Starting phenix.real_space_refine on Thu Jul 2 11:01:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w4r_65642/07_2026/9w4r_65642.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w4r_65642/07_2026/9w4r_65642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w4r_65642/07_2026/9w4r_65642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w4r_65642/07_2026/9w4r_65642.map" model { file = "/net/cci-nas-00/data/ceres_data/9w4r_65642/07_2026/9w4r_65642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w4r_65642/07_2026/9w4r_65642.cif" } resolution = 3.78 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= 0.055 sd= 0.628 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 57 5.49 5 S 49 5.16 5 C 5099 2.51 5 N 1446 2.21 5 O 1654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8309 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6095 Classifications: {'peptide': 749} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 708} Chain breaks: 3 Chain: "B" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 993 Classifications: {'peptide': 130} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 122} Chain breaks: 1 Chain: "C" Number of atoms: 1217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1217 Classifications: {'RNA': 57} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 3, 'rna3p_pur': 24, 'rna3p_pyr': 23} Link IDs: {'rna2p': 10, 'rna3p': 46} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 288 SG CYS A 306 50.930 67.911 59.045 1.00181.30 S ATOM 311 SG CYS A 309 48.624 65.345 60.705 1.00180.62 S ATOM 3436 SG CYS A 915 34.298 59.396 80.911 1.00238.58 S ATOM 3456 SG CYS A 918 37.390 57.503 80.161 1.00239.63 S ATOM 3533 SG CYS A 928 34.433 55.800 81.899 1.00258.85 S ATOM 6796 SG CYS B 139 46.390 57.123 40.122 1.00236.31 S ATOM 6822 SG CYS B 142 48.248 56.702 36.902 1.00243.32 S ATOM 6895 SG CYS B 152 49.745 55.484 40.274 1.00232.15 S ATOM 6966 SG CYS B 161 46.626 70.546 28.879 1.00289.80 S ATOM 6993 SG CYS B 164 49.136 72.453 26.862 1.00313.30 S ATOM 7064 SG CYS B 174 45.362 73.229 26.491 1.00298.22 S Time building chain proxies: 1.72, per 1000 atoms: 0.21 Number of scatterers: 8309 At special positions: 0 Unit cell: (80.925, 117.03, 136.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 49 16.00 P 57 15.00 O 1654 8.00 N 1446 7.00 C 5099 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: 0.78 Conformation dependent library (CDL) restraints added in 223.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 328 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 322 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 309 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" NE2 HIS A 923 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 915 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 918 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 928 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" ND1 HIS B 147 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 139 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 152 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 142 " pdb=" ZN B1002 " pdb="ZN ZN B1002 " - pdb=" NE2 HIS B 169 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 161 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 164 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 174 " Number of angles added : 11 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1658 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 7 sheets defined 44.1% alpha, 14.4% beta 11 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 274 through 286 removed outlier: 3.601A pdb=" N LYS A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU A 282 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 324 Processing helix chain 'A' and resid 325 through 341 Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 348 through 366 removed outlier: 4.108A pdb=" N HIS A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 3.724A pdb=" N PHE A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 424 through 439 Processing helix chain 'A' and resid 473 through 490 Processing helix chain 'A' and resid 492 through 506 removed outlier: 3.881A pdb=" N VAL A 497 " --> pdb=" O PHE A 493 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 498 " --> pdb=" O ILE A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 518 through 533 Processing helix chain 'A' and resid 551 through 557 removed outlier: 3.520A pdb=" N MET A 554 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP A 555 " --> pdb=" O LYS A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 643 removed outlier: 3.616A pdb=" N LEU A 637 " --> pdb=" O TRP A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 708 Processing helix chain 'A' and resid 901 through 907 removed outlier: 4.243A pdb=" N LEU A 905 " --> pdb=" O ASP A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 961 removed outlier: 3.617A pdb=" N CYS A 958 " --> pdb=" O VAL A 954 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE A 959 " --> pdb=" O CYS A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 987 Processing helix chain 'A' and resid 997 through 1000 Processing helix chain 'A' and resid 1026 through 1041 Processing helix chain 'A' and resid 1077 through 1092 removed outlier: 3.790A pdb=" N ASP A1092 " --> pdb=" O TYR A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1109 removed outlier: 4.233A pdb=" N GLN A1096 " --> pdb=" O ASP