Starting phenix.real_space_refine on Fri Jul 3 12:40:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8spq_40681/07_2026/8spq_40681.cif Found real_map, /net/cci-nas-00/data/ceres_data/8spq_40681/07_2026/8spq_40681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8spq_40681/07_2026/8spq_40681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8spq_40681/07_2026/8spq_40681.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8spq_40681/07_2026/8spq_40681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8spq_40681/07_2026/8spq_40681.map" } resolution = 3.26 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= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 148 5.49 5 Mg 4 5.21 5 S 22 5.16 5 C 8449 2.51 5 N 2490 2.21 5 O 3034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14147 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 11002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 11002 Classifications: {'peptide': 1341} Link IDs: {'PTRANS': 36, 'TRANS': 1304} Chain breaks: 3 Chain: "B" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2100 Classifications: {'RNA': 98} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 52, 'rna3p_pyr': 34} Link IDs: {'rna2p': 11, 'rna3p': 86} Chain: "C" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 392 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain breaks: 1 Chain: "E" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 385 Classifications: {'DNA': 19} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 18} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.83, per 1000 atoms: 0.20 Number of scatterers: 14147 At special positions: 0 Unit cell: (87.486, 122.48, 121.647, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 148 15.00 Mg 4 11.99 O 3034 8.00 N 2490 7.00 C 8449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 369.7 milliseconds 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2554 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 9 sheets defined 54.0% alpha, 9.5% beta 54 base pairs and 85 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.837A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.866A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 184 through 196 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 217 through 229 removed outlier: 4.816A pdb=" N GLU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 271 through 276 removed outlier: 3.747A pdb=" N LEU A 275 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP A 276 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.924A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.264A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.767A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.523A pdb=" N SER A 487 " --> pdb=" O ASP A 483 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 572 removed outlier: 3.950A pdb=" N PHE A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS A 571 " --> pdb=" O ASP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.590A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 642 removed outlier: 4.357A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 703 through 712 removed outlier: 3.983A pdb=" N ASP A 707 " --> pdb=" O THR A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 731 through 751 removed outlier: 4.024A pdb=" N LYS A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 779 through 792 removed outlier: 3.799A pdb=" N ARG A 783 " --> pdb=" O GLU A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 804 through 807 Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 829 through 833 removed outlier: 3.908A pdb=" N LEU A 833 " --> pdb=" O ILE A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 859 through 866 Processing helix chain 'A' and resid 872 through 888 removed outlier: 5.695A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N TYR A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 902 through 906 removed outlier: 3.550A pdb=" N GLY A 906 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 914 removed outlier: 3.505A pdb=" N LYS A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 940 removed outlier: 3.792A pdb=" N LEU A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 970 removed outlier: 3.588A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1001 Processing helix