Starting phenix.real_space_refine on Wed Feb 4 22:57:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w7v_65734/02_2026/9w7v_65734.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w7v_65734/02_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_65734/02_2026/9w7v_65734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w7v_65734/02_2026/9w7v_65734.map" model { file = "/net/cci-nas-00/data/ceres_data/9w7v_65734/02_2026/9w7v_65734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w7v_65734/02_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-2.0-5952/lib/python3.9/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: 2.45, per 1000 atoms: 0.18 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: 0.95 Conformation dependent library (CDL) restraints added in 338.8 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: 1.47 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: 2.80 Time building geometry restraints manager: 1.18 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=" CA HIS A 799 " pdb=" CB HIS A 799 " ideal model delta sigma weight residual 1.526 1.542 -0.015 1.20e-02 6.94e+03 1.66e+00 bond pdb=" CA ASP A 94 " pdb=" C ASP A 94 " ideal model delta sigma weight residual 1.522 1.534 -0.012 1.08e-02 8.57e+03 1.30e+00 bond pdb=" C3' DG B 28 " pdb=" O3' DG B 28 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.18e+00 bond pdb=" CG LEU A 419 " pdb=" CD1 LEU A 419 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.17e+00 bond pdb=" CG LEU A 158 " pdb=" CD2 LEU A 158 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.05e+00 ... (remaining 13977 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 18477 1.26 - 2.51: 823 2.51 - 3.77: 130 3.77 - 5.02: 20 5.02 - 6.28: 6 Bond angle restraints: 19456 Sorted by residual: angle pdb=" C GLY A 752 " pdb=" N ARG A 753 " pdb=" CA ARG A 753 " ideal model delta sigma weight residual 121.54 127.56 -6.02 1.91e+00 2.74e-01 9.93e+00 angle pdb=" N GLN A 709 " pdb=" CA GLN A 709 " pdb=" CB GLN A 709 " ideal model delta sigma weight residual 110.39 115.10 -4.71 1.66e+00 3.63e-01 8.07e+00 angle pdb=" CA GLN A 709 " pdb=" CB GLN A 709 " pdb=" CG GLN A 709 " ideal model delta sigma weight residual 114.10 119.38 -5.28 2.00e+00 2.50e-01 6.97e+00 angle pdb=" C ILE A 708 " pdb=" N GLN A 709 " pdb=" CA GLN A 709 " ideal model delta sigma weight residual 120.72 116.44 4.28 1.67e+00 3.59e-01 6.56e+00 angle pdb=" CA ARG A 74 " pdb=" CB ARG A 74 " pdb=" CG ARG A 74 " ideal model delta sigma weight residual 114.10 109.41 4.69 2.00e+00 2.50e-01 5.50e+00 ... (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 - 0.036: 1579 0.036 - 0.071: 480 0.071 - 0.107: 139 0.107 - 0.143: 22 0.143 - 0.178: 5 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 2.35 -2.52 -0.18 2.00e-01 2.50e+01 7.96e-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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.240 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 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= 0.178 Angle : 0.615 6.280 19456 Z= 0.352 Chirality : 0.038 0.178 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 covalent geometry : bond 0.00372 (13982) covalent geometry : angle 0.61461 (19456) hydrogen bonds : bond 0.16475 ( 643) hydrogen bonds : angle 5.90693 ( 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 : 0.379 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: 0.1226 time to fit residues: 32.6480 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 : 0.383 ------------------------------------------------------------------------------- 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: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 HIS A 817 GLN ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.050612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.031813 restraints weight = 88321.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.033117 restraints weight = 42582.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.033897 restraints weight = 27536.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.034345 restraints weight = 21302.