Starting phenix.real_space_refine on Sat Aug 23 22:13:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t76_41085/08_2025/8t76_41085.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t76_41085/08_2025/8t76_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_2025/8t76_41085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t76_41085/08_2025/8t76_41085.map" model { file = "/net/cci-nas-00/data/ceres_data/8t76_41085/08_2025/8t76_41085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t76_41085/08_2025/8t76_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-2.0-5787/lib/python3.9/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: 2.98, per 1000 atoms: 0.27 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: 0.93 Conformation dependent library (CDL) restraints added in 472.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.53 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: 3.07 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 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=" CB ASP A1344 " pdb=" CG ASP A1344 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.62e+00 bond pdb=" C ASN A 199 " pdb=" O ASN A 199 " ideal model delta sigma weight residual 1.238 1.214 0.024 1.28e-02 6.10e+03 3.47e+00 bond pdb=" CA ARG A 457 " pdb=" CB ARG A 457 " ideal model delta sigma weight residual 1.528 1.554 -0.026 1.39e-02 5.18e+03 3.40e+00 bond pdb=" CA ILE A 201 " pdb=" CB ILE A 201 " ideal model delta sigma weight residual 1.528 1.552 -0.025 1.34e-02 5.57e+03 3.35e+00 bond pdb=" CA VAL A 27 " pdb=" C VAL A 27 " ideal model delta sigma weight residual 1.526 1.512 0.014 7.90e-03 1.60e+04 3.23e+00 ... (remaining 11487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 15785 3.43 - 6.85: 208 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=" 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=" CB LYS A 755 " pdb=" CG LYS A 755 " pdb=" CD LYS A 755 " ideal model delta sigma weight residual 111.30 123.47 -12.17 2.30e+00 1.89e-01 2.80e+01 angle pdb=" CA LEU A 156 " pdb=" CB LEU A 156 " pdb=" CG LEU A 156 " ideal model delta sigma weight residual 116.30 133.43 -17.13 3.50e+00 8.16e-02 2.39e+01 angle pdb=" CA LYS A1158 " pdb=" CB LYS A1158 " pdb=" CG LYS A1158 " ideal model delta sigma weight residual 114.10 123.38 -9.28 2.00e+00 2.50e-01 2.15e+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: 1575 0.064 - 0.129: 259 0.129 - 0.193: 35 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: 5.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.230 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 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= 0.220 Angle : 1.021 17.128 16042 Z= 0.517 Chirality : 0.050 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 aren 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 covalent geometry : bond 0.00459 (11492) covalent geometry : angle 1.02102 (16042) hydrogen bonds : bond 0.12788 ( 502) hydrogen bonds : angle 6.52811 ( 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 : 0.421 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: -0.1591 (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: 0.8849 (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: 0.1280 time to fit residues: 16.7811 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 : 0.389 ------------------------------------------------------------------------------- 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: 6.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 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: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 190 GLN A 194 GLN ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 522 ASN A 940 ASN ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.077947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.054896 restraints weight = 52872.489| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 4.98 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 11492 Z= 0.414 Angle : 0.903 6.994 16042 Z= 0.473 Chirality : 0.049 0.259 1878 Planarity : 0.007 0.090 1638 Dihedral : 20.046 163.717 2768 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 20.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.65 % Allowed : 16.22 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.24), residues: 1076 helix: -0.57 (0.21), residues: 536 sheet: -0.44 (0.54), residues: 90 loop : -1.02 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1111 TYR 0.024 0.003 TYR A1187 PHE 0.026 0.003 PHE A 405 TRP 0.017 0.003 TRP A 464 HIS 0.014 0.003 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00854 (11492) covalent geometry : angle 0.90307 (16042) hydrogen bonds : bond 0.06938 ( 502) hydrogen bonds : angle 5.69664 ( 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 114 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 71 time to evaluate : 0.407 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: A 10 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7866 (m-30) REVERT: A 25 TYR cc_start: 0.8680 (m-80) cc_final: 