Starting phenix.real_space_refine on Sat Oct 11 09:21:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6x_41083/10_2025/8t6x_41083.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6x_41083/10_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_41083/10_2025/8t6x_41083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6x_41083/10_2025/8t6x_41083.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6x_41083/10_2025/8t6x_41083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6x_41083/10_2025/8t6x_41083.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 3.03, per 1000 atoms: 0.23 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: 1.00 Conformation dependent library (CDL) restraints added in 499.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.84 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: 3.25 Time building geometry restraints manager: 1.38 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: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.570 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.310 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.001 ARG A 71 TYR 0.023 0.002 TYR A 568 PHE 0.034 0.002 PHE A 518 TRP 0.011 0.001 TRP A 18 HIS 0.009 0.002 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00389 (13972) covalent geometry : angle 0.72287 (19440) hydrogen bonds : bond 0.14297 ( 592) hydrogen bonds : angle 5.91163 ( 1604) *********************** 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 : 0.477 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: 0.1130 time to fit residues: 9.9274 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 : 0.430 ------------------------------------------------------------------------------- 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 98 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 690 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.107771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.062809 restraints weight = 37603.916| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.46 r_work: 0.2773 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13972 Z= 0.238 Angle : 0.544 5.552 19440 Z= 0.293 Chirality : 0.038 0.176 2229 Planarity : 0.004 0.049 1969 Dihedral : 19.094 157.229 3310 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.82 % Allowed : 15.08 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.23), residues: 1262 helix: 0.54 (0.20), residues: 642 sheet: -0.22 (0.51), residues: 124 loop : -0.41 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 71 TYR 0.010 0.001 TYR A 568 PHE 0.013 0.001 PHE A 693 TRP 0.009 0.001 TRP A1074 HIS 0.008 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00515 (13972) covalent geometry : angle 0.54390 (19440) hydrogen bonds : bond 0.04075 ( 592) hydrogen bonds : angle 4.50742 ( 1604) *********************** 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 71 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 693 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7494 (m-80) outliers start: 21 outliers final: 11 residues processed: 64 average time/residue: 0.1221 time to fit residues: 11.7137 Evaluate side-chains 56 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 949 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1098 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 50 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 123 optimal weight: 0.0870 chunk 115 optimal weight: 0.1980 chunk 77 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 overall best weight: 1.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 HIS ** 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 = 0.3955 r_free = 0.3955 target = 0.108037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.063105 restraints weight = 37980.347| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.45 r_work: 0.2779 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1408 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= 0.182 Angle : 0.494 5.834 19440 Z= 0.267 Chirality : 0.036 0.179 2229 Planarity : 0.003 0.049 1969 Dihedral : 19.075 155.656 3308 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.91 % Allowed : 15.86 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.23), residues: 1262 helix: 0.86 (0.21), residues: 637 sheet: -0.46 (0.50), residues: 121 loop : -0.29 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 307 TYR 0.011 0.001 TYR A 155 PHE 0.016 0.001 PHE A 518 TRP 0.008 0.001 TRP A1136 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00396 (13972) covalent geometry : angle 0.49435 (19440) hydrogen bonds : bond 0.03775 ( 592) hydrogen bonds : angle 4.28158 ( 1604) *********************** 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 67 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 45 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 648 MET cc_start: 0.5959 (ptp) cc_final: 0.5469 (ptp) REVERT: A 693 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7753 (m-80) REVERT: A 822 MET cc_start: 0.6715 (tpp) cc_final: 0.5437 (tpp) REVERT: A 879 MET cc_start: -0.0554 (mmt) cc_final: -0.1552 (mtt) REVERT: A 1003 LYS cc_start: 