A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1117 Processing helix chain 'A' and resid 1120 through 1135 Processing helix chain 'A' and resid 1184 through 1196 Processing helix chain 'A' and resid 1216 through 1221 Processing helix chain 'A' and resid 1222 through 1225 Processing helix chain 'A' and resid 1239 through 1243 Processing helix chain 'A' and resid 1244 through 1261 Processing helix chain 'A' and resid 1272 through 1277 Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.750A pdb=" N VAL B 115 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 Processing sheet with id=AA1, first strand: chain 'A' and resid 289 through 291 Processing sheet with id=AA2, first strand: chain 'A' and resid 395 through 399 removed outlier: 3.939A pdb=" N ASN A 414 " --> pdb=" O TYR A 399 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL A 413 " --> pdb=" O ARG A 468 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER A 470 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE A 415 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ARG A 459 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ASP A 444 " --> pdb=" O ARG A 459 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 559 through 563 removed outlier: 4.095A pdb=" N LYS A 569 " --> pdb=" O LYS A 560 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE A 562 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE A 567 " --> pdb=" O ILE A 562 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 649 through 650 removed outlier: 4.711A pdb=" N LEU A 659 " --> pdb=" O VAL A 650 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 674 through 675 removed outlier: 4.385A pdb=" N ASP A 675 " --> pdb=" O SER A 678 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 991 through 996 removed outlier: 3.955A pdb=" N ASP A1011 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU A1010 " --> pdb=" O ASP A1070 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N SER A1072 " --> pdb=" O LEU A1010 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE A1012 " --> pdb=" O SER A1072 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE A1057 " --> pdb=" O PRO A1049 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS A1059 " --> pdb=" O ILE A1047 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE A1047 " --> pdb=" O LYS A1059 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 39 through 47 removed outlier: 6.094A pdb=" N GLY B 40 " --> pdb=" O ARG B 61 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ARG B 61 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLY B 42 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR B 59 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N CYS B 44 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N SER B 57 " --> pdb=" O CYS B 44 " (cutoff:3.500A) removed outlier: 10.287A pdb=" N PHE B 53 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 11.415A pdb=" N VAL B 72 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 9.136A pdb=" N PHE B 55 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 10.210A pdb=" N VAL B 70 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 9.860A pdb=" N SER B 57 " --> pdb=" O PRO B 68 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N THR B 59 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU B 104 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N HIS B 75 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ARG B 108 " --> pdb=" O HIS B 75 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR B 96 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL B 109 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLU B 94 " --> pdb=" O VAL B 109 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 855 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 1.36 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1857 1.33 - 1.45: 2024 1.45 - 1.57: 4548 1.57 - 1.69: 112 1.69 - 1.81: 66 Bond restraints: 8607 Sorted by residual: bond pdb=" C ILE A 494 " pdb=" N PRO A 495 " ideal model delta sigma weight residual 1.337 1.374 -0.037 1.24e-02 6.50e+03 8.88e+00 bond pdb=" C PRO A1137 " pdb=" N PRO A1138 " ideal model delta sigma weight residual 1.332 1.362 -0.030 1.12e-02 7.97e+03 7.32e+00 bond pdb=" CB VAL A 497 " pdb=" CG2 VAL A 497 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.85e+00 bond pdb=" C5 C C 41 " pdb=" C6 C C 41 " ideal model delta sigma weight residual 1.339 1.326 0.013 8.00e-03 1.56e+04 2.84e+00 bond pdb=" N9 A C 25 " pdb=" C4 A C 25 " ideal model delta sigma weight residual 1.374 1.364 0.010 6.00e-03 2.78e+04 2.64e+00 ... (remaining 8602 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 11388 1.67 - 3.34: 418 3.34 - 5.01: 54 5.01 - 6.69: 16 6.69 - 8.36: 3 Bond angle restraints: 11879 Sorted by residual: angle pdb=" N1 C C 41 " pdb=" C6 C C 41 " pdb=" C5 C C 41 " ideal model delta sigma weight residual 121.00 123.44 -2.44 5.00e-01 4.00e+00 2.38e+01 angle pdb=" N1 C C 68 " pdb=" C6 C C 68 " pdb=" C5 C C 68 " ideal model delta sigma weight residual 121.00 123.37 -2.37 5.00e-01 4.00e+00 2.25e+01 angle pdb=" N1 U C 16 " pdb=" C6 U C 16 " pdb=" C5 U C 16 " ideal model delta sigma weight residual 122.70 124.80 -2.10 5.00e-01 4.00e+00 1.77e+01 angle pdb=" C2 C C 41 " pdb=" N1 C C 41 " pdb=" C6 C C 41 " ideal model delta sigma weight residual 120.30 118.63 1.67 4.00e-01 6.25e+00 1.74e+01 angle pdb=" C8 A C 25 " pdb=" N9 A C 25 " pdb=" C4 A C 25 " ideal model delta sigma weight