Starting phenix.real_space_refine on Wed Aug 5 21:55:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t79_41088/08_2026/8t79_41088.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t79_41088/08_2026/8t79_41088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t79_41088/08_2026/8t79_41088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t79_41088/08_2026/8t79_41088.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t79_41088/08_2026/8t79_41088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t79_41088/08_2026/8t79_41088.map" } resolution = 3.04 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 118 5.49 5 S 18 5.16 5 C 7154 2.51 5 N 2083 2.21 5 O 2530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 11903 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 9406 Classifications: {'peptide': 1146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 1112} Chain breaks: 6 Chain: "B" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1905 Classifications: {'RNA': 89} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 46, 'rna3p_pyr': 32} Link IDs: {'rna2p': 10, 'rna3p': 78} Chain: "C" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 401 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 191 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Time building chain proxies: 2.91, per 1000 atoms: 0.24 Number of scatterers: 11903 At special positions: 0 Unit cell: (85.8196, 123.314, 123.314, 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 118 15.00 O 2530 8.00 N 2083 7.00 C 7154 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: 0.66 Conformation dependent library (CDL) restraints added in 359.4 milliseconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2186 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 7 sheets defined 52.8% alpha, 8.5% beta 40 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 59 through 91 removed outlier: 4.762A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (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 145 removed outlier: 3.928A 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 184 through 196 Processing helix chain 'A' and resid 208 through 213 removed outlier: 3.525A pdb=" N SER A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 229 removed outlier: 4.766A pdb=" N GLU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 289 through 306 Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 345 through 352 removed outlier: 4.578A pdb=" N GLU A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.911A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.197A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.703A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 512 through 526 removed outlier: 4.810A pdb=" N TYR A 521 " --> pdb=" O TYR A 517 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 524 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 569 removed outlier: 3.912A pdb=" N TYR A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.656A pdb=" N LEU A 616 " --> pdb=" O ASN A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 643 removed outlier: 5.266A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 643 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 654 removed outlier: 3.537A pdb=" N MET A 648 " --> pdb=" O ASP A 644 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG A 653 " --> pdb=" O LYS A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 668 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.647A pdb=" N ASN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.866A pdb=" N LYS A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 926 Processing helix chain 'A' and resid 927 through 929 No H-bonds generated for 'chain 'A' and resid 927 through 929' Processing helix chain 'A' and resid 930 through 940 Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.926A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.469A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1009 removed outlier: 3.865A pdb=" N PHE A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1047 removed outlier: 4.194A pdb=" N PHE A1045 " --> pdb=" O ILE A1042 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A1046 " --> pdb=" O MET A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1088 