Starting phenix.real_space_refine on Fri Sep 11 20:03:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5n8o_3601/09_2026/5n8o_3601_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5n8o_3601/09_2026/5n8o_3601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5n8o_3601/09_2026/5n8o_3601_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5n8o_3601/09_2026/5n8o_3601_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5n8o_3601/09_2026/5n8o_3601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5n8o_3601/09_2026/5n8o_3601.map" } resolution = 3.9 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= 0.001 sd= 0.012 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 18 5.49 5 S 45 5.16 5 C 6975 2.51 5 N 2046 2.21 5 O 2278 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11362 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11002 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1432, 10991 Classifications: {'peptide': 1432} Link IDs: {'CIS': 7, 'PCIS': 1, 'PTRANS': 51, 'TRANS': 1372} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 1432, 10991 Classifications: {'peptide': 1432} Link IDs: {'CIS': 7, 'PCIS': 1, 'PTRANS': 51, 'TRANS': 1372} Chain breaks: 5 bond proxies already assigned to first conformer: 11141 Chain: "C" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 360 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Time building chain proxies: 4.24, per 1000 atoms: 0.37 Number of scatterers: 11362 At special positions: 0 Unit cell: (113.4, 131.25, 102.9, 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 45 16.00 P 18 15.00 O 2278 8.00 N 2046 7.00 C 6975 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: 0.75 Conformation dependent library (CDL) restraints added in 957.8 milliseconds 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2632 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 18 sheets defined 36.5% alpha, 8.5% beta 0 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 11 through 18 removed outlier: 4.223A pdb=" N THR A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 41 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 100 through 120 removed outlier: 4.209A pdb=" N AARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 192 Processing helix chain 'A' and resid 192 through 212 Processing helix chain 'A' and resid 269 through 282 removed outlier: 3.853A pdb=" N ARG A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS A 282 " --> pdb=" O MET A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 304 removed outlier: 3.597A pdb=" N THR A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 336 through 347 removed outlier: 3.739A pdb=" N LEU A 340 " --> pdb=" O TYR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 354 No H-bonds generated for 'chain 'A' and resid 353 through 354' Processing helix chain 'A' and resid 356 through 367 Processing helix chain 'A' and resid 383 through 402 removed outlier: 4.131A pdb=" N ARG A 397 " --> pdb=" O ARG A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 430 removed outlier: 3.929A pdb=" N ARG A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 460 removed outlier: 3.600A pdb=" N GLN A 459 " --> pdb=" O MET A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 513 removed outlier: 3.520A pdb=" N LEU A 513 " --> pdb=" O GLY A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 527 removed outlier: 4.577A pdb=" N LEU A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 552 Processing helix chain 'A' and resid 576 through 593 Processing helix chain 'A' and resid 604 through 621 Processing helix chain 'A' and resid 696 through 698 No H-bonds generated for 'chain 'A' and resid 696 through 698' Processing helix chain 'A' and resid 763 through 767 removed outlier: 3.653A pdb=" N ALA A 767 " --> pdb=" O PRO A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 844 removed outlier: 3.844A pdb=" N GLN A 839 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 844 " --> pdb=" O ILE A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 858 removed outlier: 3.628A pdb=" N ALA A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 877 Proline residue: A 873 - end of helix Processing helix chain 'A' and resid 885 through 894 Processing helix chain 'A' and resid 901 through 914 removed outlier: 3.750A pdb=" N GLY A 905 " --> pdb=" O PHE A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 952 removed outlier: 3.545A pdb=" N GLU A 940 " --> pdb=" O SER A 936 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 942 " --> pdb=" O GLU A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 978 removed outlier: 4.011A pdb=" N THR A 977 " --> pdb=" O GLN A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1011 Processing helix chain 'A' and resid 1026 through 1036 Processing helix chain 'A' and resid 1043 through 1056 removed outlier: 3.671A pdb=" N LEU A1047 " --> pdb=" O LEU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1075 removed outlier: 3.886A pdb=" N VAL A1075 " --> pdb=" O SER A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1086 Processing helix chain 'A' and resid 1112 through 1117 Processing helix chain 'A' and resid 1133 through 1135 No H-bonds generated for 'chain 'A' and resid 1133 through 1135' Processing helix chain 'A' and resid 1136 through 1146 Processing helix chain 'A' and resid 1147 through 1155 Processing helix chain 'A' and resid 1156 through 1158 No H-bonds generated for 'chain 'A' and resid 1156 through 1158' Processing helix chain 'A' and resid 1183 through 1195 Processing helix chain 'A' and resid 1209 through 1217 removed outlier: 