Starting phenix.real_space_refine on Thu Jul 31 13:21:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6x_41083/07_2025/8t6x_41083.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6x_41083/07_2025/8t6x_41083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t6x_41083/07_2025/8t6x_41083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6x_41083/07_2025/8t6x_41083.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6x_41083/07_2025/8t6x_41083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6x_41083/07_2025/8t6x_41083.cif" } resolution = 3.08 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= 0.010 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 139 5.49 5 Mg 3 5.21 5 S 20 5.16 5 C 8043 2.51 5 N 2367 2.21 5 O 2871 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13443 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 10508 Classifications: {'peptide': 1278} Link IDs: {'PTRANS': 33, 'TRANS': 1244} Chain breaks: 7 Chain: "B" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 2058 Classifications: {'RNA': 96} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 51, 'rna3p_pyr': 34} Link IDs: {'rna2p': 10, 'rna3p': 85} Chain: "C" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 609 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "D" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 265 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.84, per 1000 atoms: 0.66 Number of scatterers: 13443 At special positions: 0 Unit cell: (87.486, 124.98, 121.647, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 20 16.00 P 139 15.00 Mg 3 11.99 O 2871 8.00 N 2367 7.00 C 8043 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: 2.95 Conformation dependent library (CDL) restraints added in 1.4 seconds 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2434 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 8 sheets defined 56.3% alpha, 7.6% beta 50 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 5.47 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.864A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.818A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 208 through 214 Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 272 through 278 removed outlier: 3.610A pdb=" N LEU A 275 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP A 276 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN A 277 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 306 Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 344 through 352 removed outlier: 4.574A pdb=" N LYS A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix removed outlier: 3.512A pdb=" N MET A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.646A pdb=" N ASN A 407 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.109A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.859A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.847A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 553 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.504A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 642 removed outlier: 4.450A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 642 " --> pdb=" O TYR A 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 638 through 642' Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 703 through 712 removed outlier: 3.828A pdb=" N ASP A 707 " --> pdb=" O THR A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 731 through 751 removed outlier: 4.167A pdb=" N LYS A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 779 through 792 Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 803 through 807 removed outlier: 3.700A pdb=" N GLN A 807 " --> pdb=" O THR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 829 through 834 removed outlier: 3.950A pdb=" N LEU A 833 " --> pdb=" O ILE A 830 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N SER A 834 " --> pdb=" O ASN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 866 Processing helix chain 'A' and resid 872 through 888 removed outlier: 3.615A pdb=" N VAL A 876 " --> pdb=" O SER A 872 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TYR A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 902 through 906 Processing helix chain 'A' and resid 909 through 914 removed outlier: 3.556A pdb=" N ALA A 914 " --> pdb=" O GLU A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 940 removed outlier: 3.820A pdb=" N LEU A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.464A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1009 Processing helix chain 'A' and resid 1030 through 1042 Processing helix chain 'A' and resid 1043 through 1047 Processing helix chain 'A' and resid 1077 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1168 through 1177 removed outlier: 4.626A pdb=" N SER A1172 " --> pdb=" O ILE A1168 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N SER A1173 " --> pdb=" O MET A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1240 Processing helix chain 'A' and resid 1248 through 1262 removed outlier: 3.668A pdb=" N