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.762A 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 1241 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1263 through 1280 removed outlier: 4.093A pdb=" N ASP A1267 " --> pdb=" O LYS A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1296 Processing helix chain 'A' and resid 1301 through 1313 Processing helix chain 'A' and resid 1314 through 1316 No H-bonds generated for 'chain 'A' and resid 1314 through 1316' Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.708A pdb=" N LEU A1343 " --> pdb=" O LYS A1340 " (cutoff:3.500A) removed outlier: 4.006A 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 958 removed outlier: 5.708A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU A 958 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE A 761 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN A 758 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU A 762 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE A 11 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 10.030A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLN A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 509 removed outlier: 4.998A pdb=" N LEU A 508 " --> pdb=" O GLY A 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 528 through 529 removed outlier: 3.848A pdb=" N ALA A 538 " --> pdb=" O TYR A 529 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1063 through 1065 Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 4.088A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS A1151 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A1158 " --> pdb=" O VAL A1149 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1324 through 1325 removed outlier: 3.857A pdb=" N PHE A1324 " --> pdb=" O ILE A1331 " (cutoff:3.500A) 406 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 196 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 0.91 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: 2671 1.33 - 1.45: 3151 1.45 - 1.57: 6280 1.57 - 1.70: 234 1.70 - 1.82: 35 Bond restraints: 12371 Sorted by residual: bond pdb=" C1' DT C 12 " pdb=" N1 DT C 12 " ideal model delta sigma weight residual 1.468 1.529 -0.061 1.40e-02 5.10e+03 1.92e+01 bond pdb=" C3' DC C 21 " pdb=" C2' DC C 21 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.52e+01 bond pdb=" C3' DC C 28 " pdb=" O3' DC C 28 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.15e+01 bond pdb=" C3' DG D 40 " pdb=" C2' DG D 40 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C1' DT C 27 " pdb=" N1 DT C 27 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.04e+01 ... (remaining 12366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 16979 3.59 - 7.18: 186 7.18 - 10.77: 24 10.77 - 14.36: 9 14.36 - 17.94: 3 Bond angle restraints: 17201 Sorted by residual: angle pdb=" C1' C B 96 " pdb=" N1 C B 96 " pdb=" C2 C B 96 " ideal model delta sigma weight residual 118.80 126.10 -7.30 1.10e+00 8.26e-01 4.40e+01 angle pdb=" CA GLU A1271 " pdb=" CB GLU A1271 " pdb=" CG GLU A1271 " ideal model delta sigma weight residual 114.10 125.93 -11.83 2.00e+00 2.50e-01 3.50e+01 angle pdb=" CB MET A 939 " pdb=" CG MET A 939 " pdb=" SD MET A 939 " ideal model delta sigma weight residual 112.70 130.11 -17.41 3.00e+00 1.11e-01 3.37e+01 angle pdb=" O4' DA C 24 " pdb=" C4' DA C 24 " pdb=" C3' DA C 24 " ideal model delta sigma weight residual 106.00 102.84 3.16 6.00e-01 2.78e+00 2.78e+01 angle pdb=" CA LEU A 651 " pdb=" CB LEU A 651 " pdb=" CG LEU A 651 " ideal model delta sigma weight residual 116.30 134.24 -17.94 3.50e+00 8.16e-02 2.63e+01 ... (remaining 17196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.41: 6971 30.41 - 60.82: 481 60.82 - 91.22: 80 91.22 - 121.63: 1 121.63 - 152.04: 1 Dihedral angle restraints: 7534 sinusoidal: 4164 harmonic: 3370 Sorted by residual: dihedral pdb=" CA PHE A 238 " pdb=" C PHE A 238 " pdb=" N GLY A 239 " pdb=" CA GLY A 239 " ideal model delta harmonic sigma weight residual 180.00 145.70 34.30 0 5.00e+00 4.00e-02 4.71e+01 dihedral pdb=" CA TYR A 517 " pdb=" C TYR A 517 " pdb=" N PHE A 518 " pdb=" CA PHE A 518 " ideal model delta harmonic sigma weight residual 180.00 157.69 22.31 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA PRO A1128 " pdb=" C PRO A1128 " pdb=" N LYS A1129 " pdb=" CA LYS A1129 " ideal model delta harmonic sigma weight residual 180.00 158.35 21.65 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 7531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1746 0.098 - 0.196: 222 0.196 - 0.294: 9 0.294 - 0.392: 1 0.392 - 0.490: 2 Chirality restraints: 1980 Sorted by residual: chirality pdb=" CB ILE A 670 " pdb=" CA ILE A 670 " pdb=" CG1 ILE A 670 " pdb=" CG2 ILE A 670 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" P DT C 23 " pdb=" OP1 DT C 23 " pdb=" OP2 DT C 23 " pdb=" O5' DT C 23 " both_signs ideal model delta sigma weight residual True 2.34 -2.73 -0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CB ILE A1309 " pdb=" CA ILE A1309 " pdb=" CG1 ILE A1309 " pdb=" CG2 ILE A1309 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 1977 not shown) Planarity restraints: 1755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A1265 " -0.022 2.00e-02 2.50e+03 4.38e-02 1.92e+01 pdb=" C TYR A1265 " 0.076 2.00e-02 2.50e+03 pdb=" O TYR A1265 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU A1266 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT C 14 " 0.025 2.00e-02 2.50e+03 2.73e-02 1.86e+01 pdb=" N1 DT C 14 " -0.071 2.00e-02 2.50e+03 pdb=" C2 DT C 14 " 0.036 2.00e-02 2.50e+03 pdb=" O2 DT C 14 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DT C 14 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT C 14 " -0.008 2.00e-02 2.50e+03 pdb=" O4 DT C 14 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DT C 14 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT C 14 " 0.018 2.00e-02 2.50e+03 pdb=" C6 DT C 14 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 655 " -0.317 9.50e-02 1.11e+02 1.43e-01 1.60e+01 pdb=" NE ARG A 655 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 655 " -0.029 2.00e-02 2.50e+03 pdb=" NH1 ARG A 655 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 655 " -0.000 2.00e-02 2.50e+03 ... (remaining 1752 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2060 2.77 - 3.30: 11117 3.30 - 3.84: 21148 3.84 - 4.37: 24800 4.37 - 4.90: 38819 Nonbonded interactions: 97944 Sorted by model distance: nonbonded pdb=" OE1 GLN A 402 " pdb=" O2' U B 44 " model vdw 2.241 3.040 nonbonded pdb=" O ALA A 299 " pdb=" OG SER A 303 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR A1167 " pdb=" OE1 GLU A1170 " model vdw 2.298 3.040 nonbonded pdb=" OD2 ASP A 618 " pdb=" OH TYR A 639 " model vdw 2.300 3.040 nonbonded pdb=" OH TYR A 373 " pdb=" O LEU A 398 " model vdw 2.302 3.040 ... (remaining 97939 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: 4.370 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: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.930 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: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 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 0.061 12371 Z= 0.303 Angle : 1.058 17.945 17201 Z= 0.661 Chirality : 0.061 0.490 1980 Planarity : 0.008 0.143 1755 Dihedral : 18.700 152.041 5348 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.39 % Allowed : 15.60 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.59 (0.22), residues: 1132 helix: -0.63 (0.21), residues: 516 sheet: -1.17 (0.47), residues: 96 loop : -1.36 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG A 655 TYR 0.033 0.002 TYR A 988 PHE 0.034 0.002 PHE A 185 TRP 0.029 0.002 TRP A1136 HIS 0.014 0.002 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.30 (12371) covalent geometry : angle 1.05760 / 0.66 (17201) hydrogen bonds : bond 0.13386 / 9.16 ( 506) hydrogen bonds : angle 6.38618 / 4.55 ( 1387) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TYR cc_start: 0.8531 (p90) cc_final: 0.8262 (p90) REVERT: A 1313 PHE cc_start: 0.8939 (m-80) cc_final: 0.8336 (m-80) outliers start: 4 outliers final: 2 residues processed: 97 average time/residue: 0.0910 time to fit residues: 13.2433 Evaluate side-chains 92 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 1095 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.0570 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 5.9990 overall best weight: 1.