4.124A pdb=" N VAL A1213 " --> pdb=" O TYR A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1224 Processing helix chain 'A' and resid 1235 through 1251 Processing helix chain 'A' and resid 1271 through 1275 removed outlier: 4.524A pdb=" N LEU A1274 " --> pdb=" O ASP A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1281 removed outlier: 3.908A pdb=" N TRP A1280 " --> pdb=" O ARG A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1392 Processing helix chain 'A' and resid 1428 through 1436 removed outlier: 3.835A pdb=" N ALA A1432 " --> pdb=" O GLY A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1451 through 1459 Processing helix chain 'A' and resid 1465 through 1469 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 34 removed outlier: 3.561A pdb=" N ARG A 32 " --> pdb=" O LEU A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 127 Processing sheet with id=AA5, first strand: chain 'A' and resid 505 through 506 removed outlier: 7.096A pdb=" N VAL A 505 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR A 535 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ALA A 434 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASP A 536 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL A 436 " --> pdb=" O ASP A 536 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 569 through 570 removed outlier: 6.207A pdb=" N THR A 569 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL A 788 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N GLU A 776 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ALA A 599 " --> pdb=" O GLU A 776 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 629 through 631 Processing sheet with id=AA8, first strand: chain 'A' and resid 655 through 660 removed outlier: 3.772A pdb=" N SER A 665 " --> pdb=" O ASN A 660 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 674 through 675 removed outlier: 3.502A pdb=" N THR A 675 " --> pdb=" O SER A 680 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 733 through 735 removed outlier: 3.800A pdb=" N ASP A 733 " --> pdb=" O VAL A 720 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 720 " --> pdb=" O ASP A 733 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 718 " --> pdb=" O LEU A 735 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 745 through 746 Processing sheet with id=AB3, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.687A pdb=" N THR A 988 " --> pdb=" O ALA A1096 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1040 through 1041 removed outlier: 6.287A pdb=" N GLY A1022 " --> pdb=" O GLN A1041 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1399 through 1401 removed outlier: 7.005A pdb=" N ALA A1413 " --> pdb=" O GLN A1444 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1260 through 1266 Processing sheet with id=AB7, first strand: chain 'A' and resid 1296 through 1301 removed outlier: 6.949A pdb=" N THR A1308 " --> pdb=" O ALA A1298 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE A1300 " --> pdb=" O LEU A1306 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU A1306 " --> pdb=" O ILE A1300 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1361 through 1363 Processing sheet with id=AB9, first strand: chain 'A' and resid 1372 through 1374 removed outlier: 3.752A pdb=" N ARG A1381 " --> pdb=" O LEU A1374 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2304 1.32 - 1.44: 2620 1.44 - 1.57: 6509 1.57 - 1.69: 37 1.69 - 1.81: 90 Bond restraints: 11560 Sorted by residual: bond pdb=" C1' DT C 7 " pdb=" N1 DT C 7 " ideal model delta sigma weight residual 1.468 1.541 -0.073 1.40e-02 5.10e+03 2.75e+01 bond pdb=" C3' DT C 9 " pdb=" O3' DT C 9 " ideal model delta sigma weight residual 1.435 1.383 0.052 1.30e-02 5.92e+03 1.58e+01 bond pdb=" C3' DT C 19 " pdb=" O3' DT C 19 " ideal model delta sigma weight residual 1.435 1.386 0.049 1.30e-02 5.92e+03 1.44e+01 bond pdb=" C3' DT C 21 " pdb=" C2' DT C 21 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.31e+01 bond pdb=" C1' DT C 17 " pdb=" N1 DT C 17 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.23e+01 ... (remaining 11555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 15408 3.84 - 7.68: 259 7.68 - 11.52: 32 11.52 - 15.36: 7 15.36 - 19.20: 2 Bond angle restraints: 15708 Sorted by residual: angle pdb=" O4' DT C 7 " pdb=" C1' DT C 7 " pdb=" N1 DT C 7 " ideal model delta sigma weight residual 108.00 112.69 -4.69 7.00e-01 2.04e+00 4.50e+01 angle pdb=" CA LEU A 818 " pdb=" CB LEU A 818 " pdb=" CG LEU A 818 " ideal model delta sigma weight residual 116.30 135.50 -19.20 3.50e+00 8.16e-02 3.01e+01 angle pdb=" C VAL A 782 " pdb=" N SER A 783 " pdb=" CA SER A 783 " ideal model delta sigma weight residual 121.54 111.24 10.30 1.91e+00 2.74e-01 2.91e+01 angle pdb=" N GLU A1471 " pdb=" CA GLU A1471 " pdb=" C GLU A1471 " ideal model delta sigma weight residual 109.81 121.55 -11.74 2.21e+00 2.05e-01 2.82e+01 angle pdb=" C ASP A1291 " pdb=" N ASN A1292 " pdb=" CA ASN A1292 " ideal model delta sigma weight residual 121.70 131.16 -9.46 1.80e+00 3.09e-01 2.76e+01 ... (remaining 15703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 6619 17.32 - 34.64: 284 34.64 - 51.96: 67 51.96 - 69.28: 21 69.28 - 86.59: 14 Dihedral angle restraints: 7005 sinusoidal: 2914 harmonic: 4091 Sorted by residual: dihedral pdb=" CA GLU A 376 " pdb=" C GLU A 376 " pdb=" N LYS A 377 " pdb=" CA LYS A 377 " ideal model delta harmonic sigma weight residual -180.00 -150.93 -29.07 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA ILE A 571 " pdb=" C ILE A 571 " pdb=" N SER A 572 " pdb=" CA SER A 572 " ideal model delta