Starting phenix.real_space_refine on Thu Aug 6 07:11:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8srs_40740/08_2026/8srs_40740.cif Found real_map, /net/cci-nas-00/data/ceres_data/8srs_40740/08_2026/8srs_40740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8srs_40740/08_2026/8srs_40740.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8srs_40740/08_2026/8srs_40740.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8srs_40740/08_2026/8srs_40740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8srs_40740/08_2026/8srs_40740.map" } resolution = 2.79 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 8450 2.51 5 N 2489 2.21 5 O 3035 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14148 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: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 268 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 388 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain breaks: 1 Chain: "c" 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.03, per 1000 atoms: 0.21 Number of scatterers: 14148 At special positions: 0 Unit cell: (87.486, 124.98, 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 3035 8.00 N 2489 7.00 C 8450 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: 1.16 Conformation dependent library (CDL) restraints added in 536.6 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 10 sheets defined 53.8% alpha, 9.8% beta 54 base pairs and 87 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 5.059A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.909A 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: 3.809A 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 215 removed outlier: 4.336A pdb=" N ALA A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 229 removed outlier: 4.854A 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: 3.680A pdb=" N LEU A 275 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.581A 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 410 removed outlier: 3.574A pdb=" N ASN A 407 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.168A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.758A 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: 3.746A 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 568 removed outlier: 3.688A pdb=" N TYR A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.580A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.600A pdb=" N LEU A 616 " --> pdb=" O ASN A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 642 removed outlier: 4.252A 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: 3.582A pdb=" N ASP A 707 " --> pdb=" O THR A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.661A pdb=" N ASN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 751 removed outlier: 4.217A pdb=" N LYS A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 776 Processing helix chain 'A' and resid 779 through 792 removed outlier: 3.554A 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 808 through 817 Processing helix chain 'A' and resid 829 through 833 removed outlier: 3.505A pdb=" N ARG A 832 " --> pdb=" O ASP A 829 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU A 833 " --> pdb=" O ILE A 830 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 829 through 833' 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: 5.544A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.663A 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 Processing helix chain 'A' and resid 909 through 914 removed outlier: 3.571A pdb=" N ALA A 914 " --> pdb=" O GLU A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 940 removed outlier: 3.794A pdb=" N LEU A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 970 removed outlier: 3.548A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.584A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1009 removed outlier: 3.663A pdb=" N PHE A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1043 removed outlier: 4.309A 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 1312 Processing helix chain 'A' and resid 1313 through 1315 No H-bonds generated for 'chain 'A' and resid 1313 through 1315' Processing helix chain 'A' and resid 1340 through 1344 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: 6.255A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU A 958 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE A 761 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N TYR A 5 " --> pdb=" O ASN A 758 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N VAL A 760 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N GLU A 762 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.548A 