Starting phenix.real_space_refine on Thu Aug 6 11:32:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t76_41085/08_2026/8t76_41085.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t76_41085/08_2026/8t76_41085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t76_41085/08_2026/8t76_41085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t76_41085/08_2026/8t76_41085.map" model { file = "/net/cci-nas-00/data/ceres_data/8t76_41085/08_2026/8t76_41085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t76_41085/08_2026/8t76_41085.cif" } resolution = 3.42 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4884 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 111 5.49 5 S 17 5.16 5 C 6629 2.51 5 N 1932 2.21 5 O 2360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 11049 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8689 Classifications: {'peptide': 1088} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 30, 'TRANS': 1057} Chain breaks: 5 Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 264 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 8, 'GLU:plan': 8, 'GLN:plan1': 1, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 108 Chain: "B" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1887 Classifications: {'RNA': 88} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 46, 'rna3p_pyr': 31} Link IDs: {'rna2p': 10, 'rna3p': 77} Chain: "C" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 268 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Time building chain proxies: 2.00, per 1000 atoms: 0.18 Number of scatterers: 11049 At special positions: 0 Unit cell: (87.486, 120.814, 121.647, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 111 15.00 O 2360 8.00 N 1932 7.00 C 6629 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: 0.92 Conformation dependent library (CDL) restraints added in 501.6 milliseconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 6 sheets defined 56.6% alpha, 10.9% beta 35 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.611A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (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: 3.919A 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 175 through 180 Processing helix chain 'A' and resid 180 through 197 removed outlier: 4.168A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 236 through 245 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 286 through 305 Processing helix chain 'A' and resid 308 through 312 removed outlier: 4.260A pdb=" N ILE A 312 " --> pdb=" O ASN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 346 through 352 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 Processing helix chain 'A' and resid 386 through 395 removed outlier: 4.837A pdb=" N LYS A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.836A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.200A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.585A 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 477 through 481 removed outlier: 3.546A pdb=" N GLU A 480 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 496 Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 637 removed outlier: 3.704A pdb=" N ILE A 632 " --> pdb=" O ASP A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 642 removed outlier: 4.265A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 652 Processing helix chain 'A' and resid 663 through 668 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 713 removed outlier: 3.575A pdb=" N ALA A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 725 Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.545A pdb=" N LYS A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 940 removed outlier: 4.548A pdb=" N ILE A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU A 935 " --> pdb=" O VAL A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 980 through 1000 removed outlier: 4.501A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.813A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 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 1261 Processing helix chain 'A' and resid 1264 through 1281 removed outlier: 4.034A pdb=" N GLU A1271 " --> pdb=" O ASP A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1317 removed outlier: 3.534A pdb=" N GLN A1305 " --> pdb=" O PRO A1301 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A1310 " --> pdb=" O ALA A1306 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N THR A1314 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU A1315 " --> pdb=" O HIS A1311 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR A1316 " --> pdb=" O LEU A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.510A pdb=" N LEU A1343 " --> pdb=" O LYS A1340 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1340 through 1344' 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: 7.073A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N GLU A 762 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 8.716A 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: 9.954A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLN A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 529 through 530 Processing sheet with id=AA4, first strand: chain 'A' and resid 1106 through 1111 removed outlier: 6.449A pdb=" N LYS A1107 " --> pdb=" O PRO A1137 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N SER A1109 " --> pdb=" O LEU A1135 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU A1135 " --> pdb=" O SER A1109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 4.030A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS A1151 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS A1158 " --> pdb=" O VAL A1149 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 4.030A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS A1151 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS A1158 " --> pdb=" O VAL A1149 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 87 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 1.22 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: 2660 1.33 - 1.46: 2907 1.46 - 1.58: 5674 1.58 - 1.70: 219 1.70 - 1.82: 32 Bond restraints: 11492 Sorted by residual: bond pdb=" C3' DT C 18 " pdb=" C2' DT C 18 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.35e+00 bond pdb=" C1' DT C 13 " pdb=" N1 DT C 13 " ideal model delta sigma weight residual 1.468 1.502 -0.034 1.40e-02 5.10e+03 5.89e+00 bond pdb=" C3' DT C 16 " pdb=" C2' DT C 16 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.87e+00 bond pdb=" C3' DT C 13 " pdb=" C2' DT C 13 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.43e+00 bond pdb=" C3' DT D 42 " pdb=" C2' DT D 42 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.41e+00 ... (remaining 11487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 15783 3.43 - 6.85: 210 6.85 - 10.28: 40 10.28 - 13.70: 6 13.70 - 17.13: 3 Bond angle restraints: 16042 Sorted by residual: angle pdb=" CA LYS A 929 " pdb=" CB LYS A 929 " pdb=" CG LYS A 929 " ideal model delta sigma weight residual 114.10 127.25 -13.15 2.00e+00 2.50e-01 4.33e+01 angle pdb=" C2 C B 20 " pdb=" N1 C B 20 " pdb=" C6 C B 20 " ideal model delta sigma weight residual 120.30 117.79 2.51 4.00e-01 6.25e+00 3.93e+01 angle pdb=" N1 U B 64 " pdb=" C2 U B 64 " pdb=" O2 U B 64 " ideal model delta sigma weight residual 122.80 127.03 -4.23 7.00e-01 2.04e+00 3.66e+01 angle pdb=" CA ARG A 457 " pdb=" CB ARG A 457 " pdb=" CG ARG A 457 " ideal model delta sigma weight residual 114.10 125.25 -11.15 2.00e+00 2.50e-01 3.11e+01 angle pdb=" O5' G B 14 " pdb=" C5' G B 14 " pdb=" C4' G B 14 " ideal model delta sigma weight residual 109.40 113.69 -4.29 8.00e-01 1.56e+00 2.88e+01 ... (remaining 16037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.75: 6387 29.75 - 59.50: 490 59.50 - 89.25: 93 89.25 - 119.00: 1 119.00 - 148.75: 1 Dihedral angle restraints: 6972 sinusoidal: 3772 harmonic: 3200 Sorted by residual: dihedral pdb=" CA GLU A1099 " pdb=" C GLU A1099 " pdb=" N VAL A1100 " pdb=" CA VAL A1100 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA PRO A 200 " pdb=" C PRO A 200 " pdb=" N ILE A 201 " pdb=" CA ILE A 201 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA PHE A 498 " pdb=" C PHE A 498 " pdb=" N ASP A 499 " pdb=" CA ASP A 499 " ideal model delta harmonic sigma weight residual -180.00 -160.49 -19.51 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 6969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1467 0.064 - 0.129: 321 0.129 - 0.193: 81 0.193 - 0.257: 6 0.257 - 0.321: 3 Chirality restraints: 1878 Sorted by residual: chirality pdb=" CG LEU A 156 " pdb=" CB LEU A 156 " pdb=" CD1 LEU A 156 " pdb=" CD2 LEU A 156 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.58e+00 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 1.71e+00 chirality pdb=" CB ILE A 201 " pdb=" CA ILE A 201 " pdb=" CG1 ILE A 201 " pdb=" CG2 ILE A 201 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1875 not shown) Planarity restraints: 