harmonic sigma weight residual -180.00 -151.05 -28.95 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA ASP A 819 " pdb=" C ASP A 819 " pdb=" N GLU A 820 " pdb=" CA GLU A 820 " ideal model delta harmonic sigma weight residual -180.00 -151.93 -28.07 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 7002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1282 0.065 - 0.129: 410 0.129 - 0.194: 79 0.194 - 0.258: 15 0.258 - 0.322: 4 Chirality restraints: 1790 Sorted by residual: chirality pdb=" CB ILE A 487 " pdb=" CA ILE A 487 " pdb=" CG1 ILE A 487 " pdb=" CG2 ILE A 487 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB THR A1308 " pdb=" CA THR A1308 " pdb=" OG1 THR A1308 " pdb=" CG2 THR A1308 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CG LEU A1287 " pdb=" CB LEU A1287 " pdb=" CD1 LEU A1287 " pdb=" CD2 LEU A1287 " both_signs ideal model delta sigma weight residual False -2.59 -2.86 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1787 not shown) Planarity restraints: 2015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A1283 " 0.044 5.00e-02 4.00e+02 6.82e-02 7.43e+00 pdb=" N PRO A1284 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A1284 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1284 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 576 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.49e+00 pdb=" C ARG A 576 " -0.041 2.00e-02 2.50e+03 pdb=" O ARG A 576 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN A 577 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 335 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.04e+00 pdb=" C THR A 335 " 0.039 2.00e-02 2.50e+03 pdb=" O THR A 335 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR A 336 " -0.013 2.00e-02 2.50e+03 ... (remaining 2012 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 71 2.48 - 3.09: 7690 3.09 - 3.69: 16792 3.69 - 4.30: 23982 4.30 - 4.90: 38556 Nonbonded interactions: 87091 Sorted by model distance: nonbonded pdb=" OG SER A1350 " pdb=" O TYR A1356 " model vdw 1.878 3.040 nonbonded pdb=" O GLY A1355 " pdb=" NH2 ARG A1381 " model vdw 2.033 3.120 nonbonded pdb=" OD2 ASP A1215 " pdb=" OH TYR A1446 " model vdw 2.093 3.040 nonbonded pdb=" ND2 ASN A1265 " pdb=" OD2 ASP A1335 " model vdw 2.119 3.120 nonbonded pdb=" OE2 GLU A 376 " pdb=" ND1 HIS A 869 " model vdw 2.123 3.120 ... (remaining 87086 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.580 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: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.810 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 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 : 0.008 0.073 11560 Z= 0.387 Angle : 1.270 19.196 15708 Z= 0.705 Chirality : 0.066 0.322 1790 Planarity : 0.007 0.068 2015 Dihedral : 11.993 86.593 4373 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 15.00 % Favored : 84.79 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.51 % 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: -5.69 (0.16), residues: 1423 helix: -3.62 (0.13), residues: 506 sheet: -3.26 (0.30), residues: 213 loop : -4.11 (0.18), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 934 TYR 0.021 0.003 TYR A 190 PHE 0.037 0.005 PHE A1412 TRP 0.028 0.004 TRP A1280 HIS 0.012 0.002 HIS A 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00774 / 0.39 (11560) covalent geometry : angle 1.26954 / 0.71 (15708) hydrogen bonds : bond 0.17517 / 10.96 ( 369) hydrogen bonds : angle 10.72234 / 7.39 ( 1047) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8587 (mtt90) cc_final: 0.8027 (ttm-80) REVERT: A 104 ASP cc_start: 0.8900 (m-30) cc_final: 0.8646 (m-30) REVERT: A 118 GLU cc_start: 0.8552 (tt0) cc_final: 0.7918 (tm-30) REVERT: A 141 MET cc_start: 0.7229 (mtm) cc_final: 0.7019 (ttm) REVERT: A 183 THR cc_start: 0.5402 (p) cc_final: 0.4842 (p) REVERT: A 202 GLU cc_start: 0.8612 (tp30) cc_final: 0.8234 (mm-30) REVERT: A 398 ASP cc_start: 0.7994 (m-30) cc_final: 0.7736 (t0) REVERT: A 402 GLN cc_start: 0.8519 (mp-120) cc_final: 0.8029 (mp10) REVERT: A 486 LEU cc_start: 0.6250 (pp) cc_final: 0.5753 (tp) REVERT: A 536 ASP cc_start: 0.7444 (t70) cc_final: 0.7233 (t0) REVERT: A 631 MET cc_start: 0.8343 (ttp) cc_final: 0.8077 (ttt) REVERT: A 667 ASP cc_start: 0.8105 (m-30) cc_final: 0.7881 (p0) REVERT: A 795 MET cc_start: 0.7755 (mtp) cc_final: 0.7426 (mtp) REVERT: A 819 ASP cc_start: 0.7300 (m-30) cc_final: 0.6965 (p0) REVERT: A 937 TYR cc_start: 0.7954 (t80) cc_final: 0.7718 (t80) REVERT: A 974 ARG cc_start: 0.7639 (ptm160) cc_final: 0.7232 (ptm160) REVERT: A 1011 MET cc_start: 0.8917 (ttt) cc_final: 0.8443 (tmm) REVERT: A 1032 GLU cc_start: 0.8418 (tt0) cc_final: 0.7841 (tm-30) REVERT: A 1070 ASP cc_start: 0.8284 (p0) cc_final: 0.6705 (p0) REVERT: A 1195 MET cc_start: 0.8017 (mmm) cc_final: 0.7475 (mmt) REVERT: A 1226 GLN cc_start: 0.6255 (tp-100) cc_final: 0.5699 (tt0) REVERT: A 1273 GLU cc_start: 0.8102 (tt0) cc_final: 0.7778 (tt0) REVERT: A 1400 ILE cc_start: 0.8072 (mp) cc_final: 0.7814 (mm) REVERT: A 1425 LEU cc_start: 0.7944 (pp) cc_final: 0.7643 (mt) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.1280 time to fit residues: 51.1528 Evaluate side-chains 172 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.0020 chunk 55 optimal weight: 0.0970 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 HIS ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 GLN A 351 ASN A 445 GLN ** A 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS A1102 GLN ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 GLN ** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.115923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.094602 restraints weight = 70152.