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.034668 restraints weight = 18399.328| |-----------------------------------------------------------------------------| r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13982 Z= 0.251 Angle : 0.642 6.683 19456 Z= 0.351 Chirality : 0.039 0.168 2225 Planarity : 0.004 0.045 1998 Dihedral : 18.660 176.889 3285 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.48 % Favored : 97.45 % Rotamer: Outliers : 1.55 % Allowed : 6.79 % Favored : 91.67 % 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: 1.30 (0.23), residues: 1292 helix: 1.38 (0.20), residues: 669 sheet: 2.25 (0.63), residues: 71 loop : 0.13 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 71 TYR 0.014 0.002 TYR A 450 PHE 0.015 0.002 PHE A 462 TRP 0.009 0.001 TRP A 659 HIS 0.007 0.002 HIS A 721 Details of bonding type rmsd covalent geometry : bond 0.00498 (13982) covalent geometry : angle 0.64188 (19456) hydrogen bonds : bond 0.05605 ( 643) hydrogen bonds : angle 4.86820 ( 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 114 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8743 (mp0) REVERT: A 161 MET cc_start: 0.9465 (OUTLIER) cc_final: 0.8826 (mmm) REVERT: A 271 TYR cc_start: 0.9415 (t80) cc_final: 0.8844 (t80) REVERT: A 303 SER cc_start: 0.9430 (t) cc_final: 0.9196 (p) REVERT: A 321 MET cc_start: 0.9449 (mmp) cc_final: 0.9124 (mmp) REVERT: A 495 MET cc_start: 0.8933 (mtp) cc_final: 0.8305 (ttm) REVERT: A 510 LYS cc_start: 0.9530 (tttt) cc_final: 0.9193 (tppt) REVERT: A 517 TYR cc_start: 0.9418 (m-80) cc_final: 0.9152 (m-80) REVERT: A 534 MET cc_start: 0.4292 (mtt) cc_final: 0.3292 (ttm) REVERT: A 648 MET cc_start: 0.9277 (mmm) cc_final: 0.8793 (mmm) REVERT: A 727 LEU cc_start: 0.9095 (mt) cc_final: 0.8566 (mp) REVERT: A 822 MET cc_start: 0.8133 (tmm) cc_final: 0.7552 (ttp) REVERT: A 939 MET cc_start: 0.9484 (mmp) cc_final: 0.9283 (mmm) REVERT: A 1087 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9213 (pp) REVERT: A 1108 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8825 (pt0) REVERT: A 1169 MET cc_start: 0.9493 (tpp) cc_final: 0.9162 (mmm) outliers start: 18 outliers final: 10 residues processed: 108 average time/residue: 0.1172 time to fit residues: 18.1325 Evaluate side-chains 89 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 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 978 ILE 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: 5.9990 chunk 90 optimal weight: 30.0000 chunk 139 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 86 optimal weight: 30.0000 chunk 20 optimal weight: 40.0000 chunk 116 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.050191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.031435 restraints weight = 88608.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.032691 restraints weight = 42151.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.033486 restraints weight = 27401.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.033924 restraints weight = 21234.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.034248 restraints weight = 18303.368| |-----------------------------------------------------------------------------| r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13982 Z= 0.171 Angle : 0.553 9.567 19456 Z= 0.298 Chirality : 0.037 0.158 2225 Planarity : 0.004 0.049 1998 Dihedral : 18.621 179.468 3285 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.71 % Favored : 97.21 % Rotamer: Outliers : 1.98 % Allowed : 7.56 % Favored : 90.46 % 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: 1.32 (0.23), residues: 1292 helix: 1.47 (0.20), residues: 675 sheet: 1.64 (0.57), residues: 86 loop : 0.08 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 71 TYR 0.010 0.001 TYR A 529 PHE 0.009 0.001 PHE A 462 TRP 0.007 0.001 TRP A 883 HIS 0.004 0.001 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00349 (13982) covalent geometry : angle 0.55342 (19456) hydrogen bonds : bond 0.04580 ( 643) hydrogen bonds : angle 4.46680 ( 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 107 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9576 (tpt) cc_final: 0.9151 (tpt) REVERT: A 156 LEU cc_start: 0.9870 (mm) cc_final: 0.9623 (mt) REVERT: A 161 MET cc_start: 0.9554 (OUTLIER) cc_final: 0.9321 (mmm) REVERT: A 271 TYR cc_start: 0.9452 (t80) cc_final: 0.8961 (t80) REVERT: A 303 SER cc_start: 0.9437 (t) cc_final: 0.9192 (p) REVERT: A 321 MET cc_start: 0.9435 (mmp) cc_final: 0.9193 (mmp) REVERT: A 495 MET cc_start: 0.8720 (mtp) cc_final: 0.8159 (ttm) REVERT: A 517 TYR cc_start: 0.9533 (m-80) cc_final: 0.9197 (m-80) REVERT: A 534 MET cc_start: 0.3786 (mtt) cc_final: 0.2762 (ttm) REVERT: A 648 MET cc_start: 0.9351 (mmm) cc_final: 0.8879 (mmm) REVERT: A 727 LEU cc_start: 0.9139 (mt) cc_final: 0.8640 (mp) REVERT: A 822 MET cc_start: 0.8120 (tmm) cc_final: 0.7617 (ttp) REVERT: A 939 MET cc_start: 0.9552 (mmp) cc_final: 0.9333 (mmm) REVERT: A 1087 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9232 (pp) REVERT: A 1108 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8901 (pt0) REVERT: A 1169 MET cc_start: 0.9446 (tpp) cc_final: 0.8967 (tpp) outliers start: 23 outliers final: 9 residues processed: 104 average time/residue: 0.0919 time to fit residues: 14.7294 Evaluate side-chains 82 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 297 SER Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 978 ILE 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 1163 LEU 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: 30.0000 chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 108 optimal weight: 0.0040 chunk 31 optimal weight: 8.9990 chunk 66 optimal weight: 0.0030 chunk 112 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 86 optimal weight: 30.0000 overall best weight: 2.6008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 HIS ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1350 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.050531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.031879 restraints weight = 88576.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.033156 restraints weight = 41397.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.033899 restraints weight = 26744.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.034430 restraints weight = 20699.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.034651 restraints weight = 17657.859| |-----------------------------------------------------------------------------| r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13982 Z= 0.131 Angle : 0.526 11.859 19456 Z= 0.281 Chirality : 0.035 0.156 2225 Planarity : 0.003 0.045 1998 Dihedral : 18.578 179.164 3285 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.71 % Favored : 97.21 % Rotamer: Outliers : 1.46 % Allowed : 8.76 % Favored : 89.78 % 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: 1.62 (0.24), residues: 1292 helix: 1.80 (0.21), residues: 662 sheet: 1.55 (0.55), residues: 89 loop : 0.16 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 71 TYR 0.011 0.001 TYR A 656 PHE 0.010 0.001 PHE A 539 TRP 0.006 0.001 TRP A 883 HIS 0.004 0.001 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00270 (13982) covalent geometry : angle 0.52577 (19456) hydrogen bonds : bond 0.04111 ( 643) hydrogen bonds : angle 4.32140 ( 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 95 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8334 (tmm) cc_final: 0.8126 (tmm) REVERT: A 90 MET cc_start: 0.9606 (tpt) cc_final: 0.9127 (tpt) REVERT: A 125 GLU cc_start: 0.9418 (OUTLIER) cc_final: 0.8353 (mm-30) REVERT: A 161 MET cc_start: 0.9529 (OUTLIER) cc_final: 0.9244 (mmm) REVERT: A 303 SER cc_start: 0.9453 (t) cc_final: 0.9210 (p) REVERT: A 495 MET cc_start: 0.8672 (mtp) cc_final: 0.8121 (ttm) REVERT: A 517 TYR cc_start: 0.9571 (m-80) cc_final: 0.9177 (m-80) REVERT: A 534 MET cc_start: 0.3832 (mtt) cc_final: 0.2804 (ttm) REVERT: A 648 MET cc_start: 0.9378 (mmm) cc_final: 0.8878 (mmm) REVERT: A 727 LEU cc_start: 0.9096 (mt) cc_final: 0.8585 (mp) REVERT: A 822 MET cc_start: 0.8022 (tmm) cc_final: 0.7613 (ttp) REVERT: A 1087 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9229 (pp) REVERT: A 1108 GLU cc_start: 