Starting phenix.real_space_refine on Mon Dec 30 22:24:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8srs_40740/12_2024/8srs_40740.cif Found real_map, /net/cci-nas-00/data/ceres_data/8srs_40740/12_2024/8srs_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8srs_40740/12_2024/8srs_40740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8srs_40740/12_2024/8srs_40740.map" model { file = "/net/cci-nas-00/data/ceres_data/8srs_40740/12_2024/8srs_40740.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8srs_40740/12_2024/8srs_40740.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 10.86, per 1000 atoms: 0.77 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: 3.88 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 5.94 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: 7.56 Time building geometry restraints manager: 3.94 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=" CB PHE A 185 " pdb=" CG PHE A 185 " ideal model delta sigma weight residual 1.502 1.548 -0.046 2.30e-02 1.89e+03 4.01e+00 bond pdb=" CB LYS A 948 " pdb=" CG LYS A 948 " ideal model delta sigma weight residual 1.520 1.580 -0.060 3.00e-02 1.11e+03 3.99e+00 bond pdb=" CG LYS A 948 " pdb=" CD LYS A 948 " ideal model delta sigma weight residual 1.520 1.578 -0.058 3.00e-02 1.11e+03 3.78e+00 bond pdb=" CB LYS A1155 " pdb=" CG LYS A1155 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.32e+00 bond pdb=" CB GLU A1253 " pdb=" CG GLU A1253 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.13e+00 ... (remaining 14708 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 20172 2.69 - 5.39: 248 5.39 - 8.08: 56 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=" CB LYS A1151 " pdb=" CG LYS A1151 " pdb=" CD LYS A1151 " ideal model delta sigma weight residual 111.30 122.09 -10.79 2.30e+00 1.89e-01 2.20e+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: 1873 0.052 - 0.103: 376 0.103 - 0.155: 77 0.155 - 0.206: 14 0.206 - 0.257: 5 Chirality restraints: 2345 Sorted by residual: 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=" 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 2.46 2.21 0.24 2.00e-01 2.50e+01 1.50e+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: 10.270 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: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 42.040 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:13.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14713 Z= 0.264 Angle : 0.830 13.463 20494 Z= 0.429 Chirality : 0.045 0.257 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.025 0.002 TRP A1136 HIS 0.028 0.002 HIS A1297 PHE 0.028 0.002 PHE A1327 TYR 0.016 0.002 TYR A 5 ARG 0.014 0.001 ARG A 884 *********************** 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 : 1.485 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: 1.3301 time to fit residues: 92.0677 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 : 1.416 ------------------------------------------------------------------------------- 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 123 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 74 optimal weight: 0.0470 chunk 59 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 132 optimal weight: 0.0670 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1057 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= 0.198 Angle : 0.533 9.263 20494 Z= 0.288 Chirality : 0.038 0.195 2345 Planarity : 0.004 0.049 2076 Dihedral : 19.284 153.978 3492 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.23 % Allowed : 18.94 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.22), residues: 1333 helix: 0.53 (0.20), residues: 648 sheet: -0.34 (0.49), residues: 120 loop : -0.40 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1136 HIS 0.007 0.001 HIS A1297 PHE 0.015 0.001 PHE A1327 TYR 0.011 0.001 TYR A 362 ARG 0.007 0.001 ARG A 653 *********************** 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 88 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 1.528 Fit side-chains REVERT: A 618 ASP cc_start: 0.8872 (t0) cc_final: 0.8623 (t0) REVERT: A 627 GLU cc_start: 0.7355 (pm20) cc_final: 0.7127 (pt0) REVERT: A 664 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8219 (tpp80) REVERT: A 802 GLU cc_start: 0.8610 (pt0) cc_final: 0.8307 (pt0) REVERT: A 1268 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8270 (mt-10) REVERT: A 1297 HIS cc_start: 0.7849 (m170) cc_final: 0.7374 (m170) outliers start: 27 outliers final: 6 residues processed: 85 average time/residue: 1.6131 time to fit residues: 149.9685 Evaluate side-chains 57 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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 664 ARG Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 1188 LYS 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 73 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 chunk 132 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 GLN ** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14713 Z= 0.270 Angle : 0.537 9.549 20494 Z= 0.289 Chirality : 0.039 0.180 2345 Planarity : 0.004 0.045 2076 Dihedral : 19.266 153.592 3487 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.81 % Allowed : 18.