0.7800 (m-80) REVERT: A 220 ARG cc_start: 0.9468 (mmp-170) cc_final: 0.9237 (mtm110) REVERT: A 383 MET cc_start: 0.6528 (ptp) cc_final: 0.6275 (ptp) REVERT: A 462 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7722 (m-80) REVERT: A 495 MET cc_start: 0.7368 (mmt) cc_final: 0.7149 (mmt) REVERT: A 763 MET cc_start: -0.0031 (mmm) cc_final: -0.0449 (mmm) REVERT: A 939 MET cc_start: 0.8823 (mmp) cc_final: 0.7892 (mmt) REVERT: A 1136 TRP cc_start: 0.8443 (m-90) cc_final: 0.8216 (m-90) outliers start: 43 outliers final: 17 residues processed: 110 average time/residue: 0.1195 time to fit residues: 18.6724 Evaluate side-chains 76 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 332 LEU 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 747 LEU Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain A residue 975 VAL 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 1299 ASP Chi-restraints excluded: chain A residue 1317 ARG 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: 0.9990 chunk 37 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 32 optimal weight: 0.3980 chunk 55 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.082691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.059638 restraints weight = 50886.545| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 4.91 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11492 Z= 0.131 Angle : 0.566 8.619 16042 Z= 0.301 Chirality : 0.038 0.209 1878 Planarity : 0.004 0.038 1638 Dihedral : 19.614 154.454 2768 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.73 % Allowed : 17.73 % Favored : 80.54 % 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 aren not related in a simple way. whole: -0.31 (0.25), residues: 1076 helix: 0.23 (0.22), residues: 545 sheet: 0.04 (0.57), residues: 83 loop : -0.66 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1317 TYR 0.014 0.001 TYR A 155 PHE 0.012 0.001 PHE A 432 TRP 0.014 0.002 TRP A1136 HIS 0.005 0.001 HIS A1311 Details of bonding type rmsd covalent geometry : bond 0.00276 (11492) covalent geometry : angle 0.56645 (16042) hydrogen bonds : bond 0.03738 ( 502) hydrogen bonds : angle 4.82587 ( 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 91 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.406 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: 0.8403 (m-80) cc_final: 0.7474 (m-80) REVERT: A 220 ARG cc_start: 0.9487 (mmp-170) cc_final: 0.9246 (mtm180) REVERT: A 625 LEU cc_start: 0.8875 (mt) cc_final: 0.8617 (mt) REVERT: A 694 MET cc_start: 0.8533 (mmm) cc_final: 0.8203 (mmt) REVERT: A 737 ILE cc_start: 0.9549 (mm) cc_final: 0.9278 (mt) REVERT: A 763 MET cc_start: -0.0550 (mmm) cc_final: -0.0847 (mmm) REVERT: A 939 MET cc_start: 0.8716 (mmp) cc_final: 0.7561 (ptp) outliers start: 16 outliers final: 13 residues processed: 85 average time/residue: 0.1311 time to fit residues: 15.6474 Evaluate side-chains 73 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 947 ASP 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 Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 90 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 79 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A 563 GLN ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.083124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.060950 restraints weight = 54802.817| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 4.72 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11492 Z= 0.184 Angle : 0.592 9.332 16042 Z= 0.309 Chirality : 0.038 0.185 1878 Planarity : 0.004 0.042 1638 Dihedral : 19.627 157.173 2768 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.70 % Allowed : 17.73 % Favored : 79.57 % 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 aren not related in a simple way. whole: -0.25 (0.25), residues: 1076 helix: 0.39 (0.22), residues: 542 sheet: -0.11 (0.56), residues: 83 loop : -0.75 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 951 TYR 0.015 0.002 TYR A 450 PHE 0.013 0.002 PHE A 352 TRP 0.015 0.002 TRP A1136 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00385 (11492) covalent geometry : angle 0.59184 (16042) hydrogen bonds : bond 0.04334 ( 502) hydrogen bonds : angle 4.77085 ( 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 87 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8689 (m-80) cc_final: 0.7650 (m-80) REVERT: A 220 ARG cc_start: 0.9532 (mmp-170) cc_final: 0.9261 (mtm110) REVERT: A 462 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7934 (m-80) REVERT: A 625 LEU cc_start: 0.8819 (mt) cc_final: 0.8571 (mt) REVERT: A 631 MET cc_start: 0.7073 (tpt) cc_final: 0.6603 (tpp) REVERT: A 642 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6764 (mt) REVERT: A 737 ILE cc_start: 0.9545 (mm) cc_final: 0.9258 (mt) REVERT: A 763 MET cc_start: -0.0496 (mmm) cc_final: -0.0832 (mmm) REVERT: A 939 MET cc_start: 0.8703 (mmp) cc_final: 0.7567 (ptp) outliers start: 25 outliers final: 18 residues processed: 85 average time/residue: 0.1298 time to fit residues: 15.1952 Evaluate side-chains 73 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 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 642 LEU Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 1098 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 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 Chi-restraints excluded: chain A residue 1362 LEU 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: 0.5980 chunk 8 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 17 optimal weight: 30.0000 chunk 20 optimal weight: 8.