HIS A1262 " --> pdb=" O PHE A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1281 Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 3.707A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.538A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 959 removed outlier: 7.413A pdb=" N TYR A 5 " --> pdb=" O ASN A 758 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N VAL A 760 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N GLU A 762 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LEU A 9 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.538A pdb=" N GLU A1357 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 836 through 840 Processing sheet with id=AA4, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA5, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 5.879A pdb=" N LYS A1156 " --> pdb=" O GLU A1150 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLU A1150 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LYS A1158 " --> pdb=" O LYS A1148 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS A1148 " --> pdb=" O LYS A1158 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A1160 " --> pdb=" O VAL A1146 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL A1146 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLU A1162 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU A1144 " --> pdb=" O GLU A1162 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU A1164 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER A1142 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE A1166 " --> pdb=" O ALA A1140 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1219 through 1222 removed outlier: 3.656A pdb=" N GLN A1219 " --> pdb=" O SER A1216 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLN A1221 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LEU A1214 " --> pdb=" O GLN A1221 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1324 through 1325 removed outlier: 3.721A pdb=" N PHE A1324 " --> pdb=" O ILE A1331 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1362 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 123 hydrogen bonds 242 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 7.64 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3104 1.33 - 1.46: 3669 1.46 - 1.58: 6885 1.58 - 1.70: 275 1.70 - 1.82: 39 Bond restraints: 13972 Sorted by residual: bond pdb=" CB PHE A1258 " pdb=" CG PHE A1258 " ideal model delta sigma weight residual 1.502 1.539 -0.037 2.30e-02 1.89e+03 2.65e+00 bond pdb=" CB ASP A 745 " pdb=" CG ASP A 745 " ideal model delta sigma weight residual 1.516 1.556 -0.040 2.50e-02 1.60e+03 2.53e+00 bond pdb=" CB LYS A 209 " pdb=" CG LYS A 209 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.11e+00 bond pdb=" CB LYS A 866 " pdb=" CG LYS A 866 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.05e+00 bond pdb=" CD1 PHE A 518 " pdb=" CE1 PHE A 518 " ideal model delta sigma weight residual 1.382 1.340 0.042 3.00e-02 1.11e+03 1.95e+00 ... (remaining 13967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 19201 2.57 - 5.14: 202 5.14 - 7.72: 25 7.72 - 10.29: 10 10.29 - 12.86: 2 Bond angle restraints: 19440 Sorted by residual: angle pdb=" CA LYS A 209 " pdb=" CB LYS A 209 " pdb=" CG LYS A 209 " ideal model delta sigma weight residual 114.10 122.72 -8.62 2.00e+00 2.50e-01 1.86e+01 angle pdb=" CB MET A 781 " pdb=" CG MET A 781 " pdb=" SD MET A 781 " ideal model delta sigma weight residual 112.70 125.56 -12.86 3.00e+00 1.11e-01 1.84e+01 angle pdb=" CB MET A 939 " pdb=" CG MET A 939 " pdb=" SD MET A 939 " ideal model delta sigma weight residual 112.70 125.43 -12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" CB LYS A 209 " pdb=" CG LYS A 209 " pdb=" CD LYS A 209 " ideal model delta sigma weight residual 111.30 120.81 -9.51 2.30e+00 1.89e-01 1.71e+01 angle pdb=" CA ILE A 300 " pdb=" CB ILE A 300 " pdb=" CG1 ILE A 300 " ideal model delta sigma weight residual 110.40 117.29 -6.89 1.70e+00 3.46e-01 1.64e+01 ... (remaining 19435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.07: 7782 30.07 - 60.15: 614 60.15 - 90.22: 99 90.22 - 120.29: 0 120.29 - 150.37: 1 Dihedral angle restraints: 8496 sinusoidal: 4741 harmonic: 3755 Sorted by residual: dihedral pdb=" CA PRO A 230 " pdb=" C PRO A 230 " pdb=" N GLY A 231 " pdb=" CA GLY A 231 " ideal model delta harmonic sigma weight residual -180.00 -159.15 -20.85 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA VAL A 647 " pdb=" C VAL A 647 " pdb=" N MET A 648 " pdb=" CA MET A 648 " ideal model delta harmonic sigma weight residual 180.00 159.88 20.12 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA ARG A 859 " pdb=" C ARG A 859 " pdb=" N SER A 860 " pdb=" CA SER A 860 " ideal model delta harmonic sigma weight residual -180.00 -159.99 -20.01 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 8493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1829 0.052 - 0.103: 331 0.103 - 0.155: 58 0.155 - 0.206: 6 0.206 - 0.258: 5 Chirality restraints: 2229 Sorted by residual: chirality pdb=" C3' A B 38 " pdb=" C4' A