Starting phenix.real_space_refine on Thu Aug 6 04:28:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6x_41083/08_2026/8t6x_41083.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6x_41083/08_2026/8t6x_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_41083/08_2026/8t6x_41083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6x_41083/08_2026/8t6x_41083.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6x_41083/08_2026/8t6x_41083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6x_41083/08_2026/8t6x_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-2.2rc3-6140/lib/python3.11/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: 2.95, per 1000 atoms: 0.22 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: 1.04 Conformation dependent library (CDL) restraints added in 488.2 milliseconds 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: 1.90 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: 3.04 Time building geometry restraints manager: 1.41 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=" C1' DC D 34 " pdb=" N1 DC D 34 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.99e+01 bond pdb=" C1' DT C 34 " pdb=" N1 DT C 34 " ideal model delta sigma weight residual 1.468 1.523 -0.055 1.40e-02 5.10e+03 1.55e+01 bond pdb=" C1' DT C 28 " pdb=" N1 DT C 28 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.24e+01 bond pdb=" C1' DC C 29 " pdb=" N1 DC C 29 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.10e+01 bond pdb=" C1' DC D 36 " pdb=" N1 DC D 36 " ideal model delta sigma weight residual 1.468 1.510 -0.042 1.40e-02 5.10e+03 9.12e+00 ... (remaining 13967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 19091 2.57 - 5.14: 311 5.14 - 7.72: 26 7.72 - 10.29: 10 10.29 - 12.86: 2 Bond angle restraints: 19440 Sorted by residual: angle pdb=" O4' DC C 21 " pdb=" C4' DC C 21 " pdb=" C3' DC C 21 " ideal model delta sigma weight residual 106.00 102.91 3.09 6.00e-01 2.78e+00 2.66e+01 angle pdb=" N1 U B 72 " pdb=" C2 U B 72 " pdb=" O2 U B 72 " ideal model delta sigma weight residual 122.80 126.21 -3.41 7.00e-01 2.04e+00 2.37e+01 angle pdb=" C3' A B 38 " pdb=" O3' A B 38 " pdb=" P G B 39 " ideal model delta sigma weight residual 119.70 125.20 -5.50 1.20e+00 6.94e-01 2.10e+01 angle pdb=" O2 U B 72 " pdb=" C2 U B 72 " pdb=" N3 U B 72 " ideal model delta sigma weight residual 122.20 119.03 3.17 7.00e-01 2.04e+00 2.06e+01 angle pdb=" O4' DC D 34 " pdb=" C1' DC D 34 " pdb=" N1 DC D 34 " ideal model delta sigma weight residual 108.00 111.16 -3.16 7.00e-01 2.04e+00 2.04e+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: 1690 0.052 - 0.103: 381 0.103 - 0.155: 144 0.155 - 0.206: 9 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: 3.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.750 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 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 0.062 13972 Z= 0.294 Angle : 0.798 12.860 19440 Z= 0.553 Chirality : 0.051 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 are 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/Z covalent geometry : bond 0.00434 / 0.29 (13972) covalent geometry : angle 0.79778 / 0.55 (19440) hydrogen bonds : bond 0.14297 / 9.70 ( 592) hydrogen bonds : angle 5.91163 / 4.38 ( 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 : 0.453 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: 0.1116 time to fit residues: 9.8350 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 : 0.431 ------------------------------------------------------------------------------- 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: 20.0000 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... A 121 ASN A 844 GLN A 920 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.109424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.065166 restraints weight = 37371.436| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.25 r_work: 0.2875 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13972 Z= 0.216 Angle : 0.555 7.486 19440 Z= 0.310 Chirality : 0.040 0.241 2229 Planarity : 0.004 0.052 1969 Dihedral : 19.156 153.092 3310 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.30 % Allowed : 15.68 % Favored : 83.02 % 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 are not related in a simple way. whole: -0.07 (0.23), residues: 1262 helix: 0.39 (0.20), residues: 642 sheet: -0.17 (0.51), residues: 124 loop : -0.42 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 71 TYR 0.011 0.001 