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 ASN ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.077841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.054377 restraints weight = 51793.069| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 4.90 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11492 Z= 0.236 Angle : 0.637 6.594 16042 Z= 0.338 Chirality : 0.040 0.198 1878 Planarity : 0.005 0.079 1638 Dihedral : 19.868 157.759 2768 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.24 % Allowed : 17.73 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.25), residues: 1076 helix: 0.35 (0.22), residues: 534 sheet: -0.54 (0.55), residues: 90 loop : -0.81 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 629 TYR 0.016 0.002 TYR A 450 PHE 0.016 0.002 PHE A1105 TRP 0.014 0.003 TRP A1136 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00487 (11492) covalent geometry : angle 0.63715 (16042) hydrogen bonds : bond 0.04825 ( 502) hydrogen bonds : angle 5.04495 ( 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 88 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 58 time to evaluate : 0.425 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: 0.8771 (m-80) cc_final: 0.7717 (m-80) REVERT: A 161 MET cc_start: 0.8360 (ttm) cc_final: 0.8114 (ttp) REVERT: A 462 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7862 (m-80) REVERT: A 737 ILE cc_start: 0.9541 (mm) cc_final: 0.9256 (mt) REVERT: A 763 MET cc_start: -0.0602 (mmm) cc_final: -0.0955 (mmm) REVERT: A 939 MET cc_start: 0.8855 (mmp) cc_final: 0.8142 (mmt) outliers start: 30 outliers final: 16 residues processed: 85 average time/residue: 0.1081 time to fit residues: 13.5569 Evaluate side-chains 72 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 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 947 ASP Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1166 ILE 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 Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 26 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 369 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.080336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.057786 restraints weight = 51155.215| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 4.78 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11492 Z= 0.128 Angle : 0.532 7.945 16042 Z= 0.279 Chirality : 0.037 0.197 1878 Planarity : 0.003 0.040 1638 Dihedral : 19.579 153.801 2768 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.38 % Allowed : 18.70 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.26), residues: 1076 helix: 0.57 (0.22), residues: 542 sheet: -0.92 (0.58), residues: 76 loop : -0.51 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 629 TYR 0.014 0.001 TYR A 450 PHE 0.010 0.001 PHE A 478 TRP 0.018 0.002 TRP A1136 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00268 (11492) covalent geometry : angle 0.53179 (16042) hydrogen bonds : bond 0.03556 ( 502) hydrogen bonds : angle 4.64970 ( 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 88 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8528 (m-80) cc_final: 0.7291 (m-80) REVERT: A 625 LEU cc_start: 0.8682 (mt) cc_final: 0.8441 (mt) REVERT: A 737 ILE cc_start: 0.9535 (mm) cc_final: 0.9227 (mt) REVERT: A 763 MET cc_start: -0.0731 (mmm) cc_final: -0.1065 (mmm) REVERT: A 939 MET cc_start: 0.8866 (mmp) cc_final: 0.7758 (ptt) REVERT: A 1108 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7476 (mp0) outliers start: 22 outliers final: 15 residues processed: 84 average time/residue: 0.1196 time to fit residues: 14.4682 Evaluate side-chains 71 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 353 ASP Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 404 THR 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 947 ASP 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 1258 PHE Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 97 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 HIS A 983 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.076944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.053816 restraints weight = 52476.415| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 4.83 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11492 Z= 0.253 Angle : 0.678 15.094 16042 Z= 0.352 Chirality : 0.041 0.191 1878 Planarity : 0.004 0.068 1638 Dihedral : 19.794 158.388 2768 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.81 % Allowed : 19.35 