B 38 " pdb=" O3' A B 38 " pdb=" C2' A B 38 " both_signs ideal model delta sigma weight residual False -2.48 -2.22 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB ILE A 679 " pdb=" CA ILE A 679 " pdb=" CG1 ILE A 679 " pdb=" CG2 ILE A 679 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILE A 548 " pdb=" CA ILE A 548 " pdb=" CG1 ILE A 548 " pdb=" CG2 ILE A 548 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 2226 not shown) Planarity restraints: 1969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 71 " -0.205 9.50e-02 1.11e+02 9.23e-02 5.63e+00 pdb=" NE ARG A 71 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 71 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 71 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 71 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 502 " -0.035 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO A 503 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 503 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 503 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 518 " -0.016 2.00e-02 2.50e+03 1.60e-02 4.46e+00 pdb=" CG PHE A 518 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 518 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 518 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 518 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 518 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 518 " -0.013 2.00e-02 2.50e+03 ... (remaining 1966 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 126 2.59 - 3.17: 10481 3.17 - 3.75: 23097 3.75 - 4.32: 31137 4.32 - 4.90: 47873 Nonbonded interactions: 112714 Sorted by model distance: nonbonded pdb=" OD1 ASP A 839 " pdb="MG MG C 101 " model vdw 2.015 2.170 nonbonded pdb=" OP1 DT C 23 " pdb="MG MG C 101 " model vdw 2.062 2.170 nonbonded pdb=" O3' DG C 22 " pdb="MG MG C 101 " model vdw 2.115 2.170 nonbonded pdb=" OP2 DC D 34 " pdb="MG MG A1401 " model vdw 2.117 2.170 nonbonded pdb=" ND1 HIS A 983 " pdb="MG MG A1401 " model vdw 2.123 2.250 ... (remaining 112709 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 39.470 Find NCS groups from input model: 0.120 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13972 Z= 0.176 Angle : 0.723 12.860 19440 Z= 0.373 Chirality : 0.042 0.258 2229 Planarity : 0.005 0.092 1969 Dihedral : 19.035 150.368 6062 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.26 % Allowed : 16.38 % Favored : 83.36 % 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: -0.80 (0.22), residues: 1262 helix: -0.43 (0.19), residues: 623 sheet: -0.12 (0.51), residues: 126 loop : -0.56 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 18 HIS 0.009 0.002 HIS A 328 PHE 0.034 0.002 PHE A 518 TYR 0.023 0.002 TYR A 568 ARG 0.011 0.001 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.14297 ( 592) hydrogen bonds : angle 5.91163 ( 1604) covalent geometry : bond 0.00389 (13972) covalent geometry : angle 0.72287 (19440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 822 MET cc_start: 0.6144 (tpp) cc_final: 0.5917 (tpp) outliers start: 3 outliers final: 1 residues processed: 56 average time/residue: 0.2668 time to fit residues: 23.3945 Evaluate side-chains 50 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 71 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 127 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 511 HIS ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 GLN A 844 GLN A 920 GLN A1308 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.107496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.062509 restraints weight = 37597.496| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.46 r_work: 0.2760 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13972 Z= 0.256 Angle : 0.556 5.730 19440 Z= 0.299 Chirality : 0.038 0.179 2229 Planarity : 0.004 0.049 1969 Dihedral : 19.107 157.227 3310 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.91 % Allowed : 15.16 % Favored : 82.93 % 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: 0.02 (0.23), residues: 1262 helix: 0.51 (0.20), residues: 642 sheet: -0.30 (0.51), residues: 119 loop : -0.40 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1074 HIS 0.009 0.001 HIS A 328 PHE 0.013 0.001 PHE A1105 TYR 0.011 0.001 TYR A 568 ARG 0.005 0.000 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 592) hydrogen bonds : angle 4.53918 ( 1604) covalent geometry : bond 0.00554 (13972) covalent geometry : angle 0.55577 (19440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 693 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7498 (m-80) outliers start: 22 outliers final: 13 residues processed: 66 average time/residue: 0.3841 time to fit residues: 38.7011 Evaluate side-chains 58 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 920 GLN Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1206 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.106190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.061119 restraints weight = 37955.070| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.52 r_work: 