Starting phenix.real_space_refine on Wed Aug 5 19:52:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6y_41084/08_2026/8t6y_41084.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6y_41084/08_2026/8t6y_41084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t6y_41084/08_2026/8t6y_41084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6y_41084/08_2026/8t6y_41084.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6y_41084/08_2026/8t6y_41084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6y_41084/08_2026/8t6y_41084.cif" } resolution = 2.88 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 109 5.49 5 S 18 5.16 5 C 6916 2.51 5 N 1994 2.21 5 O 2445 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11482 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1148, 9165 Classifications: {'peptide': 1148} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 32, 'TRANS': 1115} Chain breaks: 5 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 8, 'GLU:plan': 9, 'GLN:plan1': 1, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "B" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1885 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: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 227 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} 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: 2.64, per 1000 atoms: 0.23 Number of scatterers: 11482 At special positions: 0 Unit cell: (85.8196, 118.314, 122.48, 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 18 16.00 P 109 15.00 O 2445 8.00 N 1994 7.00 C 6916 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: 0.98 Conformation dependent library (CDL) restraints added in 425.8 milliseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2188 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 7 sheets defined 55.4% alpha, 9.8% beta 34 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.742A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 144 removed outlier: 3.860A 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 196 removed outlier: 3.600A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.715A pdb=" N ILE A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 271 through 283 Processing helix chain 'A' and resid 286 through 306 Processing helix chain 'A' and resid 307 through 311 removed outlier: 4.229A pdb=" N THR A 310 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.643A pdb=" N LEU A 334 " --> pdb=" O GLN A 330 " (cutoff:3.500A) 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: 3.521A pdb=" N VAL A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.549A pdb=" N ASN A 407 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.182A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.529A 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: 3.519A pdb=" N GLU A 480 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 481 " --> pdb=" O PHE A 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 477 through 481' Processing helix chain 'A' and resid 483 through 496 removed outlier: 3.618A pdb=" N THR A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) 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 602 Processing helix chain 'A' and resid 603 through 608 removed outlier: 3.786A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) 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: 3.708A pdb=" N ILE A 632 " --> pdb=" O ASP A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 642 removed outlier: 4.390A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 652 removed outlier: 4.411A pdb=" N GLN A 650 " --> pdb=" O LYS A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.595A pdb=" N ILE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) 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 711 removed outlier: 3.611A pdb=" N ALA A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 725 Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.879A pdb=" N LYS A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 940 removed outlier: 4.129A pdb=" N GLN A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.895A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.468A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1009 Processing helix chain 'A' and resid 1077 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.922A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 removed outlier: 3.548A pdb=" N PHE A1181 " --> pdb=" O ASN A1177 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A1185 " --> pdb=" O PHE A1181 " (cutoff:3.500A) 