0.6687 (OUTLIER) cc_final: 0.6291 (pttt) REVERT: A 1153 LYS cc_start: 0.8815 (mmtm) cc_final: 0.8322 (pttt) outliers start: 22 outliers final: 11 residues processed: 64 average time/residue: 0.1114 time to fit residues: 10.7886 Evaluate side-chains 57 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 115 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 723 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 = 0.3976 r_free = 0.3976 target = 0.109225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.064602 restraints weight = 37603.248| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.38 r_work: 0.2818 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13972 Z= 0.118 Angle : 0.449 6.421 19440 Z= 0.243 Chirality : 0.035 0.179 2229 Planarity : 0.003 0.046 1969 Dihedral : 18.953 154.146 3308 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.73 % Allowed : 15.94 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.24), residues: 1262 helix: 1.06 (0.21), residues: 640 sheet: -0.32 (0.50), residues: 126 loop : -0.20 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1114 TYR 0.011 0.001 TYR A 568 PHE 0.014 0.001 PHE A 693 TRP 0.008 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00253 (13972) covalent geometry : angle 0.44891 (19440) hydrogen bonds : bond 0.03274 ( 592) hydrogen bonds : angle 4.08985 ( 1604) *********************** 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 73 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 693 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.8011 (m-80) REVERT: A 822 MET cc_start: 0.6740 (tpp) cc_final: 0.5382 (tpp) REVERT: A 879 MET cc_start: -0.0325 (mmt) cc_final: -0.1383 (mtt) REVERT: A 1153 LYS cc_start: 0.8796 (mmtm) cc_final: 0.8380 (pttt) REVERT: A 1224 ASN cc_start: 0.9365 (OUTLIER) cc_final: 0.9100 (m110) outliers start: 20 outliers final: 7 residues processed: 71 average time/residue: 0.1169 time to fit residues: 12.5632 Evaluate side-chains 52 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 621 LEU 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 949 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1206 LEU 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 9 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 920 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.106527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.061609 restraints weight = 37901.696| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.39 r_work: 0.2748 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13972 Z= 0.251 Angle : 0.533 8.589 19440 Z= 0.284 Chirality : 0.038 0.180 2229 Planarity : 0.003 0.048 1969 Dihedral : 19.052 156.040 3308 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.08 % Allowed : 16.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.23), residues: 1262 helix: 1.03 (0.21), residues: 640 sheet: -0.43 (0.50), residues: 119 loop : -0.24 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 71 TYR 0.011 0.001 TYR A 568 PHE 0.014 0.001 PHE A 693 TRP 0.007 0.001 TRP A1074 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00546 (13972) covalent geometry : angle 0.53267 (19440) hydrogen bonds : bond 0.03987 ( 592) hydrogen bonds : angle 4.22792 ( 1604) *********************** 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 72 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 48 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 693 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7626 (m-80) REVERT: A 822 MET cc_start: 0.6724 (tpp) cc_final: 0.5349 (tpp) REVERT: A 879 MET cc_start: -0.0284 (mmt) cc_final: -0.1410 (mtt) REVERT: A 1003 LYS cc_start: 0.6541 (OUTLIER) cc_final: 0.6264 (pttt) REVERT: A 1153 LYS cc_start: 0.8858 (mmtm) cc_final: 0.8426 (pttt) REVERT: A 1224 ASN cc_start: 0.9411 (OUTLIER) cc_final: 0.9090 (m110) outliers start: 24 outliers final: 12 residues processed: 70 average time/residue: 0.1222 time to fit residues: 12.8539 Evaluate side-chains 58 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 693 PHE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 920 GLN 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 1206 LEU Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 138 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 104 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 920 GLN ** 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 = 0.3923 r_free = 0.3923 target = 0.105973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.061054 restraints weight = 38040.437| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.45 r_work: 0.2736 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2138 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= 0.261 Angle : 0.543 8.093 19440 Z= 0.287 Chirality : 0.038 0.181 2229 Planarity : 0.003 0.048 1969 Dihedral : 19.077 156.646 3308 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.82 % Allowed : 17.07 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.24), residues: 1262 helix: 0.95 (0.21), residues: 641 sheet: -0.44 (0.50), residues: 119 loop : -0.29 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 