chain 'A' and resid 1004 through 1009 removed outlier: 3.659A pdb=" N PHE A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1043 removed outlier: 4.253A pdb=" N MET A1043 " --> pdb=" O TYR A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1047 Processing helix chain 'A' and resid 1077 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1240 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1264 through 1281 Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 3.675A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.570A 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 959 removed outlier: 6.322A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU A 958 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE A 761 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLU A 762 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU A 9 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.508A pdb=" N GLU A1357 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLN A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA4, first strand: chain 'A' and resid 837 through 840 Processing sheet with id=AA5, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA6, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 3.513A pdb=" N TRP A1074 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA8, first strand: chain 'A' and resid 1156 through 1167 Processing sheet with id=AA9, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.673A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) 507 hydrogen bonds defined for protein. 1467 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 134 hydrogen bonds 264 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 85 stacking parallelities Total time for adding SS restraints: 3.49 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3515 1.34 - 1.46: 3584 1.46 - 1.58: 7278 1.58 - 1.70: 294 1.70 - 1.82: 42 Bond restraints: 14713 Sorted by residual: bond pdb=" C1' DT E 11 " pdb=" N1 DT E 11 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.98e+01 bond pdb=" C1' DC E 6 " pdb=" N1 DC E 6 " ideal model delta sigma weight residual 1.468 1.527 -0.059 1.40e-02 5.10e+03 1.80e+01 bond pdb=" C1' DC D 34 " pdb=" N1 DC D 34 " ideal model delta sigma weight residual 1.468 1.522 -0.054 1.40e-02 5.10e+03 1.48e+01 bond pdb=" C3' DG C 20 " pdb=" C2' DG C 20 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C1' DT E 0 " pdb=" N1 DT E 0 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.09e+01 ... (remaining 14708 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 20215 3.42 - 6.83: 219 6.83 - 10.25: 52 10.25 - 13.67: 6 13.67 - 17.08: 2 Bond angle restraints: 20494 Sorted by residual: angle pdb=" CA LYS A 877 " pdb=" CB LYS A 877 " pdb=" CG LYS A 877 " ideal model delta sigma weight residual 114.10 124.76 -10.66 2.00e+00 2.50e-01 2.84e+01 angle pdb=" CA LYS A 183 " pdb=" CB LYS A 183 " pdb=" CG LYS A 183 " ideal model delta sigma weight residual 114.10 124.63 -10.53 2.00e+00 2.50e-01 2.77e+01 angle pdb=" CA LYS A1255 " pdb=" CB LYS A1255 " pdb=" CG LYS A1255 " ideal model delta sigma weight residual 114.10 124.44 -10.34 2.00e+00 2.50e-01 2.68e+01 angle pdb=" CA LYS A 4 " pdb=" CB LYS A 4 " pdb=" CG LYS A 4 " ideal model delta sigma weight residual 114.10 124.30 -10.20 2.00e+00 2.50e-01 2.60e+01 angle pdb=" CB LYS A1031 " pdb=" CG LYS A1031 " pdb=" CD LYS A1031 " ideal model delta sigma weight residual 111.30 122.85 -11.55 2.30e+00 1.89e-01 2.52e+01 ... (remaining 20489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.45: 8101 29.45 - 58.90: 690 58.90 - 88.35: 117 88.35 - 117.80: 3 117.80 - 147.25: 2 Dihedral angle restraints: 8913 sinusoidal: 4969 harmonic: 3944 Sorted by residual: dihedral pdb=" CA PRO A 871 " pdb=" C PRO A 871 " pdb=" N SER A 872 " pdb=" CA SER A 872 " ideal model delta harmonic sigma weight residual -180.00 -158.71 -21.29 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ASN A 869 " pdb=" C ASN A 869 " pdb=" N VAL A 870 " pdb=" CA VAL A 870 " ideal model delta harmonic sigma weight residual 180.00 159.68 20.32 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA LEU A 444 " pdb=" C LEU A 444 " pdb=" N THR A 445 " pdb=" CA THR A 445 " ideal model delta harmonic sigma weight residual -180.00 -159.95 -20.05 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 