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 1263 through 1280 removed outlier: 4.216A pdb=" N ASP A1267 " --> pdb=" O LYS A1263 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS A1278 " --> pdb=" O SER A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1312 Processing helix chain 'A' and resid 1313 through 1315 No H-bonds generated for 'chain 'A' and resid 1313 through 1315' Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.817A pdb=" N LEU A1343 " --> pdb=" O LYS A1340 " (cutoff:3.500A) removed outlier: 3.961A 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 957 removed outlier: 6.019A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN A 758 " --> pdb=" O TYR A 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.410A pdb=" N GLU A1357 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 6.336A 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 1063 through 1065 removed outlier: 3.675A pdb=" N TRP A1074 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.827A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS A1151 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A1158 " --> pdb=" O VAL A1149 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.827A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS A1151 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A1158 " --> pdb=" O VAL A1149 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) 436 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3006 1.34 - 1.46: 3434 1.46 - 1.59: 5245 1.59 - 1.71: 211 1.71 - 1.83: 34 Bond restraints: 11930 Sorted by residual: bond pdb=" CB PRO A 503 " pdb=" CG PRO A 503 " ideal model delta sigma weight residual 1.492 1.637 -0.145 5.00e-02 4.00e+02 8.40e+00 bond pdb=" C3' DT D 42 " pdb=" C2' DT D 42 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.52e+00 bond pdb=" C3' DT C 16 " pdb=" C2' DT C 16 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.51e+00 bond pdb=" C3' DA D 40 " pdb=" O3' DA D 40 " ideal model delta sigma weight residual 1.435 1.407 0.028 1.30e-02 5.92e+03 4.70e+00 bond pdb=" O4' DA C 19 " pdb=" C1' DA C 19 " ideal model delta sigma weight residual 1.420 1.396 0.024 1.10e-02 8.26e+03 4.61e+00 ... (remaining 11925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 16438 3.90 - 7.80: 157 7.80 - 11.70: 25 11.70 - 15.61: 6 15.61 - 19.51: 1 Bond angle restraints: 16627 Sorted by residual: angle pdb=" CA PRO A 503 " pdb=" N PRO A 503 " pdb=" CD PRO A 503 " ideal model delta sigma weight residual 112.00 98.96 13.04 1.40e+00 5.10e-01 8.67e+01 angle pdb=" CA LEU A1257 " pdb=" CB LEU A1257 " pdb=" CG LEU A1257 " ideal model delta sigma weight residual 116.30 135.81 -19.51 3.50e+00 8.16e-02 3.11e+01 angle pdb=" CA LYS A 599 " pdb=" CB LYS A 599 " pdb=" CG LYS A 599 " ideal model delta sigma weight residual 114.10 124.23 -10.13 2.00e+00 2.50e-01 2.56e+01 angle pdb=" CA MET A 694 " pdb=" CB MET A 694 " pdb=" CG MET A 694 " ideal model delta sigma weight residual 114.10 124.19 -10.09 2.00e+00 2.50e-01 2.55e+01 angle pdb=" CA LYS A 961 " pdb=" CB LYS A 961 " pdb=" CG LYS A 961 " ideal model delta sigma weight residual 114.10 123.97 -9.87 2.00e+00 2.50e-01 2.44e+01 ... (remaining 16622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.78: 6642 29.78 - 59.56: 500 59.56 - 89.34: 85 89.34 - 119.12: 0 119.12 - 148.90: 1 Dihedral angle restraints: 7228 sinusoidal: 3853 harmonic: 3375 Sorted by residual: dihedral pdb=" CA PHE A 643 " pdb=" C PHE A 643 " pdb=" N ASP A 644 " pdb=" CA ASP A 644 " ideal model delta harmonic sigma weight residual -180.00 -155.10 -24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA MET A1089 " pdb=" C MET A1089 " pdb=" N PRO A1090 " pdb=" CA PRO A1090 " ideal model delta harmonic sigma weight residual -180.00 -157.49 -22.51 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ASP A 603 " pdb=" C ASP A 603 " pdb=" N LYS A 604 " pdb=" CA LYS A 604 " ideal model delta harmonic sigma weight residual -180.00 -159.23 -20.77 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 7225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1437 0.054 - 0.108: 340 0.108 - 0.162: 153 0.162 - 0.216: 11 0.216 - 0.270: 2 Chirality restraints: 1943 Sorted by residual: chirality pdb=" C3' A B 38 " pdb=" C4' A B 38 " pdb=" O3' A B 38 " pdb=" C2' A B 38 " both_signs ideal model delta sigma weight residual False -2.48 -2.21 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CG LEU A 623 " pdb=" CB LEU A 623 " pdb=" CD1 LEU A 623 " pdb=" CD2 LEU A 623 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA ASP A 304 " pdb=" N ASP A 304 " pdb=" C ASP A 304 " pdb=" CB ASP A 304 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.92e-01 ... (remaining 1940 not shown) Planarity restraints: 1722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 502 " 0.082 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO A 503 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO A 503 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 503 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U B 66 " -0.023 2.00e-02 2.50e+03 2.57e-02 1.48e+01 pdb=" N1 U B 66 " 0.061 2.00e-02 2.50e+03 pdb=" C2 U B 66 " -0.038 2.00e-02 2.50e+03 pdb=" O2 U B 66 " 0.009 2.00e-02 2.50e+03 pdb=" N3 U B 66 " 0.005 2.00e-02 2.50e+03 pdb=" C4 U B 66 " -0.001 2.00e-02 2.50e+03 pdb=" O4 U B 66 " 0.000 2.00e-02 2.50e+03 pdb=" C5 U B 66 " -0.006 2.00e-02 2.50e+03 pdb=" C6 U B 66 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 13 " 0.000 2.00e-02 2.50e+03 1.80e-02 8.88e+00 pdb=" N9 A B 13 " 0.038 2.00e-02 2.50e+03 pdb=" C8 A B 13 " -0.007 2.00e-02 2.50e+03 pdb=" N7 A B 13 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A B 13 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A B 13 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A B 13 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A B 13 " 0.007 2.00e-02 2.50e+03 pdb=" C2 A B 13 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A B 13 " 0.001 2.00e-02 2.50e+03 pdb=" C4 A B 13 " -0.044 2.00e-02 2.50e+03 ... (remaining 1719 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1139 2.75 - 3.29: 10855 3.29 - 3.82: 20288 3.82 - 4.36: 23742 4.36 - 4.90: 37900 Nonbonded interactions: 93924 Sorted by model distance: nonbonded pdb=" O VAL A 620 " pdb=" OG1 THR A 624 " model vdw 2.209 3.040 nonbonded pdb=" OG1 THR A1167 " pdb=" OE1 GLU A1170 " model vdw 2.255 3.040 nonbonded pdb=" OG SER A 541 " pdb=" OE1 GLN A 544 " model vdw 2.270 3.040 nonbonded pdb=" O SER A1088 " pdb=" OG SER A1088 " model vdw 2.311 3.040 nonbonded pdb=" NH2 ARG A1114 " pdb=" OP1 DG D 41 " model vdw 2.316 3.120 ... (remaining 93919 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.440 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:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 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 0.145 11930 Z= 0.274 Angle : 1.029 19.508 16627 Z= 0.615 Chirality : 0.056 0.270 1943 Planarity : 0.007 0.114 1722 Dihedral : 18.638 148.895 5040 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.13 % Allowed : 25.31 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.23), residues: 1136 helix: -0.82 (0.20), residues: 563 sheet: -0.38 (0.52), residues: 112 loop : -0.65 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG A 220 TYR 0.040 0.003 TYR A1001 PHE 0.034 0.002 PHE A 569 TRP 0.014 0.002 TRP A 464 HIS 0.008 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.27 (11930) covalent geometry : angle 1.02901 / 0.62 (16627) hydrogen bonds : bond 0.13253 / 8.24 ( 510) hydrogen bonds : angle 6.59914 / 4.80 ( 1446) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8452 (tp30) cc_final: 0.7972 (tp30) REVERT: A 220 ARG cc_start: 0.8972 (ptm160) cc_final: 0.8627 (ttp80) REVERT: A 959 LYS cc_start: 0.6375 (pttt) cc_final: 0.5683 (ptpp) REVERT: A 970 PHE cc_start: 0.7237 (m-10) cc_final: 0.6934 (m-10) outliers start: 11 outliers final: 3 residues processed: 67 average time/residue: 0.4905 time to fit residues: 36.5590 Evaluate side-chains 56 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 670 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.0770 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 ASN A 281 GLN A 544 GLN A 709 GLN A 971 GLN A 980 ASN ** A1297 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 = 0.3662 r_free = 0.3662 target = 0.100977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.065258 restraints weight = 25619.565| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.04 r_work: 0.2805 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11930 Z= 0.209 Angle : 0.634 12.196 16627 Z= 0.333 Chirality : 0.042 0.251 1943 Planarity : 0.004 0.052 1722 Dihedral : 18.593 150.714 2803 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 4.10 % Allowed : 18.65 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.25), residues: 1136 helix: 0.19 (0.22), residues: 556 sheet: -0.09 (0.52), residues: 111 loop : -0.40 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 220 TYR 0.014 0.002 TYR A 568 PHE 0.019 0.002 PHE A1105 TRP 0.008 0.001 TRP A 476 HIS 0.006 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (11930) covalent geometry : angle 0.63400 / 0.33 (16627) hydrogen bonds : bond 0.04775 / 3.22 ( 510) hydrogen bonds : angle 5.02884 / 3.67 ( 1446) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 58 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8286 (mp0) REVERT: A 60 GLU cc_start: 0.8606 (tp30) cc_final: 0.7989 (tp30) REVERT: A 217 SER cc_start: 0.8783 (OUTLIER) cc_final: 0.8532 (t) REVERT: A 321 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8352 (mmm) REVERT: A 682 PHE cc_start: 0.8991 (m-80) cc_final: 0.8648 (m-10) REVERT: A 1343 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8658 (mm) outliers start: 40 outliers final: 12 residues processed: 94 average time/residue: 0.4767 time to fit residues: 49.8287 Evaluate side-chains 69 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 24 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.101848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.066708 restraints weight = 25660.179| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.03 r_work: 0.2820 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11930 Z= 0.137 Angle : 0.550 10.520 16627 Z= 0.291 Chirality : 0.039 0.234 1943 Planarity : 0.004 0.053 1722 Dihedral : 18.632 151.425 2801 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.38 % Allowed : 19.67 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.25), residues: 1136 helix: 0.66 (0.23), residues: 557 sheet: 0.04 (0.53), residues: 111 loop : -0.38 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 220 TYR 0.013 0.001 TYR A1237 PHE 0.015 0.001 PHE A 432 TRP 0.007 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (11930) covalent geometry : angle 0.54993 / 0.29 (16627) hydrogen bonds : bond 0.04179 / 2.84 ( 510) hydrogen bonds : angle 4.73887 / 3.47 ( 1446) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 59 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: A 60 GLU cc_start: 0.8578 (tp30) cc_final: 0.7984 (tp30) REVERT: A 220 ARG cc_start: 0.8993 (ptm160) cc_final: 0.8651 (ttp80) REVERT: A 682 PHE cc_start: 0.8965 (m-80) cc_final: 0.8648 (m-10) REVERT: A 683 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8703 (mp) REVERT: A 1043 MET cc_start: 0.7318 (tpp) cc_final: 0.7059 (tpp) REVERT: A 1099 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8481 (mm-30) REVERT: A 1343 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8627 (mm) outliers start: 33 outliers final: 16 residues processed: 88 average time/residue: 0.5103 time to fit residues: 49.6754 Evaluate side-chains 74 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 16 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 36 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 544 GLN A1261 GLN ** A1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.101564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.066452 restraints weight = 25607.096| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.03 r_work: 0.2813 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11930 Z= 0.134 Angle : 0.523 8.698 16627 Z= 0.279 Chirality : 0.038 0.226 1943 Planarity : 0.003 0.052 1722 Dihedral : 18.645 151.800 2801 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.79 % Allowed : 19.36 % Favored : 76.84 % 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 are not related in a simple way. whole: 0.35 (0.25), residues: 1136 helix: 0.83 (0.23), residues: 557 sheet: 0.05 (0.53), residues: 111 loop : -0.33 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 220 TYR 0.015 0.001 TYR A1001 PHE 0.014 0.001 PHE A1105 TRP 0.007 0.001 TRP A 476 HIS 0.009 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (11930) covalent geometry : angle 0.52298 / 0.28 (16627) hydrogen bonds : bond 0.03976 / 2.71 ( 510) hydrogen bonds : angle 4.60098 / 3.37 ( 1446) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 59 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8268 (mp0) REVERT: A 60 GLU cc_start: 0.8561 (tp30) cc_final: 0.7935 (tp30) REVERT: A 682 PHE cc_start: 0.8963 (m-80) cc_final: 0.8691 (m-10) REVERT: A 683 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8640 (mp) REVERT: A 724 ILE cc_start: 0.6976 (OUTLIER) cc_final: 0.6710 (pt) REVERT: A 1043 MET cc_start: 0.7370 (tpp) cc_final: 0.7065 (tpp) REVERT: A 1099 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8511 (mm-30) REVERT: A 1325 LYS cc_start: 0.8503 (ptmm) cc_final: 0.7788 (tttp) REVERT: A 1343 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8638 (mm) outliers start: 37 outliers final: 17 residues processed: 93 average time/residue: 0.4752 time to fit residues: 