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: 10.011A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 6.336A 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: 3.817A 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: 3.599A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1324 through 1325 removed outlier: 3.650A pdb=" N PHE A1324 " --> pdb=" O ILE A1331 " (cutoff:3.500A) 505 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 133 hydrogen bonds 262 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 87 stacking parallelities Total time for adding SS restraints: 3.82 Time building geometry restraints manager: 1.58 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: 3071 1.33 - 1.45: 3756 1.45 - 1.57: 7547 1.57 - 1.69: 297 1.69 - 1.81: 42 Bond restraints: 14713 Sorted by residual: bond pdb=" C1' DT c 11 " pdb=" N1 DT c 11 " ideal model delta sigma weight residual 1.468 1.535 -0.067 1.40e-02 5.10e+03 2.31e+01 bond pdb=" C1' DC D 34 " pdb=" N1 DC D 34 " ideal model delta sigma weight residual 1.468 1.527 -0.059 1.40e-02 5.10e+03 1.76e+01 bond pdb=" C1' DC c 6 " pdb=" N1 DC c 6 " ideal model delta sigma weight residual 1.468 1.525 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" C1' DC D 36 " pdb=" N1 DC D 36 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.44e+01 bond pdb=" C1' DC c 13 " pdb=" N1 DC c 13 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.42e+01 ... (remaining 14708 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 20125 2.69 - 5.39: 294 5.39 - 8.08: 57 8.08 - 10.77: 14 10.77 - 13.46: 4 Bond angle restraints: 20494 Sorted by residual: angle pdb=" CB LYS A 948 " pdb=" CG LYS A 948 " pdb=" CD LYS A 948 " ideal model delta sigma weight residual 111.30 124.76 -13.46 2.30e+00 1.89e-01 3.43e+01 angle pdb=" CA LYS A1155 " pdb=" CB LYS A1155 " pdb=" CG LYS A1155 " ideal model delta sigma weight residual 114.10 124.15 -10.05 2.00e+00 2.50e-01 2.52e+01 angle pdb=" CA GLN A1254 " pdb=" CB GLN A1254 " pdb=" CG GLN A1254 " ideal model delta sigma weight residual 114.10 123.58 -9.48 2.00e+00 2.50e-01 2.25e+01 angle pdb=" CA LYS A 183 " pdb=" CB LYS A 183 " pdb=" CG LYS A 183 " ideal model delta sigma weight residual 114.10 123.56 -9.46 2.00e+00 2.50e-01 2.24e+01 angle pdb=" C1' C B 96 " pdb=" N1 C B 96 " pdb=" C2 C B 96 " ideal model delta sigma weight residual 118.80 123.98 -5.18 1.10e+00 8.26e-01 2.22e+01 ... (remaining 20489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.82: 8100 29.82 - 59.64: 711 59.64 - 89.46: 103 89.46 - 119.29: 1 119.29 - 149.11: 2 Dihedral angle restraints: 8917 sinusoidal: 4973 harmonic: 3944 Sorted by residual: dihedral pdb=" CA GLN A1261 " pdb=" C GLN A1261 " pdb=" N HIS A1262 " pdb=" CA HIS A1262 " ideal model delta harmonic sigma weight residual 180.00 150.25 29.75 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA GLU A 505 " pdb=" C GLU A 505 " pdb=" N LYS A 506 " pdb=" CA LYS A 506 " ideal model delta harmonic sigma weight residual -180.00 -160.65 -19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" C4' DT D 17 " pdb=" C3' DT D 17 " pdb=" O3' DT D 17 " pdb=" P DG D 18 " ideal model delta sinusoidal sigma weight residual 220.00 70.89 149.11 1 3.50e+01 8.16e-04 1.46e+01 ... (remaining 8914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1734 0.052 - 0.103: 418 0.103 - 0.155: 173 0.155 - 0.207: 15 0.207 - 0.258: 5 Chirality restraints: 2345 Sorted by residual: chirality pdb=" C1' A B 8 " pdb=" O4' A B 8 " pdb=" C2' A B 8 " pdb=" N9 A B 8 " both_signs ideal model delta sigma weight residual False 2.47 2.21 0.26 2.00e-01 2.50e+01 1.67e+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 -2.22 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA GLU A 630 " pdb=" N GLU A 630 " pdb=" C GLU A 630 " pdb=" CB GLU A 630 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 2342 not shown) Planarity restraints: 2076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A1298 " 0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C ARG A1298 " -0.061 2.00e-02 2.50e+03 pdb=" O ARG A1298 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP A1299 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 653 " -0.286 9.50e-02 1.11e+02 1.29e-01 1.06e+01 pdb=" NE ARG A 653 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 653 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 653 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 653 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A1297 " -0.025 2.00e-02 2.50e+03 2.60e-02 1.01e+01 pdb=" CG HIS A1297 " 0.056 2.00e-02 2.50e+03 pdb=" ND1 HIS A1297 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS A1297 