8910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2181 0.096 - 0.191: 154 0.191 - 0.287: 8 0.287 - 0.382: 1 0.382 - 0.478: 1 Chirality restraints: 2345 Sorted by residual: 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 -2.11 -0.48 2.00e-01 2.50e+01 5.70e+00 chirality pdb=" CG LEU A 444 " pdb=" CB LEU A 444 " pdb=" CD1 LEU A 444 " pdb=" CD2 LEU A 444 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" C3' A B 38 " pdb=" C4' A B 38 " pdb=" O3' A B 38 " pdb=" C2' A B 38 " both_signs ideal model delta sigma weight residual False -2.48 -2.20 -0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 2342 not shown) Planarity restraints: 2076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 1 " -0.028 2.00e-02 2.50e+03 1.27e-02 4.83e+00 pdb=" N9 G B 1 " 0.033 2.00e-02 2.50e+03 pdb=" C8 G B 1 " 0.000 2.00e-02 2.50e+03 pdb=" N7 G B 1 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G B 1 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 1 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G B 1 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G B 1 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G B 1 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G B 1 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G B 1 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G B 1 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 905 " -0.179 9.50e-02 1.11e+02 8.08e-02 4.81e+00 pdb=" NE ARG A 905 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 905 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 905 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 905 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1150 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C GLU A1150 " 0.036 2.00e-02 2.50e+03 pdb=" O GLU A1150 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS A1151 " -0.012 2.00e-02 2.50e+03 ... (remaining 2073 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 172 2.61 - 3.18: 11299 3.18 - 3.75: 24400 3.75 - 4.33: 32013 4.33 - 4.90: 49785 Nonbonded interactions: 117669 Sorted by model distance: nonbonded pdb=" OP2 DC D 34 " pdb="MG MG A1402 " model vdw 2.037 2.170 nonbonded pdb=" OP1 DC D 34 " pdb="MG MG A1401 " model vdw 2.061 2.170 nonbonded pdb=" OE1 GLN A 402 " pdb=" O2' U B 44 " model vdw 2.243 3.040 nonbonded pdb=" OD1 ASP A 672 " pdb=" OG1 THR A 703 " model vdw 2.258 3.040 nonbonded pdb=" OP3 DT E 0 " pdb="MG MG A1403 " model vdw 2.293 2.170 ... (remaining 117664 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.680 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 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 : 0.005 0.072 14713 Z= 0.304 Angle : 0.964 17.081 20494 Z= 0.598 Chirality : 0.050 0.478 2345 Planarity : 0.006 0.081 2076 Dihedral : 19.589 147.255 6359 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.33 % Allowed : 24.07 % Favored : 75.60 % 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: -1.26 (0.21), residues: 1333 helix: -0.88 (0.18), residues: 628 sheet: -0.64 (0.46), residues: 131 loop : -0.62 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG A 905 TYR 0.031 0.002 TYR A1294 PHE 0.024 0.002 PHE A 553 TRP 0.036 0.003 TRP A 883 HIS 0.017 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.30 (14713) covalent geometry : angle 0.96394 / 0.60 (20494) hydrogen bonds : bond 0.15037 / 10.06 ( 629) hydrogen bonds : angle 6.39911 / 4.76 ( 1731) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 94 ASP cc_start: 0.7666 (t0) cc_final: 0.7390 (p0) REVERT: A 221 ARG cc_start: 0.6813 (ttm170) cc_final: 0.6339 (ttp80) REVERT: A 516 GLU cc_start: 0.9241 (mm-30) cc_final: 0.8834 (mt-10) REVERT: A 947 ASP cc_start: 0.7710 (p0) cc_final: 0.7024 (t0) REVERT: A 1148 LYS cc_start: 0.9172 (mptt) cc_final: 0.8794 (mmmm) outliers start: 4 outliers final: 1 residues processed: 83 average time/residue: 0.1342 time to fit residues: 16.0954 Evaluate side-chains 66 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1302 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0270 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 794 GLN A1256 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.083889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.062529 restraints weight = 39784.293| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.11 r_work: 0.2883 