1638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 499 " 0.015 2.00e-02 2.50e+03 3.11e-02 9.69e+00 pdb=" CG ASP A 499 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASP A 499 " 0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP A 499 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 936 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.70e+00 pdb=" CG ASP A 936 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASP A 936 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP A 936 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1166 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.32e+00 pdb=" C ILE A1166 " 0.043 2.00e-02 2.50e+03 pdb=" O ILE A1166 " -0.016 2.00e-02 2.50e+03 pdb=" N THR A1167 " -0.015 2.00e-02 2.50e+03 ... (remaining 1635 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2726 2.80 - 3.33: 10104 3.33 - 3.85: 20021 3.85 - 4.38: 22954 4.38 - 4.90: 35813 Nonbonded interactions: 91618 Sorted by model distance: nonbonded pdb=" OD2 ASP A 110 " pdb=" OH TYR A1131 " model vdw 2.278 3.040 nonbonded pdb=" OG SER A 6 " pdb=" OD1 ASN A 758 " model vdw 2.307 3.040 nonbonded pdb=" OD1 ASN A 14 " pdb=" OG SER A 55 " model vdw 2.308 3.040 nonbonded pdb=" OD2 ASP A 596 " pdb=" OH TYR A 656 " model vdw 2.310 3.040 nonbonded pdb=" OG SER A 541 " pdb=" OE1 GLN A 544 " model vdw 2.312 3.040 ... (remaining 91613 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: 3.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.600 Find NCS groups from input model: 0.030 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11492 Z= 0.283 Angle : 1.073 17.128 16042 Z= 0.659 Chirality : 0.058 0.321 1878 Planarity : 0.007 0.060 1638 Dihedral : 18.986 148.749 4896 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.32 % Allowed : 21.30 % Favored : 78.38 % 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: -1.23 (0.24), residues: 1076 helix: -0.88 (0.20), residues: 524 sheet: -0.30 (0.51), residues: 102 loop : -0.62 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1317 TYR 0.037 0.003 TYR A 517 PHE 0.025 0.003 PHE A 518 TRP 0.023 0.003 TRP A 464 HIS 0.022 0.002 HIS A1297 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.28 (11492) covalent geometry : angle 1.07314 / 0.66 (16042) hydrogen bonds : bond 0.12788 / 8.24 ( 502) hydrogen bonds : angle 6.52811 / 4.65 ( 1406) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8304 (m-80) cc_final: 0.7738 (m-80) REVERT: A 335 LEU cc_start: 0.8376 (tt) cc_final: 0.7486 (pp) REVERT: A 631 MET cc_start: 0.6515 (tpt) cc_final: 0.6281 (tpt) REVERT: A 763 MET cc_start: -0.1590 (mmm) cc_final: -0.1836 (mmm) REVERT: A 939 MET cc_start: 0.8749 (mmp) cc_final: 0.8052 (mmt) REVERT: A 1124 LYS cc_start: 0.9168 (tppt) cc_final: 0.8841 (ptpp) REVERT: A 1225 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7163 (mm-30) outliers start: 3 outliers final: 1 residues processed: 94 average time/residue: 0.1061 time to fit residues: 14.0053 Evaluate side-chains 72 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1166 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN A 116 HIS A 190 GLN ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 ASN A 754 HIS A 940 ASN A 983 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.082686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.060535 restraints weight = 55700.086| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 4.86 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.135 11492 Z= 0.454 Angle : 1.045 13.249 16042 Z= 0.548 Chirality : 0.057 0.314 1878 Planarity : 0.008 0.129 1638 Dihedral : 19.625 158.569 2768 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 22.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 5.62 % Allowed : 16.00 % Favored : 78.38 % 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: -1.28 (0.24), residues: 1076 helix: -0.47 (0.21), residues: 536 sheet: -0.72 (0.52), residues: 92 loop : -1.19 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 100 TYR 0.035 0.004 TYR A1187 PHE 0.027 0.003 PHE A1105 TRP 0.011 0.003 TRP A 18 HIS 0.014 0.003 HIS A1264 Details of bonding type rmsd/Z covalent geometry : bond 0.00932 / 0.45 (11492) covalent geometry : angle 1.04497 / 0.55 (16042) hydrogen bonds : bond 0.08456 / 5.56 ( 502) hydrogen bonds : angle 5.90013 / 4.16 ( 1406) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 66 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8651 (m-80) cc_final: 0.8111 (m-80) REVERT: A 763 MET cc_start: -0.0388 (mmm) cc_final: -0.0745 (mmm) REVERT: A 1267 ASP cc_start: 