Starting phenix.real_space_refine on Fri May 16 17:02:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8umf_42378/05_2025/8umf_42378.cif Found real_map, /net/cci-nas-00/data/ceres_data/8umf_42378/05_2025/8umf_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_42378/05_2025/8umf_42378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8umf_42378/05_2025/8umf_42378.map" model { file = "/net/cci-nas-00/data/ceres_data/8umf_42378/05_2025/8umf_42378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8umf_42378/05_2025/8umf_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.82, per 1000 atoms: 0.66 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: 3.61 Conformation dependent library (CDL) restraints added in 1.5 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: 5.64 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: 9.36 Time building geometry restraints manager: 4.26 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: 0.010 Normalize map: mean=0, sd=1: 4.330 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 42.710 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.010 ------------------------------------------------------------------------------- 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= 0.232 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 Details of bonding type rmsd hydrogen bonds : bond 0.13890 ( 721) hydrogen bonds : angle 6.62360 ( 1898) covalent geometry : bond 0.00506 (15427) covalent geometry : angle 0.80164 (21619) *********************** 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 : 1.458 Fit side-chains outliers start: 0 outliers final: 2 residues processed: 106 average time/residue: 1.6837 time to fit residues: 193.1684 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 : 1.467 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.105605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.077884 restraints weight = 28084.002| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.29 r_work: 0.2961 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 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= 0.248 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 Details of bonding type rmsd hydrogen bonds : bond 0.04656 ( 721) hydrogen bonds : angle 4.82306 ( 1898) covalent geometry : bond 0.00544 (15427) covalent geometry : angle 0.62479 (21619) *********************** 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 : 1.296 Fit side-chains revert: symmetry clash REVERT: A 413 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8509 (ttp-170) REVERT: A 440 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: A 702 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7708 (tm-30) REVERT: A 982 GLN cc_start: 0.7850 (pp30) cc_final: 0.7600 (pp30) outliers start: 14 outliers final: 5 residues processed: 70 average time/residue: 1.3062 time to fit residues: 102.4707 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 : 1.263 ------------------------------------------------------------------------------- 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 122 optimal weight: 2.9990 chunk 124 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.107407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.079919 restraints weight = 27868.575| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.28 r_work: 0.3004 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 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 0.034 15427 Z= 0.155 Angle : 0.553 7.358 21619 Z= 0.297 Chirality : 0.038 0.195 2510 Planarity : 0.003 0.030 2136 Dihedral : 20.493 177.611 3900 Min Nonbonded Distance : 2.004 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 0.029 0.001 TYR A 767 ARG 0.004 0.000 ARG A 518 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 721) hydrogen bonds : angle 4.45204 ( 1898) covalent geometry : bond 0.00332 (15427) covalent geometry : angle 0.55314 (21619) *********************** 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 80 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 1.433 Fit side-chains revert: symmetry clash REVERT: A 413 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8488 (ttp-170) REVERT: A 440 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7341 (tm-30) REVERT: A 702 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7798 (tm-30) REVERT: A 910 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8584 (ttm110) REVERT: A 982 GLN cc_start: 0.7851 (pp30) cc_final: 0.7548 (pp30) outliers start: 15 outliers final: 6 residues processed: 75 average time/residue: 1.2712 time to fit residues: 106.6867 Evaluate side-chains 62 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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 765 MET Chi-restraints excluded: chain A residue 910 ARG 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 97 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.107344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.079769 restraints weight = 27918.433| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.29 r_work: 0.3000 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15427 Z= 0.168 Angle : 0.544 9.272 21619 Z= 0.290 Chirality : 0.038 0.190 2510 Planarity : 0.003 0.026 2136 Dihedral : 20.428 177.834 3900 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.54 % Allowed : 9.42 % Favored : 