0.2730 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13972 Z= 0.285 Angle : 0.562 6.368 19440 Z= 0.300 Chirality : 0.039 0.182 2229 Planarity : 0.004 0.050 1969 Dihedral : 19.171 156.979 3308 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.34 % Allowed : 15.86 % Favored : 81.80 % 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: 0.17 (0.23), residues: 1262 helix: 0.73 (0.20), residues: 636 sheet: -0.56 (0.49), residues: 119 loop : -0.37 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1136 HIS 0.009 0.001 HIS A 328 PHE 0.016 0.001 PHE A 518 TYR 0.012 0.001 TYR A 568 ARG 0.003 0.000 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 592) hydrogen bonds : angle 4.41768 ( 1604) covalent geometry : bond 0.00621 (13972) covalent geometry : angle 0.56184 (19440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 47 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 648 MET cc_start: 0.6145 (ptp) cc_final: 0.5812 (ptp) REVERT: A 693 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7790 (m-80) REVERT: A 822 MET cc_start: 0.6755 (tpp) cc_final: 0.5477 (tpp) REVERT: A 879 MET cc_start: -0.0405 (mmt) cc_final: -0.1420 (mtt) REVERT: A 1003 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6446 (pttt) outliers start: 27 outliers final: 15 residues processed: 70 average time/residue: 0.3340 time to fit residues: 35.6478 Evaluate side-chains 60 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1206 LEU Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1353 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 127 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 2 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 102 optimal weight: 0.1980 chunk 90 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN A 920 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.108349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.063526 restraints weight = 37406.373| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.44 r_work: 0.2793 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13972 Z= 0.131 Angle : 0.465 6.328 19440 Z= 0.252 Chirality : 0.035 0.180 2229 Planarity : 0.003 0.048 1969 Dihedral : 19.061 154.931 3308 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.91 % Allowed : 16.29 % Favored : 81.80 % 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: 0.44 (0.23), residues: 1262 helix: 0.98 (0.21), residues: 639 sheet: -0.43 (0.50), residues: 119 loop : -0.28 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 PHE 0.018 0.001 PHE A 518 TYR 0.012 0.001 TYR A 568 ARG 0.002 0.000 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 592) hydrogen bonds : angle 4.17742 ( 1604) covalent geometry : bond 0.00279 (13972) covalent geometry : angle 0.46496 (19440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 MET cc_start: 0.6658 (tpp) cc_final: 0.5300 (tpp) REVERT: A 879 MET cc_start: -0.0760 (mmt) cc_final: -0.1770 (mtt) REVERT: A 1153 LYS cc_start: 0.8769 (mmtm) cc_final: 0.8346 (pttt) REVERT: A 1224 ASN cc_start: 0.9383 (OUTLIER) cc_final: 0.9103 (m110) outliers start: 22 outliers final: 8 residues processed: 66 average time/residue: 0.3504 time to fit residues: 34.9367 Evaluate side-chains 54 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1224 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 1 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 123 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 ASN A 920 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.106064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.061076 restraints weight = 37870.438| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.43 r_work: 0.2732 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13972 Z= 0.268 Angle : 0.542 7.304 19440 Z= 0.289 Chirality : 0.038 0.180 2229 Planarity : 0.003 0.049 1969 Dihedral : 19.095 156.248 3308 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.99 % Allowed : 16.29 % Favored : 81.72 % 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: 0.41 (0.23), residues: 1262 helix: 0.98 (0.20), residues: 639 sheet: -0.58 (0.50), residues: 119 loop : -0.29 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1136 HIS 0.007 0.001 HIS A 328 PHE 0.010 0.001 PHE A 518 TYR 0.012 0.001 TYR A 568 ARG 0.003 0.000 ARG A 324 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 592) hydrogen bonds : angle 4.32036 ( 1604) covalent geometry : bond 0.00583 (13972) covalent geometry : angle 0.54235 (19440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 48 time to evaluate : 1.756 Fit side-chains revert: symmetry clash REVERT: A 822 MET cc_start: 0.6706 (tpp) cc_final: 0.5922 (tpp) REVERT: A 1003 LYS cc_start: 0.6648 (OUTLIER) cc_final: 0.6384 (pttt) REVERT: A 1153 LYS cc_start: 0.8863 (mmtm) cc_final: 0.8405 (pttt) REVERT: A 1224 ASN cc_start: 0.9422 (OUTLIER) cc_final: 0.9110 (m110) outliers start: 23 outliers final: 12 residues processed: 68 average time/residue: 0.4574 time to fit residues: 49.5114 Evaluate side-chains 56 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1236 