residual 105.80 104.15 1.65 4.00e-01 6.25e+00 1.71e+01 ... (remaining 11874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.97: 4917 25.97 - 51.94: 278 51.94 - 77.91: 99 77.91 - 103.87: 7 103.87 - 129.84: 1 Dihedral angle restraints: 5302 sinusoidal: 2743 harmonic: 2559 Sorted by residual: dihedral pdb=" CA ASP A 287 " pdb=" C ASP A 287 " pdb=" N HIS A 288 " pdb=" CA HIS A 288 " ideal model delta harmonic sigma weight residual 180.00 154.16 25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA HIS B 148 " pdb=" C HIS B 148 " pdb=" N ALA B 149 " pdb=" CA ALA B 149 " ideal model delta harmonic sigma weight residual -180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA ALA A 620 " pdb=" C ALA A 620 " pdb=" N LEU A 621 " pdb=" CA LEU A 621 " ideal model delta harmonic sigma weight residual 180.00 158.13 21.87 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 5299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1160 0.066 - 0.131: 173 0.131 - 0.197: 18 0.197 - 0.262: 2 0.262 - 0.328: 1 Chirality restraints: 1354 Sorted by residual: chirality pdb=" CB ILE A1229 " pdb=" CA ILE A1229 " pdb=" CG1 ILE A1229 " pdb=" CG2 ILE A1229 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CB VAL A 653 " pdb=" CA VAL A 653 " pdb=" CG1 VAL A 653 " pdb=" CG2 VAL A 653 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CB ILE A 360 " pdb=" CA ILE A 360 " pdb=" CG1 ILE A 360 " pdb=" CG2 ILE A 360 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1351 not shown) Planarity restraints: 1302 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A1055 " -0.045 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO A1056 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A1056 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1056 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 675 " -0.044 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO A 676 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 676 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 676 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1264 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.87e+00 pdb=" N PRO A1265 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A1265 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1265 " 0.030 5.00e-02 4.00e+02 ... (remaining 1299 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2170 2.80 - 3.33: 7811 3.33 - 3.85: 15878 3.85 - 4.38: 18035 4.38 - 4.90: 27897 Nonbonded interactions: 71791 Sorted by model distance: nonbonded pdb=" ND2 ASN B 48 " pdb=" O2' A C 37 " model vdw 2.276 3.120 nonbonded pdb=" O ILE A1111 " pdb=" OH TYR A1124 " model vdw 2.277 3.040 nonbonded pdb=" O GLY A1004 " pdb=" OH TYR A1100 " model vdw 2.277 3.040 nonbonded pdb=" O LYS A 385 " pdb=" OG1 THR A 389 " model vdw 2.291 3.040 nonbonded pdb=" O MET A 525 " pdb=" OH TYR A 640 " model vdw 2.296 3.040 ... (remaining 71786 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=1.00 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: 0.120 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: 0.030 Set scattering table: 0.020 Process input model: 10.150 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 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 : 0.004 0.073 8623 Z= 0.219 Angle : 0.766 8.358 11890 Z= 0.511 Chirality : 0.047 0.328 1354 Planarity : 0.006 0.068 1302 Dihedral : 17.160 129.842 3644 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.70 % Allowed : 9.18 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.27), residues: 867 helix: 0.19 (0.27), residues: 318 sheet: -1.37 (0.47), residues: 97 loop : -0.95 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 654 TYR 0.015 0.002 TYR A 502 PHE 0.026 0.002 PHE A 493 TRP 0.023 0.002 TRP A 503 HIS 0.010 0.001 HIS B 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.22 ( 8607) covalent geometry : angle 0.75931 / 0.51 (11879) hydrogen bonds : bond 0.17410 / 11.72 ( 329) hydrogen bonds : angle 6.52873 / 4.82 ( 891) metal coordination : bond 0.00977 / 0.51 ( 16) metal coordination : angle 3.39377 / 2.46 ( 11) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 LYS cc_start: 0.9049 (tttp) cc_final: 0.8398 (tptp) REVERT: A 327 ARG cc_start: 0.8572 (ttt90) cc_final: 0.8115 (tpm170) REVERT: A 329 LYS cc_start: 0.8478 (mttt) cc_final: 0.8235 (mttt) REVERT: A 377 GLN cc_start: 0.9407 (tt0) cc_final: 0.9103 (tm-30) REVERT: A 381 GLU cc_start: 0.9302 (mt-10) cc_final: 0.8816 (pt0) REVERT: A 404 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8063 (t) REVERT: A 444 ASP cc_start: 0.8989 (m-30) cc_final: 0.8789 (m-30) REVERT: A 447 SER cc_start: 0.8721 (p) cc_final: 0.8505 (p) REVERT: A 459 ARG cc_start: 0.8860 (tpp80) cc_final: 0.8641 (tpp80) REVERT: A 493 PHE cc_start: 0.7654 (t80) cc_final: 0.6925 (t80) REVERT: A 521 CYS cc_start: 0.8685 (m) cc_final: 0.8254 (m) REVERT: A 649 TYR cc_start: 0.8079 (m-80) cc_final: 0.7803 (m-80) REVERT: A 661 ARG cc_start: 0.6364 (mmm160) cc_final: 0.4619 (mmm-85) REVERT: A 679 VAL cc_start: 0.7329 (OUTLIER) cc_final: 0.7118 (t) REVERT: A 932 PHE cc_start: 0.8645 (m-80) cc_final: 0.8257 (m-10) REVERT: A 959 PHE cc_start: 0.8457 (t80) cc_final: 0.8250 (t80) REVERT: A 1105 PHE cc_start: 0.8830 (m-80) cc_final: 0.8287 (m-80) REVERT: A 1127 MET cc_start: 0.8616 (ptm) cc_final: 0.8322 (ptm) REVERT: A 1214 LEU cc_start: 0.8968 (mt) cc_final: 0.8762 (mt) REVERT: A 1252 MET cc_start: 0.9025 (mmm) cc_final: 0.8728 (mmm) REVERT: B 84 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7990 (m-80) outliers start: 29 outliers final: 9 residues processed: 205 average time/residue: 0.1312 time to fit residues: 33.5558 Evaluate side-chains 143 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 1226 CYS Chi-restraints excluded: chain A residue 1247 MET Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 160 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 50.