89.03 % 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: 0.66 (0.23), residues: 1368 helix: 1.17 (0.20), residues: 682 sheet: -0.28 (0.41), residues: 158 loop : -0.16 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1035 HIS 0.004 0.001 HIS A 58 PHE 0.024 0.001 PHE A 160 TYR 0.034 0.001 TYR A 767 ARG 0.003 0.000 ARG A1007 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 721) hydrogen bonds : angle 4.30100 ( 1898) covalent geometry : bond 0.00365 (15427) covalent geometry : angle 0.54427 (21619) *********************** 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 76 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 1.378 Fit side-chains revert: symmetry clash REVERT: A 440 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7325 (tm-30) REVERT: A 702 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7779 (tm-30) REVERT: A 910 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8442 (ttm170) REVERT: A 982 GLN cc_start: 0.7883 (pp30) cc_final: 0.7546 (pp30) outliers start: 19 outliers final: 9 residues processed: 70 average time/residue: 1.2674 time to fit residues: 99.1973 Evaluate side-chains 61 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 199 ILE 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 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 36 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.105598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.077887 restraints weight = 28282.956| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.29 r_work: 0.2962 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1777 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= 0.229 Angle : 0.570 7.350 21619 Z= 0.303 Chirality : 0.039 0.191 2510 Planarity : 0.003 0.027 2136 Dihedral : 20.400 177.639 3900 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.79 % Allowed : 9.67 % Favored : 88.55 % 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: 0.69 (0.23), residues: 1368 helix: 1.18 (0.20), residues: 682 sheet: -0.27 (0.41), residues: 158 loop : -0.12 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1035 HIS 0.006 0.001 HIS A1105 PHE 0.021 0.001 PHE A 242 TYR 0.038 0.002 TYR A 767 ARG 0.004 0.000 ARG A1007 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 721) hydrogen bonds : angle 4.32355 ( 1898) covalent geometry : bond 0.00506 (15427) covalent geometry : angle 0.57012 (21619) *********************** 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 80 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 440 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7283 (tm-30) REVERT: A 702 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7619 (tm-30) REVERT: A 910 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8357 (ttm170) REVERT: A 982 GLN cc_start: 0.7850 (pp30) cc_final: 0.7499 (pp30) REVERT: A 1288 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8276 (pm20) outliers start: 22 outliers final: 12 residues processed: 76 average time/residue: 1.3952 time to fit residues: 117.4543 Evaluate side-chains 69 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU 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 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 1073 VAL Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1288 GLN Chi-restraints excluded: chain A residue 1381 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 72 optimal weight: 0.4980 chunk 103 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.106378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.078787 restraints weight = 28571.184| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.26 r_work: 0.2993 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15427 Z= 0.192 Angle : 0.556 9.339 21619 Z= 0.296 Chirality : 0.038 0.192 2510 Planarity : 0.003 0.030 2136 Dihedral : 20.391 177.651 3900 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.87 % Allowed : 10.48 % Favored : 87.65 % 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: 0.86 (0.23), residues: 1368 helix: 1.31 (0.20), residues: 683 sheet: 0.03 (0.43), residues: 148 loop : -0.11 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1035 HIS 0.004 0.001 HIS A1105 PHE 0.020 0.001 PHE A 242 TYR 0.018 0.001 TYR A 819 ARG 0.005 0.000 ARG A1198 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 721) hydrogen bonds : angle 4.26691 ( 1898) covalent geometry : bond 0.00422 (15427) covalent geometry : angle 0.55627 (21619) *********************** 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 84 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6778 (tm130) REVERT: A 440 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7328 (tm-30) REVERT: A 564 GLU cc_start: 0.8070 (tt0) cc_final: 0.7753 (tt0) REVERT: A 702 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7585 (tm-30) REVERT: A 767 TYR cc_start: 0.7686 (p90) cc_final: 0.7388 (OUTLIER) REVERT: A 768 MET cc_start: 0.7504 (ttm) cc_final: 0.7123 (mtt) REVERT: A 910 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8361 (ttm170) REVERT: A 982 GLN cc_start: 0.7901 (pp30) cc_final: 0.7541 (pp30) outliers start: 23 outliers final: 15 residues processed: 80 average time/residue: 1.3385 time to fit residues: 119.0490 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 : 1.366 ------------------------------------------------------------------------------- 