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 87 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 113 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 82 optimal weight: 20.0000 chunk 88 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 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 342 GLN A 920 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.108335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.063558 restraints weight = 38070.270| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.43 r_work: 0.2794 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13972 Z= 0.112 Angle : 0.467 7.811 19440 Z= 0.251 Chirality : 0.035 0.181 2229 Planarity : 0.003 0.047 1969 Dihedral : 19.002 154.377 3308 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.39 % Allowed : 17.42 % Favored : 81.20 % 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: 0.64 (0.24), residues: 1262 helix: 1.18 (0.21), residues: 638 sheet: -0.41 (0.51), residues: 119 loop : -0.22 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1136 HIS 0.004 0.001 HIS A 328 PHE 0.011 0.001 PHE A 518 TYR 0.021 0.001 TYR A 568 ARG 0.002 0.000 ARG A1114 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 592) hydrogen bonds : angle 4.15661 ( 1604) covalent geometry : bond 0.00239 (13972) covalent geometry : angle 0.46692 (19440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 822 MET cc_start: 0.6590 (tpp) cc_final: 0.5678 (tpp) REVERT: A 1010 TYR cc_start: 0.6580 (t80) cc_final: 0.5952 (t80) REVERT: A 1108 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8721 (mp0) REVERT: A 1153 LYS cc_start: 0.8813 (mmtm) cc_final: 0.8394 (pttt) REVERT: A 1224 ASN cc_start: 0.9361 (OUTLIER) cc_final: 0.9114 (m110) outliers start: 16 outliers final: 8 residues processed: 59 average time/residue: 0.2628 time to fit residues: 24.3106 Evaluate side-chains 53 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1224 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 25 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 chunk 127 optimal weight: 20.0000 chunk 4 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN A1241 HIS ** A1286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.104137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.059242 restraints weight = 38185.281| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.52 r_work: 0.2695 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 13972 Z= 0.377 Angle : 0.629 8.761 19440 Z= 0.332 Chirality : 0.042 0.183 2229 Planarity : 0.004 0.052 1969 Dihedral : 19.185 157.592 3308 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.51 % Allowed : 16.55 % Favored : 80.94 % 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: 0.32 (0.23), residues: 1262 helix: 0.92 (0.20), residues: 639 sheet: -0.61 (0.50), residues: 119 loop : -0.37 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1074 HIS 0.007 0.001 HIS A 328 PHE 0.011 0.002 PHE A 518 TYR 0.014 0.002 TYR A 568 ARG 0.004 0.001 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.04769 ( 592) hydrogen bonds : angle 4.48828 ( 1604) covalent geometry : bond 0.00819 (13972) covalent geometry : angle 0.62926 (19440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 50 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 822 MET cc_start: 0.6558 (tpp) cc_final: 0.5617 (tpp) REVERT: A 1003 LYS cc_start: 0.6613 (OUTLIER) cc_final: 0.6278 (pttt) REVERT: A 1153 LYS cc_start: 0.8904 (mmtm) cc_final: 0.8488 (pttt) REVERT: A 1224 ASN cc_start: 0.9443 (OUTLIER) cc_final: 0.9119 (m110) REVERT: A 1278 LYS cc_start: 0.9788 (OUTLIER) cc_final: 0.9505 (mtmm) outliers start: 29 outliers final: 19 residues processed: 76 average time/residue: 0.2557 time to fit residues: 29.7158 Evaluate side-chains 67 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 45 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1206 LEU Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1278 LYS Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain A residue 1353 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 94 optimal weight: 20.0000 chunk 13 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 4 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 34 optimal weight: 0.0570 chunk 133 optimal weight: 2.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS A 920 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.107685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.062985 restraints weight = 37945.242| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.47 r_work: 0.2790 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13972 Z= 0.113 Angle : 0.488 9.027 19440 Z= 0.259 Chirality : 0.035 0.185 2229 Planarity : 0.003 0.045 1969 Dihedral : 19.026 154.801 3308 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.56 % Allowed : 17.85 % Favored : 80.59 % 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: 0.64 (0.24), residues: 1262 helix: 1.16 (0.21), residues: 638 sheet: -0.52 (0.50), residues: 119 loop : -0.15 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1136 