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 ASN A1046 ASN ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 HIS ** B 147 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 = 0.4186 r_free = 0.4186 target = 0.104588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.079460 restraints weight = 40373.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.082060 restraints weight = 24568.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.083794 restraints weight = 17238.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.084996 restraints weight = 13298.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.085660 restraints weight = 11021.794| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8623 Z= 0.251 Angle : 0.828 34.457 11890 Z= 0.401 Chirality : 0.044 0.225 1354 Planarity : 0.007 0.127 1302 Dihedral : 18.345 138.203 1853 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 24.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.95 % Allowed : 16.07 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.28), residues: 867 helix: -0.16 (0.27), residues: 332 sheet: -1.68 (0.47), residues: 102 loop : -0.74 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1259 TYR 0.013 0.002 TYR A 695 PHE 0.023 0.002 PHE A 406 TRP 0.033 0.003 TRP A1189 HIS 0.007 0.002 HIS B 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.25 ( 8607) covalent geometry : angle 0.74508 / 0.39 (11879) hydrogen bonds : bond 0.07572 / 5.03 ( 329) hydrogen bonds : angle 5.87040 / 4.37 ( 891) metal coordination : bond 0.01664 / 1.15 ( 16) metal coordination : angle 11.91495 / 9.22 ( 11) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 LEU cc_start: 0.9413 (tp) cc_final: 0.9168 (tp) REVERT: A 284 LEU cc_start: 0.9407 (mm) cc_final: 0.8875 (tp) REVERT: A 324 LYS cc_start: 0.9146 (tttp) cc_final: 0.8247 (tptp) REVERT: A 329 LYS cc_start: 0.8127 (mttt) cc_final: 0.7704 (mmtt) REVERT: A 361 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8729 (pt0) REVERT: A 404 THR cc_start: 0.8645 (p) cc_final: 0.8267 (t) REVERT: A 414 ASN cc_start: 0.6441 (m110) cc_final: 0.5871 (m-40) REVERT: A 493 PHE cc_start: 0.7657 (t80) cc_final: 0.6998 (t80) REVERT: A 521 CYS cc_start: 0.8535 (m) cc_final: 0.8126 (m) REVERT: A 619 LEU cc_start: 0.5824 (OUTLIER) cc_final: 0.5524 (tt) REVERT: A 649 TYR cc_start: 0.8158 (m-80) cc_final: 0.7892 (m-80) REVERT: A 661 ARG cc_start: 0.6440 (mmm160) cc_final: 0.5819 (mmm-85) REVERT: A 668 LYS cc_start: 0.8993 (mptt) cc_final: 0.8788 (mptt) REVERT: A 679 VAL cc_start: 0.7601 (OUTLIER) cc_final: 0.7331 (t) REVERT: A 909 LYS cc_start: 0.7064 (tttm) cc_final: 0.6725 (tmtt) REVERT: A 943 MET cc_start: 0.7304 (mmt) cc_final: 0.6931 (mmp) REVERT: A 1128 VAL cc_start: 0.9440 (OUTLIER) cc_final: 0.9113 (t) REVERT: A 1187 GLU cc_start: 0.9349 (tp30) cc_final: 0.9133 (tp30) REVERT: A 1194 ARG cc_start: 0.9400 (ttp-110) cc_final: 0.9127 (ttm110) REVERT: A 1212 LYS cc_start: 0.9060 (pptt) cc_final: 0.8795 (ptmm) REVERT: A 1222 TRP cc_start: 0.7639 (m100) cc_final: 0.7435 (m100) REVERT: A 1250 PHE cc_start: 0.9189 (t80) cc_final: 0.8827 (m-80) outliers start: 31 outliers final: 13 residues processed: 159 average time/residue: 0.1141 time to fit residues: 22.7296 Evaluate side-chains 131 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 971 ASN Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1226 CYS Chi-restraints excluded: chain A residue 1249 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 52 optimal weight: 20.0000 chunk 73 optimal weight: 0.9980 chunk 42 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 85 optimal weight: 30.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 532 GLN A 688 ASN ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.106812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.081423 restraints weight = 41131.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.084098 restraints weight = 24914.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.085823 restraints weight = 17484.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.086925 restraints weight = 13562.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.087729 restraints weight = 11367.437| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8623 Z= 0.160 Angle : 0.735 22.796 11890 Z= 0.367 Chirality : 0.044 0.235 1354 Planarity : 0.006 0.098 1302 Dihedral : 18.226 144.190 1830 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 23.