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 201 GLN Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 288 LYS 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 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 106 optimal weight: 2.9990 chunk 63 optimal weight: 0.0670 chunk 22 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 123 optimal weight: 0.3980 chunk 84 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1288 GLN ** A1392 ASN ** 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 = 0.3614 r_free = 0.3614 target = 0.108294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.080697 restraints weight = 28733.253| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.31 r_work: 0.3049 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15427 Z= 0.138 Angle : 0.526 7.569 21619 Z= 0.280 Chirality : 0.037 0.193 2510 Planarity : 0.003 0.029 2136 Dihedral : 20.377 177.791 3900 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.95 % Allowed : 10.80 % Favored : 87.25 % 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: 1.07 (0.23), residues: 1368 helix: 1.51 (0.20), residues: 684 sheet: 0.04 (0.42), residues: 148 loop : -0.02 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1214 HIS 0.004 0.001 HIS A1406 PHE 0.017 0.001 PHE A 242 TYR 0.017 0.001 TYR A 819 ARG 0.005 0.000 ARG A1198 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 721) hydrogen bonds : angle 4.14759 ( 1898) covalent geometry : bond 0.00299 (15427) covalent geometry : angle 0.52613 (21619) *********************** 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 92 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.6608 (tm130) REVERT: A 231 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8315 (pm20) REVERT: A 440 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7287 (tm-30) REVERT: A 564 GLU cc_start: 0.8063 (tt0) cc_final: 0.7686 (mm-30) REVERT: A 702 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7469 (tm-30) REVERT: A 768 MET cc_start: 0.7524 (ttm) cc_final: 0.7263 (mtp) REVERT: A 910 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8312 (ttm170) REVERT: A 982 GLN cc_start: 0.7920 (pp30) cc_final: 0.7562 (pp30) REVERT: A 1288 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8570 (pm20) REVERT: A 1394 MET cc_start: 0.8393 (mpp) cc_final: 0.8175 (mpt) outliers start: 24 outliers final: 9 residues processed: 85 average time/residue: 1.3254 time to fit residues: 124.9932 Evaluate side-chains 74 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 1.460 ------------------------------------------------------------------------------- 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 201 GLN Chi-restraints excluded: chain A residue 231 GLU 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 1288 GLN Chi-restraints excluded: chain A residue 1290 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 61 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 77 optimal weight: 0.0570 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 GLN A1288 GLN ** A1392 ASN ** 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 = 0.3603 r_free = 0.3603 target = 0.107715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.080166 restraints weight = 28669.874| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.27 r_work: 0.3038 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15427 Z= 0.167 Angle : 0.541 10.392 21619 Z= 0.286 Chirality : 0.037 0.193 2510 Planarity : 0.003 0.031 2136 Dihedral : 20.346 177.748 3900 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.71 % Allowed : 11.86 % Favored : 86.43 % 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: 1.11 (0.23), residues: 1368 helix: 1.54 (0.20), residues: 684 sheet: 0.09 (0.43), residues: 148 loop : -0.02 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1214 HIS 0.005 0.001 HIS A1406 PHE 0.020 0.001 PHE A 160 TYR 0.016 0.001 TYR A 819 ARG 0.007 0.000 ARG A1198 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 721) hydrogen bonds : angle 4.14156 ( 1898) covalent geometry : bond 0.00365 (15427) covalent geometry : angle 0.54104 (21619) *********************** 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 81 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 GLN cc_start: 0.6929 (OUTLIER) cc_final: 0.6646 (tm130) REVERT: A 440 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: A 564 GLU cc_start: 0.8038 (tt0) cc_final: 0.7690 (mm-30) REVERT: A 702 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7454 (tm-30) REVERT: A 910 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8331 (ttm170) REVERT: A 982 GLN cc_start: 0.7925 (pp30) cc_final: 0.7564 (pp30) REVERT: A 1288 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8570 (pm20) REVERT: A 1394 MET cc_start: 0.8367 (mpp) cc_final: 0.8157 (mpt) outliers start: 21 outliers final: 14 residues processed: 77 average time/residue: 1.3829 time to fit residues: 117.6364 Evaluate side-chains 77 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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 201 GLN 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 1288 GLN Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1381 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.108201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.080726 restraints weight = 28474.677| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.26 