0.9523 (OUTLIER) cc_final: 0.9178 (p0) outliers start: 52 outliers final: 25 residues processed: 111 average time/residue: 0.1018 time to fit residues: 15.9695 Evaluate side-chains 83 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 57 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1325 LYS Chi-restraints excluded: chain A residue 1330 THR Chi-restraints excluded: chain A residue 1355 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 107 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 72 optimal weight: 0.0970 chunk 32 optimal weight: 0.8980 chunk 55 optimal weight: 0.0970 chunk 6 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 GLN A1350 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.084740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.061750 restraints weight = 50853.683| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 5.02 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11492 Z= 0.139 Angle : 0.620 10.020 16042 Z= 0.333 Chirality : 0.040 0.257 1878 Planarity : 0.004 0.047 1638 Dihedral : 19.567 154.743 2768 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.41 % Allowed : 17.30 % Favored : 81.30 % 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: -0.47 (0.25), residues: 1076 helix: 0.11 (0.21), residues: 533 sheet: -0.48 (0.54), residues: 99 loop : -0.63 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 61 TYR 0.017 0.002 TYR A 155 PHE 0.018 0.002 PHE A1105 TRP 0.012 0.002 TRP A1136 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (11492) covalent geometry : angle 0.62006 / 0.33 (16042) hydrogen bonds : bond 0.04278 / 2.86 ( 502) hydrogen bonds : angle 5.03791 / 3.58 ( 1406) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8345 (m-80) cc_final: 0.7789 (m-80) REVERT: A 625 LEU cc_start: 0.8960 (mt) cc_final: 0.8737 (mt) REVERT: A 694 MET cc_start: 0.8265 (mmm) cc_final: 0.7981 (mmt) REVERT: A 763 MET cc_start: -0.0415 (mmm) cc_final: -0.0781 (mmm) REVERT: A 939 MET cc_start: 0.8525 (mmp) cc_final: 0.7777 (mmt) REVERT: A 1166 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8106 (mp) REVERT: A 1176 LYS cc_start: 0.9357 (mmmt) cc_final: 0.9145 (pttm) outliers start: 13 outliers final: 8 residues processed: 79 average time/residue: 0.1124 time to fit residues: 12.8013 Evaluate side-chains 68 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1299 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 90 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.082256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.059386 restraints weight = 51373.518| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 4.92 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11492 Z= 0.197 Angle : 0.628 7.625 16042 Z= 0.337 Chirality : 0.041 0.227 1878 Planarity : 0.004 0.052 1638 Dihedral : 19.434 155.945 2768 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.49 % Allowed : 17.73 % Favored : 79.78 % 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: -0.40 (0.25), residues: 1076 helix: 0.30 (0.22), residues: 537 sheet: -0.16 (0.56), residues: 84 loop : -0.86 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 635 TYR 0.015 0.002 TYR A 450 PHE 0.017 0.002 PHE A1105 TRP 0.010 0.002 TRP A1126 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.20 (11492) covalent geometry : angle 0.62794 / 0.34 (16042) hydrogen bonds : bond 0.05005 / 3.30 ( 502) hydrogen bonds : angle 4.98157 / 3.55 ( 1406) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8583 (m-80) cc_final: 0.7565 (m-80) REVERT: A 462 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.7930 (m-80) REVERT: A 521 TYR cc_start: 0.6598 (OUTLIER) cc_final: 0.5987 (m-80) REVERT: A 625 LEU cc_start: 0.8988 (mt) cc_final: 0.8760 (mt) REVERT: A 631 MET cc_start: 0.6904 (tpt) cc_final: 0.6510 (tpp) REVERT: A 763 MET cc_start: -0.0528 (mmm) cc_final: -0.0743 (mmm) REVERT: A 939 MET cc_start: 0.8543 (mmp) cc_final: 0.7741 (mmt) REVERT: A 1176 LYS cc_start: 0.9335 (mmmt) cc_final: 0.9106 (pttp) outliers start: 23 outliers final: 16 residues processed: 82 average time/residue: 0.1023 time to fit residues: 12.3190 Evaluate side-chains 73 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 521 TYR Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1299 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 85 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 114 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 HIS ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.080965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.058100 