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.099991 restraints weight = 30249.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.102652 restraints weight = 14103.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.102926 restraints weight = 9385.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.103616 restraints weight = 8758.450| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11560 Z= 0.158 Angle : 0.869 18.430 15708 Z= 0.445 Chirality : 0.048 0.300 1790 Planarity : 0.006 0.068 2015 Dihedral : 13.135 89.317 1749 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.68 % Favored : 87.25 % Rotamer: Outliers : 2.31 % Allowed : 8.90 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.51 % 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: -4.38 (0.19), residues: 1423 helix: -1.88 (0.20), residues: 508 sheet: -2.96 (0.30), residues: 231 loop : -3.75 (0.20), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1093 TYR 0.031 0.002 TYR A1141 PHE 0.029 0.002 PHE A 380 TRP 0.025 0.002 TRP A 560 HIS 0.008 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (11560) covalent geometry : angle 0.86923 / 0.44 (15708) hydrogen bonds : bond 0.04131 / 2.67 ( 369) hydrogen bonds : angle 6.67728 / 4.54 ( 1047) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 209 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8263 (mtt90) cc_final: 0.7803 (ttm-80) REVERT: A 100 LYS cc_start: 0.8801 (mttt) cc_final: 0.8221 (tmmt) REVERT: A 104 ASP cc_start: 0.8412 (m-30) cc_final: 0.8058 (m-30) REVERT: A 118 GLU cc_start: 0.8006 (tt0) cc_final: 0.7689 (mm-30) REVERT: A 183 THR cc_start: 0.5586 (p) cc_final: 0.5353 (p) REVERT: A 202 GLU cc_start: 0.8304 (tp30) cc_final: 0.8038 (mm-30) REVERT: A 402 GLN cc_start: 0.8302 (mp-120) cc_final: 0.7914 (mp10) REVERT: A 772 ASN cc_start: 0.7094 (t0) cc_final: 0.6668 (t0) REVERT: A 884 MET cc_start: 0.6197 (mmm) cc_final: 0.5522 (mmm) REVERT: A 1011 MET cc_start: 0.8730 (ttt) cc_final: 0.8367 (tmm) REVERT: A 1070 ASP cc_start: 0.7750 (p0) cc_final: 0.7484 (p0) REVERT: A 1099 ASP cc_start: 0.6421 (t70) cc_final: 0.5664 (t70) REVERT: A 1195 MET cc_start: 0.7693 (mmm) cc_final: 0.7310 (mmt) REVERT: A 1212 ILE cc_start: 0.7877 (mp) cc_final: 0.7651 (mp) REVERT: A 1226 GLN cc_start: 0.6142 (tp-100) cc_final: 0.5620 (tt0) REVERT: A 1273 GLU cc_start: 0.7914 (tt0) cc_final: 0.7472 (tt0) REVERT: A 1459 ASN cc_start: 0.8363 (m110) cc_final: 0.8032 (m-40) outliers start: 27 outliers final: 13 residues processed: 223 average time/residue: 0.1102 time to fit residues: 34.3819 Evaluate side-chains 158 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1429 PHE Chi-restraints excluded: chain A residue 1445 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 127 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 HIS ** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1444 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.113615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.093130 restraints weight = 50616.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.096592 restraints weight = 24679.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.098989 restraints weight = 14897.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.100630 restraints weight = 10346.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.101751 restraints weight = 7988.524| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11560 Z= 0.152 Angle : 0.828 17.164 15708 Z= 0.421 Chirality : 0.047 0.225 1790 Planarity : 0.006 0.065 2015 Dihedral : 12.912 89.305 1749 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.61 % Favored : 87.32 % Rotamer: Outliers : 1.88 % Allowed : 12.83 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.51 % 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: -3.82 (0.20), residues: 1423 helix: -1.10 (0.22), residues: 522 sheet: -2.77 (0.30), residues: 238 loop : -3.70 (0.20), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1093 TYR 0.033 0.002 TYR A1141 PHE 0.020 0.002 PHE A 380 TRP 0.017 0.002 TRP A 702 HIS 0.007 0.001 HIS A 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (11560) covalent geometry : angle 0.82763 / 0.42 (15708) hydrogen bonds : bond 0.03672 / 2.44 ( 369) hydrogen bonds : angle 5.99389 / 4.11 ( 1047) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8263 (mtt90) cc_final: 0.7924 (ttm-80) REVERT: A 100 LYS cc_start: 0.8749 (mttt) cc_final: 0.8169 (tmmt) REVERT: A 104 ASP cc_start: 0.8659 (m-30) cc_final: 0.8178 (m-30) REVERT: A 118 GLU cc_start: 0.8157 (tt0) cc_final: 0.7817 (mm-30) REVERT: A 183 THR cc_start: 0.5468 (p) cc_final: 0.5259 (p) REVERT: A 486 LEU cc_start: 0.6162 (pp) cc_final: 0.5407 (tp) REVERT: A 772 ASN cc_start: 0.7254 (t0) cc_final: 0.6765 (t0) REVERT: A 884 MET cc_start: 0.6193 (mmm) cc_final: 0.5813 (mmm) REVERT: A 1011 MET cc_start: 0.8773 (ttt) cc_final: 0.8384 (tmm) REVERT: A 1033 MET cc_start: 0.7986 (mtp) cc_final: 0.7386 (mtt) REVERT: A 1070 ASP cc_start: 0.8060 (p0) cc_final: 0.7780 (p0) REVERT: A 1099 ASP cc_start: 0.6194 (t70) cc_final: 0.4697 (t0) REVERT: A 1226 GLN cc_start: 0.6356 (tp-100) cc_final: 0.6031 (tt0) REVERT: A 1260 MET cc_start: 0.7826 (mmm) cc_final: 0.7438 (mmm) REVERT: A 1392 GLN cc_start: 0.8558 (mm110) cc_final: 0.8002 (mp10) REVERT: A 1459 ASN cc_start: 0.8373 (m110) cc_final: 0.8079 (m-40) outliers start: 22 outliers final: 11 residues processed: 184 average time/residue: 0.1013 time to fit residues: 26.7456 Evaluate side-chains 154 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1429 PHE Chi-restraints excluded: chain A residue 1445 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 20 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 2 optimal weight: 0.0980 chunk 43 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 51 optimal weight: 0.0000 overall best weight: 2.