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14713 Z= 0.165 Angle : 0.605 9.468 20494 Z= 0.329 Chirality : 0.040 0.214 2345 Planarity : 0.004 0.051 2076 Dihedral : 19.546 152.487 3485 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.99 % Allowed : 19.44 % Favored : 78.58 % 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: -0.24 (0.22), residues: 1333 helix: 0.23 (0.20), residues: 644 sheet: -0.49 (0.48), residues: 123 loop : -0.37 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 535 TYR 0.024 0.001 TYR A 132 PHE 0.010 0.001 PHE A1038 TRP 0.012 0.001 TRP A 883 HIS 0.006 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (14713) covalent geometry : angle 0.60452 / 0.33 (20494) hydrogen bonds : bond 0.04579 / 3.12 ( 629) hydrogen bonds : angle 4.81554 / 3.52 ( 1731) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 94 ASP cc_start: 0.7502 (t0) cc_final: 0.7126 (p0) REVERT: A 221 ARG cc_start: 0.6981 (ttm170) cc_final: 0.6682 (ttm170) REVERT: A 296 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8324 (pp) REVERT: A 307 ARG cc_start: 0.7465 (mmm160) cc_final: 0.6975 (mmm160) REVERT: A 534 MET cc_start: 0.8223 (pmt) cc_final: 0.7081 (ptt) REVERT: A 781 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7613 (tmm) REVERT: A 947 ASP cc_start: 0.7823 (p0) cc_final: 0.7088 (t0) REVERT: A 1148 LYS cc_start: 0.9063 (mptt) cc_final: 0.8746 (mmmm) outliers start: 24 outliers final: 11 residues processed: 88 average time/residue: 0.1204 time to fit residues: 15.6674 Evaluate side-chains 75 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1216 SER Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1364 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 75 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 144 optimal weight: 20.0000 chunk 123 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.078457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.056837 restraints weight = 41122.515| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.98 r_work: 0.2746 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 14713 Z= 0.234 Angle : 0.621 7.572 20494 Z= 0.339 Chirality : 0.042 0.194 2345 Planarity : 0.004 0.052 2076 Dihedral : 19.292 154.136 3485 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.39 % Allowed : 17.12 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.23), residues: 1333 helix: 0.72 (0.20), residues: 649 sheet: -0.67 (0.45), residues: 125 loop : -0.32 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 629 TYR 0.016 0.002 TYR A1294 PHE 0.014 0.002 PHE A 553 TRP 0.011 0.001 TRP A 659 HIS 0.006 0.001 HIS A 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.23 (14713) covalent geometry : angle 0.62076 / 0.34 (20494) hydrogen bonds : bond 0.04780 / 3.22 ( 629) hydrogen bonds : angle 4.53763 / 3.30 ( 1731) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 58 time to evaluate : 0.365 Fit side-chains REVERT: A 296 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8534 (pp) REVERT: A 307 ARG cc_start: 0.7495 (mmm160) cc_final: 0.6993 (mmm160) REVERT: A 465 MET cc_start: 0.8914 (tmm) cc_final: 0.8675 (tmm) REVERT: A 534 MET cc_start: 0.7911 (pmt) cc_final: 0.7394 (ptt) REVERT: A 781 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7631 (tmm) REVERT: A 943 TYR cc_start: 0.7947 (OUTLIER) cc_final: 0.7740 (p90) REVERT: A 1148 LYS cc_start: 0.9119 (mptt) cc_final: 0.8706 (mmmm) REVERT: A 1254 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8252 (tm-30) outliers start: 41 outliers final: 18 residues processed: 93 average time/residue: 0.1152 time to fit residues: 15.8078 Evaluate side-chains 72 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1216 SER Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1364 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 2 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 105 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 140 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.080167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.058530 restraints weight = 40676.463| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.01 r_work: 0.2785 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14713 Z= 0.122 Angle : 0.498 7.389 20494 Z= 0.281 Chirality : 0.038 0.199 2345 Planarity : 0.003 0.048 2076 Dihedral : 19.247 