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.25), residues: 1076 helix: 0.38 (0.22), residues: 535 sheet: -0.13 (0.58), residues: 83 loop : -0.83 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 629 TYR 0.017 0.002 TYR A 450 PHE 0.018 0.002 PHE A1105 TRP 0.014 0.003 TRP A1126 HIS 0.006 0.001 HIS A1264 Details of bonding type rmsd covalent geometry : bond 0.00525 (11492) covalent geometry : angle 0.67796 (16042) hydrogen bonds : bond 0.05121 ( 502) hydrogen bonds : angle 5.01698 ( 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 82 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8585 (m-80) cc_final: 0.8029 (m-80) REVERT: A 462 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7847 (m-80) REVERT: A 737 ILE cc_start: 0.9541 (mm) cc_final: 0.9240 (mt) REVERT: A 763 MET cc_start: -0.0627 (mmm) cc_final: -0.0874 (mmm) REVERT: A 929 LYS cc_start: 0.9292 (tptt) cc_final: 0.9063 (tptp) REVERT: A 939 MET cc_start: 0.8886 (mmp) cc_final: 0.7773 (ptt) REVERT: A 1108 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7315 (mp0) outliers start: 26 outliers final: 21 residues processed: 78 average time/residue: 0.1077 time to fit residues: 12.4049 Evaluate side-chains 77 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 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 474 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 529 TYR 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 1143 VAL Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1330 THR Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain A residue 1355 LEU Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 27 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.078496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.055228 restraints weight = 51751.498| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 4.85 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11492 Z= 0.168 Angle : 0.600 13.067 16042 Z= 0.308 Chirality : 0.039 0.257 1878 Planarity : 0.004 0.043 1638 Dihedral : 19.658 154.670 2768 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.16 % Allowed : 20.32 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.26), residues: 1076 helix: 0.56 (0.22), residues: 537 sheet: -0.35 (0.56), residues: 83 loop : -0.66 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 629 TYR 0.016 0.001 TYR A 450 PHE 0.016 0.001 PHE A 98 TRP 0.019 0.003 TRP A1136 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00355 (11492) covalent geometry : angle 0.60035 (16042) hydrogen bonds : bond 0.03954 ( 502) hydrogen bonds : angle 4.77572 ( 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 79 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8489 (m-80) cc_final: 0.7893 (m-80) REVERT: A 220 ARG cc_start: 0.9491 (mmp-170) cc_final: 0.9258 (mtm180) REVERT: A 462 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7851 (m-80) REVERT: A 737 ILE cc_start: 0.9494 (mm) cc_final: 0.9184 (mt) REVERT: A 763 MET cc_start: -0.0838 (mmm) cc_final: -0.1039 (mmm) REVERT: A 929 LYS cc_start: 0.9290 (tptt) cc_final: 0.8984 (tptp) REVERT: A 939 MET cc_start: 0.8868 (mmp) cc_final: 0.7781 (ptt) REVERT: A 1108 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7222 (mp0) outliers start: 20 outliers final: 17 residues processed: 76 average time/residue: 0.0979 time to fit residues: 11.4995 Evaluate side-chains 75 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 339 VAL 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 529 TYR 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 1098 THR 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 1299 ASP Chi-restraints excluded: chain A residue 1330 THR Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain A residue 1362 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: 7.9990 chunk 46 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 44 optimal weight: 0.0270 overall best weight: 2.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1335 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.076609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.053599 restraints weight = 52747.459| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 4.81 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.5991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11492 Z= 0.241 Angle : 0.673 12.055 16042 Z= 0.347 Chirality : 0.041 0.192 1878 Planarity : 0.004 0.058 1638 Dihedral : 19.814 157.684 2768 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.38 % Allowed : 20.86 % 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 aren not related in a simple way. whole: -0.31 (0.25), residues: 1076 helix: 0.40 (0.22), residues: 530 sheet: -0.17 (0.58), residues: 83 loop : -0.83 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 629 TYR 0.017 0.002 TYR A 155 PHE 0.018 0.002 PHE A1105 TRP 0.031 0.004 TRP A 476 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00503 (11492) covalent geometry : angle 0.67306 (16042) hydrogen bonds : bond 0.04959 ( 502) hydrogen bonds : angle 4.98200 ( 