HIS 0.004 0.001 HIS A 328 PHE 0.012 0.001 PHE A 518 TYR 0.014 0.001 TYR A 568 ARG 0.003 0.000 ARG A1114 Details of bonding type rmsd hydrogen bonds : bond 0.03444 ( 592) hydrogen bonds : angle 4.23252 ( 1604) covalent geometry : bond 0.00240 (13972) covalent geometry : angle 0.48768 (19440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 MET cc_start: 0.6379 (tpp) cc_final: 0.5473 (tpp) REVERT: A 1153 LYS cc_start: 0.8872 (mmtm) cc_final: 0.8510 (pttt) REVERT: A 1224 ASN cc_start: 0.9367 (OUTLIER) cc_final: 0.9115 (m110) outliers start: 18 outliers final: 11 residues processed: 65 average time/residue: 0.2781 time to fit residues: 27.7314 Evaluate side-chains 59 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 920 GLN Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1312 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 37 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 47 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.106046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.061579 restraints weight = 37833.026| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.41 r_work: 0.2742 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13972 Z= 0.230 Angle : 0.545 9.586 19440 Z= 0.286 Chirality : 0.037 0.201 2229 Planarity : 0.003 0.045 1969 Dihedral : 18.999 155.728 3308 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.47 % Allowed : 18.02 % Favored : 80.50 % 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: 0.60 (0.24), residues: 1262 helix: 1.15 (0.21), residues: 637 sheet: -0.54 (0.50), residues: 119 loop : -0.21 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1136 HIS 0.006 0.001 HIS A 328 PHE 0.010 0.001 PHE A 693 TYR 0.013 0.001 TYR A 155 ARG 0.006 0.000 ARG A 919 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 592) hydrogen bonds : angle 4.24330 ( 1604) covalent geometry : bond 0.00501 (13972) covalent geometry : angle 0.54462 (19440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 822 MET cc_start: 0.6335 (tpp) cc_final: 0.5404 (tpp) REVERT: A 1010 TYR cc_start: 0.6777 (t80) cc_final: 0.6202 (t80) REVERT: A 1153 LYS cc_start: 0.8916 (mmtm) cc_final: 0.8541 (pttt) REVERT: A 1224 ASN cc_start: 0.9427 (OUTLIER) cc_final: 0.9107 (m110) outliers start: 17 outliers final: 13 residues processed: 65 average time/residue: 0.2633 time to fit residues: 26.6982 Evaluate side-chains 62 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1353 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.107261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.062441 restraints weight = 37771.161| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.50 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13972 Z= 0.142 Angle : 0.498 9.857 19440 Z= 0.262 Chirality : 0.036 0.192 2229 Planarity : 0.003 0.045 1969 Dihedral : 18.929 154.696 3308 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.30 % Allowed : 18.20 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.24), residues: 1262 helix: 1.25 (0.21), residues: 638 sheet: -0.44 (0.50), residues: 119 loop : -0.15 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1136 HIS 0.005 0.001 HIS A 723 PHE 0.009 0.001 PHE A 693 TYR 0.012 0.001 TYR A 155 ARG 0.002 0.000 ARG A1114 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 592) hydrogen bonds : angle 4.14414 ( 1604) covalent geometry : bond 0.00309 (13972) covalent geometry : angle 0.49829 (19440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 MET cc_start: 0.6174 (tpp) cc_final: 0.5292 (tpp) REVERT: A 1153 LYS cc_start: 0.8888 (mmtm) cc_final: 0.8574 (pttt) REVERT: A 1224 ASN cc_start: 0.9247 (OUTLIER) cc_final: 0.8978 (m110) outliers start: 15 outliers final: 13 residues processed: 62 average time/residue: 0.2684 time to fit residues: 25.9528 Evaluate side-chains 61 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 126 optimal weight: 0.3980 chunk 108 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 ASN A 920 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.107016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.062609 restraints weight = 38014.846| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.39 r_work: 0.2773 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13972 Z= 0.162 Angle : 0.508 9.843 19440 Z= 0.266 Chirality : 0.036 0.198 2229 Planarity : 0.003 0.045 1969 Dihedral : 18.893 154.705 3308 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.47 % Allowed : 18.11 % Favored : 80.42 % 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 (0.24), residues: 1262 helix: 1.29 (0.21), residues: 638 sheet: -0.45 (0.50), residues: 119 loop : -0.13 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 PHE 0.008 0.001 PHE A 693 TYR 0.013 0.001 TYR A 155 ARG 0.001 0.000 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 592) hydrogen bonds : angle 4.16463 ( 1604) covalent geometry : bond 0.00353 (13972) covalent geometry : angle 0.50783 (19440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8894.16 seconds wall clock time: 162 minutes 57.15 seconds (9777.15 seconds total)