Starting phenix.real_space_refine on Thu Jun 12 17:18:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8srs_40740/06_2025/8srs_40740.cif Found real_map, /net/cci-nas-00/data/ceres_data/8srs_40740/06_2025/8srs_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_40740/06_2025/8srs_40740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8srs_40740/06_2025/8srs_40740.map" model { file = "/net/cci-nas-00/data/ceres_data/8srs_40740/06_2025/8srs_40740.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8srs_40740/06_2025/8srs_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.43, per 1000 atoms: 0.74 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: 3.56 Conformation dependent library (CDL) restraints added in 1.3 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: 5.68 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: 7.95 Time building geometry restraints manager: 4.23 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: 9.310 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: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 42.450 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.860 ------------------------------------------------------------------------------- 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= 0.186 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 Details of bonding type rmsd hydrogen bonds : bond 0.14710 ( 626) hydrogen bonds : angle 6.04717 ( 1726) covalent geometry : bond 0.00416 (14713) covalent geometry : angle 0.83036 (20494) *********************** 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 : 1.445 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: 1.2508 time to fit residues: 86.7817 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 : 1.409 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.099603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.067585 restraints weight = 26836.061| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.34 r_work: 0.2780 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 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= 0.144 Angle : 0.533 9.263 20494 Z= 0.288 Chirality : 0.038 0.195 2345 Planarity : 0.004 0.049 2076 Dihedral : 19.283 153.977 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 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 626) hydrogen bonds : angle 4.52179 ( 1726) covalent geometry : bond 0.00318 (14713) covalent geometry : angle 0.53257 (20494) *********************** 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 : 1.408 Fit side-chains REVERT: A 618 ASP cc_start: 0.8922 (t0) cc_final: 0.8658 (t0) REVERT: A 627 GLU cc_start: 0.7417 (pm20) cc_final: 0.7204 (pt0) REVERT: A 664 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8393 (tpp80) REVERT: A 802 GLU cc_start: 0.8786 (pt0) cc_final: 0.8476 (pt0) REVERT: A 1268 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8434 (mt-10) REVERT: A 1297 HIS cc_start: 0.7876 (m170) cc_final: 0.7382 (m170) outliers start: 27 outliers final: 6 residues processed: 85 average time/residue: 1.6186 time to fit residues: 150.1138 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 : 1.559 ------------------------------------------------------------------------------- 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 28 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 105 optimal weight: 0.0570 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.097344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.065234 restraints weight = 26928.675| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.34 r_work: 0.2737 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14713 Z= 0.155 Angle : 0.509 9.192 20494 Z= 0.276 Chirality : 0.038 0.180 2345 Planarity : 0.003 0.044 2076 Dihedral : 19.219 153.476 3487 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.56 % Allowed : 18.69 % 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 (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: 0.30 (0.23), residues: 1333 helix: 0.84 (0.20), residues: 653 sheet: -0.19 (0.48), residues: 120 loop : -0.36 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1136 HIS 0.005 0.001 HIS A1297 PHE 0.008 0.001 PHE A 164 TYR 0.023 0.001 TYR A1242 ARG 0.005 0.000 ARG A 783 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 626) hydrogen bonds : angle 4.29778 ( 1726) covalent geometry : bond 0.00349 (14713) covalent geometry : angle 0.50922 (20494) *********************** 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 89 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 58 time to evaluate : 1.842 Fit side-chains REVERT: A 523 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8431 (tt0) REVERT: A 548 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8847 (pt) REVERT: A 618 ASP cc_start: 0.8914 (t0) cc_final: 0.8677 (t0) REVERT: A 652 LYS cc_start: 0.8575 (pttt) cc_final: 0.8322 (ptmm) REVERT: A 664 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8443 (tpp80) REVERT: A 1268 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.7735 (mp0) outliers start: 31 outliers final: 9 residues processed: 80 average time/residue: 1.4708 time to fit residues: 128.9488 Evaluate side-chains 63 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 495 MET 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 130 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.092520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.060689 restraints weight = 26718.464| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 2.23 r_work: 0.2645 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 14713 Z= 0.285 Angle : 0.590 9.738 20494 Z= 0.315 Chirality : 0.042 0.179 2345 Planarity : 0.004 0.047 2076 Dihedral : 19.330 154.371 3487 