restraints weight = 51497.957| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 4.86 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11492 Z= 0.215 Angle : 0.643 8.704 16042 Z= 0.345 Chirality : 0.042 0.233 1878 Planarity : 0.005 0.068 1638 Dihedral : 19.525 156.162 2768 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.46 % Allowed : 17.95 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.50 (0.25), residues: 1076 helix: 0.23 (0.22), residues: 538 sheet: -0.64 (0.58), residues: 71 loop : -0.85 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 629 TYR 0.016 0.002 TYR A 450 PHE 0.018 0.002 PHE A1105 TRP 0.024 0.003 TRP A1136 HIS 0.010 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.22 (11492) covalent geometry : angle 0.64255 / 0.35 (16042) hydrogen bonds : bond 0.04889 / 3.27 ( 502) hydrogen bonds : angle 5.07591 / 3.61 ( 1406) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 62 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8644 (m-80) cc_final: 0.7624 (m-80) REVERT: A 399 LEU cc_start: 0.8307 (mt) cc_final: 0.7830 (pp) REVERT: A 462 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7883 (m-80) REVERT: A 621 LEU cc_start: 0.7959 (mt) cc_final: 0.7729 (mm) REVERT: A 625 LEU cc_start: 0.8929 (mt) cc_final: 0.8611 (mt) REVERT: A 694 MET cc_start: 0.8432 (mmm) cc_final: 0.8156 (mmt) REVERT: A 737 ILE cc_start: 0.9572 (mm) cc_final: 0.9298 (mt) REVERT: A 763 MET cc_start: -0.0051 (mmm) cc_final: -0.0332 (mmm) REVERT: A 939 MET cc_start: 0.8629 (mmp) cc_final: 0.7536 (ptp) REVERT: A 1176 LYS cc_start: 0.9300 (mmmt) cc_final: 0.9072 (pptt) outliers start: 32 outliers final: 23 residues processed: 90 average time/residue: 0.0795 time to fit residues: 10.6053 Evaluate side-chains 80 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1330 THR Chi-restraints excluded: chain A residue 1355 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 26 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 0.0570 chunk 68 optimal weight: 0.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.080642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.058234 restraints weight = 50487.530| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 4.75 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11492 Z= 0.192 Angle : 0.604 9.620 16042 Z= 0.325 Chirality : 0.041 0.231 1878 Planarity : 0.004 0.047 1638 Dihedral : 19.518 156.380 2768 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.92 % Allowed : 18.92 % Favored : 78.16 % 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: -0.44 (0.25), residues: 1076 helix: 0.33 (0.22), residues: 543 sheet: -0.72 (0.58), residues: 71 loop : -0.86 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 635 TYR 0.016 0.002 TYR A 450 PHE 0.031 0.002 PHE A1105 TRP 0.017 0.003 TRP A1136 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 (11492) covalent geometry : angle 0.60432 / 0.33 (16042) hydrogen bonds : bond 0.04688 / 3.10 ( 502) hydrogen bonds : angle 4.97100 / 3.53 ( 1406) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8626 (m-80) cc_final: 0.7604 (m-80) REVERT: A 399 LEU cc_start: 0.8502 (mt) cc_final: 0.8047 (pp) REVERT: A 462 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.7933 (m-80) REVERT: A 625 LEU cc_start: 0.8925 (mt) cc_final: 0.8644 (mt) REVERT: A 631 MET cc_start: 0.7018 (tpt) cc_final: 0.6703 (tpt) REVERT: A 659 TRP cc_start: 0.8494 (m100) cc_final: 0.8232 (m100) REVERT: A 737 ILE cc_start: 0.9582 (mm) cc_final: 0.9325 (mt) REVERT: A 939 MET cc_start: 0.8710 (mmp) cc_final: 0.8033 (mmt) REVERT: A 951 ARG cc_start: 0.8851 (mmm-85) cc_final: 0.8642 (mmm160) REVERT: A 1169 MET cc_start: 0.8826 (mmm) cc_final: 0.8560 (mmm) outliers start: 27 outliers final: 23 residues processed: 89 average time/residue: 0.0894 time to fit residues: 11.7851 Evaluate side-chains 83 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 967 ARG Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1355 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 97 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 504 ASN ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.077729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.055072 restraints weight = 52744.596| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 4.74 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 11492 Z= 0.344 Angle : 0.790 15.149 16042 Z= 0.418 Chirality : 0.048 0.228 1878 Planarity : 0.006 0.093 1638 Dihedral : 19.708 158.138 2768 