TYR A 155 PHE 0.011 0.001 PHE A1105 TRP 0.010 0.001 TRP A1136 HIS 0.007 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.22 (13972) covalent geometry : angle 0.55547 / 0.31 (19440) hydrogen bonds : bond 0.04852 / 3.27 ( 592) hydrogen bonds : angle 4.70528 / 3.50 ( 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 65 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 693 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.7580 (m-80) outliers start: 15 outliers final: 9 residues processed: 59 average time/residue: 0.1147 time to fit residues: 10.3864 Evaluate side-chains 57 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 920 GLN Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1108 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 50 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 HIS A 690 ASN ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1308 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.107344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.062124 restraints weight = 38104.367| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.51 r_work: 0.2747 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 13972 Z= 0.260 Angle : 0.569 6.896 19440 Z= 0.312 Chirality : 0.040 0.226 2229 Planarity : 0.004 0.053 1969 Dihedral : 19.158 154.343 3308 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.51 % Allowed : 15.60 % Favored : 81.89 % 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 are not related in a simple way. whole: 0.15 (0.23), residues: 1262 helix: 0.69 (0.20), residues: 637 sheet: -0.44 (0.51), residues: 119 loop : -0.38 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 324 TYR 0.015 0.001 TYR A 568 PHE 0.015 0.001 PHE A 693 TRP 0.008 0.001 TRP A1136 HIS 0.010 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.26 (13972) covalent geometry : angle 0.56886 / 0.31 (19440) hydrogen bonds : bond 0.04661 / 3.13 ( 592) hydrogen bonds : angle 4.51097 / 3.34 ( 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 76 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 47 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 693 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7566 (m-80) REVERT: A 1003 LYS cc_start: 0.6723 (OUTLIER) cc_final: 0.6363 (pttt) outliers start: 29 outliers final: 15 residues processed: 70 average time/residue: 0.1026 time to fit residues: 11.0803 Evaluate side-chains 62 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 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 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 1206 LEU 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 115 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 chunk 121 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3958 r_free = 0.3958 target = 0.108289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.063402 restraints weight = 37559.505| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.42 r_work: 0.2787 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13972 Z= 0.151 Angle : 0.483 6.986 19440 Z= 0.273 Chirality : 0.037 0.222 2229 Planarity : 0.003 0.051 1969 Dihedral : 19.166 153.500 3308 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.65 % Allowed : 16.20 % Favored : 82.15 % 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 are not related in a simple way. whole: 0.36 (0.23), residues: 1262 helix: 0.91 (0.21), residues: 638 sheet: -0.49 (0.50), residues: 121 loop : -0.30 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 976 TYR 0.012 0.001 TYR A 568 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/Z covalent geometry : bond 0.00314 / 0.15 (13972) covalent geometry : angle 0.48303 / 0.27 (19440) hydrogen bonds : bond 0.04026 / 2.70 ( 592) hydrogen bonds : angle 4.30703 / 3.20 ( 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 67 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 693 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.8004 (m-80) REVERT: A 822 MET cc_start: 0.6595 (tpp) cc_final: 0.5354 (tpp) REVERT: A 879 MET cc_start: -0.0294 (mmt) cc_final: -0.1353 (mtt) REVERT: A 1003 LYS cc_start: 0.6666 (OUTLIER) cc_final: 0.6284 (pttt) REVERT: A 1224 ASN cc_start: 0.9375 (OUTLIER) cc_final: 0.9095 (m110) outliers start: 19 outliers final: 9 residues processed: 64 average time/residue: 0.1160 time to fit residues: 11.5044 Evaluate side-chains 58 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 404 THR 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 