 PHE 0.015 0.001 PHE A 168 TRP 0.006 0.001 TRP A 883 HIS 0.009 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.16 (13982) covalent geometry : angle 0.57395 / 0.31 (19456) hydrogen bonds : bond 0.04562 / 3.09 ( 643) hydrogen bonds : angle 4.53593 / 3.27 ( 1788) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8089 (tmm) cc_final: 0.7699 (tmm) REVERT: A 90 MET cc_start: 0.9399 (tpp) cc_final: 0.9009 (tpp) REVERT: A 161 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.8696 (mmm) REVERT: A 300 ILE cc_start: 0.9351 (pt) cc_final: 0.9056 (pt) REVERT: A 303 SER cc_start: 0.9471 (t) cc_final: 0.9220 (p) REVERT: A 398 LEU cc_start: 0.9601 (tp) cc_final: 0.8999 (mt) REVERT: A 495 MET cc_start: 0.8873 (mtp) cc_final: 0.8224 (ttm) REVERT: A 510 LYS cc_start: 0.9520 (tttt) cc_final: 0.9289 (ptmm) REVERT: A 517 TYR cc_start: 0.9460 (m-80) cc_final: 0.9057 (m-80) REVERT: A 534 MET cc_start: 0.3668 (mtt) cc_final: 0.2272 (ttt) REVERT: A 648 MET cc_start: 0.9433 (mmm) cc_final: 0.8987 (mmm) REVERT: A 781 MET cc_start: 0.5850 (ptp) cc_final: 0.5601 (ptm) REVERT: A 822 MET cc_start: 0.8177 (tmm) cc_final: 0.7716 (ttp) REVERT: A 833 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7588 (mm) REVERT: A 908 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7689 (pp) REVERT: A 1108 GLU cc_start: 0.9333 (mt-10) cc_final: 0.9003 (pt0) REVERT: A 1169 MET cc_start: 0.9461 (tpp) cc_final: 0.8999 (tpp) outliers start: 15 outliers final: 12 residues processed: 79 average time/residue: 0.1168 time to fit residues: 14.1834 Evaluate side-chains 79 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1236 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 68 optimal weight: 40.0000 chunk 27 optimal weight: 30.0000 chunk 122 optimal weight: 0.4980 chunk 107 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 HIS ** A 844 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 = 0.3155 r_free = 0.3155 target = 0.049594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.031232 restraints weight = 88097.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.032486 restraints weight = 41489.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.033225 restraints weight = 26718.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.033627 restraints weight = 20658.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.033872 restraints weight = 17991.272| |-----------------------------------------------------------------------------| r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13982 Z= 0.132 Angle : 0.583 14.845 19456 Z= 0.310 Chirality : 0.039 0.304 2225 Planarity : 0.003 0.035 1998 Dihedral : 18.810 178.766 3285 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.86 % Favored : 97.06 % Rotamer: Outliers : 1.29 % Allowed : 11.68 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.19 (0.24), residues: 1292 helix: 1.48 (0.20), residues: 669 sheet: 1.16 (0.53), residues: 85 loop : -0.07 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 783 TYR 0.007 0.001 TYR A 656 PHE 0.009 0.001 PHE A 970 TRP 0.007 0.001 TRP A 883 HIS 0.008 0.001 HIS A 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (13982) covalent geometry : angle 0.58281 / 0.31 (19456) hydrogen bonds : bond 0.04392 / 2.98 ( 643) hydrogen bonds : angle 4.47423 / 3.23 ( 1788) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2358.88 seconds wall clock time: 41 minutes 39.30 seconds (2499.30 seconds total)