324 TYR 0.020 0.001 TYR A 568 PHE 0.016 0.001 PHE A 693 TRP 0.008 0.001 TRP A1136 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00568 (13972) covalent geometry : angle 0.54255 (19440) hydrogen bonds : bond 0.04067 ( 592) hydrogen bonds : angle 4.22121 ( 1604) *********************** 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 68 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 47 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 MET cc_start: 0.6504 (tpp) cc_final: 0.5648 (tpp) REVERT: A 1003 LYS cc_start: 0.6581 (OUTLIER) cc_final: 0.6280 (pttt) REVERT: A 1153 LYS cc_start: 0.8917 (mmtm) cc_final: 0.8494 (pttt) REVERT: A 1224 ASN cc_start: 0.9435 (OUTLIER) cc_final: 0.9133 (m110) outliers start: 21 outliers final: 14 residues processed: 64 average time/residue: 0.1216 time to fit residues: 12.0252 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 : 0.401 ------------------------------------------------------------------------------- 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 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 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 1312 LEU Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 9 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 6 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 105 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.107351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.062589 restraints weight = 37522.928| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.47 r_work: 0.2775 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 0.035 13972 Z= 0.149 Angle : 0.484 8.447 19440 Z= 0.258 Chirality : 0.036 0.180 2229 Planarity : 0.003 0.046 1969 Dihedral : 18.989 155.104 3308 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.99 % Allowed : 17.16 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.24), residues: 1262 helix: 1.17 (0.21), residues: 634 sheet: -0.37 (0.50), residues: 119 loop : -0.23 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1114 TYR 0.033 0.001 TYR A 517 PHE 0.009 0.001 PHE A 693 TRP 0.009 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00322 (13972) covalent geometry : angle 0.48386 (19440) hydrogen bonds : bond 0.03498 ( 592) hydrogen bonds : angle 4.13345 ( 1604) *********************** 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 71 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 48 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 822 MET cc_start: 0.6517 (tpp) cc_final: 0.5532 (tpp) REVERT: A 1010 TYR cc_start: 0.6581 (t80) cc_final: 0.6003 (t80) REVERT: A 1153 LYS cc_start: 0.8880 (mmtm) cc_final: 0.8494 (pttt) REVERT: A 1224 ASN cc_start: 0.9384 (OUTLIER) cc_final: 0.9140 (m110) outliers start: 23 outliers final: 14 residues processed: 69 average time/residue: 0.1107 time to fit residues: 12.0475 Evaluate side-chains 60 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU 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 693 PHE 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 1098 THR 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 1312 LEU Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 3 optimal weight: 2.9990 chunk 50 optimal weight: 0.0770 chunk 9 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 134 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 920 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.106308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.061329 restraints weight = 37808.994| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.46 r_work: 0.2750 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13972 Z= 0.214 Angle : 0.520 8.521 19440 Z= 0.276 Chirality : 0.037 0.194 2229 Planarity : 0.003 0.046 1969 Dihedral : 18.996 155.710 3308 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.73 % Allowed : 17.59 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.24), residues: 1262 helix: 1.15 (0.21), residues: 634 sheet: -0.44 (0.51), residues: 119 loop : -0.23 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 324 TYR 0.031 0.001 TYR A 517 PHE 0.008 0.001 PHE A 446 TRP 0.008 0.001 TRP A1136 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00465 (13972) covalent geometry : angle 0.52008 (19440) hydrogen bonds : bond 0.03825 ( 592) hydrogen bonds : angle 4.21127 ( 1604) *********************** 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 71 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 693 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7322 (m-80) REVERT: A 822 MET cc_start: 0.6391 (tpp) cc_final: 0.5447 (tpp) REVERT: A 1010 TYR cc_start: 0.6646 (t80) cc_final: 0.6075 (t80) REVERT: A 1153 LYS cc_start: 0.8920 (mmtm) cc_final: 0.8515 (pttt) REVERT: A 1224 ASN cc_start: 0.9427 (OUTLIER) cc_final: 0.9111 (m110) outliers start: 20 outliers final: 13 residues processed: 67 average time/residue: 0.1188 time to fit residues: 12.1463 Evaluate side-chains 63 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 23 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 22 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 920 GLN A1241 