48.8174 Evaluate side-chains 74 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 0.0870 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 544 GLN A1261 GLN ** A1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.098735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.062994 restraints weight = 25686.314| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.00 r_work: 0.2753 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11930 Z= 0.223 Angle : 0.587 13.860 16627 Z= 0.308 Chirality : 0.042 0.228 1943 Planarity : 0.004 0.049 1722 Dihedral : 18.627 152.132 2799 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.48 % Allowed : 19.77 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.25), residues: 1136 helix: 0.87 (0.23), residues: 559 sheet: 0.03 (0.53), residues: 111 loop : -0.30 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 220 TYR 0.018 0.001 TYR A 568 PHE 0.021 0.002 PHE A1105 TRP 0.009 0.001 TRP A 476 HIS 0.006 0.002 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.22 (11930) covalent geometry : angle 0.58719 / 0.31 (16627) hydrogen bonds : bond 0.04417 / 3.02 ( 510) hydrogen bonds : angle 4.62769 / 3.38 ( 1446) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 56 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8292 (mp0) REVERT: A 60 GLU cc_start: 0.8597 (tp30) cc_final: 0.7932 (tp30) REVERT: A 220 ARG cc_start: 0.9019 (ptm160) cc_final: 0.8720 (ttp80) REVERT: A 331 ASP cc_start: 0.8945 (m-30) cc_final: 0.8687 (m-30) REVERT: A 682 PHE cc_start: 0.8989 (m-80) cc_final: 0.8772 (m-10) REVERT: A 683 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8717 (mp) REVERT: A 1325 LYS cc_start: 0.8614 (ptmm) cc_final: 0.7921 (tttp) REVERT: A 1343 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8698 (mm) outliers start: 34 outliers final: 17 residues processed: 87 average time/residue: 0.5260 time to fit residues: 50.3256 Evaluate side-chains 69 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN A1261 GLN ** A1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.099746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.063889 restraints weight = 25633.892| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.03 r_work: 0.2774 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11930 Z= 0.126 Angle : 0.536 12.267 16627 Z= 0.282 Chirality : 0.038 0.223 1943 Planarity : 0.003 0.047 1722 Dihedral : 18.631 152.276 2799 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.87 % Allowed : 20.90 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.25), residues: 1136 helix: 1.02 (0.23), residues: 558 sheet: 0.16 (0.52), residues: 109 loop : -0.24 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 220 TYR 0.017 0.001 TYR A1242 PHE 0.019 0.001 PHE A 518 TRP 0.008 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (11930) covalent geometry : angle 0.53556 / 0.28 (16627) hydrogen bonds : bond 0.03919 / 2.67 ( 510) hydrogen bonds : angle 4.53126 / 3.33 ( 1446) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 51 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8296 (mp0) REVERT: A 60 GLU cc_start: 0.8549 (tp30) cc_final: 0.7991 (tp30) REVERT: A 220 ARG cc_start: 0.9007 (ptm160) cc_final: 0.8698 (ttp80) REVERT: A 331 ASP cc_start: 0.8947 (m-30) cc_final: 0.8704 (m-30) REVERT: A 683 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8698 (mp) REVERT: A 1325 LYS cc_start: 0.8623 (ptmm) cc_final: 0.7940 (tttp) REVERT: A 1343 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8630 (mm) outliers start: 28 outliers final: 16 residues processed: 77 average time/residue: 0.4747 time to fit residues: 40.3111 Evaluate side-chains 66 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 16 optimal weight: 0.4980 chunk 119 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN ** A1297 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 = 0.3634 r_free = 0.3634 target = 0.099281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.063932 restraints weight = 25390.515| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.97 r_work: 0.2764 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11930 Z= 0.145 Angle : 0.530 10.537 16627 Z= 0.281 Chirality : 0.039 0.219 1943 Planarity : 0.004 0.068 1722 Dihedral : 18.542 152.631 2797 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.66 % Allowed : 21.31 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.25), residues: 1136 helix: 1.09 (0.23), residues: 558 sheet: 0.11 (0.51), residues: 109 loop : -0.19 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1303 TYR 0.022 0.001 TYR A1242 