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.64 % Allowed : 18.11 % 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: 0.21 (0.23), residues: 1333 helix: 0.79 (0.20), residues: 651 sheet: -0.44 (0.44), residues: 130 loop : -0.37 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1136 HIS 0.007 0.001 HIS A 167 PHE 0.011 0.002 PHE A 498 TYR 0.016 0.002 TYR A 362 ARG 0.005 0.001 ARG A 976 Details of bonding type rmsd hydrogen bonds : bond 0.04704 ( 626) hydrogen bonds : angle 4.40658 ( 1726) covalent geometry : bond 0.00654 (14713) covalent geometry : angle 0.59009 (20494) *********************** 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 97 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 53 time to evaluate : 1.342 Fit side-chains REVERT: A 523 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8491 (tt0) REVERT: A 548 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8907 (pt) REVERT: A 618 ASP cc_start: 0.8895 (t0) cc_final: 0.8654 (t0) REVERT: A 627 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7755 (pt0) REVERT: A 631 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8790 (mtp) REVERT: A 652 LYS cc_start: 0.8638 (pttt) cc_final: 0.8375 (ptmm) REVERT: A 879 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7073 (mtp) REVERT: A 1191 LYS cc_start: 0.8844 (mmmt) cc_final: 0.8418 (mmtm) outliers start: 44 outliers final: 11 residues processed: 91 average time/residue: 1.3600 time to fit residues: 136.1895 Evaluate side-chains 64 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 1.385 ------------------------------------------------------------------------------- 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 495 MET 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 627 GLU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 647 VAL 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 1188 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 69 optimal weight: 0.0270 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 75 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN A 690 ASN ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.096475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.064888 restraints weight = 26602.325| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.26 r_work: 0.2731 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14713 Z= 0.115 Angle : 0.489 7.991 20494 Z= 0.264 Chirality : 0.036 0.174 2345 Planarity : 0.003 0.045 2076 Dihedral : 19.130 154.144 3487 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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: 0.49 (0.23), residues: 1333 helix: 1.10 (0.20), residues: 650 sheet: -0.28 (0.47), residues: 120 loop : -0.36 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1136 HIS 0.005 0.001 HIS A1297 PHE 0.007 0.001 PHE A 446 TYR 0.009 0.001 TYR A 155 ARG 0.002 0.000 ARG A 783 Details of bonding type rmsd hydrogen bonds : bond 0.03617 ( 626) hydrogen bonds : angle 4.17157 ( 1726) covalent geometry : bond 0.00248 (14713) covalent geometry : angle 0.48937 (20494) *********************** 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 79 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 51 time to evaluate : 2.108 Fit side-chains REVERT: A 548 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8893 (pt) REVERT: A 618 ASP cc_start: 0.8894 (t0) cc_final: 0.8644 (t0) REVERT: A 652 LYS cc_start: 0.8564 (pttt) cc_final: 0.8263 (ptmm) REVERT: A 1257 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8430 (mm) REVERT: A 1268 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8343 (mt-10) outliers start: 28 outliers final: 6 residues processed: 70 average time/residue: 1.5102 time to fit residues: 117.8799 Evaluate side-chains 56 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 574 CYS 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 1257 LEU 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 122 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.093779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.062150 restraints weight = 26887.212| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.25 r_work: 0.2661 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14713 Z= 0.201 Angle : 0.524 8.704 20494 Z= 0.279 Chirality : 0.039 0.175 2345 Planarity : 0.003 0.046 2076 Dihedral : 19.039 154.403 3487 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.81 % Allowed : 18.86 % 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: 0.48 (0.23), residues: 1333 helix: 1.09 (0.20), residues: 651 sheet: -0.27 (0.47), residues: 120 loop : -0.36 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1136 HIS 0.005 0.001 HIS A 167 PHE 0.008 0.001 PHE A 164 TYR 0.013 0.001 TYR A 362 ARG 0.003 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.04048 ( 626) hydrogen bonds : angle 4.19354 ( 1726) covalent geometry : bond 0.00456 (14713) covalent geometry : angle 0.52363 (20494) *********************** 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 80 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 46 time to evaluate : 1.369 Fit side-chains REVERT: A 321 MET cc_start: 0.9263 (mmt) cc_final: 0.9057 (mmt) REVERT: A 523 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8430 (tt0) REVERT: A 548 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8897 (pt) REVERT: A 618 ASP cc_start: 0.8912 (t0) cc_final: 0.8645 (t0) REVERT: A 652 LYS cc_start: 0.8592 (pttt) cc_final: 0.8377 (ptmm) REVERT: A 671 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.7670 (mtp85) REVERT: A 879 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.7085 (mtp) REVERT: A 1268 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8395 (mt-10) outliers start: 34 outliers final: 10 residues processed: 74 