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.105692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.060991 restraints weight = 38166.742| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.46 r_work: 0.2728 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13972 Z= 0.264 Angle : 0.575 11.109 19440 Z= 0.303 Chirality : 0.038 0.191 2229 Planarity : 0.003 0.046 1969 Dihedral : 19.060 156.747 3308 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.82 % Allowed : 17.94 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.24), residues: 1262 helix: 1.05 (0.21), residues: 632 sheet: -0.53 (0.50), residues: 119 loop : -0.20 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 324 TYR 0.032 0.001 TYR A 517 PHE 0.009 0.001 PHE A 518 TRP 0.007 0.001 TRP A1136 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00575 (13972) covalent geometry : angle 0.57510 (19440) hydrogen bonds : bond 0.04146 ( 592) hydrogen bonds : angle 4.35201 ( 1604) *********************** 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 70 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 49 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 MET cc_start: 0.6302 (tpp) cc_final: 0.5381 (tpp) REVERT: A 1003 LYS cc_start: 0.6396 (OUTLIER) cc_final: 0.6196 (pttt) REVERT: A 1010 TYR cc_start: 0.6728 (t80) cc_final: 0.6352 (t80) REVERT: A 1153 LYS cc_start: 0.8971 (mmtm) cc_final: 0.8574 (pttt) REVERT: A 1224 ASN cc_start: 0.9446 (OUTLIER) cc_final: 0.9141 (m110) outliers start: 21 outliers final: 17 residues processed: 67 average time/residue: 0.1213 time to fit residues: 12.4244 Evaluate side-chains 65 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 621 LEU Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 920 GLN 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 1206 LEU Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1225 GLU 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 61 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 97 optimal weight: 0.0170 chunk 104 optimal weight: 0.5980 chunk 112 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.0820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 920 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.107427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.062690 restraints weight = 37565.094| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.46 r_work: 0.2783 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13972 Z= 0.137 Angle : 0.506 9.938 19440 Z= 0.267 Chirality : 0.036 0.198 2229 Planarity : 0.003 0.045 1969 Dihedral : 18.986 154.717 3308 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.30 % Allowed : 18.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.24), residues: 1262 helix: 1.17 (0.21), residues: 632 sheet: -0.41 (0.51), residues: 119 loop : -0.10 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 919 TYR 0.029 0.001 TYR A 517 PHE 0.009 0.001 PHE A 693 TRP 0.010 0.001 TRP A1136 HIS 0.005 0.001 HIS A 723 Details of bonding type rmsd covalent geometry : bond 0.00297 (13972) covalent geometry : angle 0.50591 (19440) hydrogen bonds : bond 0.03487 ( 592) hydrogen bonds : angle 4.20700 ( 1604) ********************** 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 63 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 MET cc_start: 0.6182 (tpp) cc_final: 0.5337 (tpp) REVERT: A 1153 LYS cc_start: 0.8926 (mmtm) cc_final: 0.8545 (pttt) REVERT: A 1224 ASN cc_start: 0.9396 (OUTLIER) cc_final: 0.9127 (m110) outliers start: 15 outliers final: 11 residues processed: 60 average time/residue: 0.1231 time to fit residues: 11.2308 Evaluate side-chains 60 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 920 GLN Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1206 LEU Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1225 GLU 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 0 optimal weight: 4.9990 chunk 119 optimal weight: 0.3980 chunk 47 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 chunk 127 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 920 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.105505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.060652 restraints weight = 38171.090| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.43 r_work: 0.2736 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13972 Z= 0.256 Angle : 0.565 9.843 19440 Z= 0.296 Chirality : 0.038 0.203 2229 Planarity : 0.003 0.045 1969 Dihedral : 18.997 156.097 3308 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.56 % Allowed : 17.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.24), residues: 1262 helix: 1.12 (0.21), residues: 632 sheet: -0.50 (0.50), residues: 119 loop : -0.17 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 919 TYR 0.026 0.001 TYR A 517 PHE 0.020 0.001 PHE A 693 TRP 0.008 0.001 TRP A1074 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00557 (13972) covalent geometry : angle 0.56541 (19440) hydrogen bonds : bond 0.04038 ( 592) hydrogen bonds : angle 4.29919 ( 1604) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4131.09 seconds wall clock time: 71 minutes 30.93 seconds (4290.93 seconds total)