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS A1297 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A1297 " -0.008 2.00e-02 2.50e+03 ... (remaining 2073 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 146 2.60 - 3.18: 11005 3.18 - 3.75: 23987 3.75 - 4.33: 33112 4.33 - 4.90: 50694 Nonbonded interactions: 118944 Sorted by model distance: nonbonded pdb=" OP2 DC D 34 " pdb="MG MG A1402 " model vdw 2.029 2.170 nonbonded pdb=" OP1 DC D 34 " pdb="MG MG A1401 " model vdw 2.066 2.170 nonbonded pdb=" OE2 GLU A 762 " pdb="MG MG A1401 " model vdw 2.081 2.170 nonbonded pdb=" OD1 ASP A 839 " pdb="MG MG A1403 " model vdw 2.085 2.170 nonbonded pdb=" OD1 ASP A 10 " pdb="MG MG A1401 " model vdw 2.100 2.170 ... (remaining 118939 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: 10.620 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.120 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 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 0.067 14713 Z= 0.304 Angle : 0.897 13.463 20494 Z= 0.594 Chirality : 0.054 0.258 2345 Planarity : 0.006 0.129 2076 Dihedral : 19.788 149.107 6363 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.58 % Allowed : 23.66 % Favored : 75.77 % 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 (0.21), residues: 1333 helix: -0.63 (0.18), residues: 637 sheet: -0.34 (0.49), residues: 120 loop : -0.59 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 884 TYR 0.016 0.002 TYR A 5 PHE 0.028 0.002 PHE A1327 TRP 0.025 0.002 TRP A1136 HIS 0.028 0.002 HIS A1297 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.30 (14713) covalent geometry : angle 0.89697 / 0.59 (20494) hydrogen bonds : bond 0.14710 / 9.76 ( 626) hydrogen bonds : angle 6.04717 / 4.42 ( 1726) *********************** 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 66 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.477 Fit side-chains REVERT: A 1254 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8297 (tm-30) outliers start: 7 outliers final: 1 residues processed: 62 average time/residue: 0.6501 time to fit residues: 44.7675 Evaluate side-chains 55 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 1254 GLN 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: 0.0870 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 674 GLN ** A1261 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 = 0.3501 r_free = 0.3501 target = 0.099753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.067676 restraints weight = 26851.650| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.36 r_work: 0.2784 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14713 Z= 0.156 Angle : 0.571 9.670 20494 Z= 0.319 Chirality : 0.041 0.232 2345 Planarity : 0.004 0.056 2076 Dihedral : 19.357 151.017 3492 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.40 % Allowed : 18.86 % Favored : 78.74 % 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: -0.09 (0.22), residues: 1333 helix: 0.39 (0.20), residues: 650 sheet: -0.17 (0.49), residues: 117 loop : -0.43 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 864 TYR 0.011 0.001 TYR A 362 PHE 0.011 0.001 PHE A1327 TRP 0.017 0.001 TRP A1136 HIS 0.007 0.001 HIS A1297 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (14713) covalent geometry : angle 0.57066 / 0.32 (20494) hydrogen bonds : bond 0.04969 / 3.35 ( 626) hydrogen bonds : angle 4.74342 / 3.48 ( 1726) *********************** 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 86 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 0.527 Fit side-chains REVERT: A 4 LYS cc_start: 0.9044 (mmtp) cc_final: 0.8842 (mptp) REVERT: A 618 ASP cc_start: 0.8924 (t0) cc_final: 0.8721 (t0) REVERT: A 664 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8321 (tpp80) REVERT: A 1268 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8354 (mt-10) REVERT: A 1297 HIS cc_start: 0.7810 (m170) cc_final: 0.7603 (m170) outliers start: 29 outliers final: 5 residues processed: 81 average time/residue: 0.6745 time to fit residues: 60.0646 Evaluate side-chains 57 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 1268 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 44 optimal weight: 0.0670 chunk 107 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 121 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 674 GLN A1261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.099159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.067426 restraints weight = 26953.135| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.32 r_work: 0.2773 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14713 Z= 0.134 Angle : 0.508 8.538 20494 Z= 0.287 Chirality : 0.039 0.217 2345 