Starting phenix.real_space_refine on Tue Dec 31 03:28:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8umf_42378/12_2024/8umf_42378.cif Found real_map, /net/cci-nas-00/data/ceres_data/8umf_42378/12_2024/8umf_42378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8umf_42378/12_2024/8umf_42378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8umf_42378/12_2024/8umf_42378.map" model { file = "/net/cci-nas-00/data/ceres_data/8umf_42378/12_2024/8umf_42378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8umf_42378/12_2024/8umf_42378.cif" } resolution = 2.9 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= 0.014 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 172 5.49 5 Mg 7 5.21 5 S 37 5.16 5 C 8725 2.51 5 N 2621 2.21 5 O 3242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 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: 14804 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 11159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1376, 11159 Classifications: {'peptide': 1376} Link IDs: {'PTRANS': 38, 'TRANS': 1337} Chain breaks: 3 Chain: "B" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2568 Classifications: {'RNA': 121} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 58, 'rna3p_pyr': 48} Link IDs: {'rna2p': 15, 'rna3p': 105} Chain: "C" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 372 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "D" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 395 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "E" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 303 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 10.54, per 1000 atoms: 0.71 Number of scatterers: 14804 At special positions: 0 Unit cell: (91.53, 113.4, 139.32, 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 37 16.00 P 172 15.00 Mg 7 11.99 O 3242 8.00 N 2621 7.00 C 8725 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: 4.36 Conformation dependent library (CDL) restraints added in 1.6 seconds 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2628 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 10 sheets defined 55.3% alpha, 10.3% beta 65 base pairs and 119 stacking pairs defined. Time for finding SS restraints: 7.15 Creating SS restraints... Processing helix chain 'A' and resid 50 through 82 Processing helix chain 'A' and resid 86 through 98 Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.518A pdb=" N LEU A 114 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 removed outlier: 3.775A pdb=" N PHE A 121 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A 123 " --> pdb=" O GLY A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 148 Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 167 through 178 Processing helix chain 'A' and resid 181 through 200 removed outlier: 3.632A pdb=" N SER A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.651A pdb=" N GLU A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 248 Processing helix chain 'A' and resid 250 through 259 Processing helix chain 'A' and resid 260 through 266 removed outlier: 3.634A pdb=" N ASN A 265 " --> pdb=" O SER A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 282 Processing helix chain 'A' and resid 290 through 303 removed outlier: 3.541A pdb=" N ASN A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 350 through 361 removed outlier: 3.841A pdb=" N ILE A 354 " --> pdb=" O ASP A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 397 through 412 Processing helix chain 'A' and resid 421 through 426 Processing helix chain 'A' and resid 432 through 448 removed outlier: 4.025A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 471 Processing helix chain 'A' and resid 472 through 477 removed outlier: 5.426A pdb=" N PHE A 475 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 506 removed outlier: 3.556A pdb=" N ARG A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 517 Processing helix chain 'A' and resid 526 through 541 Processing helix chain 'A' and resid 543 through 557 Processing helix chain 'A' and resid 562 through 586 Processing helix chain 'A' and resid 589 through 594 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 620 through 632 Processing helix chain 'A' and resid 652 through 674 Processing helix chain 'A' and resid 699 through 707 removed outlier: 4.281A pdb=" N LYS A 705 " --> pdb=" O ALA A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 738 removed outlier: 3.834A pdb=" N SER A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 769 Processing helix chain 'A' and resid 774 through 776 No H-bonds generated for 'chain 'A' and resid 774 through 776' Processing helix chain 'A' and resid 782 through 788 Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 800 through 809 Processing helix chain 'A' and resid 812 through 826 Processing helix chain 'A' and resid 828 through 834 Processing helix chain 'A' and resid 835 through 838 Processing helix chain 'A' and resid 839 through 849 Processing helix chain 'A' and resid 850 through 852 No H-bonds generated for 'chain 'A' and resid 850 through 852' Processing helix chain 'A' and resid 856 through 866 removed outlier: 3.561A pdb=" N ARG A 864 " --> pdb=" O ARG A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 873 Processing helix chain 'A' and resid 877 through 893 Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 913 through 920 Processing helix chain 'A' and resid 920 through 928 Processing helix chain 'A' and resid 929 through 932 Processing helix chain 'A' and resid 940 through 956 removed outlier: 4.102A pdb=" N HIS A 944 " --> pdb=" O PRO A 940 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA A 945 " --> pdb=" O ILE A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 966 removed outlier: 4.092A pdb=" N VAL A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 981 removed outlier: 3.588A pdb=" N ASN A 976 " --> pdb=" O ALA A 972 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1007 Processing helix chain 'A' and resid 1046 through 1052 Processing helix chain 'A' and resid 1074 through 1088 removed outlier: 3.683A pdb=" N PHE A1086 " --> pdb=" O LEU A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1104 Processing helix chain 'A' and resid 1126 through 1131 Processing helix chain 'A' and resid 1132 through 1135 Processing helix chain 'A' and resid 1156 through 1166 removed outlier: 4.075A pdb=" N GLU A1160 " --> pdb=" O PRO A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1197 removed outlier: 3.529A pdb=" N LEU A1192 " --> pdb=" O ASP A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1333 Processing helix chain 'A' and resid 1338 through 1342 Processing helix chain 'A' and resid 1349 through 1361 Processing helix chain 'A' and resid 1368 through 1370 No H-bonds generated for 'chain 'A' and resid 1368 through 1370' Processing helix chain 'A' and resid 1392 through 1409 removed outlier: 3.597A pdb=" N GLN A1409 " --> pdb=" O VAL A1405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 903 through 912 removed outlier: 3.906A pdb=" N GLU A 690 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA A 35 " --> pdb=" O ASN A 989 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE A 991 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL A 37 " --> pdb=" O ILE A 991 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AA3, first strand: chain 'A' and resid 519 through 521 removed outlier: 7.110A pdb=" N SER A 524 " --> pdb=" O VAL A 520 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 754 through 757 Processing sheet with id=AA5, first strand: chain 'A' and resid 1215 through 1218 removed outlier: 6.411A pdb=" N ASN A1110 " --> pdb=" O ILE A1014 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N ILE A1014 " --> pdb=" O ASN A1110 " (cutoff:3.500A) removed outlier: 13.686A pdb=" N SER A1112 " --> pdb=" O GLU A1012 " (cutoff:3.500A) removed outlier: 18.968A pdb=" N GLU A1012 " --> pdb=" O SER A1112 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLY A1013 " --> pdb=" O MET A1243 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N MET A1243 " --> pdb=" O GLY A1013 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A1241 " --> pdb=" O PHE A1015 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLU A1017 " --> pdb=" O TYR A1239 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N TYR A1239 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 15.770A pdb=" N PHE A1019 " --> pdb=" O ASP A1237 " (cutoff:3.500A) removed outlier: 20.399A pdb=" N ASP A1237 " --> pdb=" O PHE A1019 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1040 through 1042 Processing sheet with id=AA7, first strand: chain 'A' and resid 1117 through 1118 Processing sheet with id=AA8, first strand: chain 'A' and resid 1137 through 1141 Processing sheet with id=AA9, first strand: chain 'A' and resid 1266 through 1267 removed outlier: 7.788A pdb=" N LEU A1266 " --> pdb=" O LYS A1250 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLN A1288 " --> pdb=" O VAL A1254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1296 through 1297 removed outlier: 6.555A pdb=" N LYS A1383 " --> pdb=" O ILE A1376 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N CYS A1387 " --> pdb=" O GLN A1372 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLN A1372 " --> pdb=" O CYS A1387 " (cutoff:3.500A) 561 hydrogen bonds defined for protein. 