PHE 0.024 0.002 PHE A 682 TRP 0.008 0.001 TRP A 476 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (11930) covalent geometry : angle 0.53029 / 0.28 (16627) hydrogen bonds : bond 0.03897 / 2.65 ( 510) hydrogen bonds : angle 4.47012 / 3.28 ( 1446) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 54 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8559 (tp30) cc_final: 0.7895 (tp30) REVERT: A 202 ASN cc_start: 0.9107 (OUTLIER) cc_final: 0.8830 (t0) REVERT: A 331 ASP cc_start: 0.8976 (m-30) cc_final: 0.8722 (m-30) REVERT: A 682 PHE cc_start: 0.8602 (m-10) cc_final: 0.8389 (m-10) REVERT: A 723 HIS cc_start: 0.6835 (OUTLIER) cc_final: 0.6378 (m-70) REVERT: A 1325 LYS cc_start: 0.8673 (ptmm) cc_final: 0.7965 (tttp) REVERT: A 1343 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8636 (mm) outliers start: 26 outliers final: 16 residues processed: 76 average time/residue: 0.4261 time to fit residues: 35.9901 Evaluate side-chains 66 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 723 HIS Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 61 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 102 optimal weight: 0.1980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 556 ASN A 563 GLN ** A1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.099108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.063797 restraints weight = 25521.206| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.98 r_work: 0.2763 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11930 Z= 0.147 Angle : 0.538 9.852 16627 Z= 0.283 Chirality : 0.039 0.225 1943 Planarity : 0.003 0.051 1722 Dihedral : 18.496 152.570 2797 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.97 % Allowed : 21.00 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.25), residues: 1136 helix: 1.17 (0.23), residues: 559 sheet: 0.01 (0.50), residues: 109 loop : -0.20 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 220 TYR 0.020 0.001 TYR A1242 PHE 0.016 0.001 PHE A1105 TRP 0.008 0.001 TRP A 476 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (11930) covalent geometry : angle 0.53813 / 0.28 (16627) hydrogen bonds : bond 0.03868 / 2.64 ( 510) hydrogen bonds : angle 4.45498 / 3.28 ( 1446) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 54 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8578 (tp30) cc_final: 0.8016 (tp30) REVERT: A 202 ASN cc_start: 0.9104 (OUTLIER) cc_final: 0.8840 (t0) REVERT: A 220 ARG cc_start: 0.9007 (ptm160) cc_final: 0.8749 (ttp80) REVERT: A 331 ASP cc_start: 0.8991 (m-30) cc_final: 0.8713 (m-30) REVERT: A 556 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.7638 (p0) REVERT: A 682 PHE cc_start: 0.8666 (m-10) cc_final: 0.8449 (m-10) REVERT: A 683 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8707 (mp) REVERT: A 724 ILE cc_start: 0.7160 (OUTLIER) cc_final: 0.6756 (pt) REVERT: A 1047 LYS cc_start: 0.4340 (pptt) cc_final: 0.3980 (tmtt) REVERT: A 1205 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8590 (tt0) REVERT: A 1325 LYS cc_start: 0.8720 (ptmm) cc_final: 0.8035 (tttp) REVERT: A 1343 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8633 (mm) outliers start: 29 outliers final: 16 residues processed: 79 average time/residue: 0.4356 time to fit residues: 38.1692 Evaluate side-chains 71 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1205 GLU Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 0 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.099430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.064211 restraints weight = 25296.369| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.96 r_work: 0.2781 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11930 Z= 0.125 Angle : 0.526 9.691 16627 Z= 0.278 Chirality : 0.038 0.217 1943 Planarity : 0.003 0.050 1722 Dihedral : 18.498 152.640 2797 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.56 % Allowed : 21.21 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.25), residues: 1136 helix: 1.21 (0.23), residues: 559 sheet: 0.01 (0.50), residues: 109 loop : -0.17 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 220 TYR 0.018 0.001 TYR A1242 PHE 0.025 0.001 PHE A 518 TRP 0.007 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (11930) covalent geometry : angle 0.52612 / 0.28 (16627) hydrogen bonds : bond 0.03761 / 2.56 ( 510) hydrogen bonds : angle 4.43083 / 3.26 ( 1446) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 50 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8524 (tp30) cc_final: 0.7957 (tp30) REVERT: A 202 ASN cc_start: 0.9113 (OUTLIER) cc_final: 