Planarity : 0.004 0.051 2076 Dihedral : 19.256 151.905 3487 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.23 % Allowed : 18.78 % 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: 0.30 (0.23), residues: 1333 helix: 0.86 (0.20), residues: 648 sheet: -0.22 (0.48), residues: 120 loop : -0.36 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 976 TYR 0.015 0.001 TYR A1242 PHE 0.016 0.001 PHE A1327 TRP 0.013 0.001 TRP A1136 HIS 0.006 0.001 HIS A1297 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (14713) covalent geometry : angle 0.50803 / 0.29 (20494) hydrogen bonds : bond 0.04308 / 2.89 ( 626) hydrogen bonds : angle 4.42869 / 3.25 ( 1726) *********************** 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 87 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.510 Fit side-chains REVERT: A 523 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8401 (tt0) REVERT: A 618 ASP cc_start: 0.8947 (t0) cc_final: 0.8711 (t0) REVERT: A 627 GLU cc_start: 0.7489 (pm20) cc_final: 0.7258 (pp20) REVERT: A 652 LYS cc_start: 0.8559 (pttt) cc_final: 0.8263 (ptmm) REVERT: A 664 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8335 (tpp80) REVERT: A 802 GLU cc_start: 0.8802 (pt0) cc_final: 0.8494 (pt0) REVERT: A 1150 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8088 (mp0) REVERT: A 1268 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8429 (mt-10) REVERT: A 1296 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.9108 (pptt) REVERT: A 1297 HIS cc_start: 0.8116 (m170) cc_final: 0.7870 (m170) outliers start: 27 outliers final: 9 residues processed: 80 average time/residue: 0.7019 time to fit residues: 61.4369 Evaluate side-chains 66 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1296 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 48 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.097732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.065548 restraints weight = 26882.472| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.34 r_work: 0.2740 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14713 Z= 0.154 Angle : 0.522 9.598 20494 Z= 0.290 Chirality : 0.039 0.208 2345 Planarity : 0.004 0.046 2076 Dihedral : 19.219 151.965 3487 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.56 % Allowed : 19.02 % Favored : 78.41 % 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: 0.44 (0.23), residues: 1333 helix: 1.05 (0.20), residues: 649 sheet: -0.06 (0.48), residues: 120 loop : -0.42 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 629 TYR 0.012 0.001 TYR A 362 PHE 0.023 0.001 PHE A1327 TRP 0.012 0.001 TRP A1136 HIS 0.004 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (14713) covalent geometry : angle 0.52168 / 0.29 (20494) hydrogen bonds : bond 0.04198 / 2.82 ( 626) hydrogen bonds : angle 4.32954 / 3.17 ( 1726) *********************** 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: 31 poor density : 55 time to evaluate : 0.490 Fit side-chains REVERT: A 275 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7090 (pp) REVERT: A 523 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8425 (tt0) REVERT: A 548 ILE cc_start: 0.9079 (pt) cc_final: 0.8860 (pt) REVERT: A 618 ASP cc_start: 0.8955 (t0) cc_final: 0.8717 (t0) REVERT: A 652 LYS cc_start: 0.8551 (pttt) cc_final: 0.8312 (ptmm) REVERT: A 664 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8385 (tpp80) REVERT: A 671 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7729 (mtp85) REVERT: A 879 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7087 (mtp) REVERT: A 1268 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8366 (mt-10) outliers start: 31 outliers final: 10 residues processed: 80 average time/residue: 0.6577 time to fit residues: 57.8118 Evaluate side-chains 68 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1268 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 97 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 142 optimal weight: 9.9990 chunk 99 optimal weight: 0.0980 chunk 144 optimal weight: 9.9990 chunk 93 optimal weight: 0.0980 chunk 87 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 108 optimal weight: 0.0050 chunk 105 optimal weight: 0.0570 chunk 6 optimal weight: 0.9990 overall best weight: 0.1712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 674 GLN A 690 ASN ** A1262 HIS ** 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 = 0.3493 r_free = 0.3493 target = 0.099252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.067664 restraints weight = 26860.453| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.28 r_work: 0.2792 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14713 Z= 0.103 Angle : 0.480 8.074 20494 Z= 0.271 Chirality : 0.037 0.209 2345 Planarity : 0.003 0.044 2076 Dihedral : 19.230 151.719 3487 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.48 % Allowed : 19.52 % Favored : 78.00 % 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: 0.62 (0.23), residues: 1333 helix: 1.22 (0.21), residues: 648 sheet: -0.00 (0.49), residues: 120 loop : -0.35 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 783 TYR 0.008 0.001 TYR A 155 PHE 0.007 0.001 PHE A 916 TRP 0.011 0.001 TRP A1136 HIS 0.004 0.001 HIS A1297 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.10 (14713) covalent geometry : angle 0.47989 / 0.27 (20494) hydrogen bonds : bond 0.03850 / 2.61 ( 626) hydrogen bonds : angle 4.23282 / 3.10 ( 1726) *********************** 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: 30 poor density : 59 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 275 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7105 (pp) REVERT: A 523 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8385 (tt0) REVERT: A 548 ILE cc_start: 0.9034 (pt) cc_final: 0.8817 (pt) REVERT: A 618 ASP cc_start: 0.8925 (t0) cc_final: 0.8682 (t0) REVERT: A 648 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8238 (mmm) REVERT: A 652 LYS cc_start: 0.8515 (pttt) cc_final: 0.8231 (ptmm) REVERT: A 664 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8348 (tpp80) REVERT: A 671 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7654 (mtp85) REVERT: A 1150 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8037 (mp0) REVERT: A 1268 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.7673 (mp0) outliers start: 30 outliers final: 12 residues processed: 81 average time/residue: 0.6336 time to fit residues: 56.7393 Evaluate side-chains 73 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1261 GLN Chi-restraints excluded: chain A residue 1268 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 29 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 674 GLN ** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.094627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.063151 restraints weight = 26924.028| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.23 r_work: 0.2682 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14713 Z= 0.247 Angle : 0.584 8.982 20494 Z= 0.316 Chirality : 0.043 0.201 2345 Planarity : 0.004 0.046 2076 Dihedral : 19.150 152.652 3487 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.06 % Allowed : 19.35 % Favored : 77.58 % 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: 0.51 (0.23), residues: 1333 helix: 1.10 (0.20), residues: 651 sheet: -0.03 (0.47), residues: 120 loop : -0.40 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 586 TYR 0.018 0.002 TYR A 362 PHE 0.010 0.001 PHE A 164 TRP 0.011 0.002 TRP A1136 HIS 0.006 0.001 HIS A1241 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.25 (14713) covalent geometry : angle 0.58353 / 0.32 (20494) hydrogen bonds : bond 0.04621 / 3.10 ( 626) hydrogen bonds : angle 4.31422 / 3.16 ( 1726) *********************** 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 85 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 48 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 275 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7026 (pp) REVERT: A 523 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8455 (tt0) REVERT: A 548 ILE cc_start: 0.9123 (pt) cc_final: 0.8905 (pt) REVERT: A 618 ASP cc_start: 0.8949 (t0) cc_final: 0.8699 (t0) REVERT: A 652 LYS cc_start: 0.8563 (pttt) cc_final: 0.8312 (ptmm) REVERT: A 664 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8461 (tpp80) outliers start: 37 outliers final: 12 residues processed: 79 average time/residue: 0.6791 time to fit residues: 58.9585 Evaluate side-chains 61 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1261 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 119 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 46 optimal weight: 0.0870 chunk 112 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 chunk 54 optimal weight: 0.0070 chunk 105 optimal weight: 0.8980 chunk 93 optimal weight: 0.2980 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 674 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.097706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.066026 restraints weight = 26476.879| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.25 r_work: 0.2752 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14713 Z= 0.107 Angle : 0.483 9.059 20494 Z= 0.270 Chirality : 0.037 0.209 2345 Planarity : 0.003 0.045 2076 Dihedral : 19.198 151.616 3487 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.65 % Allowed : 20.35 % Favored : 78.00 % 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: 0.69 (0.23), residues: 1333 helix: 1.28 (0.21), residues: 650 sheet: -0.09 (0.48), residues: 120 loop : -0.30 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 783 TYR 0.010 0.001 TYR A1242 PHE 0.007 0.001 PHE A1038 TRP 0.013 0.001 TRP A1136 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.11 (14713) covalent geometry : angle 0.48311 / 0.27 (20494) hydrogen bonds : bond 0.03904 / 2.65 ( 626) hydrogen bonds : angle 4.19873 / 3.07 ( 1726) *********************** 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 68 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 275 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.7030 (pp) REVERT: A 523 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8380 (tt0) REVERT: A 548 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8848 (pt) REVERT: A 618 ASP cc_start: 0.8909 (t0) cc_final: 0.8647 (t0) REVERT: A 652 LYS cc_start: 0.8523 (pttt) cc_final: 0.8215 (ptmm) REVERT: A 664 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8408 (tpp80) REVERT: A 1150 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7969 (mp0) REVERT: A 1268 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.7726 (mp0) outliers start: 20 outliers final: 7 residues processed: 65 average time/residue: 0.6434 time to fit residues: 45.8635 Evaluate side-chains 60 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1261 GLN Chi-restraints excluded: chain A residue 1268 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 74 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 128 optimal weight: 0.5980 chunk 77 optimal weight: 0.0770 chunk 11 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 127 optimal weight: 0.3980 chunk 89 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.097453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.065810 restraints weight = 26540.996| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.26 r_work: 0.2749 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14713 Z= 0.122 Angle : 0.484 8.589 20494 Z= 0.268 Chirality : 0.037 0.203 2345 Planarity : 0.003 0.045 2076 Dihedral : 19.120 152.092 3487 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.82 % Allowed : 20.26 % Favored : 77.92 % 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: 0.76 (0.23), residues: 1333 helix: 1.35 (0.21), residues: 650 sheet: -0.05 (0.48), residues: 120 loop : -0.28 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 783 TYR 0.010 0.001 TYR A 155 PHE 0.006 0.001 PHE A 446 TRP 0.012 0.001 TRP A1136 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (14713) covalent geometry : angle 0.48380 / 0.27 (20494) hydrogen bonds : bond 0.03843 / 2.59 ( 626) hydrogen bonds : angle 4.14550 / 3.04 ( 1726) *********************** 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 72 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 171 GLU cc_start: 0.7746 (pm20) cc_final: 0.7401 (mp0) REVERT: A 275 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6997 (pp) REVERT: A 434 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8682 (ttmm) REVERT: A 523 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8340 (tt0) REVERT: A 548 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8852 (pt) REVERT: A 618 ASP cc_start: 0.8909 (t0) cc_final: 0.8659 (t0) REVERT: A 664 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8363 (tpp80) REVERT: A 827 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8327 (mm-30) REVERT: A 1150 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7962 (mp0) REVERT: A 1268 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7751 (mp0) outliers start: 22 outliers final: 8 residues processed: 71 average time/residue: 0.6897 time to fit residues: 53.7458 Evaluate side-chains 61 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1261 GLN Chi-restraints excluded: chain A residue 1268 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 130 optimal weight: 0.6980 chunk 141 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 77 optimal weight: 0.0170 chunk 19 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 108 optimal weight: 0.0030 overall best weight: 0.4228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.097992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.066339 restraints weight = 26553.201| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.27 r_work: 0.2761 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14713 Z= 0.113 Angle : 0.475 9.466 20494 Z= 0.264 Chirality : 0.037 0.204 2345 Planarity : 0.003 0.045 2076 Dihedral : 19.109 151.885 3487 