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 GLN A 721 HIS A1264 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.120801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.076349 restraints weight = 29101.176| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 3.36 r_work: 0.3068 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12371 Z= 0.193 Angle : 0.630 10.292 17201 Z= 0.343 Chirality : 0.042 0.248 1980 Planarity : 0.004 0.062 1755 Dihedral : 18.956 155.027 2897 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.81 % Allowed : 12.02 % Favored : 85.17 % 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: -0.85 (0.24), residues: 1132 helix: 0.06 (0.22), residues: 533 sheet: -0.82 (0.48), residues: 100 loop : -1.10 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1122 TYR 0.018 0.002 TYR A 988 PHE 0.012 0.001 PHE A 185 TRP 0.014 0.001 TRP A1136 HIS 0.006 0.001 HIS A 982 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (12371) covalent geometry : angle 0.63003 / 0.34 (17201) hydrogen bonds : bond 0.05130 / 3.48 ( 506) hydrogen bonds : angle 5.01142 / 3.55 ( 1387) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TYR cc_start: 0.8521 (p90) cc_final: 0.8247 (p90) REVERT: A 156 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9192 (mm) REVERT: A 370 GLU cc_start: 0.9261 (tp30) cc_final: 0.9030 (tp30) REVERT: A 517 TYR cc_start: 0.9060 (m-80) cc_final: 0.8827 (m-80) REVERT: A 630 GLU cc_start: 0.8951 (pm20) cc_final: 0.8744 (pm20) REVERT: A 1001 TYR cc_start: 0.6318 (m-10) cc_final: 0.6090 (m-10) REVERT: A 1297 HIS cc_start: 0.9151 (m90) cc_final: 0.8910 (m-70) REVERT: A 1313 PHE cc_start: 0.9025 (m-80) cc_final: 0.8779 (m-80) outliers start: 29 outliers final: 16 residues processed: 114 average time/residue: 0.0806 time to fit residues: 13.8166 Evaluate side-chains 109 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1353 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 12 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 413 GLN A1066 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.118708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.073410 restraints weight = 29417.269| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.38 r_work: 0.2987 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12371 Z= 0.230 Angle : 0.626 6.278 17201 Z= 0.339 Chirality : 0.042 0.247 1980 Planarity : 0.004 0.062 1755 Dihedral : 18.976 155.481 2894 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.10 % Allowed : 12.69 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.24), residues: 1132 helix: 0.27 (0.22), residues: 532 sheet: -0.61 (0.50), residues: 105 loop : -0.97 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 69 TYR 0.018 0.002 TYR A 362 PHE 0.040 0.002 PHE A 682 TRP 0.011 0.001 TRP A1136 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.23 (12371) covalent geometry : angle 0.62607 / 0.34 (17201) hydrogen bonds : bond 0.04910 / 3.35 ( 506) hydrogen bonds : angle 4.83906 / 3.42 ( 1387) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TYR cc_start: 0.8623 (p90) cc_final: 0.8348 (p90) REVERT: A 370 GLU cc_start: 0.9298 (tp30) cc_final: 0.9061 (tp30) REVERT: A 517 TYR cc_start: 0.9149 (m-80) cc_final: 0.8675 (m-80) REVERT: A 630 GLU cc_start: 0.8951 (pm20) cc_final: 0.8597 (pm20) REVERT: A 1297 HIS cc_start: 0.9058 (m90) cc_final: 0.8823 (m-70) outliers start: 32 outliers final: 27 residues processed: 109 average time/residue: 0.0807 time to fit residues: 13.2023 Evaluate side-chains 118 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1286 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 24 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 72 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 26 optimal weight: 0.0050 chunk 101 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 HIS A 983 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.120033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.076334 restraints weight = 28887.783| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.28 r_work: 0.3041 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12371 Z= 0.128 Angle : 0.533 7.817 17201 Z= 0.291 Chirality : 0.039 0.247 1980 Planarity : 0.003 0.059 1755 Dihedral : 18.962 153.432 2894 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.42 % Allowed : 14.34 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.24), residues: 