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 GLN ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 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 = 0.3704 r_free = 0.3704 target = 0.111967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.091205 restraints weight = 68687.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.096705 restraints weight = 28889.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.098088 restraints weight = 13767.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.100229 restraints weight = 9437.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.100156 restraints weight = 8177.046| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11560 Z= 0.167 Angle : 0.824 16.157 15708 Z= 0.418 Chirality : 0.047 0.205 1790 Planarity : 0.005 0.065 2015 Dihedral : 12.808 89.172 1749 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.82 % Favored : 87.11 % Rotamer: Outliers : 2.48 % Allowed : 12.23 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.51 % 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: -3.40 (0.21), residues: 1423 helix: -0.64 (0.22), residues: 523 sheet: -2.43 (0.31), residues: 231 loop : -3.63 (0.20), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 298 TYR 0.018 0.002 TYR A1141 PHE 0.025 0.002 PHE A 894 TRP 0.025 0.002 TRP A1453 HIS 0.006 0.001 HIS A 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (11560) covalent geometry : angle 0.82383 / 0.42 (15708) hydrogen bonds : bond 0.03587 / 2.38 ( 369) hydrogen bonds : angle 5.64431 / 3.87 ( 1047) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8400 (mtt90) cc_final: 0.7870 (ttm-80) REVERT: A 100 LYS cc_start: 0.8715 (mttt) cc_final: 0.8127 (tmmt) REVERT: A 104 ASP cc_start: 0.8720 (m-30) cc_final: 0.8213 (m-30) REVERT: A 118 GLU cc_start: 0.8279 (tt0) cc_final: 0.7903 (mm-30) REVERT: A 183 THR cc_start: 0.5698 (p) cc_final: 0.5484 (p) REVERT: A 486 LEU cc_start: 0.6221 (pp) cc_final: 0.5462 (tp) REVERT: A 772 ASN cc_start: 0.7362 (t0) cc_final: 0.6866 (t0) REVERT: A 960 ARG cc_start: 0.5929 (tpt90) cc_final: 0.4906 (mmm-85) REVERT: A 1011 MET cc_start: 0.8805 (ttt) cc_final: 0.8367 (ppp) REVERT: A 1033 MET cc_start: 0.7988 (mtp) cc_final: 0.7535 (mtp) REVERT: A 1210 GLU cc_start: 0.8184 (mp0) cc_final: 0.7851 (mp0) REVERT: A 1226 GLN cc_start: 0.6362 (tp-100) cc_final: 0.6091 (tt0) REVERT: A 1238 ARG cc_start: 0.7709 (ttm-80) cc_final: 0.7193 (ttt-90) REVERT: A 1392 GLN cc_start: 0.8645 (mm110) cc_final: 0.8000 (mp10) REVERT: A 1451 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.7104 (tp40) REVERT: A 1453 TRP cc_start: 0.8109 (t60) cc_final: 0.7789 (t60) REVERT: A 1459 ASN cc_start: 0.8489 (m110) cc_final: 0.8230 (m-40) outliers start: 29 outliers final: 18 residues processed: 179 average time/residue: 0.1110 time to fit residues: 27.8534 Evaluate side-chains 165 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 974 ARG Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1451 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 107 optimal weight: 0.0670 chunk 87 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.2980 chunk 74 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 132 optimal weight: 0.3980 chunk 103 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1403 HIS ** A1444 GLN ** 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 = 0.3743 r_free = 0.3743 target = 0.114480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.093392 restraints weight = 59763.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.097145 restraints weight = 27340.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.099718 restraints weight = 15878.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.101457 restraints weight = 10733.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.102674 restraints weight = 8099.234| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11560 Z= 0.137 Angle : 0.796 16.320 15708 Z= 0.398 Chirality : 0.045 0.183 1790 Planarity : 0.005 0.061 2015 Dihedral : 12.632 88.728 1749 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.32 % Favored : 87.61 % Rotamer: Outliers : 1.88 % Allowed : 12.92 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.51 % 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: -3.11 (0.21), residues: 1423 helix: -0.33 (0.23), residues: 520 sheet: -2.29 (0.31), residues: 238 loop : -3.50 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 934 TYR 0.016 0.001 TYR A1209 PHE 0.017 0.002 PHE A 380 TRP 0.018 0.001 TRP A1170 HIS 0.005 0.001 HIS A 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (11560) covalent geometry : angle 0.79594 / 0.40 (15708) hydrogen bonds : bond 0.03283 / 2.20 ( 369) hydrogen bonds : angle 5.36957 / 3.68 ( 1047) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8372 (mtt90) cc_final: 0.7873 (ttm-80) REVERT: A 92 MET cc_start: 0.8679 (ttp) cc_final: 0.8334 (tmm) REVERT: A 100 LYS cc_start: 0.8668 (mttt) cc_final: 0.8123 (tmmt) REVERT: A 104 ASP cc_start: 0.8696 (m-30) cc_final: 0.8242 (m-30) REVERT: A 118 GLU cc_start: 0.8198 (tt0) cc_final: 0.7876 (mm-30) REVERT: A 486 LEU cc_start: 0.6078 (pp) cc_final: 0.5438 (tp) REVERT: A 772 ASN cc_start: 0.7299 (t0) cc_final: 0.6811 (t0) REVERT: A 884 MET cc_start: 0.6190 (mmm) cc_final: 0.5749 (mmm) REVERT: A 985 ASP cc_start: 0.7743 (t70) cc_final: 0.7157 (m-30) REVERT: A 1011 MET cc_start: 0.8639 (ttt) cc_final: 0.8341 (ppp) REVERT: A 1099 ASP cc_start: 0.5803 (OUTLIER) cc_final: 0.5526 (t0) REVERT: A 1210 GLU cc_start: 0.8172 (mp0) cc_final: 0.7613 (tp30) REVERT: A 1392 GLN cc_start: 0.8666 (mm110) cc_final: 0.7848 (mp10) outliers start: 22 outliers final: 11 residues processed: 182 average time/residue: 0.0989 time to fit residues: 26.2041 Evaluate side-chains 160 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1396 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 130 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 HIS ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 GLN ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 HIS ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1226 GLN A1283 ASN ** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 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 = 0.3664 r_free = 0.3664 target = 0.109273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.087748 restraints weight = 71635.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.091846 restraints weight = 31646.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.093749 restraints weight = 18201.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.096236 restraints weight = 12867.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.097566 restraints weight = 8281.422| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3468 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 11560 Z= 0.223 Angle : 0.879 14.759 15708 Z= 0.443 Chirality : 0.049 0.194 1790 Planarity : 0.005 0.063 2015 Dihedral : 12.805 86.945 1749 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.24 % Favored : 86.62 % Rotamer: Outliers : 2.22 % Allowed : 13.94 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.51 % 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: -3.11 (0.21), residues: 1423 helix: -0.35 (0.23), residues: 525 sheet: -2.37 (0.32), residues: 224 loop : -3.47 (0.21), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1214 TYR 0.014 0.002 TYR A1398 PHE 0.035 0.002 PHE A 894 TRP 0.048 0.003 TRP A1170 HIS 0.008 0.002 HIS A 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 (11560) covalent geometry : angle 0.87926 / 0.44 (15708) hydrogen bonds : bond 0.03668 / 2.44 ( 369) hydrogen bonds : angle 5.45067 / 3.74 ( 1047) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8309 (mtt90) cc_final: 0.7874 (ttm-80) REVERT: A 92 MET cc_start: 0.8651 (ttp) cc_final: 0.8378 (tmm) REVERT: A 93 MET cc_start: 0.8420 (mmm) cc_final: 0.8044 (mmm) REVERT: A 100 LYS cc_start: 0.8699 (mttt) cc_final: 0.8122 (tmmt) REVERT: A 104 ASP cc_start: 0.8617 (m-30) cc_final: 0.8166 (m-30) REVERT: A 118 GLU cc_start: 0.8236 (tt0) cc_final: 0.8019 (mm-30) REVERT: A 631 MET cc_start: 0.8248 (tpt) cc_final: 0.7485 (tpt) REVERT: A 772 ASN cc_start: 0.7678 (t0) cc_final: 0.7151 (t0) REVERT: A 1011 MET cc_start: 0.8582 (ttt) cc_final: 0.8289 (ppp) REVERT: A 1070 ASP cc_start: 0.8254 (p0) cc_final: 0.7857 (p0) REVERT: A 1099 ASP cc_start: 0.6418 (t70) cc_final: 0.5581 (t0) REVERT: A 1167 GLU cc_start: 0.7926 (pt0) cc_final: 0.7352 (tm-30) REVERT: A 1210 GLU cc_start: 0.8319 (mp0) cc_final: 0.7946 (mp0) REVERT: A 1453 TRP cc_start: 0.8321 (t60) cc_final: 0.7894 (t60) outliers start: 26 outliers final: 19 residues processed: 163 average time/residue: 0.1047 time to fit residues: 24.5842 Evaluate side-chains 153 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1429 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 88 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1444 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 = 0.3715 r_free = 0.3715 target = 0.112480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.090851 restraints weight = 70484.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.095164 restraints weight = 29981.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.097096 restraints weight = 17465.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.099898 restraints weight = 12118.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.101155 restraints weight = 7603.740| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11560 Z= 0.145 Angle : 0.812 14.520 15708 Z= 0.405 Chirality : 0.046 0.171 1790 Planarity : 0.005 0.062 2015 Dihedral : 12.636 87.340 1749 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.04 % Favored : 87.96 % Rotamer: Outliers : 1.88 % Allowed : 14.54 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.51 % 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: -2.92 (0.21), residues: 1423 helix: -0.20 (0.23), residues: 522 sheet: -2.20 (0.31), residues: 241 loop : -3.38 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 934 TYR 0.011 0.001 TYR A1209 PHE 0.019 0.002 PHE A1412 TRP 0.061 0.002 TRP A1170 HIS 0.006 0.001 HIS A 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (11560) covalent geometry : angle 0.81173 / 0.41 (15708) hydrogen bonds : bond 0.03222 / 2.14 ( 369) hydrogen bonds : angle 5.25106 / 3.58 ( 1047) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8777 (ttp) cc_final: 0.8487 (tmm) REVERT: A 100 LYS cc_start: 0.8657 (mttt) cc_final: 0.8099 (tmmt) REVERT: A 104 ASP cc_start: 0.8774 (m-30) cc_final: 0.8223 (m-30) REVERT: A 118 GLU cc_start: 0.8231 (tt0) cc_final: 0.7903 (mm-30) REVERT: A 486 LEU cc_start: 0.6152 (pp) cc_final: 0.5470 (tp) REVERT: A 631 MET cc_start: 0.8161 (tpt) cc_final: 0.7474 (tpt) REVERT: A 772 ASN cc_start: 0.7558 (t0) cc_final: 0.6949 (t0) REVERT: A 857 LYS cc_start: 0.8848 (tptp) cc_final: 