average time/residue: 1.4440 time to fit residues: 118.2242 Evaluate side-chains 58 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU 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 548 ILE 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 627 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 67 optimal weight: 0.0000 chunk 37 optimal weight: 0.2980 chunk 111 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 141 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.095658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.064290 restraints weight = 26665.119| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.24 r_work: 0.2716 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2618 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= 0.134 Angle : 0.487 8.736 20494 Z= 0.261 Chirality : 0.037 0.174 2345 Planarity : 0.003 0.045 2076 Dihedral : 18.966 154.134 3487 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.89 % Allowed : 18.20 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.23 (0.21), residues: 650 sheet: -0.24 (0.47), residues: 120 loop : -0.33 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1136 HIS 0.003 0.001 HIS A 328 PHE 0.007 0.001 PHE A 446 TYR 0.010 0.001 TYR A 155 ARG 0.002 0.000 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 626) hydrogen bonds : angle 4.10874 ( 1726) covalent geometry : bond 0.00299 (14713) covalent geometry : angle 0.48750 (20494) *********************** 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 80 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 45 time to evaluate : 1.398 Fit side-chains REVERT: A 321 MET cc_start: 0.9244 (mmt) cc_final: 0.9041 (mmt) REVERT: A 434 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8711 (ttmm) REVERT: A 523 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8407 (tt0) REVERT: A 548 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8882 (pt) REVERT: A 618 ASP cc_start: 0.8909 (t0) cc_final: 0.8637 (t0) REVERT: A 646 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8558 (tptt) REVERT: A 652 LYS cc_start: 0.8567 (pttt) cc_final: 0.8347 (ptmm) REVERT: A 671 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7616 (mtp85) REVERT: A 879 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.7078 (mtp) REVERT: A 1068 GLU cc_start: 0.8808 (mp0) cc_final: 0.7875 (tm-30) REVERT: A 1268 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8356 (mt-10) outliers start: 35 outliers final: 12 residues processed: 76 average time/residue: 1.5664 time to fit residues: 132.9683 Evaluate side-chains 64 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 225 LEU 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 548 ILE 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 627 GLU 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 870 VAL Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain A residue 890 LYS 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 85 optimal weight: 0.3980 chunk 137 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 21 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.095293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.063810 restraints weight = 26462.989| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.25 r_work: 0.2710 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2714 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= 0.141 Angle : 0.484 8.860 20494 Z= 0.260 Chirality : 0.037 0.174 2345 Planarity : 0.003 0.045 2076 Dihedral : 18.933 154.139 3487 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.99 % Allowed : 19.02 % 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 (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: 0.66 (0.23), residues: 1333 helix: 1.27 (0.21), residues: 650 sheet: -0.18 (0.48), residues: 120 loop : -0.31 (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 0.009 0.001 PHE A 290 TYR 0.010 0.001 TYR A 155 ARG 0.003 0.000 ARG A 820 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 626) hydrogen bonds : angle 4.09357 ( 1726) covalent geometry : bond 0.00318 (14713) covalent geometry : angle 0.48434 (20494) *********************** 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 70 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 46 time to evaluate : 1.525 Fit side-chains REVERT: A 523 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8404 (tt0) REVERT: A 548 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8870 (pt) REVERT: A 618 ASP cc_start: 0.8905 (t0) cc_final: 0.8637 (t0) REVERT: A 646 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8584 (tptt) REVERT: A 652 LYS cc_start: 0.8550 (pttt) cc_final: 0.8303 (ptmm) REVERT: A 671 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7579 (mtp85) REVERT: A 879 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.7029 (mtp) REVERT: A 1268 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8318 (mt-10) outliers start: 24 outliers final: 11 residues processed: 66 average time/residue: 1.5189 time to fit residues: 110.1852 Evaluate side-chains 61 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 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 548 ILE 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 870 VAL Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain A residue 890 LYS 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 76 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.093634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.061981 restraints weight = 26474.281| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.26 r_work: 0.2665 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14713 Z= 0.194 Angle : 0.518 8.937 20494 Z= 0.276 Chirality : 0.039 0.175 2345 Planarity : 0.003 0.046 2076 Dihedral : 18.979 154.284 3487 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.82 % Allowed : 19.19 % 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 (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: 0.54 (0.23), residues: 1333 helix: 1.15 (0.21), residues: 651 sheet: -0.21 (0.47), residues: 120 loop : -0.37 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1136 HIS 0.004 0.001 HIS A 167 PHE 0.007 0.001 PHE A 491 TYR 0.012 0.001 TYR A 362 ARG 0.003 0.000 ARG A 820 Details of bonding type rmsd hydrogen bonds : bond 0.03991 ( 626) hydrogen bonds : angle 4.17524 ( 1726) covalent geometry : bond 0.00442 (14713) covalent geometry : angle 0.51834 (20494) *********************** 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 69 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 1.722 Fit side-chains REVERT: A 523 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8425 (tt0) REVERT: A 548 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8887 (pt) REVERT: A 618 ASP cc_start: 0.8902 (t0) cc_final: 0.8636 (t0) REVERT: A 646 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8588 (tptt) REVERT: A 652 LYS cc_start: 0.8587 (pttt) cc_final: 0.8329 (ptmm) REVERT: A 671 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7678 (mtp85) REVERT: A 879 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7108 (mtp) REVERT: A 1068 GLU cc_start: 0.8801 (mp0) cc_final: 0.7789 (tm-30) REVERT: A 1268 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8354 (mt-10) outliers start: 22 outliers final: 9 residues processed: 66 average time/residue: 1.9036 time to fit residues: 138.2176 Evaluate side-chains 60 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 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 548 ILE 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 870 VAL Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 879 MET 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 37 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 141 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.095344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.064036 restraints weight = 26460.329| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.24 r_work: 0.2710 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2861 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= 0.140 Angle : 0.489 9.559 20494 Z= 0.262 Chirality : 0.037 0.174 2345 Planarity : 0.003 0.045 2076 Dihedral : 18.937 154.068 3487 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.82 % Allowed : 19.44 % 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 (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: 0.62 (0.23), residues: 1333 helix: 1.20 (0.20), residues: 657 sheet: -0.18 (0.48), residues: 120 loop : -0.31 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1136 HIS 0.003 0.001 HIS A 328 PHE 0.007 0.001 PHE A 290 TYR 0.010 0.001 TYR A 155 ARG 0.005 0.000 ARG A1317 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 626) hydrogen bonds : angle 4.10975 ( 1726) covalent geometry : bond 0.00314 (14713) covalent geometry : angle 0.48864 (20494) ********************** 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 70 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 2.349 Fit side-chains REVERT: A 523 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8389 (tt0) REVERT: A 548 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8879 (pt) REVERT: A 618 ASP cc_start: 0.8896 (t0) cc_final: 0.8623 (t0) REVERT: A 646 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8596 (tptt) REVERT: A 652 LYS cc_start: 0.8568 (pttt) cc_final: 0.8324 (ptmm) REVERT: A 671 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7590 (mtp85) REVERT: A 879 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7020 (mtp) REVERT: A 1268 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8335 (mt-10) outliers start: 22 outliers final: 10 residues processed: 67 average time/residue: 1.7404 time to fit residues: 128.7363 Evaluate side-chains 60 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 1.360 ------------------------------------------------------------------------------- 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 548 ILE 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 870 VAL Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 952 GLU 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 90 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 0.0060 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 77 optimal weight: 0.0770 overall best weight: 0.4754 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.096178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.064954 restraints weight = 26534.507| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.25 r_work: 0.2736 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2900 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= 0.123 Angle : 0.478 9.695 20494 Z= 0.256 Chirality : 0.036 0.174 2345 Planarity : 0.003 0.044 2076 Dihedral : 18.886 153.819 3487 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.90 % Allowed : 19.69 % 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: 0.69 (0.23), residues: 1333 helix: 1.28 (0.21), residues: 657 sheet: -0.15 (0.48), residues: 120 loop : -0.30 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1136 HIS 0.004 0.001 HIS A 328 PHE 0.008 0.001 PHE A1327 TYR 0.009 0.001 TYR A 155 ARG 0.005 0.000 ARG A1317 Details of bonding type rmsd hydrogen bonds : bond 0.03431 ( 626) hydrogen bonds : angle 4.03783 ( 1726) covalent geometry : bond 0.00273 (14713) covalent geometry : angle 0.47782 (20494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10155.82 seconds wall clock time: 179 minutes 14.79 seconds (10754.79 seconds total)