1003 LYS Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1329 THR 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: 0.9980 chunk 67 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 80 optimal weight: 0.2980 chunk 44 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.108423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.063584 restraints weight = 37596.691| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.41 r_work: 0.2790 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13972 Z= 0.140 Angle : 0.471 9.182 19440 Z= 0.264 Chirality : 0.037 0.216 2229 Planarity : 0.003 0.050 1969 Dihedral : 19.123 153.327 3308 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.82 % Allowed : 16.29 % Favored : 81.89 % 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 are not related in a simple way. whole: 0.52 (0.24), residues: 1262 helix: 1.06 (0.21), residues: 638 sheet: -0.48 (0.50), residues: 121 loop : -0.24 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 71 TYR 0.017 0.001 TYR A 639 PHE 0.015 0.001 PHE A 518 TRP 0.008 0.001 TRP A1136 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (13972) covalent geometry : angle 0.47127 / 0.26 (19440) hydrogen bonds : bond 0.03863 / 2.58 ( 592) hydrogen bonds : angle 4.22580 / 3.15 ( 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 69 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 648 MET cc_start: 0.6063 (ptp) cc_final: 0.5736 (ptp) REVERT: A 822 MET cc_start: 0.6741 (tpp) cc_final: 0.5475 (tpp) REVERT: A 879 MET cc_start: -0.0355 (mmt) cc_final: -0.1354 (mtt) REVERT: A 1003 LYS cc_start: 0.6627 (OUTLIER) cc_final: 0.6213 (pttt) REVERT: A 1224 ASN cc_start: 0.9389 (OUTLIER) cc_final: 0.9071 (m110) outliers start: 21 outliers final: 12 residues processed: 65 average time/residue: 0.1153 time to fit residues: 11.5975 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 : 0.271 ------------------------------------------------------------------------------- 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 619 ILE 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 1329 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 138 optimal weight: 30.0000 chunk 117 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 127 optimal weight: 40.0000 chunk 74 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 123 optimal weight: 0.5980 chunk 139 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.105960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.060862 restraints weight = 38108.003| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.46 r_work: 0.2725 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 13972 Z= 0.309 Angle : 0.608 8.135 19440 Z= 0.324 Chirality : 0.042 0.214 2229 Planarity : 0.004 0.050 1969 Dihedral : 19.154 154.659 3308 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.34 % Allowed : 16.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.23), residues: 1262 helix: 0.89 (0.20), residues: 638 sheet: -0.55 (0.50), residues: 119 loop : -0.39 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 324 TYR 0.024 0.002 TYR A 568 PHE 0.014 0.002 PHE A1105 TRP 0.007 0.001 TRP A1074 HIS 0.008 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.31 (13972) covalent geometry : angle 0.60771 / 0.32 (19440) hydrogen bonds : bond 0.04696 / 3.15 ( 592) hydrogen bonds : angle 4.39569 / 3.26 ( 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 75 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 48 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 MET cc_start: 0.6781 (tpp) cc_final: 0.5496 (tpp) REVERT: A 879 MET cc_start: -0.0500 (mmt) cc_final: -0.1519 (mtt) REVERT: A 1003 LYS cc_start: 0.6778 (OUTLIER) cc_final: 0.6324 (pttt) REVERT: A 1153 LYS cc_start: 0.8801 (mmtm) cc_final: 0.8352 (pttt) REVERT: A 1224 ASN cc_start: 0.9422 (OUTLIER) cc_final: 0.9114 (m110) outliers start: 27 outliers final: 21 residues processed: 69 average time/residue: 0.0975 time to fit residues: 10.3238 Evaluate side-chains 66 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 43 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 380 LEU Chi-restraints excluded: chain A residue 404 THR 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 733 ILE Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 931 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 1206 LEU Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1236 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: 1.9990 chunk 40 