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.46 % Allowed : 20.00 % Favored : 76.54 % 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: -0.81 (0.25), residues: 1076 helix: 0.12 (0.22), residues: 540 sheet: -0.75 (0.53), residues: 95 loop : -1.21 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 629 TYR 0.021 0.003 TYR A 450 PHE 0.030 0.003 PHE A1105 TRP 0.012 0.003 TRP A1136 HIS 0.012 0.002 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.34 (11492) covalent geometry : angle 0.79032 / 0.42 (16042) hydrogen bonds : bond 0.06576 / 4.36 ( 502) hydrogen bonds : angle 5.44600 / 3.86 ( 1406) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 60 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8734 (m-80) cc_final: 0.7713 (m-80) REVERT: A 462 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.7897 (m-80) REVERT: A 625 LEU cc_start: 0.8977 (mt) cc_final: 0.8720 (mt) REVERT: A 643 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.5270 (p90) REVERT: A 694 MET cc_start: 0.8691 (mmm) cc_final: 0.8375 (mmt) REVERT: A 763 MET cc_start: 0.0144 (mmm) cc_final: -0.0375 (mmm) REVERT: A 939 MET cc_start: 0.8764 (mmp) cc_final: 0.8073 (mmt) REVERT: A 951 ARG cc_start: 0.8829 (mmm-85) cc_final: 0.8610 (mmm160) outliers start: 32 outliers final: 23 residues processed: 87 average time/residue: 0.0818 time to fit residues: 10.5768 Evaluate side-chains 79 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 967 ARG Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1330 THR Chi-restraints excluded: chain A residue 1355 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 27 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 115 optimal weight: 20.0000 chunk 42 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.080666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.057780 restraints weight = 50741.599| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 4.80 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11492 Z= 0.138 Angle : 0.600 14.799 16042 Z= 0.322 Chirality : 0.039 0.250 1878 Planarity : 0.004 0.035 1638 Dihedral : 19.676 155.717 2768 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.70 % Allowed : 20.54 % Favored : 76.76 % 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: -0.50 (0.25), residues: 1076 helix: 0.28 (0.21), residues: 543 sheet: -1.02 (0.56), residues: 84 loop : -0.83 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 629 TYR 0.042 0.002 TYR A 521 PHE 0.036 0.002 PHE A1105 TRP 0.023 0.003 TRP A1126 HIS 0.005 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (11492) covalent geometry : angle 0.60033 / 0.32 (16042) hydrogen bonds : bond 0.04377 / 2.90 ( 502) hydrogen bonds : angle 5.00582 / 3.57 ( 1406) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8616 (m-80) cc_final: 0.7586 (m-80) REVERT: A 462 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7993 (m-80) REVERT: A 625 LEU cc_start: 0.8878 (mt) cc_final: 0.8612 (mt) REVERT: A 631 MET cc_start: 0.6941 (tpt) cc_final: 0.6457 (tpp) REVERT: A 643 PHE cc_start: 0.6569 (OUTLIER) cc_final: 0.5137 (p90) REVERT: A 694 MET cc_start: 0.8665 (mmm) cc_final: 0.8420 (mmt) REVERT: A 763 MET cc_start: 0.0202 (mmm) cc_final: -0.0115 (mmm) REVERT: A 939 MET cc_start: 0.8804 (mmp) cc_final: 0.7693 (ptt) REVERT: A 951 ARG cc_start: 0.8841 (mmm-85) cc_final: 0.8603 (mmm160) REVERT: A 1169 MET cc_start: 0.8814 (mmm) cc_final: 0.8580 (mmm) outliers start: 25 outliers final: 18 residues processed: 82 average time/residue: 0.1140 time to fit residues: 13.4122 Evaluate side-chains 74 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 967 ARG Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1355 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 8 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 87 optimal weight: 0.3980 chunk 82 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.079232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.056546 restraints weight = 51490.052| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 4.72 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11492 Z= 0.202 Angle : 0.625 13.016 16042 Z= 0.333 Chirality : 0.041 0.233 1878 Planarity : 0.004 0.063 1638 Dihedral : 19.628 155.554 2768 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.59 % Allowed : 20.97 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.42 (0.25), residues: 1076 helix: 0.37 (0.22), residues: 535 sheet: -0.56 (0.55), residues: 95 loop : -0.91 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 40 TYR 0.031 0.002 TYR A 521 PHE 