Starting phenix.real_space_refine on Tue Dec 31 06:44:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t76_41085/12_2024/8t76_41085.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t76_41085/12_2024/8t76_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_41085/12_2024/8t76_41085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t76_41085/12_2024/8t76_41085.map" model { file = "/net/cci-nas-00/data/ceres_data/8t76_41085/12_2024/8t76_41085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t76_41085/12_2024/8t76_41085.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 1, 'ASP:plan': 5, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 8} 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: 7.75, per 1000 atoms: 0.70 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: 2.97 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 4.25 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: 5.47 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 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: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 33.150 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.780 ------------------------------------------------------------------------------- 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= 0.295 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 : 4.93 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.023 0.003 TRP A 464 HIS 0.022 0.002 HIS A1297 PHE 0.025 0.003 PHE A 518 TYR 0.037 0.003 TYR A 517 ARG 0.013 0.001 ARG A1317 *********************** 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 : 1.099 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 631 MET cc_start: 0.6515 (tpt) cc_final: 0.6288 (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: 0.2736 time to fit residues: 35.8957 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 : 1.163 ------------------------------------------------------------------------------- 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 99 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 60 optimal weight: 0.0570 chunk 47 optimal weight: 0.0670 chunk 92 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 overall best weight: 1.3238 ------------------------------------------------------------------------------- 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 522 ASN A 940 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1682 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= 0.200 Angle : 0.593 7.515 16042 Z= 0.314 Chirality : 0.038 0.187 1878 Planarity : 0.004 0.043 1638 Dihedral : 19.061 156.127 2768 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.70 % Allowed : 16.43 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.25), residues: 1076 helix: 0.04 (0.22), residues: 537 sheet: -0.26 (0.53), residues: 97 loop : -0.41 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1136 HIS 0.005 0.001 HIS A 129 PHE 0.013 0.002 PHE A 432 TYR 0.016 0.001 TYR A 517 ARG 0.005 0.001 ARG A 403 *********************** 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 102 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 1.169 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: 0.8403 (m-80) cc_final: 0.7791 (m-80) REVERT: A 220 ARG cc_start: 0.9490 (mmp-170) cc_final: 0.9290 (mtm180) REVERT: A 495 MET cc_start: 0.7123 (mmt) cc_final: 0.6914 (mmt) REVERT: A 625 LEU cc_start: 0.8990 (mt) cc_final: 0.8770 (mt) REVERT: A 631 MET cc_start: 0.6884 (tpt) cc_final: 0.6507 (tpp) REVERT: A 976 ARG cc_start: 0.8019 (mmt90) cc_final: 0.7736 (mmt-90) REVERT: A 1170 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7891 (pt0) outliers start: 25 outliers final: 12 residues processed: 98 average time/residue: 0.2617 time to fit residues: 36.2801 Evaluate side-chains 78 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 482 VAL Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1106 SER 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 1317 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1350 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11492 Z= 0.175 Angle : 0.540 9.648 16042 Z= 0.286 Chirality : 0.037 0.188 1878 Planarity : 0.004 0.038 1638 Dihedral : 19.102 154.568 2768 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.95 % Allowed : 16.54 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.25), residues: 1076 helix: 0.49 (0.22), residues: 542 sheet: 0.23 (0.58), residues: 81 loop : -0.48 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1136 HIS 0.004 0.001 HIS A1297 PHE 0.012 0.001 PHE A 432 TYR 0.011 0.001 TYR A 517 ARG 0.005 0.001 ARG A 629 *********************** 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 89 