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 84 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8621 (m-80) cc_final: 0.7471 (m-80) REVERT: A 220 ARG cc_start: 0.9493 (mmp-170) cc_final: 0.9239 (mtm180) REVERT: A 462 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7850 (m-80) REVERT: A 579 GLU cc_start: 0.9496 (mm-30) cc_final: 0.9291 (mp0) REVERT: A 599 LYS cc_start: 0.8751 (tptp) cc_final: 0.8390 (ptmt) REVERT: A 621 LEU cc_start: 0.8434 (mm) cc_final: 0.7997 (tt) REVERT: A 763 MET cc_start: -0.0761 (mmm) cc_final: -0.1017 (mmm) REVERT: A 929 LYS cc_start: 0.9265 (tptt) cc_final: 0.9001 (tptt) REVERT: A 939 MET cc_start: 0.8882 (mmp) cc_final: 0.8079 (mmt) REVERT: A 947 ASP cc_start: 0.9080 (OUTLIER) cc_final: 0.8651 (p0) REVERT: A 1108 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7242 (mp0) outliers start: 22 outliers final: 18 residues processed: 80 average time/residue: 0.1046 time to fit residues: 12.8359 Evaluate side-chains 79 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 339 VAL 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 625 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 1098 THR 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 1299 ASP Chi-restraints excluded: chain A residue 1330 THR Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 64 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 90 optimal weight: 0.4980 chunk 76 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4022 r_free = 0.4022 target = 0.077981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.054944 restraints weight = 52525.504| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 4.80 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.6041 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= 0.182 Angle : 0.631 15.711 16042 Z= 0.323 Chirality : 0.039 0.197 1878 Planarity : 0.004 0.047 1638 Dihedral : 19.696 155.051 2768 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.05 % Allowed : 21.41 % 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 aren not related in a simple way. whole: -0.24 (0.25), residues: 1076 helix: 0.45 (0.22), residues: 538 sheet: -0.80 (0.53), residues: 95 loop : -0.64 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 629 TYR 0.018 0.001 TYR A 155 PHE 0.029 0.002 PHE A1105 TRP 0.026 0.004 TRP A 476 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00386 (11492) covalent geometry : angle 0.63084 (16042) hydrogen bonds : bond 0.04221 ( 502) hydrogen bonds : angle 4.81709 ( 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: 19 poor density : 62 time to evaluate : 0.393 Fit side-chains REVERT: A 25 TYR cc_start: 0.8590 (m-80) cc_final: 0.7408 (m-80) REVERT: A 220 ARG cc_start: 0.9487 (mmp-170) cc_final: 0.9229 (mtm180) REVERT: A 462 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7855 (m-80) REVERT: A 621 LEU cc_start: 0.8296 (mm) cc_final: 0.7879 (tt) REVERT: A 763 MET cc_start: -0.0746 (mmm) cc_final: -0.0973 (mmm) REVERT: A 929 LYS cc_start: 0.9254 (tptt) cc_final: 0.8973 (tptt) REVERT: A 939 MET cc_start: 0.8890 (mmp) cc_final: 0.7754 (ptt) REVERT: A 947 ASP cc_start: 0.9098 (OUTLIER) cc_final: 0.8659 (p0) REVERT: A 1108 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7249 (mp0) outliers start: 19 outliers final: 17 residues processed: 77 average time/residue: 0.0941 time to fit residues: 11.3342 Evaluate side-chains 77 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 339 VAL 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 529 TYR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 1098 THR 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 1299 ASP Chi-restraints excluded: chain A residue 1330 THR Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 8 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 74 optimal weight: 0.0030 chunk 19 optimal weight: 5.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.078939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.055939 restraints weight = 51848.702| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 4.83 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.6087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11492 Z= 0.147 Angle : 0.593 13.242 16042 Z= 0.306 Chirality : 0.038 0.199 1878 Planarity : 0.003 0.040 1638 Dihedral : 19.537 153.653 2768 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.16 % Allowed : 21.41 % 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 aren not related in a simple way. whole: -0.03 (0.26), residues: 1076 helix: 0.64 (0.22), residues: 538 sheet: -0.74 (0.53), residues: 95 loop : -0.55 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 629 TYR 0.017 0.001 TYR A 155 PHE 0.024 0.001 PHE A1105 TRP 0.026 0.004 TRP A 476 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00314 (11492) covalent geometry : angle 0.59335 (16042) hydrogen bonds : bond 0.03855 ( 502) hydrogen bonds : angle 4.71594 ( 1406) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2442.54 seconds wall clock time: 43 minutes 4.27 seconds (2584.27 seconds total)