0.9314 (mt-10) cc_final: 0.8926 (pt0) REVERT: A 1169 MET cc_start: 0.9449 (tpp) cc_final: 0.8991 (tpp) REVERT: A 1213 MET cc_start: 0.9408 (tpp) cc_final: 0.9185 (tpp) outliers start: 17 outliers final: 10 residues processed: 92 average time/residue: 0.0872 time to fit residues: 12.4260 Evaluate side-chains 82 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 448 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 958 LEU Chi-restraints excluded: chain A residue 978 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 24 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 0.1980 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 ASN ** 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 = 0.3148 r_free = 0.3148 target = 0.049109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.030668 restraints weight = 91221.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.031907 restraints weight = 42690.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.032658 restraints weight = 27521.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.033133 restraints weight = 21297.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.033335 restraints weight = 18218.530| |-----------------------------------------------------------------------------| r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13982 Z= 0.198 Angle : 0.566 11.829 19456 Z= 0.303 Chirality : 0.037 0.196 2225 Planarity : 0.003 0.044 1998 Dihedral : 18.632 179.699 3285 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.25 % Favored : 96.67 % Rotamer: Outliers : 1.37 % Allowed : 10.14 % Favored : 88.49 % 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: 1.35 (0.24), residues: 1292 helix: 1.53 (0.20), residues: 679 sheet: 1.41 (0.54), residues: 91 loop : 0.04 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.009 0.001 TYR A 812 PHE 0.013 0.001 PHE A 970 TRP 0.004 0.001 TRP A1074 HIS 0.005 0.001 HIS A1262 Details of bonding type rmsd covalent geometry : bond 0.00404 (13982) covalent geometry : angle 0.56560 (19456) hydrogen bonds : bond 0.04443 ( 643) hydrogen bonds : angle 4.46320 ( 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 86 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.370 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 90 MET cc_start: 0.9607 (tpt) cc_final: 0.9259 (tpt) REVERT: A 125 GLU cc_start: 0.9293 (OUTLIER) cc_final: 0.8240 (mm-30) REVERT: A 161 MET cc_start: 0.9531 (OUTLIER) cc_final: 0.9280 (mmm) REVERT: A 303 SER cc_start: 0.9498 (t) cc_final: 0.9253 (p) REVERT: A 399 LEU cc_start: 0.9775 (mp) cc_final: 0.9418 (mt) REVERT: A 495 MET cc_start: 0.8845 (mtp) cc_final: 0.8150 (ttm) REVERT: A 517 TYR cc_start: 0.9632 (m-80) cc_final: 0.9279 (m-80) REVERT: A 534 MET cc_start: 0.4057 (mtt) cc_final: 0.3235 (ttm) REVERT: A 648 MET cc_start: 0.9478 (mmm) cc_final: 0.8975 (mmm) REVERT: A 806 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6970 (mm) REVERT: A 822 MET cc_start: 0.8181 (tmm) cc_final: 0.7720 (ttp) REVERT: A 833 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7653 (mm) REVERT: A 1169 MET cc_start: 0.9421 (tpp) cc_final: 0.8817 (tpp) REVERT: A 1213 MET cc_start: 0.9444 (tpp) cc_final: 0.9183 (tpp) REVERT: A 1228 LEU cc_start: 0.9517 (tp) cc_final: 0.9308 (tp) outliers start: 16 outliers final: 9 residues processed: 83 average time/residue: 0.0890 time to fit residues: 11.5924 Evaluate side-chains 79 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 448 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 958 LEU Chi-restraints excluded: chain A residue 978 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 77 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 ASN ** 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 = 0.3140 r_free = 0.3140 target = 0.048726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.030402 restraints weight = 89349.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.031616 restraints weight = 42007.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.032283 restraints weight = 27087.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.032800 restraints weight = 21186.