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8449 (m-80) cc_final: 0.7893 (m-80) REVERT: A 83 GLN cc_start: 0.8997 (mt0) cc_final: 0.8487 (mp10) REVERT: A 220 ARG cc_start: 0.9490 (mmp-170) cc_final: 0.9274 (mtm180) REVERT: A 495 MET cc_start: 0.7306 (mmt) cc_final: 0.7100 (mmt) REVERT: A 625 LEU cc_start: 0.8920 (mt) cc_final: 0.8707 (mt) REVERT: A 631 MET cc_start: 0.6918 (tpt) cc_final: 0.6528 (tpp) REVERT: A 737 ILE cc_start: 0.9549 (mm) cc_final: 0.9264 (mt) REVERT: A 763 MET cc_start: 0.0854 (mmt) cc_final: 0.0540 (mmm) REVERT: A 939 MET cc_start: 0.8551 (mmp) cc_final: 0.7914 (mmt) REVERT: A 976 ARG cc_start: 0.8064 (mmt90) cc_final: 0.7720 (mmt-90) REVERT: A 1166 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7908 (mp) REVERT: A 1170 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7938 (pt0) outliers start: 18 outliers final: 10 residues processed: 86 average time/residue: 0.2686 time to fit residues: 32.8972 Evaluate side-chains 74 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1106 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.0970 chunk 80 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11492 Z= 0.215 Angle : 0.570 15.048 16042 Z= 0.297 Chirality : 0.037 0.184 1878 Planarity : 0.004 0.037 1638 Dihedral : 19.356 156.739 2768 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.27 % Allowed : 16.65 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1076 helix: 0.67 (0.22), residues: 543 sheet: 0.17 (0.56), residues: 81 loop : -0.51 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1136 HIS 0.006 0.001 HIS A1349 PHE 0.015 0.002 PHE A1105 TYR 0.012 0.001 TYR A1187 ARG 0.006 0.001 ARG A 629 *********************** 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 91 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 1.160 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 25 TYR cc_start: 0.8637 (m-80) cc_final: 0.7585 (m-80) REVERT: A 462 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7788 (m-80) REVERT: A 625 LEU cc_start: 0.8885 (mt) cc_final: 0.8671 (mt) REVERT: A 737 ILE cc_start: 0.9550 (mm) cc_final: 0.9250 (mt) REVERT: A 761 ILE cc_start: 0.7714 (mm) cc_final: 0.7435 (tt) REVERT: A 763 MET cc_start: 0.0720 (mmt) cc_final: 0.0248 (mmm) REVERT: A 939 MET cc_start: 0.8615 (mmp) cc_final: 0.7893 (mmt) REVERT: A 1170 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7893 (pt0) outliers start: 21 outliers final: 10 residues processed: 86 average time/residue: 0.2465 time to fit residues: 30.7270 Evaluate side-chains 73 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 518 PHE 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 1105 PHE Chi-restraints excluded: chain A residue 1106 SER 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 94 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1350 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11492 Z= 0.187 Angle : 0.535 10.025 16042 Z= 0.278 Chirality : 0.037 0.191 1878 Planarity : 0.003 0.058 1638 Dihedral : 19.375 154.564 2768 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.73 % Allowed : 17.08 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1076 helix: 0.84 (0.22), residues: 543 sheet: -0.06 (0.62), residues: 66 loop : -0.51 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1136 HIS 0.005 0.001 HIS A 511 PHE 0.013 0.001 PHE A1105 TYR 0.014 0.001 TYR A 639 ARG 0.009 0.000 ARG A 629 *********************** 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 86 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 1.214 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: A 25 TYR cc_start: 0.8679 (m-80) cc_final: 0.7556 (m-80) REVERT: A 462 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.7831 (m-80) REVERT: A 631 MET cc_start: 0.6718 (tpt) cc_final: 0.6387 (tpp) REVERT: A 737 ILE cc_start: 0.9540 (mm) cc_final: 0.9246 (mt) REVERT: A 761 ILE cc_start: 0.7945 (mm) cc_final: 0.7735 (tt) REVERT: A 763 MET cc_start: 0.0707 (mmt) cc_final: 0.0417 (mmm) REVERT: A 939 MET cc_start: 0.8658 (mmp) cc_final: 0.7609 (ptt) REVERT: A 976 ARG cc_start: 0.8252 (mmt90) cc_final: 0.7912 (mmt-90) REVERT: A 1124 LYS cc_start: 0.9150 (tppt) cc_final: 0.8862 (mtmm) REVERT: A 1170 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7854 (pt0) REVERT: A 1225 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8085 (mm-30) outliers start: 16 outliers final: 11 residues processed: 82 average time/residue: 0.2484 time to fit residues: 29.5586 Evaluate side-chains 76 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 518 PHE 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 1105 PHE 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 1299 ASP Chi-restraints excluded: chain A residue 1330 