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.06 % Allowed : 17.60 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.28), residues: 867 helix: -0.11 (0.27), residues: 332 sheet: -1.63 (0.47), residues: 104 loop : -0.68 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 699 TYR 0.015 0.001 TYR A 502 PHE 0.038 0.002 PHE A 406 TRP 0.018 0.002 TRP A 503 HIS 0.004 0.001 HIS B 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 ( 8607) covalent geometry : angle 0.69356 / 0.36 (11879) hydrogen bonds : bond 0.06477 / 4.33 ( 329) hydrogen bonds : angle 5.59530 / 4.19 ( 891) metal coordination : bond 0.01287 / 0.84 ( 16) metal coordination : angle 8.03707 / 6.06 ( 11) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 LEU cc_start: 0.9223 (tp) cc_final: 0.8798 (tp) REVERT: A 284 LEU cc_start: 0.9368 (mm) cc_final: 0.8853 (tp) REVERT: A 404 THR cc_start: 0.8697 (p) cc_final: 0.8240 (t) REVERT: A 414 ASN cc_start: 0.6324 (m110) cc_final: 0.5764 (m-40) REVERT: A 493 PHE cc_start: 0.7522 (t80) cc_final: 0.6776 (t80) REVERT: A 521 CYS cc_start: 0.8465 (m) cc_final: 0.8047 (m) REVERT: A 565 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8585 (mm-30) REVERT: A 661 ARG cc_start: 0.6147 (mmm160) cc_final: 0.5600 (mmm160) REVERT: A 668 LYS cc_start: 0.8826 (mptt) cc_final: 0.8536 (mptt) REVERT: A 679 VAL cc_start: 0.7502 (OUTLIER) cc_final: 0.7273 (t) REVERT: A 921 ASP cc_start: 0.8125 (p0) cc_final: 0.7649 (t0) REVERT: A 932 PHE cc_start: 0.8710 (m-80) cc_final: 0.8182 (m-10) REVERT: A 1187 GLU cc_start: 0.9301 (tp30) cc_final: 0.8776 (tm-30) REVERT: A 1196 TYR cc_start: 0.8572 (m-80) cc_final: 0.8156 (m-80) REVERT: A 1212 LYS cc_start: 0.9153 (pptt) cc_final: 0.8898 (ptmm) REVERT: A 1250 PHE cc_start: 0.9166 (t80) cc_final: 0.8924 (m-80) REVERT: A 1252 MET cc_start: 0.8965 (mmm) cc_final: 0.8093 (mmm) outliers start: 24 outliers final: 16 residues processed: 149 average time/residue: 0.1157 time to fit residues: 21.4376 Evaluate side-chains 135 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1226 CYS Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 52 optimal weight: 6.9990 chunk 76 optimal weight: 50.0000 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 73 optimal weight: 0.1980 chunk 81 optimal weight: 0.0470 chunk 69 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 91 optimal weight: 30.0000 overall best weight: 2.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 GLN ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 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 = 0.4209 r_free = 0.4209 target = 0.106127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.080618 restraints weight = 41464.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.083244 restraints weight = 25072.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.084990 restraints weight = 17466.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.086132 restraints weight = 13429.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.086903 restraints weight = 11159.289| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8623 Z= 0.166 Angle : 0.734 18.269 11890 Z= 0.374 Chirality : 0.044 0.304 1354 Planarity : 0.006 0.089 1302 Dihedral : 18.193 145.903 1830 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 23.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.08 % Allowed : 18.88 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.28), residues: 867 helix: -0.05 (0.27), residues: 331 sheet: -1.70 (0.48), residues: 104 loop : -0.68 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 295 TYR 0.028 0.002 TYR A 649 PHE 0.026 0.002 PHE A 406 TRP 0.017 0.002 TRP A 503 HIS 0.005 0.001 HIS B 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 ( 8607) covalent geometry : angle 0.70842 / 0.37 (11879) hydrogen bonds : bond 0.06109 / 4.10 ( 329) hydrogen bonds : angle 5.60721 / 4.18 ( 891) metal coordination : bond 0.01316 / 0.82 ( 16) metal coordination : angle 6.34476 / 4.75 ( 11) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6019 (tpm170) REVERT: A 335 LYS cc_start: 0.8771 (tppt) cc_final: 0.8442 (pptt) REVERT: A 404 THR cc_start: 0.8765 (p) cc_final: 0.8455 (p) REVERT: A 414 ASN cc_start: 0.6368 (m110) cc_final: 0.5797 (m-40) REVERT: A 459 ARG cc_start: 0.8521 (tpp80) cc_final: 0.8320 (tpp80) REVERT: A 493 PHE cc_start: 0.7466 (t80) cc_final: 0.6857 (t80) REVERT: A 521 CYS cc_start: 0.8512 (m) cc_final: 0.8077 (m) REVERT: A 565 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8552 (mm-30) REVERT: A 668 LYS cc_start: 0.8809 (mptt) cc_final: 0.8515 (mptt) REVERT: A 679 VAL cc_start: 0.7535 (OUTLIER) cc_final: 0.7311 (t) REVERT: A 921 ASP cc_start: 0.8143 (p0) cc_final: 0.7922 (t0) REVERT: A 932 PHE cc_start: 0.8773 (m-80) cc_final: 0.8217 (m-10) REVERT: A 1187 GLU cc_start: 0.9216 (tp30) cc_final: 0.8759 (tm-30) REVERT: A 1189 TRP cc_start: 0.9072 (t-100) cc_final: 0.8832 (t-100) REVERT: A 1212 LYS cc_start: 0.9167 (pptt) cc_final: 0.8925 (ptmm) REVERT: A 1252 MET cc_start: 0.9110 (mmm) cc_final: 0.8345 (mmm) outliers start: 32 outliers final: 15 residues processed: 146 average time/residue: 0.1221 time to fit residues: 22.5335 Evaluate side-chains 128 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1226 CYS Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 52 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 83 optimal weight: 0.0970 chunk 38 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 GLN ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 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 = 0.4217 r_free = 0.4217 target = 0.106799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.081641 restraints weight = 40285.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.084308 restraints weight = 24301.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.086057 restraints weight = 16969.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.087221 restraints weight = 12997.