r_work: 0.3048 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15427 Z= 0.149 Angle : 0.546 9.730 21619 Z= 0.289 Chirality : 0.037 0.227 2510 Planarity : 0.003 0.047 2136 Dihedral : 20.334 177.741 3900 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.71 % Allowed : 11.78 % 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: 1.13 (0.23), residues: 1368 helix: 1.56 (0.20), residues: 684 sheet: 0.10 (0.43), residues: 148 loop : 0.00 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 139 HIS 0.005 0.001 HIS A1406 PHE 0.017 0.001 PHE A 242 TYR 0.016 0.001 TYR A 819 ARG 0.011 0.000 ARG A1198 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 721) hydrogen bonds : angle 4.11758 ( 1898) covalent geometry : bond 0.00326 (15427) covalent geometry : angle 0.54593 (21619) *********************** 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 82 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 GLN cc_start: 0.6895 (OUTLIER) cc_final: 0.6602 (tm130) REVERT: A 440 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7304 (tm-30) REVERT: A 564 GLU cc_start: 0.8020 (tt0) cc_final: 0.7723 (mm-30) REVERT: A 702 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7433 (tm-30) REVERT: A 767 TYR cc_start: 0.7842 (p90) cc_final: 0.7358 (p90) REVERT: A 910 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8306 (ttm170) REVERT: A 982 GLN cc_start: 0.7943 (pp30) cc_final: 0.7577 (pp30) REVERT: A 1394 MET cc_start: 0.8355 (mpp) cc_final: 0.8140 (mpt) outliers start: 21 outliers final: 12 residues processed: 79 average time/residue: 1.3012 time to fit residues: 114.1076 Evaluate side-chains 72 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 1.510 ------------------------------------------------------------------------------- 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 201 GLN Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 231 GLU 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 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 84 optimal weight: 0.5980 chunk 16 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.106172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.078578 restraints weight = 28763.620| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.26 r_work: 0.2991 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2055 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= 0.217 Angle : 0.577 9.600 21619 Z= 0.304 Chirality : 0.039 0.228 2510 Planarity : 0.004 0.057 2136 Dihedral : 20.309 177.528 3900 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.54 % Allowed : 12.02 % Favored : 86.43 % 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: 1.08 (0.23), residues: 1368 helix: 1.51 (0.20), residues: 683 sheet: 0.14 (0.43), residues: 148 loop : -0.04 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 139 HIS 0.006 0.001 HIS A1406 PHE 0.020 0.001 PHE A 160 TYR 0.015 0.002 TYR A 281 ARG 0.011 0.000 ARG A1198 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 721) hydrogen bonds : angle 4.22704 ( 1898) covalent geometry : bond 0.00479 (15427) covalent geometry : angle 0.57694 (21619) ********************** 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 80 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.6726 (tm130) REVERT: A 440 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7290 (tm-30) REVERT: A 564 GLU cc_start: 0.8050 (tt0) cc_final: 0.7704 (mm-30) REVERT: A 702 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7346 (tm-30) REVERT: A 767 TYR cc_start: 0.7881 (p90) cc_final: 0.7624 (OUTLIER) REVERT: A 910 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8324 (ttm170) REVERT: A 982 GLN cc_start: 0.7977 (pp30) cc_final: 0.7594 (pp30) REVERT: A 1394 MET cc_start: 0.8388 (mpp) cc_final: 0.8102 (mpt) outliers start: 19 outliers final: 15 residues processed: 78 average time/residue: 1.3407 time to fit residues: 117.0482 Evaluate side-chains 76 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 1.545 ------------------------------------------------------------------------------- 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 201 GLN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 70 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 92 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.107919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.080492 restraints weight = 28785.409| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.27 r_work: 0.3046 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15427 Z= 0.151 Angle : 0.555 9.164 21619 Z= 0.292 Chirality : 0.037 0.247 2510 Planarity : 0.003 0.048 2136 Dihedral : 20.304 177.667 3900 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.46 % Allowed : 12.19 % 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: 1.20 (0.23), residues: 1368 helix: 1.61 (0.20), residues: 684 sheet: 0.20 (0.43), residues: 148 loop : 0.01 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 139 HIS 0.006 0.001 HIS A1406 PHE 0.017 0.001 PHE A 242 TYR 0.015 0.001 TYR A 819 ARG 0.010 0.000 ARG A1198 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 721) hydrogen bonds : angle 4.14839 ( 1898) covalent geometry : bond 0.00331 (15427) covalent geometry : angle 0.55479 (21619) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9417.66 seconds wall clock time: 163 minutes 13.68 seconds (9793.68 seconds total)