1596 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 160 hydrogen bonds 302 hydrogen bond angles 0 basepair planarities 65 basepair parallelities 119 stacking parallelities Total time for adding SS restraints: 10.12 Time building geometry restraints manager: 4.68 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: 2957 1.33 - 1.45: 4318 1.45 - 1.57: 7754 1.57 - 1.69: 341 1.69 - 1.81: 57 Bond restraints: 15427 Sorted by residual: bond pdb=" C3' C B 57 " pdb=" O3' C B 57 " ideal model delta sigma weight residual 1.427 1.457 -0.030 1.50e-02 4.44e+03 3.87e+00 bond pdb=" CB ARG A 70 " pdb=" CG ARG A 70 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.65e+00 bond pdb=" CB VAL A1226 " pdb=" CG1 VAL A1226 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.35e+00 bond pdb=" CG LYS A 888 " pdb=" CD LYS A 888 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.10e+00 bond pdb=" CD LYS A 888 " pdb=" CE LYS A 888 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.02e+00 ... (remaining 15422 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 20876 1.92 - 3.83: 624 3.83 - 5.75: 89 5.75 - 7.66: 22 7.66 - 9.58: 8 Bond angle restraints: 21619 Sorted by residual: angle pdb=" C3' C B 57 " pdb=" O3' C B 57 " pdb=" P U B 58 " ideal model delta sigma weight residual 120.20 127.50 -7.30 1.50e+00 4.44e-01 2.37e+01 angle pdb=" C LYS A 679 " pdb=" N ASN A 680 " pdb=" CA ASN A 680 " ideal model delta sigma weight residual 122.46 128.25 -5.79 1.41e+00 5.03e-01 1.69e+01 angle pdb=" C ASN A 766 " pdb=" N TYR A 767 " pdb=" CA TYR A 767 " ideal model delta sigma weight residual 122.54 115.91 6.63 1.65e+00 3.67e-01 1.62e+01 angle pdb=" N GLU A 370 " pdb=" CA GLU A 370 " pdb=" C GLU A 370 " ideal model delta sigma weight residual 111.02 115.62 -4.60 1.22e+00 6.72e-01 1.42e+01 angle pdb=" N GLN A 158 " pdb=" CA GLN A 158 " pdb=" CB GLN A 158 " ideal model delta sigma weight residual 110.39 116.52 -6.13 1.66e+00 3.63e-01 1.36e+01 ... (remaining 21614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 8827 35.51 - 71.02: 477 71.02 - 106.53: 45 106.53 - 142.03: 1 142.03 - 177.54: 5 Dihedral angle restraints: 9355 sinusoidal: 5304 harmonic: 4051 Sorted by residual: dihedral pdb=" O4' U B 101 " pdb=" C1' U B 101 " pdb=" N1 U B 101 " pdb=" C2 U B 101 " ideal model delta sinusoidal sigma weight residual 200.00 50.64 149.36 1 1.50e+01 4.44e-03 7.94e+01 dihedral pdb=" O4' U B 108 " pdb=" C1' U B 108 " pdb=" N1 U B 108 " pdb=" C2 U B 108 " ideal model delta sinusoidal sigma weight residual -128.00 49.54 -177.54 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 85 " pdb=" C1' U B 85 " pdb=" N1 U B 85 " pdb=" C2 U B 85 " ideal model delta sinusoidal sigma weight residual -128.00 47.17 -175.17 1 1.70e+01 3.46e-03 6.63e+01 ... (remaining 9352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2058 0.057 - 0.115: 380 0.115 - 0.172: 61 0.172 - 0.230: 9 0.230 - 0.287: 2 Chirality restraints: 2510 Sorted by residual: chirality pdb=" CB THR A1381 " pdb=" CA THR A1381 " pdb=" OG1 THR A1381 " pdb=" CG2 THR A1381 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C3' C B 57 " pdb=" C4' C B 57 " pdb=" O3' C B 57 " pdb=" C2' C B 57 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB VAL A 575 " pdb=" CA VAL A 575 " pdb=" CG1 VAL A 575 " pdb=" CG2 VAL A 575 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 2507 not shown) Planarity restraints: 2136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 15 " 0.058 2.00e-02 2.50e+03 2.46e-02 1.82e+01 pdb=" N9 G B 15 " -0.058 2.00e-02 2.50e+03 pdb=" C8 G B 15 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G B 15 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B 15 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B 15 " 0.009 2.00e-02 2.50e+03 pdb=" O6 G B 15 " 0.013 2.00e-02 2.50e+03 pdb=" N1 G B 15 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G B 15 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G B 15 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G B 15 " -0.012 2.00e-02 2.50e+03 pdb=" C4 G B 15 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 99 " -0.046 2.00e-02 2.50e+03 1.93e-02 1.12e+01 pdb=" N9 G B 99 " 0.045 2.00e-02 2.50e+03 pdb=" C8 G B 99 " 0.007 2.00e-02 2.50e+03 pdb=" N7 G B 99 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G B 99 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G B 99 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G B 99 " -0.016 2.00e-02 2.50e+03 pdb=" N1 G B 99 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G B 99 " 0.004 2.00e-02 2.50e+03 pdb=" N2 G B 99 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G B 99 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G B 99 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 106 " -0.014 2.00e-02 2.50e+03 