154.582 3485 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.65 % Allowed : 18.36 % Favored : 78.99 % 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: 0.42 (0.23), residues: 1333 helix: 0.94 (0.21), residues: 647 sheet: -0.64 (0.47), residues: 123 loop : -0.16 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 221 TYR 0.013 0.001 TYR A1242 PHE 0.012 0.001 PHE A 553 TRP 0.007 0.001 TRP A1136 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (14713) covalent geometry : angle 0.49848 / 0.28 (20494) hydrogen bonds : bond 0.03945 / 2.66 ( 629) hydrogen bonds : angle 4.42405 / 3.22 ( 1731) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 54 time to evaluate : 0.452 Fit side-chains REVERT: A 94 ASP cc_start: 0.7574 (t0) cc_final: 0.7215 (p0) REVERT: A 296 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8608 (pp) REVERT: A 301 LEU cc_start: 0.9316 (mm) cc_final: 0.9078 (mp) REVERT: A 307 ARG cc_start: 0.7554 (mmm160) cc_final: 0.7058 (mmm160) REVERT: A 465 MET cc_start: 0.8834 (tmm) cc_final: 0.8628 (tmm) REVERT: A 534 MET cc_start: 0.7622 (pmt) cc_final: 0.7263 (ptt) REVERT: A 781 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7929 (tmm) REVERT: A 943 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.7696 (p90) REVERT: A 947 ASP cc_start: 0.7955 (p0) cc_final: 0.7157 (t0) REVERT: A 1326 TYR cc_start: 0.8628 (t80) cc_final: 0.8427 (t80) outliers start: 32 outliers final: 19 residues processed: 80 average time/residue: 0.1109 time to fit residues: 13.2773 Evaluate side-chains 72 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1043 MET Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1216 SER Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 71 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 99 optimal weight: 0.0870 chunk 144 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 930 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.077904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.056423 restraints weight = 40846.562| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.96 r_work: 0.2721 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14713 Z= 0.203 Angle : 0.551 8.307 20494 Z= 0.302 Chirality : 0.040 0.188 2345 Planarity : 0.003 0.050 2076 Dihedral : 19.065 154.662 3485 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.89 % Allowed : 18.53 % Favored : 78.58 % 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: 0.45 (0.23), residues: 1333 helix: 1.02 (0.20), residues: 654 sheet: -0.62 (0.48), residues: 122 loop : -0.24 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1337 TYR 0.015 0.001 TYR A1242 PHE 0.013 0.001 PHE A1105 TRP 0.010 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (14713) covalent geometry : angle 0.55096 / 0.30 (20494) hydrogen bonds : bond 0.04281 / 2.89 ( 629) hydrogen bonds : angle 4.41189 / 3.20 ( 1731) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 54 time to evaluate : 0.533 Fit side-chains REVERT: A 94 ASP cc_start: 0.7618 (t0) cc_final: 0.7215 (p0) REVERT: A 221 ARG cc_start: 0.6916 (ttm170) cc_final: 0.6606 (tmm160) REVERT: A 294 LYS cc_start: 0.9069 (tttt) cc_final: 0.8573 (ttmt) REVERT: A 301 LEU cc_start: 0.9329 (mm) cc_final: 0.9089 (mp) REVERT: A 307 ARG cc_start: 0.7593 (mmm160) cc_final: 0.7102 (mmm160) REVERT: A 534 MET cc_start: 0.7931 (pmt) cc_final: 0.7515 (ptt) REVERT: A 781 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7627 (tmm) REVERT: A 913 LYS cc_start: 0.8124 (tttt) cc_final: 0.7631 (ttmt) REVERT: A 943 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.7744 (p90) REVERT: A 947 ASP cc_start: 0.8145 (p0) cc_final: 0.7358 (t0) REVERT: A 1124 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8796 (ttpt) REVERT: A 1326 TYR cc_start: 0.8799 (t80) cc_final: 0.8473 (t80) outliers start: 35 outliers final: 22 residues processed: 83 average time/residue: 0.1287 time to fit residues: 15.5867 Evaluate side-chains 71 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 46 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1043 MET Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1124 LYS Chi-restraints excluded: chain A residue 1216 SER Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 133 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.079300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.057844 