1132 helix: 0.53 (0.23), residues: 532 sheet: -0.51 (0.51), residues: 107 loop : -0.85 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 494 TYR 0.012 0.001 TYR A 515 PHE 0.020 0.001 PHE A 682 TRP 0.008 0.001 TRP A1136 HIS 0.004 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (12371) covalent geometry : angle 0.53273 / 0.29 (17201) hydrogen bonds : bond 0.04201 / 2.85 ( 506) hydrogen bonds : angle 4.59898 / 3.26 ( 1387) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 TYR cc_start: 0.8578 (p90) cc_final: 0.8357 (p90) REVERT: A 156 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9190 (mm) REVERT: A 370 GLU cc_start: 0.9288 (tp30) cc_final: 0.9039 (tp30) REVERT: A 517 TYR cc_start: 0.9138 (m-80) cc_final: 0.8569 (m-80) REVERT: A 630 GLU cc_start: 0.8939 (pm20) cc_final: 0.8591 (pm20) REVERT: A 751 MET cc_start: 0.8877 (mtp) cc_final: 0.8499 (mtp) REVERT: A 933 GLN cc_start: 0.8841 (mt0) cc_final: 0.8509 (mp10) REVERT: A 1297 HIS cc_start: 0.9075 (m90) cc_final: 0.8815 (m-70) outliers start: 25 outliers final: 18 residues processed: 108 average time/residue: 0.0770 time to fit residues: 12.8138 Evaluate side-chains 107 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1242 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 30 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 ASN A 240 ASN A 641 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.118383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.073415 restraints weight = 29406.377| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.35 r_work: 0.2990 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12371 Z= 0.198 Angle : 0.572 6.791 17201 Z= 0.306 Chirality : 0.040 0.237 1980 Planarity : 0.004 0.058 1755 Dihedral : 18.909 153.809 2894 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.91 % Allowed : 15.31 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.25), residues: 1132 helix: 0.57 (0.23), residues: 532 sheet: -0.61 (0.50), residues: 114 loop : -0.76 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 69 TYR 0.015 0.001 TYR A 362 PHE 0.015 0.002 PHE A 478 TRP 0.019 0.002 TRP A 659 HIS 0.006 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.20 (12371) covalent geometry : angle 0.57179 / 0.31 (17201) hydrogen bonds : bond 0.04427 / 3.05 ( 506) hydrogen bonds : angle 4.62159 / 3.27 ( 1387) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TYR cc_start: 0.8632 (p90) cc_final: 0.8406 (p90) REVERT: A 156 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9232 (mm) REVERT: A 370 GLU cc_start: 0.9317 (tp30) cc_final: 0.9066 (tp30) REVERT: A 517 TYR cc_start: 0.9178 (m-80) cc_final: 0.8528 (m-80) REVERT: A 630 GLU cc_start: 0.8979 (pm20) cc_final: 0.8666 (pm20) REVERT: A 933 GLN cc_start: 0.8845 (mt0) cc_final: 0.8507 (mp10) REVERT: A 1297 HIS cc_start: 0.9065 (m90) cc_final: 0.8830 (m-70) outliers start: 30 outliers final: 21 residues processed: 107 average time/residue: 0.0767 time to fit residues: 12.2187 Evaluate side-chains 113 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1286 ASN Chi-restraints excluded: chain A residue 1347 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 6 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 102 optimal weight: 0.0870 chunk 87 optimal weight: 1.9990 chunk 17 optimal weight: 0.0570 chunk 92 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 8 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.120184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.076703 restraints weight = 28898.362| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.26 r_work: 0.3054 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12371 Z= 0.107 Angle : 0.510 8.279 17201 Z= 0.276 Chirality : 0.038 0.244 1980 Planarity : 0.003 0.053 1755 Dihedral : 18.823 151.360 2894 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.03 % Allowed : 15.99 % Favored : 81.98 % 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: -0.01 (0.25), residues: 1132 helix: 0.76 (0.23), residues: 532 sheet: -0.35 (0.51), residues: 112 loop : -0.68 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 494 TYR 0.012 0.001 TYR A 515 PHE 0.016 0.001 PHE A1313 TRP 0.008 0.001 TRP A 464 HIS 0.006 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.11 (12371) covalent geometry : angle 0.50968 / 0.28 (17201) hydrogen bonds : bond 0.03845 / 2.63 ( 506) hydrogen bonds : angle 4.47009 / 3.17 ( 1387) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.9280 (tp30) cc_final: 0.9032 (tp30) REVERT: A 510 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8789 (tmmt) REVERT: A 517 TYR cc_start: 0.9171 (m-80) cc_final: 0.8688 (m-80) REVERT: A 751 MET cc_start: 0.8840 (mtp) cc_final: 0.8518 (mtp) REVERT: A 933 GLN cc_start: 0.8835 (mt0) cc_final: 0.8488 (mp10) REVERT: A 1297 HIS cc_start: 0.9079 (m90) cc_final: 0.8821 (m-70) outliers start: 21 outliers final: 15 residues processed: 105 average time/residue: 0.0790 time to fit residues: 12.6360 Evaluate side-chains 102 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1286 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 55 optimal weight: 30.0000 chunk 29 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 27 optimal weight: 0.0570 chunk 108 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 121 optimal weight: 20.0000 overall best weight: 1.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.118856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.075221 restraints weight = 28473.121| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.20 r_work: 0.3022 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12371 Z= 0.154 Angle : 0.547 9.465 17201 Z= 0.291 Chirality : 0.039 0.236 1980 Planarity : 0.003 0.052 1755 Dihedral : 18.714 151.848 2894 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.84 % Allowed : 17.05 % Favored : 81.10 % 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: 0.05 (0.25), residues: 1132 helix: 0.83 (0.23), residues: 529 sheet: -0.28 (0.53), residues: 107 loop : -0.69 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 494 TYR 0.011 0.001 TYR A 362 PHE 0.016 0.001 PHE A1313 TRP 0.007 0.001 TRP A1136 HIS 0.005 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (12371) covalent geometry : angle 0.54668 / 0.29 (17201) hydrogen bonds : bond 0.03936 / 2.70 ( 506) hydrogen bonds : angle 4.49986 / 3.19 ( 1387) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.9298 (tp30) cc_final: 0.9045 (tp30) REVERT: A 517 TYR cc_start: 0.9196 (m-80) cc_final: 0.8681 (m-80) REVERT: A 649 LYS cc_start: 0.8680 (mmtm) cc_final: 0.8161 (tmtt) REVERT: A 933 GLN cc_start: 0.8848 (mt0) cc_final: 0.8499 (mp10) REVERT: A 1297 HIS cc_start: 0.9093 (m90) cc_final: 0.8865 (m-70) outliers start: 19 outliers final: 14 residues processed: 100 average time/residue: 0.0883 time to fit residues: 13.5968 Evaluate side-chains 101 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1286 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 63 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 53 optimal weight: 30.0000 chunk 10 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.118053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.074302 restraints weight = 28507.711| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.20 r_work: 0.3003 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12371 Z= 0.177 Angle : 0.556 9.544 17201 Z= 0.296 Chirality : 0.040 0.246 1980 Planarity : 0.003 0.051 1755 Dihedral : 18.707 152.186 2894 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.03 % Allowed : 16.76 % Favored : 81.20 % 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: 0.05 (0.25), residues: 1132 helix: 0.82 (0.23), residues: 529 sheet: -0.30 (0.53), residues: 107 loop : -0.68 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 494 TYR 0.036 0.001 TYR A 5 PHE 0.015 0.001 PHE A1313 TRP 0.007 0.001 TRP A1136 HIS 0.005 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (12371) covalent geometry : angle 0.55619 / 0.30 (17201) hydrogen bonds : bond 0.04039 / 2.77 ( 506) hydrogen bonds : angle 4.51819 / 3.21 ( 1387) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.9324 (tp30) cc_final: 0.9074 (tp30) REVERT: A 517 TYR cc_start: 0.9177 (m-80) cc_final: 0.8658 (m-80) REVERT: A 933 GLN cc_start: 0.8861 (mt0) cc_final: 0.8380 (mp10) outliers start: 21 outliers final: 15 residues processed: 95 average time/residue: 0.0846 time to fit residues: 12.1817 Evaluate side-chains 100 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1286 