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.23), residues: 1333 helix: 0.77 (0.20), residues: 653 sheet: -0.26 (0.48), residues: 120 loop : -0.38 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1136 HIS 0.007 0.001 HIS A1297 PHE 0.012 0.001 PHE A1327 TYR 0.016 0.001 TYR A1242 ARG 0.011 0.001 ARG A 221 *********************** 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 91 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 57 time to evaluate : 1.418 Fit side-chains REVERT: A 434 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8636 (ttmm) REVERT: A 436 ASN cc_start: 0.8207 (OUTLIER) cc_final: 0.7658 (p0) REVERT: A 523 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8301 (tt0) REVERT: A 618 ASP cc_start: 0.8842 (t0) cc_final: 0.8581 (t0) REVERT: A 652 LYS cc_start: 0.8480 (pttt) cc_final: 0.8185 (ptmm) REVERT: A 664 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8294 (tpp80) REVERT: A 837 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8255 (t0) REVERT: A 1261 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8071 (pp30) outliers start: 34 outliers final: 11 residues processed: 85 average time/residue: 1.4767 time to fit residues: 137.7282 Evaluate side-chains 65 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 495 MET 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 647 VAL Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 738 LEU 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 1116 SER Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1261 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 GLN A 690 ASN A1297 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14713 Z= 0.266 Angle : 0.517 8.966 20494 Z= 0.277 Chirality : 0.039 0.175 2345 Planarity : 0.003 0.046 2076 Dihedral : 19.224 154.368 3487 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.39 % Allowed : 18.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.23), residues: 1333 helix: 0.99 (0.20), residues: 650 sheet: -0.28 (0.47), residues: 120 loop : -0.32 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1136 HIS 0.004 0.001 HIS A 167 PHE 0.008 0.001 PHE A 164 TYR 0.011 0.001 TYR A 362 ARG 0.003 0.000 ARG A1303 *********************** 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 94 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 53 time to evaluate : 1.516 Fit side-chains REVERT: A 618 ASP cc_start: 0.8848 (t0) cc_final: 0.8548 (t0) REVERT: A 652 LYS cc_start: 0.8491 (pttt) cc_final: 0.8179 (ptmm) REVERT: A 664 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8347 (tpp80) REVERT: A 1188 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8407 (ptpp) REVERT: A 1191 LYS cc_start: 0.8810 (mmmt) cc_final: 0.8383 (mmtm) REVERT: A 1254 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8634 (mm-40) REVERT: A 1268 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8233 (mt-10) outliers start: 41 outliers final: 9 residues processed: 88 average time/residue: 1.3793 time to fit residues: 133.7726 Evaluate side-chains 59 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 664 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 1116 SER Chi-restraints excluded: chain A residue 1188 LYS 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 117 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 0.0070 chunk 105 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 126 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14713 Z= 0.179 Angle : 0.484 8.481 20494 Z= 0.260 Chirality : 0.037 0.174 2345 Planarity : 0.003 0.045 2076 Dihedral : 19.067 154.085 3487 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.32 % Allowed : 19.52 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.23), residues: 1333 helix: 1.18 (0.21), residues: 651 sheet: -0.20 (0.48), residues: 120 loop : -0.28 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1136 HIS 0.004 0.001 HIS A 328 PHE 0.007 0.001 PHE A 446 TYR 0.009 0.001 TYR A 155 ARG 0.003 0.000 ARG A1303 *********************** 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 76 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 48 time to evaluate : 1.509 Fit side-chains REVERT: A 618 ASP cc_start: 0.8860 (t0) cc_final: 0.8574 (t0) REVERT: A 664 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8348 (tpp80) REVERT: A 1254 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8683 (mm-40) REVERT: A 1268 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8163 (mt-10) outliers start: 28 outliers final: 8 residues processed: 70 average time/residue: 1.4746 time to fit residues: 114.1355 Evaluate side-chains 53 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 551 LEU 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 802 GLU Chi-restraints excluded: chain A residue 1116 SER 