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.033057 restraints weight = 18063.150| |-----------------------------------------------------------------------------| r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13982 Z= 0.185 Angle : 0.555 12.057 19456 Z= 0.298 Chirality : 0.036 0.143 2225 Planarity : 0.003 0.043 1998 Dihedral : 18.669 179.372 3285 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.94 % Favored : 96.98 % Rotamer: Outliers : 1.46 % Allowed : 10.65 % Favored : 87.89 % 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: 1.29 (0.24), residues: 1292 helix: 1.51 (0.20), residues: 678 sheet: 1.26 (0.52), residues: 91 loop : 0.01 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.011 0.001 TYR A 973 PHE 0.027 0.001 PHE A 916 TRP 0.005 0.001 TRP A 883 HIS 0.004 0.001 HIS A1262 Details of bonding type rmsd covalent geometry : bond 0.00376 (13982) covalent geometry : angle 0.55539 (19456) hydrogen bonds : bond 0.04236 ( 643) hydrogen bonds : angle 4.44419 ( 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 84 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8258 (tmm) cc_final: 0.8053 (tmm) REVERT: A 90 MET cc_start: 0.9600 (tpt) cc_final: 0.9264 (tpt) REVERT: A 125 GLU cc_start: 0.9281 (OUTLIER) cc_final: 0.8490 (mm-30) REVERT: A 161 MET cc_start: 0.9537 (OUTLIER) cc_final: 0.9278 (mmm) REVERT: A 398 LEU cc_start: 0.9618 (tp) cc_final: 0.9031 (mt) REVERT: A 495 MET cc_start: 0.8868 (mtp) cc_final: 0.8173 (ttm) REVERT: A 517 TYR cc_start: 0.9656 (m-80) cc_final: 0.9303 (m-80) REVERT: A 534 MET cc_start: 0.4014 (mtt) cc_final: 0.3037 (ttm) REVERT: A 648 MET cc_start: 0.9534 (mmm) cc_final: 0.9045 (mmm) REVERT: A 664 ARG cc_start: 0.9727 (ttt180) cc_final: 0.9504 (tpt90) REVERT: A 822 MET cc_start: 0.8141 (tmm) cc_final: 0.7669 (ttp) REVERT: A 833 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7408 (mm) REVERT: A 879 MET cc_start: -0.1626 (mmt) cc_final: -0.2016 (mmt) REVERT: A 1108 GLU cc_start: 0.9308 (mt-10) cc_final: 0.8923 (pt0) REVERT: A 1169 MET cc_start: 0.9450 (tpp) cc_final: 0.8947 (tpp) REVERT: A 1213 MET cc_start: 0.9456 (tpp) cc_final: 0.9205 (tpp) REVERT: A 1228 LEU cc_start: 0.9494 (tp) cc_final: 0.9276 (tp) outliers start: 17 outliers final: 12 residues processed: 82 average time/residue: 0.0869 time to fit residues: 11.1662 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 : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 448 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 958 LEU Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1167 THR 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: 10.0000 chunk 23 optimal weight: 40.0000 chunk 87 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 78 optimal weight: 50.0000 chunk 99 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 ASN ** 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 = 0.3140 r_free = 0.3140 target = 0.048494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.030143 restraints weight = 88740.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.031344 restraints weight = 41860.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.032028 restraints weight = 27104.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.032509 restraints weight = 21156.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.032779 restraints weight = 18293.345| |-----------------------------------------------------------------------------| r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13982 Z= 0.195 Angle : 0.568 12.841 19456 Z= 0.304 Chirality : 0.037 0.221 2225 Planarity : 0.003 0.042 1998 Dihedral : 18.716 178.257 3285 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.02 % Favored : 96.90 % Rotamer: Outliers : 1.80 % Allowed : 11.34 % Favored : 86.86 % 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: 1.27 (0.24), residues: 1292 helix: 1.52 (0.20), residues: 675 sheet: 1.21 (0.51), residues: 89 loop : -0.01 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 778 TYR 0.011 0.001 TYR A1237 PHE 0.013 0.001 PHE A 970 TRP 0.005 0.001 TRP A1074 HIS 0.005 0.001 HIS A1262 Details