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 105 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.107320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.062284 restraints weight = 37578.643| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.42 r_work: 0.2761 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13972 Z= 0.163 Angle : 0.499 8.633 19440 Z= 0.276 Chirality : 0.037 0.220 2229 Planarity : 0.003 0.050 1969 Dihedral : 19.189 153.695 3308 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.91 % Allowed : 17.07 % Favored : 81.02 % 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 are not related in a simple way. whole: 0.46 (0.24), residues: 1262 helix: 1.03 (0.21), residues: 638 sheet: -0.52 (0.50), residues: 119 loop : -0.30 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 71 TYR 0.023 0.001 TYR A 568 PHE 0.009 0.001 PHE A 518 TRP 0.008 0.001 TRP A1136 HIS 0.006 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (13972) covalent geometry : angle 0.49873 / 0.28 (19440) hydrogen bonds : bond 0.04115 / 2.76 ( 592) hydrogen bonds : angle 4.25799 / 3.17 ( 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 67 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 45 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 648 MET cc_start: 0.6068 (ptp) cc_final: 0.5676 (ptp) REVERT: A 822 MET cc_start: 0.6721 (tpp) cc_final: 0.5379 (tpp) REVERT: A 879 MET cc_start: -0.0616 (mmt) cc_final: -0.1623 (mtt) REVERT: A 1003 LYS cc_start: 0.6646 (OUTLIER) cc_final: 0.6246 (pttt) REVERT: A 1153 LYS cc_start: 0.8812 (mmtm) cc_final: 0.8387 (pttt) REVERT: A 1224 ASN cc_start: 0.9381 (OUTLIER) cc_final: 0.9082 (m110) outliers start: 22 outliers final: 12 residues processed: 64 average time/residue: 0.1390 time to fit residues: 13.1347 Evaluate side-chains 59 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 3 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 60 optimal weight: 0.0970 chunk 23 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 127 optimal weight: 40.0000 chunk 134 optimal weight: 20.0000 chunk 93 optimal weight: 0.0670 overall best weight: 1.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.107086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.062064 restraints weight = 37683.213| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.43 r_work: 0.2755 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13972 Z= 0.184 Angle : 0.504 8.540 19440 Z= 0.277 Chirality : 0.038 0.218 2229 Planarity : 0.003 0.049 1969 Dihedral : 19.172 153.627 3308 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.91 % Allowed : 17.07 % Favored : 81.02 % 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 are not related in a simple way. whole: 0.46 (0.24), residues: 1262 helix: 1.03 (0.21), residues: 638 sheet: -0.53 (0.50), residues: 119 loop : -0.29 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1303 TYR 0.023 0.001 TYR A 568 PHE 0.011 0.001 PHE A 518 TRP 0.008 0.001 TRP A1136 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (13972) covalent geometry : angle 0.50432 / 0.28 (19440) hydrogen bonds : bond 0.04051 / 2.71 ( 592) hydrogen bonds : angle 4.24214 / 3.15 ( 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 68 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 46 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 MET cc_start: 0.6646 (tpp) cc_final: 0.5890 (tpp) REVERT: A 1003 LYS cc_start: 0.6523 (OUTLIER) cc_final: 0.6211 (pttt) REVERT: A 1153 LYS cc_start: 0.8823 (mmtm) cc_final: 0.8398 (pttt) REVERT: A 1224 ASN cc_start: 0.9394 (OUTLIER) cc_final: 0.9119 (m110) outliers start: 22 outliers final: 15 residues processed: 65 average time/residue: 0.1169 time to fit residues: 11.6423 Evaluate side-chains 62 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 380 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 737 ILE 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 1206 LEU Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1236 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: 4.9990 chunk 122 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 14 optimal weight: 0.3980 chunk 86 optimal weight: 0.0030 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.108190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.063332 restraints weight = 37708.976| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.46 r_work: 0.2783 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13972 Z= 0.115 Angle : 0.473 9.460 19440 Z= 0.261 