0.8606 (tptm) REVERT: A 960 ARG cc_start: 0.5694 (tpt90) cc_final: 0.4768 (mmm-85) REVERT: A 985 ASP cc_start: 0.7828 (t70) cc_final: 0.7150 (m-30) REVERT: A 1011 MET cc_start: 0.8626 (ttt) cc_final: 0.8275 (ppp) REVERT: A 1070 ASP cc_start: 0.8330 (p0) cc_final: 0.7810 (p0) REVERT: A 1099 ASP cc_start: 0.6172 (t70) cc_final: 0.5610 (t0) REVERT: A 1167 GLU cc_start: 0.7922 (pt0) cc_final: 0.7281 (tm-30) REVERT: A 1210 GLU cc_start: 0.8061 (mp0) cc_final: 0.7650 (mp0) REVERT: A 1392 GLN cc_start: 0.8489 (mm-40) cc_final: 0.7678 (mp10) outliers start: 22 outliers final: 14 residues processed: 160 average time/residue: 0.1005 time to fit residues: 23.2440 Evaluate side-chains 152 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1429 PHE Chi-restraints excluded: chain A residue 1465 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 14 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 30 optimal weight: 0.0980 chunk 69 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 GLN ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.106142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.085565 restraints weight = 56029.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.088828 restraints weight = 27351.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.091097 restraints weight = 16600.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.092669 restraints weight = 11622.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.093717 restraints weight = 9018.332| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 11560 Z= 0.286 Angle : 0.949 14.002 15708 Z= 0.482 Chirality : 0.052 0.228 1790 Planarity : 0.006 0.067 2015 Dihedral : 12.967 87.098 1749 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 14.58 % Favored : 85.21 % Rotamer: Outliers : 2.48 % Allowed : 14.29 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.51 % 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: -3.17 (0.21), residues: 1423 helix: -0.50 (0.22), residues: 527 sheet: -2.32 (0.32), residues: 230 loop : -3.46 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 829 TYR 0.021 0.002 TYR A 937 PHE 0.042 0.003 PHE A 894 TRP 0.058 0.003 TRP A1170 HIS 0.009 0.002 HIS A 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.29 (11560) covalent geometry : angle 0.94936 / 0.48 (15708) hydrogen bonds : bond 0.04083 / 2.71 ( 369) hydrogen bonds : angle 5.58361 / 3.85 ( 1047) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8200 (mtt90) cc_final: 0.7996 (ttm-80) REVERT: A 92 MET cc_start: 0.8543 (ttp) cc_final: 0.8289 (tmm) REVERT: A 93 MET cc_start: 0.8381 (mmm) cc_final: 0.7991 (mmm) REVERT: A 100 LYS cc_start: 0.8624 (mttt) cc_final: 0.8125 (tmmt) REVERT: A 104 ASP cc_start: 0.8579 (m-30) cc_final: 0.8154 (m-30) REVERT: A 486 LEU cc_start: 0.6232 (pp) cc_final: 0.5435 (tp) REVERT: A 631 MET cc_start: 0.8103 (tpt) cc_final: 0.7331 (tpt) REVERT: A 772 ASN cc_start: 0.7896 (t0) cc_final: 0.7506 (t0) REVERT: A 985 ASP cc_start: 0.7932 (t70) cc_final: 0.7250 (m-30) REVERT: A 1011 MET cc_start: 0.8585 (ttt) cc_final: 0.8359 (ppp) REVERT: A 1099 ASP cc_start: 0.6561 (t70) cc_final: 0.5744 (t0) REVERT: A 1167 GLU cc_start: 0.8062 (pt0) cc_final: 0.7663 (tm-30) REVERT: A 1210 GLU cc_start: 0.8190 (mp0) cc_final: 0.7839 (mp0) REVERT: A 1453 TRP cc_start: 0.8475 (t60) cc_final: 0.8137 (t60) outliers start: 29 outliers final: 23 residues processed: 153 average time/residue: 0.0955 time to fit residues: 21.7451 Evaluate side-chains 151 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1429 PHE Chi-restraints excluded: chain A residue 1443 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 70 optimal weight: 20.0000 chunk 130 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 128 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 141 optimal weight: 8.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 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 = 0.3629 r_free = 0.3629 target = 0.107144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.085842 restraints weight = 59905.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.089336 restraints weight = 28143.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.091772 restraints weight = 16707.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.093428 restraints weight = 11511.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.094485 restraints weight = 8854.724| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 11560 Z= 0.238 Angle : 0.908 14.040 15708 Z= 0.457 Chirality : 0.050 0.213 1790 Planarity : 0.006 0.138 2015 Dihedral : 12.922 85.732 1749 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.87 % Favored : 85.99 % Rotamer: Outliers : 2.22 % Allowed : 14.71 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.51 % 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: -3.16 (0.21), residues: 1423 helix: -0.52 (0.22), residues: 529 sheet: -2.28 (0.32), residues: 221 loop : -3.43 (0.22), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 934 TYR 0.024 0.002 TYR A 937 PHE 0.033 0.002 PHE A 894 TRP 0.050 0.002 TRP A1170 HIS 0.008 0.001 HIS A 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.24 (11560) covalent geometry : angle 0.90765 / 0.46 (15708) hydrogen bonds : bond 0.03802 / 2.52 ( 369) hydrogen bonds : angle 5.47057 / 3.76 ( 1047) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8686 (ttp) cc_final: 0.8403 (tmm) REVERT: A 100 LYS cc_start: 0.8664 (mttt) cc_final: 0.8111 (tmmt) REVERT: A 104 ASP cc_start: 0.8690 (m-30) cc_final: 0.8215 (m-30) REVERT: A 486 LEU cc_start: 0.6287 (pp) cc_final: 0.5532 (tp) REVERT: A 631 MET cc_start: 0.8066 (tpt) cc_final: 0.7319 (tpt) REVERT: A 772 ASN cc_start: 0.7892 (t0) cc_final: 0.7484 (t0) REVERT: A 857 LYS cc_start: 0.8968 (tptp) cc_final: 0.8608 (tptm) REVERT: A 985 ASP cc_start: 0.8021 (t70) cc_final: 0.7389 (m-30) REVERT: A 1011 MET cc_start: 0.8685 (ttt) cc_final: 0.8395 (ppp) REVERT: A 1070 ASP cc_start: 0.8369 (p0) cc_final: 0.7891 (p0) REVERT: A 1099 ASP cc_start: 0.6366 (t70) cc_final: 0.5703 (t0) REVERT: A 1167 GLU cc_start: 0.8159 (pt0) cc_final: 0.7690 (tm-30) REVERT: A 1210 GLU cc_start: 0.8176 (mp0) cc_final: 0.7753 (mp0) REVERT: A 1392 GLN cc_start: 0.8540 (mm-40) cc_final: 0.7771 (mp10) REVERT: A 1453 TRP cc_start: 0.8499 (t60) cc_final: 0.8177 (t60) outliers start: 26 outliers final: 24 residues processed: 149 average time/residue: 0.0879 time to fit residues: 19.8224 Evaluate side-chains 152 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1429 PHE Chi-restraints excluded: chain A residue 1443 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 97 optimal weight: 0.0040 chunk 32 optimal weight: 8.9990 chunk 143 optimal weight: 20.0000 chunk 118 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.110469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.089561 restraints weight = 60733.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.093136 restraints weight = 28496.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.095621 restraints weight = 16803.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.097280 restraints weight = 11498.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.098428 restraints weight = 8791.098| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11560 Z= 0.155 Angle : 0.852 14.610 15708 Z= 0.425 Chirality : 0.047 0.182 1790 Planarity : 0.005 0.065 2015 Dihedral : 12.713 86.571 1749 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.52 % Favored : 86.48 % Rotamer: Outliers : 1.45 % Allowed : 15.91 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.51 % 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: -2.93 (0.21), residues: 1423 helix: -0.24 (0.22), residues: 527 sheet: -2.23 (0.31), residues: 236 loop : -3.36 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 829 TYR 0.027 0.002 TYR A 937 PHE 0.020 0.002 PHE A 894 TRP 0.039 0.002 TRP A1170 HIS 0.006 0.001 HIS A 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (11560) covalent geometry : angle 0.85173 / 0.42 (15708) hydrogen bonds : bond 0.03386 / 2.26 ( 369) hydrogen bonds : angle 5.22811 / 3.59 ( 1047) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8205 (mtt90) cc_final: 0.7914 (ttm-80) REVERT: A 92 MET cc_start: 0.8546 (ttp) cc_final: 0.8294 (tmm) REVERT: A 100 LYS cc_start: 0.8577 (mttt) cc_final: 0.8143 (tmmt) REVERT: A 104 ASP cc_start: 0.8509 (m-30) cc_final: 0.8136 (m-30) REVERT: A 486 LEU cc_start: 0.6111 (pp) cc_final: 0.5423 (tp) REVERT: A 631 MET cc_start: 0.8155 (tpt) cc_final: 0.7495 (tpt) REVERT: A 772 ASN cc_start: 0.7773 (t0) cc_final: 0.7295 (t0) REVERT: A 857 LYS cc_start: 0.8915 (tptp) cc_final: 0.8659 (tptm) REVERT: A 945 ARG cc_start: 0.8049 (mmm160) cc_final: 0.7815 (mmm160) REVERT: A 960 ARG cc_start: 0.5911 (tpt90) cc_final: 0.4824 (mmm-85) REVERT: A 985 ASP cc_start: 0.7962 (t70) cc_final: 0.7285 (m-30) REVERT: A 1070 ASP cc_start: 0.8248 (p0) cc_final: 0.7812 (p0) REVERT: A 1099 ASP cc_start: 0.6297 (t70) cc_final: 0.5811 (t0) REVERT: A 1110 GLN cc_start: 0.7656 (pp30) cc_final: 0.7437 (pm20) REVERT: A 1167 GLU cc_start: 0.8056 (pt0) cc_final: 0.7673 (tm-30) REVERT: A 1210 GLU cc_start: 0.7975 (mp0) cc_final: 0.7589 (mp0) REVERT: A 1392 GLN cc_start: 0.8472 (mm-40) cc_final: 0.7672 (mp10) outliers start: 17 outliers final: 15 residues processed: 153 average time/residue: 0.1024 time to fit residues: 22.8361 Evaluate side-chains 150 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1429 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 109 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 105 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 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 = 0.3687 r_free = 0.3687 target = 0.111058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.090986 restraints weight = 48612.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.094237 restraints weight = 24472.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.096477 restraints weight = 15141.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.097999 restraints weight = 10753.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.099093 restraints weight = 8416.079| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11560 Z= 0.151 Angle : 0.837 14.439 15708 Z= 0.416 Chirality : 0.046 0.182 1790 Planarity : 0.005 0.063 2015 Dihedral : 12.639 86.609 1749 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.10 % Favored : 86.90 % Rotamer: Outliers : 1.28 % Allowed : 16.25 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.51 % 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: -2.78 (0.22), residues: 1423 helix: -0.13 (0.23), residues: 526 sheet: -2.00 (0.32), residues: 227 loop : -3.31 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 934 TYR 0.027 0.002 TYR A 937 PHE 0.020 0.002 PHE A 894 TRP 0.058 0.003 TRP A1453 HIS 0.007 0.001 HIS A 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (11560) covalent geometry : angle 0.83663 / 0.42 (15708) hydrogen bonds : bond 0.03329 / 2.21 ( 369) hydrogen bonds : angle 5.12537 / 3.53 ( 1047) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1795.14 seconds wall clock time: 31 minutes 46.22 seconds (1906.22 seconds total)