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 47 optimal weight: 0.5980 chunk 127 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 0.0570 chunk 141 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2495 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= 0.213 Angle : 0.488 8.355 20494 Z= 0.261 Chirality : 0.037 0.174 2345 Planarity : 0.003 0.045 2076 Dihedral : 19.021 154.198 3487 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.23), residues: 1333 helix: 1.25 (0.21), residues: 651 sheet: -0.17 (0.48), residues: 120 loop : -0.26 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1136 HIS 0.004 0.001 HIS A 328 PHE 0.007 0.001 PHE A 164 TYR 0.011 0.001 TYR A 155 ARG 0.003 0.000 ARG A 820 *********************** 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 70 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 46 time to evaluate : 1.359 Fit side-chains REVERT: A 523 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8230 (tt0) REVERT: A 618 ASP cc_start: 0.8849 (t0) cc_final: 0.8554 (t0) REVERT: A 664 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8343 (tpp80) REVERT: A 671 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7555 (mtp85) REVERT: A 1254 GLN cc_start: 0.8958 (mm-40) cc_final: 0.8672 (mm-40) REVERT: A 1268 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8149 (mt-10) outliers start: 24 outliers final: 9 residues processed: 68 average time/residue: 1.4950 time to fit residues: 111.9578 Evaluate side-chains 55 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 551 LEU 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 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 1116 SER Chi-restraints excluded: chain A residue 1268 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 118 optimal weight: 0.0980 chunk 78 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14713 Z= 0.178 Angle : 0.475 8.697 20494 Z= 0.254 Chirality : 0.036 0.174 2345 Planarity : 0.003 0.044 2076 Dihedral : 18.951 154.080 3487 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.15 % Allowed : 19.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.23), residues: 1333 helix: 1.34 (0.21), residues: 650 sheet: -0.13 (0.48), residues: 120 loop : -0.24 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1136 HIS 0.004 0.001 HIS A 328 PHE 0.007 0.001 PHE A 290 TYR 0.010 0.001 TYR A 155 ARG 0.003 0.000 ARG A 820 *********************** 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 73 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 47 time to evaluate : 1.467 Fit side-chains REVERT: A 434 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8553 (ttmm) REVERT: A 523 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: A 534 MET cc_start: 0.7889 (pmt) cc_final: 0.7660 (pmt) REVERT: A 618 ASP cc_start: 0.8849 (t0) cc_final: 0.8550 (t0) REVERT: A 664 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8349 (tpp80) REVERT: A 671 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7552 (mtp85) REVERT: A 1068 GLU cc_start: 0.8606 (mp0) cc_final: 0.7816 (tm-30) REVERT: A 1254 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8702 (mm-40) REVERT: A 1268 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8128 (mt-10) outliers start: 26 outliers final: 6 residues processed: 69 average time/residue: 1.4555 time to fit residues: 111.3739 Evaluate side-chains 54 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LYS 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 559 VAL Chi-restraints excluded: chain A residue 574 CYS 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 1116 SER 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 87 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 69 optimal weight: 0.0570 chunk 13 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14713 Z= 0.197 Angle : 0.476 8.546 20494 Z= 0.255 Chirality : 0.037 0.174 2345 Planarity : 0.003 0.045 2076 Dihedral : 18.932 154.107 3487 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.57 % Allowed : 20.18 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.23), residues: 1333 helix: 1.32 (0.21), residues: 651 sheet: -0.13 (0.48), residues: 120 loop : -0.23 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1136 HIS 0.003 0.001 HIS A 328 PHE 0.008 0.001 PHE A 290 TYR 0.010 0.001 TYR A 155 ARG 0.003 0.000 ARG A1317 *********************** 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 65 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 1.465 Fit side-chains REVERT: A 434 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8527 (ttmm) REVERT: A 523 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8239 (tt0) REVERT: A 534 MET cc_start: 0.7920 (pmt) cc_final: 0.7698 (pmt) REVERT: A 618 ASP cc_start: 0.8833 (t0) cc_final: 0.8542 (t0) REVERT: A 646 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8616 (tptt) REVERT: A 671 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7559 (mtp85) REVERT: A 1068 GLU cc_start: 0.8593 (mp0) cc_final: 0.7810 (tm-30) REVERT: A 1254 