0.033 0.002 PHE A1105 TRP 0.023 0.003 TRP A1126 HIS 0.005 0.001 HIS A1264 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.20 (11492) covalent geometry : angle 0.62503 / 0.33 (16042) hydrogen bonds : bond 0.05083 / 3.40 ( 502) hydrogen bonds : angle 5.05979 / 3.59 ( 1406) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8715 (m-80) cc_final: 0.7666 (m-80) REVERT: A 462 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.7898 (m-80) REVERT: A 625 LEU cc_start: 0.8897 (mt) cc_final: 0.8622 (mt) REVERT: A 763 MET cc_start: 0.0205 (mmm) cc_final: -0.0162 (mmm) REVERT: A 939 MET cc_start: 0.8807 (mmp) cc_final: 0.7667 (ptt) REVERT: A 951 ARG cc_start: 0.8837 (mmm-85) cc_final: 0.8618 (mmm160) outliers start: 24 outliers final: 19 residues processed: 79 average time/residue: 0.1148 time to fit residues: 13.0463 Evaluate side-chains 72 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 967 ARG Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1258 PHE Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1355 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 64 optimal weight: 0.0170 chunk 69 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.080633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.057916 restraints weight = 51343.253| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 4.80 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11492 Z= 0.138 Angle : 0.594 13.516 16042 Z= 0.313 Chirality : 0.039 0.265 1878 Planarity : 0.004 0.037 1638 Dihedral : 19.613 154.070 2768 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.27 % Allowed : 21.62 % Favored : 76.11 % 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: -0.39 (0.25), residues: 1076 helix: 0.35 (0.21), residues: 543 sheet: -0.91 (0.57), residues: 84 loop : -0.77 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 629 TYR 0.047 0.002 TYR A 521 PHE 0.037 0.002 PHE A1105 TRP 0.022 0.003 TRP A1136 HIS 0.004 0.001 HIS A 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (11492) covalent geometry : angle 0.59361 / 0.31 (16042) hydrogen bonds : bond 0.04165 / 2.75 ( 502) hydrogen bonds : angle 4.93940 / 3.51 ( 1406) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8645 (m-80) cc_final: 0.7589 (m-80) REVERT: A 462 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.8029 (m-80) REVERT: A 625 LEU cc_start: 0.8839 (mt) cc_final: 0.8596 (mt) REVERT: A 694 MET cc_start: 0.8733 (mmm) cc_final: 0.8411 (mmt) REVERT: A 712 GLN cc_start: 0.8947 (mm-40) cc_final: 0.8335 (pp30) REVERT: A 763 MET cc_start: 0.0212 (mmm) cc_final: -0.0152 (mmm) REVERT: A 951 ARG cc_start: 0.8850 (mmm-85) cc_final: 0.8647 (mmm160) REVERT: A 1108 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7614 (mp0) outliers start: 21 outliers final: 18 residues processed: 78 average time/residue: 0.0963 time to fit residues: 11.0827 Evaluate side-chains 75 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 967 ARG Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1258 PHE Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1355 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 8 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 32 optimal weight: 0.0020 chunk 21 optimal weight: 10.0000 chunk 115 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 overall best weight: 3.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1350 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.081281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.059315 restraints weight = 55266.844| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 4.67 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 11492 Z= 0.249 Angle : 0.680 12.324 16042 Z= 0.360 Chirality : 0.043 0.228 1878 Planarity : 0.005 0.071 1638 Dihedral : 19.613 155.741 2768 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.59 % Allowed : 21.84 % Favored : 75.57 % 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: -0.50 (0.25), residues: 1076 helix: 0.32 (0.22), residues: 535 sheet: -0.62 (0.55), residues: 95 loop : -0.97 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 629 TYR 0.030 0.002 TYR A 521 PHE 0.041 0.002 PHE A1105 TRP 0.023 0.004 TRP A1126 HIS 0.006 0.001 HIS A1264 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.25 (11492) covalent geometry : angle 0.68016 / 0.36 (16042) hydrogen bonds : bond 0.05351 / 3.68 ( 502) hydrogen bonds : angle 5.13755 / 3.63 ( 1406) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2034.86 seconds wall clock time: 35 minutes 52.29 seconds (2152.29 seconds total)