0.8860 (t0) REVERT: A 220 ARG cc_start: 0.9018 (ptm160) cc_final: 0.8706 (ttp80) REVERT: A 331 ASP cc_start: 0.8977 (m-30) cc_final: 0.8702 (m-30) REVERT: A 556 ASN cc_start: 0.8810 (OUTLIER) cc_final: 0.8008 (p0) REVERT: A 682 PHE cc_start: 0.8614 (m-10) cc_final: 0.8400 (m-10) REVERT: A 683 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8777 (mp) REVERT: A 724 ILE cc_start: 0.7121 (OUTLIER) cc_final: 0.6847 (pp) REVERT: A 1047 LYS cc_start: 0.4244 (pptt) cc_final: 0.3914 (tmtt) REVERT: A 1205 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8581 (tt0) REVERT: A 1263 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8331 (tppp) REVERT: A 1325 LYS cc_start: 0.8709 (ptmm) cc_final: 0.8037 (tttp) REVERT: A 1343 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8647 (mm) outliers start: 25 outliers final: 14 residues processed: 73 average time/residue: 0.5312 time to fit residues: 42.8307 Evaluate side-chains 69 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1205 GLU Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.096629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.061621 restraints weight = 25808.166| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.95 r_work: 0.2701 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 11930 Z= 0.288 Angle : 0.651 10.298 16627 Z= 0.339 Chirality : 0.045 0.254 1943 Planarity : 0.004 0.051 1722 Dihedral : 18.563 152.428 2797 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.36 % Allowed : 21.31 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.25), residues: 1136 helix: 0.99 (0.23), residues: 555 sheet: 0.02 (0.51), residues: 109 loop : -0.32 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 220 TYR 0.017 0.002 TYR A 155 PHE 0.025 0.002 PHE A1105 TRP 0.011 0.001 TRP A 476 HIS 0.009 0.002 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.29 (11930) covalent geometry : angle 0.65113 / 0.34 (16627) hydrogen bonds : bond 0.04985 / 3.40 ( 510) hydrogen bonds : angle 4.63098 / 3.39 ( 1446) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 54 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8488 (mp0) REVERT: A 60 GLU cc_start: 0.8645 (tp30) cc_final: 0.7936 (tp30) REVERT: A 90 MET cc_start: 0.9114 (tpp) cc_final: 0.8588 (ttp) REVERT: A 202 ASN cc_start: 0.9115 (OUTLIER) cc_final: 0.8863 (t0) REVERT: A 220 ARG cc_start: 0.9022 (ptm160) cc_final: 0.8759 (ttp80) REVERT: A 331 ASP cc_start: 0.9043 (m-30) cc_final: 0.8754 (m-30) REVERT: A 682 PHE cc_start: 0.8698 (m-10) cc_final: 0.8410 (m-10) REVERT: A 1042 ILE cc_start: 0.7705 (tp) cc_final: 0.7497 (tp) REVERT: A 1047 LYS cc_start: 0.4547 (pptt) cc_final: 0.4189 (tmtt) REVERT: A 1205 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8668 (tt0) REVERT: A 1263 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8428 (mmmm) REVERT: A 1325 LYS cc_start: 0.8783 (ptmm) cc_final: 0.8125 (tttp) REVERT: A 1343 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8749 (mm) outliers start: 23 outliers final: 13 residues processed: 76 average time/residue: 0.4107 time to fit residues: 34.4707 Evaluate side-chains 68 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1205 GLU Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 58 optimal weight: 0.9980 chunk 30 optimal weight: 0.1980 chunk 41 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 122 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 971 GLN ** A1297 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 = 0.3626 r_free = 0.3626 target = 0.098660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.063325 restraints weight = 25598.228| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.98 r_work: 0.2763 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11930 Z= 0.121 Angle : 0.548 10.708 16627 Z= 0.288 Chirality : 0.039 0.223 1943 Planarity : 0.003 0.046 1722 Dihedral : 18.558 152.670 2797 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.54 % Allowed : 22.44 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.25), residues: 1136 helix: 1.14 (0.23), residues: 560 sheet: -0.02 (0.50), residues: 109 loop : -0.14 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 220 TYR 0.022 0.001 TYR A1242 PHE 0.023 0.001 PHE A 518 TRP 0.008 0.001 TRP A 464 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (11930) covalent geometry : angle 0.54764 / 0.29 (16627) hydrogen bonds : bond 0.03874 / 2.63 ( 510) hydrogen bonds : angle 4.45015 / 3.28 ( 1446) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2913.52 seconds wall clock time: 50 minutes 34.67 seconds (3034.67 seconds total)