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8693 (mm-40) REVERT: A 1268 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8135 (mt-10) outliers start: 19 outliers final: 9 residues processed: 63 average time/residue: 1.5172 time to fit residues: 106.1875 Evaluate side-chains 57 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LYS 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 646 LYS 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 1116 SER 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 134 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 78 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 40 optimal weight: 0.0050 chunk 118 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14713 Z= 0.186 Angle : 0.474 9.217 20494 Z= 0.253 Chirality : 0.036 0.174 2345 Planarity : 0.003 0.045 2076 Dihedral : 18.916 153.985 3487 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.57 % Allowed : 20.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.23), residues: 1333 helix: 1.30 (0.20), residues: 657 sheet: -0.11 (0.49), residues: 120 loop : -0.25 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1136 HIS 0.004 0.001 HIS A 328 PHE 0.006 0.001 PHE A 446 TYR 0.010 0.001 TYR A 155 ARG 0.005 0.000 ARG A1317 *********************** 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 63 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 1.466 Fit side-chains REVERT: A 523 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: A 618 ASP cc_start: 0.8832 (t0) cc_final: 0.8539 (t0) REVERT: A 646 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8611 (tptt) REVERT: A 671 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.7444 (mtp85) REVERT: A 1068 GLU cc_start: 0.8608 (mp0) cc_final: 0.7709 (tm-30) REVERT: A 1254 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8701 (mm-40) REVERT: A 1268 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8103 (mt-10) outliers start: 19 outliers final: 8 residues processed: 61 average time/residue: 1.4235 time to fit residues: 96.5600 Evaluate side-chains 54 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 559 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 646 LYS 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 1116 SER 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 138 optimal weight: 2.9990 chunk 84 optimal weight: 0.1980 chunk 65 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14713 Z= 0.226 Angle : 0.488 9.610 20494 Z= 0.261 Chirality : 0.037 0.174 2345 Planarity : 0.003 0.045 2076 Dihedral : 18.930 154.072 3487 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.16 % Allowed : 20.60 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.23), residues: 1333 helix: 1.27 (0.20), residues: 657 sheet: -0.11 (0.48), residues: 120 loop : -0.25 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1136 HIS 0.004 0.001 HIS A 328 PHE 0.008 0.001 PHE A 290 TYR 0.011 0.001 TYR A 155 ARG 0.005 0.000 ARG A1317 ********************** 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 57 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 1.539 Fit side-chains REVERT: A 523 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8244 (tt0) REVERT: A 618 ASP cc_start: 0.8838 (t0) cc_final: 0.8544 (t0) REVERT: A 646 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8622 (tptt) REVERT: A 671 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7562 (mtp85) REVERT: A 1068 GLU cc_start: 0.8634 (mp0) cc_final: 0.7753 (tm-30) REVERT: A 1254 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8694 (mm-40) REVERT: A 1268 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8136 (mt-10) outliers start: 14 outliers final: 7 residues processed: 55 average time/residue: 1.5358 time to fit residues: 93.4746 Evaluate side-chains 53 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 559 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 671 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 1268 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 116 optimal weight: 0.1980 chunk 48 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3420 r_free = 0.3420 target = 0.094458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.063055 restraints weight = 26406.142| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.17 r_work: 0.2703 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14713 Z= 0.214 Angle : 0.485 9.574 20494 Z= 0.259 Chirality : 0.037 0.175 2345 Planarity : 0.003 0.045 2076 Dihedral : 18.921 154.016 3487 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.08 % Allowed : 20.68 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.23), residues: 1333 helix: 1.25 (0.20), residues: 657 sheet: -0.11 (0.49), residues: 120 loop : -0.26 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1136 HIS 0.004 0.001 HIS A 328 PHE 0.006 0.001 PHE A 164 TYR 0.011 0.001 TYR A 155 ARG 0.005 0.000 ARG A1317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3612.35 seconds wall clock time: 67 minutes 2.43 seconds (4022.43 seconds total)