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.088016 restraints weight = 10743.175| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 8623 Z= 0.161 Angle : 0.757 19.144 11890 Z= 0.383 Chirality : 0.047 0.528 1354 Planarity : 0.005 0.065 1302 Dihedral : 18.154 146.314 1830 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 23.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.93 % Allowed : 20.54 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.29), residues: 867 helix: 0.02 (0.27), residues: 329 sheet: -1.61 (0.48), residues: 104 loop : -0.66 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 699 TYR 0.016 0.001 TYR A 704 PHE 0.035 0.002 PHE A 406 TRP 0.014 0.001 TRP A 503 HIS 0.012 0.002 HIS A1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 8607) covalent geometry : angle 0.73325 / 0.38 (11879) hydrogen bonds : bond 0.05861 / 3.96 ( 329) hydrogen bonds : angle 5.55422 / 4.13 ( 891) metal coordination : bond 0.01038 / 0.66 ( 16) metal coordination : angle 6.22487 / 4.67 ( 11) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.5837 (tpm170) REVERT: A 404 THR cc_start: 0.8715 (p) cc_final: 0.8437 (p) REVERT: A 414 ASN cc_start: 0.6326 (m110) cc_final: 0.5748 (m-40) REVERT: A 459 ARG cc_start: 0.8398 (tpp80) cc_final: 0.8178 (tpp80) REVERT: A 493 PHE cc_start: 0.7298 (t80) cc_final: 0.6844 (t80) REVERT: A 521 CYS cc_start: 0.8495 (m) cc_final: 0.8071 (m) REVERT: A 668 LYS cc_start: 0.8791 (mptt) cc_final: 0.8522 (mptt) REVERT: A 679 VAL cc_start: 0.7453 (OUTLIER) cc_final: 0.7222 (t) REVERT: A 932 PHE cc_start: 0.8725 (m-80) cc_final: 0.8187 (m-10) REVERT: A 1187 GLU cc_start: 0.9160 (tp30) cc_final: 0.8745 (tm-30) REVERT: A 1194 ARG cc_start: 0.9299 (ttm110) cc_final: 0.9083 (ptp-170) REVERT: A 1212 LYS cc_start: 0.9147 (pptt) cc_final: 0.8905 (ptmm) REVERT: A 1250 PHE cc_start: 0.9347 (t80) cc_final: 0.9029 (m-80) REVERT: A 1252 MET cc_start: 0.9078 (mmm) cc_final: 0.8290 (mmm) REVERT: B 58 MET cc_start: -0.1375 (ttt) cc_final: -0.2189 (tpp) outliers start: 23 outliers final: 14 residues processed: 132 average time/residue: 0.1157 time to fit residues: 19.3684 Evaluate side-chains 119 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1226 CYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 88 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.104974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.079355 restraints weight = 41229.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.081926 restraints weight = 25104.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.083645 restraints weight = 17734.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.084756 restraints weight = 13761.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.085498 restraints weight = 11518.238| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 8623 Z= 0.201 Angle : 0.756 16.974 11890 Z= 0.385 Chirality : 0.045 0.358 1354 Planarity : 0.006 0.069 1302 Dihedral : 18.152 146.538 1830 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 26.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.68 % Allowed : 21.81 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.29), residues: 867 helix: -0.04 (0.27), residues: 331 sheet: -1.81 (0.50), residues: 94 loop : -0.68 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 699 TYR 0.012 0.002 TYR A 649 PHE 0.027 0.002 PHE A 406 TRP 0.051 0.003 TRP A1189 HIS 0.011 0.002 HIS A 970 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 ( 8607) covalent geometry : angle 0.73575 / 0.38 (11879) hydrogen bonds : bond 0.06035 / 4.15 ( 329) hydrogen bonds : angle 5.65930 / 4.14 ( 891) metal coordination : bond 0.01500 / 0.97 ( 16) metal coordination : angle 5.74832 / 4.32 ( 11) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 LEU cc_start: 0.9362 (tp) cc_final: 0.9039 (pp) REVERT: A 404 THR cc_start: 0.8706 (p) cc_final: 0.8411 (p) REVERT: A 414 ASN cc_start: 0.6419 (m110) cc_final: 0.5809 (m-40) REVERT: A 459 ARG cc_start: 0.8590 (tpp80) cc_final: 0.8373 (tpp80) REVERT: A 493 PHE cc_start: 0.7289 (t80) cc_final: 0.6904 (t80) REVERT: A 521 CYS cc_start: 0.8523 (m) cc_final: 0.8087 (m) REVERT: A 661 ARG cc_start: 0.6443 (mmm160) cc_final: 0.5627 (mmm160) REVERT: A 668 LYS cc_start: 0.8852 (mptt) cc_final: 0.8558 (mptt) REVERT: A 932 PHE cc_start: 0.8856 (m-80) cc_final: 0.8423 (m-10) REVERT: A 1187 GLU cc_start: 0.9172 (tp30) cc_final: 0.8836 (tm-30) REVERT: A 1212 LYS cc_start: 0.9169 (pptt) cc_final: 0.8961 (ptmm) REVERT: A 1250 PHE cc_start: 0.9380 (t80) cc_final: 0.9068 (m-80) REVERT: A 1252 MET cc_start: 0.9160 (mmm) cc_final: 0.8415 (mmm) REVERT: B 58 MET cc_start: -0.1231 (ttt) cc_final: -0.1718 (tpp) outliers start: 21 outliers final: 17 residues processed: 125 average time/residue: 0.1273 time to fit residues: 19.8978 Evaluate side-chains 114 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1127 MET Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1226 CYS Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 170 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 71 optimal weight: 30.0000 chunk 69 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 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 = 0.4194 r_free = 0.4194 target = 0.105364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.079336 restraints weight = 41120.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.081951 restraints weight = 25188.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.083665 restraints weight = 17739.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.084791 restraints weight = 13823.