of bonding type rmsd covalent geometry : bond 0.00396 (13982) covalent geometry : angle 0.56766 (19456) hydrogen bonds : bond 0.04358 ( 643) hydrogen bonds : angle 4.49029 ( 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 87 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9585 (tpt) cc_final: 0.9261 (tpt) REVERT: A 125 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8470 (mm-30) REVERT: A 161 MET cc_start: 0.9518 (OUTLIER) cc_final: 0.9255 (mmm) REVERT: A 398 LEU cc_start: 0.9641 (tp) cc_final: 0.9105 (mt) REVERT: A 495 MET cc_start: 0.8910 (mtp) cc_final: 0.8072 (ttm) REVERT: A 517 TYR cc_start: 0.9677 (m-80) cc_final: 0.9344 (m-80) REVERT: A 534 MET cc_start: 0.4041 (mtt) cc_final: 0.3138 (ttm) REVERT: A 648 MET cc_start: 0.9581 (mmm) cc_final: 0.9121 (mmm) REVERT: A 822 MET cc_start: 0.8096 (tmm) cc_final: 0.7656 (ttp) REVERT: A 833 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7351 (mm) REVERT: A 986 ASP cc_start: 0.9161 (m-30) cc_final: 0.8936 (p0) REVERT: A 1169 MET cc_start: 0.9433 (tpp) cc_final: 0.8929 (tpp) REVERT: A 1213 MET cc_start: 0.9446 (tpp) cc_final: 0.9217 (tpp) REVERT: A 1228 LEU cc_start: 0.9477 (tp) cc_final: 0.9253 (tp) outliers start: 21 outliers final: 16 residues processed: 84 average time/residue: 0.0825 time to fit residues: 11.1130 Evaluate side-chains 84 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 364 ASP Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 474 THR 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 958 LEU Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 39 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 40.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** A 985 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.048015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.029771 restraints weight = 89107.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.030953 restraints weight = 42208.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.031672 restraints weight = 27431.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.032081 restraints weight = 21314.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.032365 restraints weight = 18555.731| |-----------------------------------------------------------------------------| r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13982 Z= 0.212 Angle : 0.594 13.073 19456 Z= 0.316 Chirality : 0.038 0.254 2225 Planarity : 0.003 0.041 1998 Dihedral : 18.784 178.690 3285 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.71 % Favored : 97.21 % Rotamer: Outliers : 1.63 % Allowed : 11.68 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.24), residues: 1292 helix: 1.43 (0.20), residues: 675 sheet: 1.05 (0.52), residues: 89 loop : -0.07 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 664 TYR 0.012 0.001 TYR A 812 PHE 0.013 0.001 PHE A 970 TRP 0.006 0.001 TRP A1074 HIS 0.005 0.001 HIS A 754 Details of bonding type rmsd covalent geometry : bond 0.00431 (13982) covalent geometry : angle 0.59436 (19456) hydrogen bonds : bond 0.04373 ( 643) hydrogen bonds : angle 4.53941 ( 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 86 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9593 (tpt) cc_final: 0.9269 (tpt) REVERT: A 125 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8463 (mm-30) REVERT: A 161 MET cc_start: 0.9533 (OUTLIER) cc_final: 0.9267 (mmm) REVERT: A 398 LEU cc_start: 0.9647 (tp) cc_final: 0.9122 (mt) REVERT: A 495 MET cc_start: 0.8964 (mtp) cc_final: 0.8122 (ttm) REVERT: A 517 TYR cc_start: 0.9692 (m-80) cc_final: 0.9356 (m-80) REVERT: A 534 MET cc_start: 0.4101 (mtt) cc_final: 0.3200 (ttm) REVERT: A 648 MET cc_start: 0.9614 (mmm) cc_final: 0.9172 (mmm) REVERT: A 822 MET cc_start: 0.8094 (tmm) cc_final: 0.7672 (ttp) REVERT: A 833 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7258 (mm) REVERT: A 879 MET cc_start: -0.1648 (mmt) cc_final: -0.2132 (mmt) REVERT: A 1108 GLU cc_start: 0.9307 (mt-10) cc_final: 0.8923 (pt0) REVERT: A 1169 MET cc_start: 0.9438 (tpp) cc_final: 0.8931 (tpp) REVERT: A 1213 MET cc_start: 0.9451 (tpp) cc_final: 0.9226 (tpp) REVERT: A 1228 LEU cc_start: 0.9479 (tp) cc_final: 0.9223 (tp) outliers start: 19 outliers final: 16 residues processed: 84 average time/residue: 0.0910 time to fit residues: 11.7474 Evaluate side-chains 80 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 364 ASP Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 474 THR 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 958 LEU Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 94 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 19 optimal weight: 0.0770 chunk 128 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 overall best weight: 5.