2.92e-02 8.52e+00 pdb=" C GLU A 106 " 0.050 2.00e-02 2.50e+03 pdb=" O GLU A 106 " -0.019 2.00e-02 2.50e+03 pdb=" N SER A 107 " -0.017 2.00e-02 2.50e+03 ... (remaining 2133 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 315 2.65 - 3.21: 12606 3.21 - 3.77: 26154 3.77 - 4.34: 36347 4.34 - 4.90: 54274 Nonbonded interactions: 129696 Sorted by model distance: nonbonded pdb=" OD1 ASP A 756 " pdb="MG MG A1503 " model vdw 2.087 2.170 nonbonded pdb=" OD2 ASP A 10 " pdb="MG MG A1502 " model vdw 2.102 2.170 nonbonded pdb=" OP1 DC C 43 " pdb="MG MG A1502 " model vdw 2.125 2.170 nonbonded pdb=" OP2 DC C 43 " pdb="MG MG A1501 " model vdw 2.142 2.170 nonbonded pdb=" OG SER A 94 " pdb=" OP1 A B 72 " model vdw 2.189 3.040 ... (remaining 129691 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: 10.040 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: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 46.490 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: 0.000 Load rotamer database and sin/cos tables:12.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15427 Z= 0.320 Angle : 0.802 9.576 21619 Z= 0.436 Chirality : 0.047 0.287 2510 Planarity : 0.005 0.044 2136 Dihedral : 19.052 177.543 6727 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.20 (0.21), residues: 1368 helix: -0.80 (0.17), residues: 673 sheet: -0.23 (0.42), residues: 155 loop : -0.72 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 516 HIS 0.009 0.002 HIS A 206 PHE 0.022 0.002 PHE A 242 TYR 0.027 0.002 TYR A 819 ARG 0.018 0.001 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 1.573 Fit side-chains outliers start: 0 outliers final: 2 residues processed: 106 average time/residue: 1.7520 time to fit residues: 201.8567 Evaluate side-chains 57 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 1047 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 604 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15427 Z= 0.342 Angle : 0.625 7.285 21619 Z= 0.335 Chirality : 0.041 0.209 2510 Planarity : 0.004 0.038 2136 Dihedral : 20.558 177.778 3904 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.14 % Allowed : 6.42 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.11 (0.22), residues: 1368 helix: 0.36 (0.19), residues: 680 sheet: -0.06 (0.42), residues: 150 loop : -0.47 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1035 HIS 0.006 0.001 HIS A1105 PHE 0.023 0.001 PHE A 160 TYR 0.016 0.002 TYR A 281 ARG 0.006 0.001 ARG A 655 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 1.506 Fit side-chains revert: symmetry clash REVERT: A 413 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8613 (ttp-170) REVERT: A 440 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7574 (tm-30) outliers start: 14 outliers final: 5 residues processed: 70 average time/residue: 1.3553 time to fit residues: 105.7594 Evaluate side-chains 63 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 767 TYR Chi-restraints excluded: chain A residue 926 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 110 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A1392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15427 Z= 0.199 Angle : 0.552 6.929 21619 Z= 0.296 Chirality : 0.038 0.196 2510 Planarity : 0.003 0.030 2136 Dihedral : 20.497 177.618 3900 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.22 % Allowed : 8.61 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.38 (0.23), residues: 1368 helix: 0.89 (0.20), residues: 682 sheet: -0.21 (0.41), residues: 155 loop : -0.30 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1035 HIS 0.004 0.001 HIS A 206 PHE 0.016 0.001 PHE A 242 TYR 0.039 0.001 TYR A 767 ARG 0.003 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 1.567 Fit side-chains revert: symmetry clash REVERT: A 413 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8606 (ttp-170) REVERT: A 440 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7613 (tm-30) outliers start: 15 outliers final: 5 residues processed: 74 average time/residue: 1.2915 time to fit residues: 107.2484 Evaluate side-chains 58 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1009 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 15427 Z= 0.360 Angle : 0.596 9.414 21619 Z= 0.317 Chirality : 0.041 0.190 2510 Planarity : 0.004 0.033 2136 Dihedral : 20.426 177.647 3900 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.38 % Allowed : 9.67 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.51 (0.23), residues: 1368 helix: 1.01 (0.20), residues: 682 sheet: -0.19 (0.42), residues: 155 loop : -0.24 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1035 HIS 0.007 0.001 HIS A1105 PHE 0.022 0.001 PHE A 160 TYR 0.031 0.002 TYR A 767 ARG 0.004 0.000 ARG