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.99 % Allowed : 20.10 % Favored : 77.92 % 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: 0.82 (0.23), residues: 1333 helix: 1.40 (0.21), residues: 650 sheet: -0.03 (0.49), residues: 120 loop : -0.25 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 783 TYR 0.009 0.001 TYR A 155 PHE 0.007 0.001 PHE A 916 TRP 0.012 0.001 TRP A1136 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (14713) covalent geometry : angle 0.47499 / 0.26 (20494) hydrogen bonds : bond 0.03721 / 2.52 ( 626) hydrogen bonds : angle 4.10545 / 3.01 ( 1726) *********************** 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 72 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 48 time to evaluate : 0.516 Fit side-chains REVERT: A 171 GLU cc_start: 0.7795 (pm20) cc_final: 0.7456 (mp0) REVERT: A 523 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8338 (tt0) REVERT: A 548 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8840 (pt) REVERT: A 618 ASP cc_start: 0.8905 (t0) cc_final: 0.8648 (t0) REVERT: A 827 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8349 (mm-30) REVERT: A 1150 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8038 (mp0) REVERT: A 1268 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.7735 (mp0) outliers start: 24 outliers final: 7 residues processed: 71 average time/residue: 0.6515 time to fit residues: 51.1121 Evaluate side-chains 57 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1268 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 135 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.094452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.063021 restraints weight = 26823.412| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.23 r_work: 0.2679 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14713 Z= 0.230 Angle : 0.569 9.379 20494 Z= 0.307 Chirality : 0.042 0.200 2345 Planarity : 0.004 0.046 2076 Dihedral : 19.111 152.665 3487 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.99 % Allowed : 20.93 % 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: 0.62 (0.23), residues: 1333 helix: 1.20 (0.20), residues: 651 sheet: -0.17 (0.45), residues: 130 loop : -0.30 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 864 TYR 0.016 0.001 TYR A 362 PHE 0.009 0.001 PHE A1235 TRP 0.009 0.001 TRP A1136 HIS 0.006 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.23 (14713) covalent geometry : angle 0.56866 / 0.31 (20494) hydrogen bonds : bond 0.04444 / 2.99 ( 626) hydrogen bonds : angle 4.22618 / 3.09 ( 1726) ********************** 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 62 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.404 Fit side-chains REVERT: A 523 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8412 (tt0) REVERT: A 548 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8917 (pt) REVERT: A 618 ASP cc_start: 0.8931 (t0) cc_final: 0.8687 (t0) REVERT: A 1150 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7935 (mp0) REVERT: A 1191 LYS cc_start: 0.8833 (mmmt) cc_final: 0.8433 (mmtm) REVERT: A 1242 TYR cc_start: 0.8161 (t80) cc_final: 0.7880 (t80) outliers start: 12 outliers final: 6 residues processed: 60 average time/residue: 0.6902 time to fit residues: 45.1524 Evaluate side-chains 52 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 1188 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 102 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 106 optimal weight: 0.0070 chunk 115 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 674 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.096078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.064331 restraints weight = 26479.260| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.25 r_work: 0.2715 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14713 Z= 0.137 Angle : 0.505 9.657 20494 Z= 0.279 Chirality : 0.038 0.203 2345 Planarity : 0.003 0.046 2076 Dihedral : 19.152 151.992 3487 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.08 % Allowed : 20.84 % 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: 0.68 (0.23), residues: 1333 helix: 1.28 (0.21), residues: 650 sheet: -0.12 (0.48), residues: 120 loop : -0.32 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 783 TYR 0.010 0.001 TYR A 155 PHE 0.007 0.001 PHE A 446 TRP 0.012 0.001 TRP A1136 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (14713) covalent geometry : angle 0.50509 / 0.28 (20494) hydrogen bonds : bond 0.04013 / 2.71 ( 626) hydrogen bonds : angle 4.17210 / 3.06 ( 1726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4697.57 seconds wall clock time: 81 minutes 6.59 seconds (4866.59 seconds total)