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3121 r_free = 0.3121 target = 0.047689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.029540 restraints weight = 90231.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.030715 restraints weight = 42719.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.031382 restraints weight = 27604.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.031858 restraints weight = 21573.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.032024 restraints weight = 18563.583| |-----------------------------------------------------------------------------| r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13982 Z= 0.219 Angle : 0.617 13.513 19456 Z= 0.326 Chirality : 0.038 0.287 2225 Planarity : 0.003 0.041 1998 Dihedral : 18.845 178.739 3285 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.10 % Favored : 96.83 % Rotamer: Outliers : 1.72 % Allowed : 12.29 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.01 (0.24), residues: 1292 helix: 1.31 (0.20), residues: 675 sheet: 0.95 (0.52), residues: 89 loop : -0.12 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 664 TYR 0.011 0.001 TYR A 812 PHE 0.014 0.001 PHE A 970 TRP 0.007 0.001 TRP A1074 HIS 0.005 0.001 HIS A1262 Details of bonding type rmsd covalent geometry : bond 0.00445 (13982) covalent geometry : angle 0.61669 (19456) hydrogen bonds : bond 0.04448 ( 643) hydrogen bonds : angle 4.59006 ( 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 82 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.9585 (tpt) cc_final: 0.9270 (tpt) REVERT: A 125 GLU cc_start: 0.9209 (OUTLIER) cc_final: 0.8471 (mm-30) REVERT: A 161 MET cc_start: 0.9523 (OUTLIER) cc_final: 0.9248 (mmm) REVERT: A 398 LEU cc_start: 0.9644 (tp) cc_final: 0.9126 (mt) REVERT: A 495 MET cc_start: 0.8998 (mtp) cc_final: 0.8100 (ttm) REVERT: A 517 TYR cc_start: 0.9686 (m-80) cc_final: 0.9347 (m-80) REVERT: A 534 MET cc_start: 0.4084 (mtt) cc_final: 0.3063 (ttt) REVERT: A 648 MET cc_start: 0.9638 (mmm) cc_final: 0.9230 (mmm) REVERT: A 693 PHE cc_start: 0.9567 (t80) cc_final: 0.9114 (p90) REVERT: A 822 MET cc_start: 0.8045 (tmm) cc_final: 0.7646 (ttp) REVERT: A 833 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7253 (mm) REVERT: A 879 MET cc_start: -0.1393 (mmt) cc_final: -0.1843 (mmt) REVERT: A 1108 GLU cc_start: 0.9347 (mt-10) cc_final: 0.8948 (pt0) REVERT: A 1169 MET cc_start: 0.9437 (tpp) cc_final: 0.8925 (tpp) REVERT: A 1213 MET cc_start: 0.9434 (tpp) cc_final: 0.9209 (tpp) REVERT: A 1228 LEU cc_start: 0.9461 (tp) cc_final: 0.9205 (tp) outliers start: 20 outliers final: 16 residues processed: 80 average time/residue: 0.0769 time to fit residues: 10.3320 Evaluate side-chains 80 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 364 ASP Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 474 THR 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 958 LEU Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 94 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 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 = 0.3124 r_free = 0.3124 target = 0.047764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.029627 restraints weight = 89334.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.030807 restraints weight = 42097.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.031464 restraints weight = 27284.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.031918 restraints weight = 21400.