restraints weight = 40482.186| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.96 r_work: 0.2766 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14713 Z= 0.115 Angle : 0.491 7.658 20494 Z= 0.274 Chirality : 0.037 0.184 2345 Planarity : 0.003 0.047 2076 Dihedral : 19.061 154.269 3485 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.23 % Allowed : 18.86 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.23), residues: 1333 helix: 1.16 (0.21), residues: 654 sheet: -0.72 (0.49), residues: 118 loop : -0.08 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 221 TYR 0.015 0.001 TYR A1242 PHE 0.012 0.001 PHE A1105 TRP 0.007 0.001 TRP A1136 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 (14713) covalent geometry : angle 0.49084 / 0.27 (20494) hydrogen bonds : bond 0.03742 / 2.52 ( 629) hydrogen bonds : angle 4.30616 / 3.13 ( 1731) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 55 time to evaluate : 0.374 Fit side-chains REVERT: A 94 ASP cc_start: 0.7620 (t0) cc_final: 0.7254 (p0) REVERT: A 294 LYS cc_start: 0.9109 (tttt) cc_final: 0.8601 (ttmt) REVERT: A 301 LEU cc_start: 0.9323 (mm) cc_final: 0.9080 (mp) REVERT: A 307 ARG cc_start: 0.7647 (mmm160) cc_final: 0.7185 (mmm160) REVERT: A 534 MET cc_start: 0.7885 (pmt) cc_final: 0.7469 (ptt) REVERT: A 781 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7756 (tmm) REVERT: A 913 LYS cc_start: 0.8095 (tttt) cc_final: 0.7591 (ttmt) REVERT: A 943 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.7659 (p90) REVERT: A 947 ASP cc_start: 0.7928 (p0) cc_final: 0.7177 (t0) REVERT: A 1213 MET cc_start: 0.9368 (OUTLIER) cc_final: 0.9140 (mtp) REVERT: A 1254 GLN cc_start: 0.8609 (tm-30) cc_final: 0.7924 (tm-30) outliers start: 27 outliers final: 17 residues processed: 75 average time/residue: 0.1186 time to fit residues: 13.4260 Evaluate side-chains 70 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1043 MET Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 122 optimal weight: 0.0470 chunk 140 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 overall best weight: 1.4882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.078271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.056701 restraints weight = 40820.766| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.97 r_work: 0.2734 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14713 Z= 0.157 Angle : 0.505 7.670 20494 Z= 0.280 Chirality : 0.038 0.189 2345 Planarity : 0.003 0.048 2076 Dihedral : 18.980 153.958 3485 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.73 % Allowed : 18.28 % Favored : 78.99 % 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: 0.62 (0.23), residues: 1333 helix: 1.23 (0.21), residues: 655 sheet: -0.59 (0.49), residues: 122 loop : -0.23 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 221 TYR 0.013 0.001 TYR A1242 PHE 0.012 0.001 PHE A1105 TRP 0.009 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (14713) covalent geometry : angle 0.50493 / 0.28 (20494) hydrogen bonds : bond 0.03911 / 2.63 ( 629) hydrogen bonds : angle 4.28823 / 3.11 ( 1731) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 56 time to evaluate : 0.469 Fit side-chains REVERT: A 94 ASP cc_start: 0.7678 (t0) cc_final: 0.7225 (p0) REVERT: A 221 ARG cc_start: 0.6763 (ttm170) cc_final: 0.6027 (ttp80) REVERT: A 294 LYS cc_start: 0.9199 (tttt) cc_final: 0.8692 (ttmt) REVERT: A 301 LEU cc_start: 0.9324 (mm) cc_final: 0.9057 (mp) REVERT: A 307 ARG cc_start: 0.7625 (mmm160) cc_final: 0.7171 (mmm160) REVERT: A 534 MET cc_start: 0.7925 (pmt) cc_final: 0.7502 (ptt) REVERT: A 548 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8866 (mp) REVERT: A 781 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7754 (tmm) REVERT: A 798 GLU cc_start: 0.8938 (tp30) cc_final: 0.8691 (tp30) REVERT: A 913 LYS cc_start: 0.8168 (tttt) cc_final: 0.7672 (ttmt) REVERT: A 943 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7629 (p90) REVERT: A 947 ASP cc_start: 0.8063 (p0) cc_final: 0.7264 (t0) REVERT: A 1213 MET cc_start: 0.9399 (OUTLIER) cc_final: 0.9185 (mtp) REVERT: A 1254 GLN cc_start: 0.8636 (tm-30) cc_final: 0.7938 (tm-30) outliers start: 33 outliers final: 23 residues processed: 81 average time/residue: 0.0988 time to fit residues: 12.4940 Evaluate side-chains 79 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 