A1007 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 1.529 Fit side-chains revert: symmetry clash REVERT: A 50 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7279 (mmp) REVERT: A 413 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8608 (ttp-170) REVERT: A 440 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7578 (tm-30) outliers start: 17 outliers final: 9 residues processed: 66 average time/residue: 1.4216 time to fit residues: 104.6176 Evaluate side-chains 57 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 767 TYR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1381 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 131 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1288 GLN ** A1392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 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 : 0.003 0.044 15427 Z= 0.190 Angle : 0.534 7.882 21619 Z= 0.285 Chirality : 0.037 0.192 2510 Planarity : 0.003 0.029 2136 Dihedral : 20.433 177.768 3900 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.95 % Allowed : 9.26 % Favored : 88.79 % 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: 1368 helix: 1.26 (0.20), residues: 683 sheet: -0.18 (0.42), residues: 153 loop : -0.12 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1035 HIS 0.003 0.001 HIS A1406 PHE 0.017 0.001 PHE A 242 TYR 0.035 0.001 TYR A 767 ARG 0.004 0.000 ARG A1198 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 413 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8603 (ttp-170) REVERT: A 440 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7592 (tm-30) REVERT: A 910 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8272 (ttm170) REVERT: A 982 GLN cc_start: 0.7722 (pp30) cc_final: 0.7490 (pp30) outliers start: 24 outliers final: 8 residues processed: 82 average time/residue: 1.3774 time to fit residues: 125.6266 Evaluate side-chains 69 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1140 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 0.0980 chunk 12 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15427 Z= 0.308 Angle : 0.568 9.340 21619 Z= 0.302 Chirality : 0.039 0.192 2510 Planarity : 0.003 0.027 2136 Dihedral : 20.377 177.732 3900 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.03 % Allowed : 10.07 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.80 (0.23), residues: 1368 helix: 1.31 (0.20), residues: 683 sheet: -0.15 (0.42), residues: 153 loop : -0.15 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1035 HIS 0.006 0.001 HIS A1406 PHE 0.021 0.001 PHE A 242 TYR 0.021 0.002 TYR A 819 ARG 0.005 0.000 ARG A1198 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7439 (mmp) REVERT: A 413 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8628 (ttp-170) REVERT: A 440 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: A 910 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8125 (ttm170) REVERT: A 982 GLN cc_start: 0.7716 (pp30) cc_final: 0.7461 (pp30) outliers start: 25 outliers final: 16 residues processed: 80 average time/residue: 1.3961 time to fit residues: 123.9075 Evaluate side-chains 75 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 767 TYR Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1381 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 15427 Z= 0.346 Angle : 0.589 7.718 21619 Z= 0.313 Chirality : 0.040 0.213 2510 Planarity : 0.004 0.043 2136 Dihedral : 20.376 177.573 3900 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.95 % Allowed : 10.72 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.79 (0.23), residues: 1368 helix: 1.28 (0.20), residues: 683 sheet: -0.12 (0.42), residues: 153 loop : -0.15 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1035 HIS 0.006 0.001 HIS A1105 PHE 0.022 0.001 PHE A 242 TYR 0.019 0.002 TYR A 767 ARG 0.009 0.000 ARG A1198 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7284 (mmp) REVERT: A 413 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8606 (ttp-170) REVERT: A 440 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7577 (tm-30) REVERT: A 564 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6859 (tp30) REVERT: A 910 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8054 (ttm170) REVERT: A 982 GLN cc_start: 0.7690 (pp30) cc_final: 0.7439 (pp30) outliers start: 24 outliers final: 13 residues processed: 77 average time/residue: 1.4254 time to fit residues: 121.7563 Evaluate side-chains 73 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1381 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 133 optimal weight: 0.5980 chunk 140 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15427 Z= 0.315 Angle : 0.571 7.584 21619 Z= 0.303 Chirality : 0.039 0.192 2510 Planarity : 0.003 