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.119000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.075537 restraints weight = 28427.710| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.16 r_work: 0.3032 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12371 Z= 0.122 Angle : 0.527 9.683 17201 Z= 0.282 Chirality : 0.038 0.238 1980 Planarity : 0.003 0.049 1755 Dihedral : 18.676 151.148 2894 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.84 % Allowed : 17.15 % Favored : 81.01 % 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: 0.16 (0.25), residues: 1132 helix: 0.90 (0.23), residues: 529 sheet: -0.23 (0.53), residues: 107 loop : -0.61 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 494 TYR 0.040 0.001 TYR A 5 PHE 0.017 0.001 PHE A1313 TRP 0.007 0.001 TRP A 464 HIS 0.005 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (12371) covalent geometry : angle 0.52734 / 0.28 (17201) hydrogen bonds : bond 0.03768 / 2.58 ( 506) hydrogen bonds : angle 4.45666 / 3.17 ( 1387) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.9308 (tp30) cc_final: 0.9062 (tp30) REVERT: A 517 TYR cc_start: 0.9166 (m-80) cc_final: 0.8632 (m-80) REVERT: A 933 GLN cc_start: 0.8865 (mt0) cc_final: 0.8393 (mp10) outliers start: 19 outliers final: 17 residues processed: 96 average time/residue: 0.0848 time to fit residues: 12.1000 Evaluate side-chains 103 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1286 ASN Chi-restraints excluded: chain A residue 1290 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 84 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.117932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.074369 restraints weight = 28574.854| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.19 r_work: 0.3004 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12371 Z= 0.173 Angle : 0.558 9.056 17201 Z= 0.296 Chirality : 0.039 0.232 1980 Planarity : 0.003 0.050 1755 Dihedral : 18.644 151.913 2894 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.74 % Allowed : 17.25 % Favored : 81.01 % 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: 0.11 (0.25), residues: 1132 helix: 0.89 (0.23), residues: 529 sheet: -0.35 (0.52), residues: 107 loop : -0.64 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1171 TYR 0.013 0.001 TYR A 362 PHE 0.016 0.002 PHE A1313 TRP 0.008 0.001 TRP A1136 HIS 0.005 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (12371) covalent geometry : angle 0.55785 / 0.30 (17201) hydrogen bonds : bond 0.03990 / 2.74 ( 506) hydrogen bonds : angle 4.48396 / 3.18 ( 1387) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 370 GLU cc_start: 0.9324 (tp30) cc_final: 0.9083 (tp30) REVERT: A 517 TYR cc_start: 0.9201 (m-80) cc_final: 0.8654 (m-80) REVERT: A 649 LYS cc_start: 0.8713 (mmtm) cc_final: 0.8148 (tmtt) REVERT: A 933 GLN cc_start: 0.8875 (mt0) cc_final: 0.8401 (mp10) REVERT: A 968 LYS cc_start: 0.9351 (ptpp) cc_final: 0.8922 (mtmm) outliers start: 18 outliers final: 17 residues processed: 96 average time/residue: 0.0908 time to fit residues: 13.2091 Evaluate side-chains 103 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1242 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.118625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.074815 restraints weight = 28758.746| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.22 r_work: 0.3019 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12371 Z= 0.132 Angle : 0.534 9.144 17201 Z= 0.285 Chirality : 0.038 0.237 1980 Planarity : 0.003 0.049 1755 Dihedral : 18.651 151.023 2894 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.74 % Allowed : 17.15 % Favored : 81.10 % 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: 0.19 (0.25), residues: 1132 helix: 0.95 (0.23), residues: 529 sheet: -0.31 (0.52), residues: 107 loop : -0.60 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 629 TYR 0.012 0.001 TYR A 521 PHE 0.017 0.001 PHE A1313 TRP 0.007 0.001 TRP A1136 HIS 0.005 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (12371) covalent geometry : angle 0.53426 / 0.28 (17201) hydrogen bonds : bond 0.03792 / 2.60 ( 506) hydrogen bonds : angle 4.44984 / 3.16 ( 1387) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2905.35 seconds wall clock time: 50 minutes 22.56 seconds (3022.56 seconds total)