Chirality : 0.036 0.219 2229 Planarity : 0.003 0.047 1969 Dihedral : 19.166 152.509 3308 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.47 % Allowed : 17.42 % 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 are not related in a simple way. whole: 0.58 (0.24), residues: 1262 helix: 1.13 (0.21), residues: 639 sheet: -0.46 (0.51), residues: 119 loop : -0.24 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1303 TYR 0.018 0.001 TYR A 568 PHE 0.020 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/Z covalent geometry : bond 0.00234 / 0.12 (13972) covalent geometry : angle 0.47315 / 0.26 (19440) hydrogen bonds : bond 0.03747 / 2.51 ( 592) hydrogen bonds : angle 4.15674 / 3.11 ( 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 64 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 MET cc_start: 0.6580 (tpp) cc_final: 0.5769 (tpp) REVERT: A 1153 LYS cc_start: 0.8839 (mmtm) cc_final: 0.8386 (pttt) REVERT: A 1224 ASN cc_start: 0.9362 (OUTLIER) cc_final: 0.9086 (m110) outliers start: 17 outliers final: 13 residues processed: 63 average time/residue: 0.1167 time to fit residues: 11.5188 Evaluate side-chains 59 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 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 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 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: 6.9990 chunk 89 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.105926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.060931 restraints weight = 37884.678| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.45 r_work: 0.2730 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 13972 Z= 0.278 Angle : 0.580 9.782 19440 Z= 0.309 Chirality : 0.041 0.216 2229 Planarity : 0.004 0.048 1969 Dihedral : 19.158 154.203 3308 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.65 % Allowed : 17.68 % 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 are not related in a simple way. whole: 0.41 (0.24), residues: 1262 helix: 0.99 (0.21), residues: 638 sheet: -0.58 (0.50), residues: 119 loop : -0.30 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 324 TYR 0.017 0.001 TYR A 568 PHE 0.030 0.002 PHE A 518 TRP 0.009 0.001 TRP A1074 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.28 (13972) covalent geometry : angle 0.58050 / 0.31 (19440) hydrogen bonds : bond 0.04520 / 3.04 ( 592) hydrogen bonds : angle 4.28869 / 3.17 ( 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 69 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 MET cc_start: 0.6575 (tpp) cc_final: 0.5762 (tpp) REVERT: A 1003 LYS cc_start: 0.6644 (OUTLIER) cc_final: 0.6344 (pttt) REVERT: A 1153 LYS cc_start: 0.8855 (mmtm) cc_final: 0.8420 (pttt) REVERT: A 1224 ASN cc_start: 0.9426 (OUTLIER) cc_final: 0.9118 (m110) outliers start: 19 outliers final: 13 residues processed: 66 average time/residue: 0.1098 time to fit residues: 11.0255 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 : 0.372 ------------------------------------------------------------------------------- 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 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 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 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: 2.9990 chunk 119 optimal weight: 4.9990 chunk 47 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 104 optimal weight: 0.5980 chunk 127 optimal weight: 40.0000 chunk 99 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.107400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.062585 restraints weight = 38004.148| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.46 r_work: 0.2769 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13972 Z= 0.137 Angle : 0.487 9.786 19440 Z= 0.269 Chirality : 0.037 0.219 2229 Planarity : 0.003 0.047 1969 Dihedral : 19.184 152.981 3308 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.24), residues: 1262 helix: 1.14 (0.21), residues: 632 sheet: -0.51 (0.50), residues: 119 loop : -0.23 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1303 TYR 0.046 0.001 TYR A 517 PHE 0.024 0.001 PHE A 518 TRP 0.009 0.001 TRP A1136 HIS 0.007 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (13972) covalent geometry : angle 0.48670 / 0.27 (19440) hydrogen bonds : bond 0.03891 / 2.61 ( 592) hydrogen bonds : angle 4.19674 / 3.12 ( 1604) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3757.03 seconds wall clock time: 64 minutes 59.33 seconds (3899.33 seconds total)