52 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1043 MET Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1364 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 75 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 99 optimal weight: 0.0570 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.079502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.057666 restraints weight = 40433.955| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.02 r_work: 0.2759 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14713 Z= 0.114 Angle : 0.479 8.099 20494 Z= 0.268 Chirality : 0.037 0.186 2345 Planarity : 0.003 0.047 2076 Dihedral : 18.998 153.626 3485 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.82 % Allowed : 19.11 % Favored : 79.07 % 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: 0.71 (0.23), residues: 1333 helix: 1.27 (0.21), residues: 655 sheet: -0.69 (0.49), residues: 118 loop : -0.12 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 221 TYR 0.014 0.001 TYR A1242 PHE 0.010 0.001 PHE A1105 TRP 0.008 0.001 TRP A1136 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (14713) covalent geometry : angle 0.47904 / 0.27 (20494) hydrogen bonds : bond 0.03588 / 2.43 ( 629) hydrogen bonds : angle 4.23812 / 3.08 ( 1731) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.429 Fit side-chains REVERT: A 94 ASP cc_start: 0.7734 (t0) cc_final: 0.7217 (p0) REVERT: A 221 ARG cc_start: 0.6813 (ttm170) cc_final: 0.6605 (tmm160) REVERT: A 294 LYS cc_start: 0.9202 (tttt) cc_final: 0.8657 (ttpt) REVERT: A 301 LEU cc_start: 0.9338 (mm) cc_final: 0.9079 (mp) REVERT: A 307 ARG cc_start: 0.7703 (mmm160) cc_final: 0.7259 (mmm160) REVERT: A 781 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7816 (tmm) REVERT: A 798 GLU cc_start: 0.8996 (tp30) cc_final: 0.8743 (tp30) REVERT: A 913 LYS cc_start: 0.8108 (tttt) cc_final: 0.7597 (ttmt) REVERT: A 947 ASP cc_start: 0.8004 (p0) cc_final: 0.7232 (t0) REVERT: A 1213 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.9122 (mtp) REVERT: A 1254 GLN cc_start: 0.8636 (tm-30) cc_final: 0.7931 (tm-30) outliers start: 22 outliers final: 15 residues processed: 73 average time/residue: 0.1205 time to fit residues: 12.9631 Evaluate side-chains 71 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1043 MET Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1216 SER Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 21 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 56 optimal weight: 0.0570 chunk 33 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 31 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 overall best weight: 2.1104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1264 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.077658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.055915 restraints weight = 41187.067| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.98 r_work: 0.2715 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14713 Z= 0.197 Angle : 0.534 7.928 20494 Z= 0.292 Chirality : 0.039 0.190 2345 Planarity : 0.003 0.049 2076 Dihedral : 18.967 153.795 3485 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.99 % Allowed : 19.35 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.23), residues: 1333 helix: 1.24 (0.21), residues: 660 sheet: -0.70 (0.48), residues: 123 loop : -0.21 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 535 TYR 0.012 0.001 TYR A 155 PHE 0.012 0.001 PHE A1105 TRP 0.010 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.20 (14713) covalent geometry : angle 0.53378 / 0.29 (20494) hydrogen bonds : bond 0.03965 / 2.68 ( 629) hydrogen bonds : angle 4.27883 / 3.10 ( 1731) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 0.381 Fit side-chains REVERT: A 94 ASP cc_start: 0.7847 (t0) cc_final: 0.7356 (p0) REVERT: A 221 ARG cc_start: 0.6870 (ttm170) cc_final: 0.6264 (ttp80) REVERT: A 294 LYS cc_start: 0.9232 (tttt) cc_final: 0.8716 (ttpt) REVERT: A 301 LEU cc_start: 0.9362 (mm) cc_final: 0.9115 (mp) REVERT: A 307 ARG cc_start: 0.7683 (mmm160) cc_final: 0.7215 (mmm160) REVERT: A 534 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.7893 (pmm) REVERT: A 781 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7779 (tmm) REVERT: A 798 GLU cc_start: 0.9053 (tp30) cc_final: 0.8789 (tp30) REVERT: A 913 LYS cc_start: 0.8216 (tttt) cc_final: 0.7738 (ttmt) REVERT: A 943 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.7574 (p90) REVERT: A 947 ASP cc_start: 0.8130 (p0) cc_final: 0.7372 (t0) REVERT: A 1213 MET cc_start: 0.9402 (OUTLIER) cc_final: 0.9190 (mtp) REVERT: A 1245 LEU cc_start: 0.7340 (tt) cc_final: 0.6894 (mp) REVERT: A 1254 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8002 (tm-30) outliers start: 24 outliers final: 20 residues processed: 71 average time/residue: 0.1131 time to fit residues: 12.1268 Evaluate side-chains 77 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1043 MET Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1216 SER Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 142 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 135 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.078105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.056536 restraints weight = 40690.060| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.96 r_work: 0.2728 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14713 Z= 0.153 Angle : 0.512 8.546 20494 Z= 0.282 Chirality : 0.038 0.188 2345 Planarity : 0.003 0.049 2076 Dihedral : 19.009 153.757 3485 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.99 % Allowed : 19.69 % Favored : 78.33 % 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: 0.66 (0.23), residues: 1333 helix: 1.28 (0.21), residues: 659 sheet: -0.79 (0.49), residues: 118 loop : -0.20 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 535 TYR 0.014 0.001 TYR A1242 PHE 0.012 0.001 PHE A1105 TRP 0.009 0.001 TRP A1136 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (14713) covalent geometry : angle 0.51234 / 0.28 (20494) hydrogen bonds : bond 0.03764 / 2.55 ( 629) hydrogen bonds : angle 4.24617 / 3.08 ( 1731) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 94 ASP cc_start: 0.7821 (t0) cc_final: 0.7334 (p0) REVERT: A 221 ARG cc_start: 0.6891 (ttm170) cc_final: 0.6274 (ttp80) REVERT: A 294 LYS cc_start: 0.9269 (tttt) cc_final: 0.8774 (ttpt) REVERT: A 301 LEU cc_start: 0.9353 (mm) cc_final: 0.9110 (mp) REVERT: A 307 ARG cc_start: 0.7665 (mmm160) cc_final: 0.7192 (mmm160) REVERT: A 534 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.7194 (pmm) REVERT: A 548 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.9039 (mp) REVERT: A 781 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7800 (tmm) REVERT: A 798 GLU cc_start: 0.9058 (tp30) cc_final: 0.8788 (tp30) REVERT: A 913 LYS cc_start: 0.8239 (tttt) cc_final: 0.7712 (ttmt) REVERT: A 947 ASP cc_start: 0.8113 (p0) cc_final: 0.7378 (t0) REVERT: A 1213 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.9157 (mtp) REVERT: A 1245 LEU cc_start: 0.7341 (tt) cc_final: 0.6883 (mp) REVERT: A 1254 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8020 (tm-30) outliers start: 24 outliers final: 18 residues processed: 75 average time/residue: 0.1204 time to fit residues: 13.2987 Evaluate side-chains 78 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1216 SER Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 112 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 240 ASN ** 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 = 0.3321 r_free = 0.3321 target = 0.075908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.054312 restraints weight = 41104.040| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.94 r_work: 0.2687 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 14713 Z= 0.230 Angle : 0.574 8.426 20494 Z= 0.312 Chirality : 0.040 0.201 2345 Planarity : 0.004 0.050 2076 Dihedral : 19.001 153.949 3485 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.07 % Allowed : 19.85 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.23), residues: 1333 helix: 1.21 (0.20), residues: 658 sheet: -0.83 (0.50), residues: 118 loop : -0.22 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 221 TYR 0.012 0.001 TYR A 155 PHE 0.014 0.001 PHE A1105 TRP 0.010 0.001 TRP A1136 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.23 (14713) covalent geometry : angle 0.57442 / 0.31 (20494) hydrogen bonds : bond 0.04262 / 2.88 ( 629) hydrogen bonds : angle 4.36002 / 3.16 ( 1731) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2515.49 seconds wall clock time: 44 minutes 18.31 seconds (2658.31 seconds total)