0.034 2136 Dihedral : 20.362 177.530 3900 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.11 % Allowed : 10.89 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.83 (0.23), residues: 1368 helix: 1.31 (0.20), residues: 683 sheet: -0.14 (0.42), residues: 153 loop : -0.13 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 139 HIS 0.005 0.001 HIS A1105 PHE 0.021 0.001 PHE A 242 TYR 0.041 0.002 TYR A 767 ARG 0.004 0.000 ARG A1198 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7353 (mmp) REVERT: A 413 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8638 (ttp-170) REVERT: A 440 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7574 (tm-30) REVERT: A 910 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8022 (ttm170) REVERT: A 982 GLN cc_start: 0.7689 (pp30) cc_final: 0.7446 (pp30) outliers start: 26 outliers final: 13 residues processed: 81 average time/residue: 1.3577 time to fit residues: 122.0691 Evaluate side-chains 75 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 767 TYR Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1290 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.5980 chunk 136 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15427 Z= 0.214 Angle : 0.561 11.200 21619 Z= 0.297 Chirality : 0.037 0.194 2510 Planarity : 0.003 0.048 2136 Dihedral : 20.355 177.673 3900 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.62 % Allowed : 11.86 % Favored : 86.52 % 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: 0.98 (0.23), residues: 1368 helix: 1.41 (0.20), residues: 683 sheet: 0.08 (0.43), residues: 148 loop : -0.05 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 139 HIS 0.007 0.001 HIS A1406 PHE 0.019 0.001 PHE A 242 TYR 0.033 0.001 TYR A 767 ARG 0.011 0.000 ARG A1198 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 440 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7557 (tm-30) REVERT: A 564 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6900 (tp30) REVERT: A 910 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7965 (ttm170) REVERT: A 982 GLN cc_start: 0.7677 (pp30) cc_final: 0.7432 (pp30) outliers start: 20 outliers final: 12 residues processed: 82 average time/residue: 1.4282 time to fit residues: 129.7493 Evaluate side-chains 73 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1290 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 12 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15427 Z= 0.227 Angle : 0.555 11.017 21619 Z= 0.294 Chirality : 0.038 0.216 2510 Planarity : 0.003 0.045 2136 Dihedral : 20.314 177.723 3900 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.54 % Allowed : 12.10 % Favored : 86.35 % 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: 1.07 (0.23), residues: 1368 helix: 1.49 (0.20), residues: 683 sheet: 0.11 (0.43), residues: 148 loop : -0.02 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 139 HIS 0.009 0.001 HIS A1406 PHE 0.023 0.001 PHE A 160 TYR 0.017 0.001 TYR A 819 ARG 0.010 0.000 ARG A1198 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 1.528 Fit side-chains revert: symmetry clash REVERT: A 440 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7567 (tm-30) REVERT: A 564 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6924 (tp30) REVERT: A 910 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7965 (ttm170) REVERT: A 982 GLN cc_start: 0.7678 (pp30) cc_final: 0.7443 (pp30) outliers start: 19 outliers final: 14 residues processed: 76 average time/residue: 1.3279 time to fit residues: 113.2970 Evaluate side-chains 73 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 767 TYR Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1290 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 33 optimal weight: 0.0470 chunk 120 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.108505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.081196 restraints weight = 28641.777| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.27 r_work: 0.3062 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15427 Z= 0.185 Angle : 0.551 10.471 21619 Z= 0.291 Chirality : 0.037 0.223 2510 Planarity : 0.003 0.044 2136 Dihedral : 20.266 177.820 3900 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.30 % Allowed : 12.35 % Favored : 86.35 % 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: 1.18 (0.23), residues: 1368 helix: 1.59 (0.20), residues: 684 sheet: 0.15 (0.43), residues: 148 loop : 0.02 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 139 HIS 0.009 0.001 HIS A1406 PHE 0.017 0.001 PHE A 242 TYR 0.017 0.001 TYR A 819 ARG 0.009 0.000 ARG A1198 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3638.06 seconds wall clock time: 67 minutes 24.15 seconds (4044.15 seconds total)