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 66 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 52 optimal weight: 0.0040 chunk 9 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11492 Z= 0.134 Angle : 0.508 9.828 16042 Z= 0.262 Chirality : 0.035 0.191 1878 Planarity : 0.003 0.037 1638 Dihedral : 19.214 152.632 2768 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.41 % Allowed : 17.95 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.26), residues: 1076 helix: 0.96 (0.23), residues: 544 sheet: -0.00 (0.62), residues: 66 loop : -0.43 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1136 HIS 0.004 0.001 HIS A1349 PHE 0.013 0.001 PHE A 626 TYR 0.011 0.001 TYR A 155 ARG 0.005 0.000 ARG A 629 *********************** 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 84 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8675 (m-80) cc_final: 0.7822 (m-80) REVERT: A 83 GLN cc_start: 0.9006 (mt0) cc_final: 0.8502 (mp10) REVERT: A 631 MET cc_start: 0.6638 (tpt) cc_final: 0.6298 (tpp) REVERT: A 737 ILE cc_start: 0.9508 (mm) cc_final: 0.9183 (mt) REVERT: A 763 MET cc_start: 0.0636 (mmt) cc_final: 0.0336 (mmm) REVERT: A 939 MET cc_start: 0.8672 (mmp) cc_final: 0.7672 (ptt) REVERT: A 976 ARG cc_start: 0.8253 (mmt90) cc_final: 0.7751 (mmt-90) REVERT: A 1124 LYS cc_start: 0.9161 (tppt) cc_final: 0.8888 (mtmm) REVERT: A 1170 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7478 (pt0) REVERT: A 1225 GLU cc_start: 0.8215 (mm-30) cc_final: 0.8015 (mm-30) outliers start: 13 outliers final: 9 residues processed: 80 average time/residue: 0.2652 time to fit residues: 30.4250 Evaluate side-chains 72 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1330 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 65 optimal weight: 20.0000 chunk 83 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 63 optimal weight: 0.2980 chunk 113 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 GLN A1350 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11492 Z= 0.209 Angle : 0.556 8.679 16042 Z= 0.286 Chirality : 0.037 0.190 1878 Planarity : 0.003 0.042 1638 Dihedral : 19.331 154.935 2766 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.84 % Allowed : 18.27 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.26), residues: 1076 helix: 0.98 (0.23), residues: 551 sheet: -0.01 (0.62), residues: 66 loop : -0.50 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1136 HIS 0.004 0.001 HIS A 129 PHE 0.016 0.002 PHE A1105 TYR 0.012 0.001 TYR A 450 ARG 0.004 0.000 ARG A 629 *********************** 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 80 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.9063 (mt0) cc_final: 0.8746 (mt0) REVERT: A 737 ILE cc_start: 0.9527 (mm) cc_final: 0.9226 (mt) REVERT: A 763 MET cc_start: 0.0705 (mmt) cc_final: 0.0309 (mmm) REVERT: A 939 MET cc_start: 0.8689 (mmp) cc_final: 0.7680 (ptt) REVERT: A 1124 LYS cc_start: 0.9151 (tppt) cc_final: 0.8872 (ptpp) REVERT: A 1170 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7680 (pt0) REVERT: A 1225 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7733 (mm-30) outliers start: 17 outliers final: 10 residues processed: 77 average time/residue: 0.2083 time to fit residues: 24.3883 Evaluate side-chains 69 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 518 PHE 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 1194 LEU Chi-restraints excluded: chain A residue 1258 PHE Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1330 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 77 optimal weight: 0.0270 chunk 56 optimal weight: 6.9990 chunk 10 optimal weight: 0.0970 chunk 89 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11492 Z= 0.137 Angle : 0.529 9.066 16042 Z= 0.268 Chirality : 0.036 0.195 1878 Planarity : 0.003 0.037 1638 Dihedral : 19.196 151.948 2766 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.97 % Allowed : 19.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1076 helix: 1.13 (0.23), residues: 541 sheet: 0.06 (0.64), residues: 66 loop : -0.44 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 476 HIS 0.003 0.001 HIS A1349 PHE 0.012 0.001 PHE A1105 TYR 0.012 0.001 TYR A 155 ARG 0.004 0.000 ARG A 629 *********************** 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 73 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.9005 (mt0) cc_final: 0.8560 (mp10) REVERT: A 737 ILE cc_start: 0.9473 (mm) cc_final: 0.9143 (mt) REVERT: A 763 MET cc_start: 0.0544 (mmt) cc_final: 0.0178 (mmm) REVERT: A 939 MET cc_start: 0.8699 (mmp) cc_final: 0.7689 (ptt) REVERT: A 1108 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7578 (mp0) REVERT: A 1170 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7370 (pt0) outliers start: 9 outliers final: 8 residues processed: 73 average time/residue: 0.2184 time to fit residues: 24.4767 Evaluate side-chains 67 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1258 PHE Chi-restraints excluded: chain A residue 1330 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 105 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 HIS ** A1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11492 Z= 0.247 Angle : 0.597 9.120 16042 Z= 0.307 Chirality : 0.038 0.190 1878 Planarity : 0.004 0.051 1638 Dihedral : 19.417 155.968 2766 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.73 % Allowed : 18.16 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1076 helix: 0.95 (0.23), residues: 541 sheet: 0.03 (0.63), residues: 66 loop : -0.58 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 476 HIS 0.005 0.001 HIS A 129 PHE 0.022 0.002 PHE A1105 TYR 0.012 0.001 TYR A 639 ARG 0.004 0.000 ARG A 629 *********************** 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 77 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8534 (m-80) cc_final: 0.7362 (m-80) REVERT: A 161 MET cc_start: 0.7948 (ttm) cc_final: 0.7715 (ttp) REVERT: A 763 MET cc_start: 0.0866 (mmt) cc_final: 0.0374 (mmm) REVERT: A 939 MET cc_start: 0.8659 (mmp) cc_final: 0.7665 (ptt) REVERT: A 1108 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7557 (mp0) REVERT: A 1124 LYS cc_start: 0.9162 (tppt) cc_final: 0.8906 (ptpp) REVERT: A 1170 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7646 (pt0) REVERT: A 1225 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7893 (mm-30) outliers start: 16 outliers final: 13 residues processed: 73 average time/residue: 0.2155 time to fit residues: 24.1169 Evaluate side-chains 70 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 761 ILE 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 1194 LEU Chi-restraints excluded: chain A residue 1258 PHE Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1330 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 77 optimal weight: 0.0270 chunk 117 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 72 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 overall best weight: 2.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11492 Z= 0.265 Angle : 0.624 10.176 16042 Z= 0.322 Chirality : 0.039 0.207 1878 Planarity : 0.004 0.051 1638 Dihedral : 19.557 155.992 2766 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.62 % Allowed : 18.70 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.25), residues: 1076 helix: 0.87 (0.22), residues: 546 sheet: -0.04 (0.63), residues: 66 loop : -0.72 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 476 HIS 0.004 0.001 HIS A 129 PHE 0.026 0.002 PHE A1105 TYR 0.012 0.002 TYR A 639 ARG 0.005 0.001 ARG A 629 ********************** 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 78 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8532 (m-80) cc_final: 0.7339 (m-80) REVERT: A 161 MET cc_start: 0.7957 (ttm) cc_final: 0.7635 (ttp) REVERT: A 763 MET cc_start: 0.0705 (mmt) cc_final: 0.0244 (mmm) REVERT: A 939 MET cc_start: 0.8649 (mmp) cc_final: 0.7699 (ptt) REVERT: A 986 ASP cc_start: 0.9045 (m-30) cc_final: 0.8546 (p0) REVERT: A 1124 LYS cc_start: 0.9149 (tppt) cc_final: 0.8840 (ptpp) REVERT: A 1170 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7644 (pt0) outliers start: 15 outliers final: 13 residues processed: 74 average time/residue: 0.2138 time to fit residues: 24.0637 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 : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 761 ILE 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 1194 LEU Chi-restraints excluded: chain A residue 1258 PHE Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1330 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.079792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.056546 restraints weight = 51185.355| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 4.88 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11492 Z= 0.222 Angle : 0.591 10.324 16042 Z= 0.303 Chirality : 0.038 0.195 1878 Planarity : 0.003 0.043 1638 Dihedral : 19.502 154.648 2766 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.51 % Allowed : 19.03 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1076 helix: 0.90 (0.22), residues: 542 sheet: 0.22 (0.58), residues: 77 loop : -0.77 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 476 HIS 0.003 0.001 HIS A 167 PHE 0.037 0.002 PHE A1105 TYR 0.011 0.001 TYR A 155 ARG 0.004 0.000 ARG A 629 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2174.05 seconds wall clock time: 40 minutes 53.56 seconds (2453.56 seconds total)