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.032246 restraints weight = 18570.815| |-----------------------------------------------------------------------------| r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13982 Z= 0.200 Angle : 0.612 14.218 19456 Z= 0.322 Chirality : 0.038 0.305 2225 Planarity : 0.003 0.041 1998 Dihedral : 18.884 179.326 3285 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.02 % Favored : 96.90 % Rotamer: Outliers : 1.72 % Allowed : 12.11 % Favored : 86.17 % 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: 0.99 (0.24), residues: 1292 helix: 1.32 (0.20), residues: 674 sheet: 0.88 (0.52), residues: 89 loop : -0.15 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.011 0.001 TYR A 812 PHE 0.012 0.001 PHE A 970 TRP 0.007 0.001 TRP A1074 HIS 0.005 0.001 HIS A1262 Details of bonding type rmsd covalent geometry : bond 0.00408 (13982) covalent geometry : angle 0.61190 (19456) hydrogen bonds : bond 0.04272 ( 643) hydrogen bonds : angle 4.59433 ( 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 85 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.9598 (tpt) cc_final: 0.9283 (tpt) REVERT: A 125 GLU cc_start: 0.9231 (OUTLIER) cc_final: 0.8492 (mm-30) REVERT: A 161 MET cc_start: 0.9509 (OUTLIER) cc_final: 0.9205 (mmm) REVERT: A 398 LEU cc_start: 0.9651 (tp) cc_final: 0.9135 (mt) REVERT: A 495 MET cc_start: 0.9059 (mtp) cc_final: 0.8159 (ttm) REVERT: A 517 TYR cc_start: 0.9692 (m-80) cc_final: 0.9364 (m-80) REVERT: A 534 MET cc_start: 0.4074 (mtt) cc_final: 0.3172 (ttt) REVERT: A 648 MET cc_start: 0.9649 (mmm) cc_final: 0.9252 (mmm) REVERT: A 693 PHE cc_start: 0.9577 (t80) cc_final: 0.9109 (p90) REVERT: A 822 MET cc_start: 0.7880 (tmm) cc_final: 0.7519 (ttp) REVERT: A 833 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7077 (mm) REVERT: A 879 MET cc_start: -0.1257 (mmt) cc_final: -0.1716 (mmt) REVERT: A 1108 GLU cc_start: 0.9363 (mt-10) cc_final: 0.8961 (pt0) REVERT: A 1169 MET cc_start: 0.9436 (tpp) cc_final: 0.8892 (tpp) REVERT: A 1213 MET cc_start: 0.9454 (tpp) cc_final: 0.9215 (tpp) REVERT: A 1228 LEU cc_start: 0.9460 (tp) cc_final: 0.9202 (tp) outliers start: 20 outliers final: 15 residues processed: 83 average time/residue: 0.0770 time to fit residues: 10.6214 Evaluate side-chains 77 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 364 ASP Chi-restraints excluded: chain A residue 474 THR 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 958 LEU Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1120 ILE Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 3.9990 chunk 112 optimal weight: 0.4980 chunk 110 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.048354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.030118 restraints weight = 88919.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.031316 restraints weight = 41678.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.031998 restraints weight = 26880.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.032497 restraints weight = 20980.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.032751 restraints weight = 18039.330| |-----------------------------------------------------------------------------| r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13982 Z= 0.152 Angle : 0.597 14.585 19456 Z= 0.310 Chirality : 0.037 0.304 2225 Planarity : 0.003 0.041 1998 Dihedral : 18.855 179.291 3285 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.94 % Favored : 96.98 % Rotamer: Outliers : 1.55 % Allowed : 12.71 % Favored : 85.74 % 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 (0.24), residues: 1292 helix: 1.42 (0.20), residues: 674 sheet: 0.98 (0.51), residues: 91 loop : -0.13 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 63 TYR 0.009 0.001 TYR A 812 PHE 0.031 0.001 PHE A 916 TRP 0.008 0.001 TRP A 883 HIS 0.004 0.001 HIS A1262 Details of bonding type rmsd covalent geometry : bond 0.00317 (13982) covalent geometry : angle 0.59677 (19456) hydrogen bonds : bond 0.03971 ( 643) hydrogen bonds : angle 4.46833 ( 1788) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2029.68 seconds wall clock time: 35 minutes 56.76 seconds (2156.76 seconds total)