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.085545 restraints weight = 11510.308| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 8623 Z= 0.169 Angle : 0.740 15.426 11890 Z= 0.378 Chirality : 0.045 0.353 1354 Planarity : 0.006 0.060 1302 Dihedral : 18.127 145.356 1829 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 25.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.42 % Allowed : 22.07 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.29), residues: 867 helix: 0.06 (0.27), residues: 326 sheet: -1.76 (0.50), residues: 98 loop : -0.72 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A1194 TYR 0.019 0.002 TYR A 299 PHE 0.047 0.002 PHE A 406 TRP 0.032 0.002 TRP A1189 HIS 0.009 0.002 HIS B 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 8607) covalent geometry : angle 0.72251 / 0.38 (11879) hydrogen bonds : bond 0.05714 / 3.93 ( 329) hydrogen bonds : angle 5.60124 / 4.09 ( 891) metal coordination : bond 0.01238 / 0.88 ( 16) metal coordination : angle 5.28861 / 3.92 ( 11) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 LEU cc_start: 0.9295 (tp) cc_final: 0.9045 (pp) REVERT: A 307 LYS cc_start: 0.9112 (mtmm) cc_final: 0.8882 (mtmt) REVERT: A 324 LYS cc_start: 0.8996 (tttp) cc_final: 0.8501 (tptp) REVERT: A 404 THR cc_start: 0.8768 (p) cc_final: 0.8477 (p) REVERT: A 414 ASN cc_start: 0.6372 (m110) cc_final: 0.5774 (m-40) REVERT: A 459 ARG cc_start: 0.8585 (tpp80) cc_final: 0.8355 (tpp80) REVERT: A 493 PHE cc_start: 0.7199 (t80) cc_final: 0.6928 (t80) REVERT: A 521 CYS cc_start: 0.8499 (m) cc_final: 0.8061 (m) REVERT: A 565 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8661 (mm-30) REVERT: A 661 ARG cc_start: 0.6210 (mmm160) cc_final: 0.5574 (mmm160) REVERT: A 668 LYS cc_start: 0.8836 (mptt) cc_final: 0.8558 (mptt) REVERT: A 932 PHE cc_start: 0.8878 (m-80) cc_final: 0.8288 (m-10) REVERT: A 1187 GLU cc_start: 0.9133 (tp30) cc_final: 0.8798 (tm-30) REVERT: A 1212 LYS cc_start: 0.9174 (pptt) cc_final: 0.8958 (ptmm) REVERT: A 1250 PHE cc_start: 0.9424 (t80) cc_final: 0.9072 (m-80) REVERT: A 1252 MET cc_start: 0.9131 (mmm) cc_final: 0.8385 (mmm) REVERT: B 58 MET cc_start: 0.0344 (ttt) cc_final: -0.0785 (tpt) REVERT: B 159 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7669 (tptp) outliers start: 19 outliers final: 14 residues processed: 123 average time/residue: 0.1044 time to fit residues: 16.1730 Evaluate side-chains 115 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1127 MET Chi-restraints excluded: chain A residue 1226 CYS Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 170 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 42 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 chunk 76 optimal weight: 50.0000 chunk 11 optimal weight: 0.1980 chunk 62 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 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 = 0.4219 r_free = 0.4219 target = 0.106462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.081378 restraints weight = 40607.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.083952 restraints weight = 24646.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.085677 restraints weight = 17215.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.086847 restraints weight = 13263.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.087566 restraints weight = 11023.599| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8623 Z= 0.145 Angle : 0.740 13.687 11890 Z= 0.376 Chirality : 0.045 0.341 1354 Planarity : 0.006 0.057 1302 Dihedral : 18.065 143.877 1829 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 22.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.04 % Allowed : 21.68 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.29), residues: 867 helix: 0.20 (0.27), residues: 326 sheet: -1.53 (0.52), residues: 98 loop : -0.76 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 699 TYR 0.018 0.002 TYR A 649 PHE 0.035 0.002 PHE B 163 TRP 0.021 0.002 TRP A1189 HIS 0.010 0.001 HIS B 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 8607) covalent geometry : angle 0.72713 / 0.37 (11879) hydrogen bonds : bond 0.05407 / 3.72 ( 329) hydrogen bonds : angle 5.49282 / 4.01 ( 891) metal coordination : bond 0.01018 / 0.74 ( 16) metal coordination : angle 4.64864 / 3.40 ( 11) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 ARG cc_start: 0.8513 (ttm-80) cc_final: 0.8157 (mtm-85) REVERT: A 312 HIS cc_start: 0.7576 (m170) cc_final: 0.7360 (m170) REVERT: A 313 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8562 (tp) REVERT: A 324 LYS cc_start: 0.8962 (tttp) cc_final: 0.8559 (tptt) REVERT: A 414 ASN cc_start: 0.6176 (m110) cc_final: 0.5576 (m-40) REVERT: A 459 ARG cc_start: 0.8493 (tpp80) cc_final: 0.8259 (tpp80) REVERT: A 521 CYS cc_start: 0.8552 (m) cc_final: 0.8120 (m) REVERT: A 565 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8620 (mm-30) REVERT: A 656 GLN cc_start: 0.8442 (tm-30) cc_final: 0.7893 (tm-30) REVERT: A 668 LYS cc_start: 0.8760 (mptt) cc_final: 0.8543 (mptt) REVERT: A 669 ARG cc_start: 0.7665 (mtt-85) cc_final: 0.7353 (mtt-85) REVERT: A 932 PHE cc_start: 0.8824 (m-80) cc_final: 0.8379 (m-10) REVERT: A 1014 MET cc_start: 0.7705 (mmp) cc_final: 0.7135 (mmp) REVERT: A 1073 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6553 (pt) REVERT: A 1187 GLU cc_start: 0.9104 (tp30) cc_final: 0.8799 (tm-30) REVERT: A 1196 TYR cc_start: 0.8386 (m-80) cc_final: 0.8046 (m-80) REVERT: A 1212 LYS cc_start: 0.9125 (pptt) cc_final: 0.8913 (ptmm) REVERT: A 1250 PHE cc_start: 0.9419 (t80) cc_final: 0.8903 (m-80) REVERT: A 1252 MET cc_start: 0.9151 (mmm) cc_final: 0.8309 (mmm) REVERT: B 58 MET cc_start: -0.1949 (ttt) cc_final: -0.2557 (tpt) REVERT: B 159 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7528 (tptp) outliers start: 16 outliers final: 13 residues processed: 121 average time/residue: 0.1129 time to fit residues: 17.2375 Evaluate side-chains 117 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1127 MET Chi-restraints excluded: chain A residue 1226 CYS Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 170 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 8 optimal weight: 0.0270 chunk 84 optimal weight: 30.0000 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 74 optimal weight: 50.0000 chunk 27 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 overall best weight: 2.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 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 = 0.4206 r_free = 0.4206 target = 0.106101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.080946 restraints weight = 40247.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.083535 restraints weight = 24580.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.085235 restraints weight = 17235.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.086323 restraints weight = 13360.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.087076 restraints weight = 11104.401| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8623 Z= 0.157 Angle : 0.755 13.544 11890 Z= 0.385 Chirality : 0.045 0.326 1354 Planarity : 0.005 0.051 1302 Dihedral : 18.039 143.319 1829 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 25.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.17 % Allowed : 22.45 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.28), residues: 867 helix: 0.24 (0.27), residues: 326 sheet: -1.53 (0.51), residues: 98 loop : -0.87 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 274 TYR 0.028 0.002 TYR A1205 PHE 0.059 0.002 PHE A 406 TRP 0.017 0.002 TRP A1189 HIS 0.011 0.002 HIS B 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 8607) covalent geometry : angle 0.74118 / 0.38 (11879) hydrogen bonds : bond 0.05373 / 3.70 ( 329) hydrogen bonds : angle 5.50568 / 3.99 ( 891) metal coordination : bond 0.01294 / 0.93 ( 16) metal coordination : angle 4.86836 / 3.72 ( 11) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 ARG cc_start: 0.8580 (ttm-80) cc_final: 0.8223 (mtm-85) REVERT: A 313 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8600 (tp) REVERT: A 324 LYS cc_start: 0.8966 (tttp) cc_final: 0.8552 (tptt) REVERT: A 414 ASN cc_start: 0.6351 (m110) cc_final: 0.5818 (m110) REVERT: A 459 ARG cc_start: 0.8569 (tpp80) cc_final: 0.8309 (tpp80) REVERT: A 521 CYS cc_start: 0.8587 (m) cc_final: 0.8149 (m) REVERT: A 565 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8664 (mm-30) REVERT: A 656 GLN cc_start: 0.8467 (tm-30) cc_final: 0.7921 (tm-30) REVERT: A 668 LYS cc_start: 0.8818 (mptt) cc_final: 0.8487 (mptt) REVERT: A 932 PHE cc_start: 0.8876 (m-80) cc_final: 0.8436 (m-10) REVERT: A 1014 MET cc_start: 0.7910 (mmp) cc_final: 0.7514 (mmp) REVERT: A 1073 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6562 (pt) REVERT: A 1187 GLU cc_start: 0.9105 (tp30) cc_final: 0.8829 (tm-30) REVERT: A 1196 TYR cc_start: 0.8411 (m-80) cc_final: 0.7954 (m-80) REVERT: A 1212 LYS cc_start: 0.9141 (pptt) cc_final: 0.8934 (ptmm) REVERT: A 1250 PHE cc_start: 0.9313 (t80) cc_final: 0.8889 (m-80) REVERT: A 1252 MET cc_start: 0.9186 (mmm) cc_final: 0.8174 (mmm) REVERT: B 159 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7561 (tptp) outliers start: 17 outliers final: 13 residues processed: 114 average time/residue: 0.1305 time to fit residues: 18.7094 Evaluate side-chains 117 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1127 MET Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1226 CYS Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 170 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 79 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 84 optimal weight: 40.0000 chunk 68 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 60 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 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 = 0.4225 r_free = 0.4225 target = 0.107311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.081447 restraints weight = 40605.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.084048 restraints weight = 24846.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.085727 restraints weight = 17634.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.086884 restraints weight = 13781.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.087551 restraints weight = 11559.750| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8623 Z= 0.146 Angle : 0.756 13.065 11890 Z= 0.386 Chirality : 0.045 0.300 1354 Planarity : 0.005 0.056 1302 Dihedral : 18.014 142.064 1829 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 24.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.17 % Allowed : 22.58 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.28), residues: 867 helix: 0.27 (0.28), residues: 326 sheet: -1.41 (0.55), residues: 88 loop : -0.87 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 274 TYR 0.025 0.002 TYR A1205 PHE 0.050 0.002 PHE B 163 TRP 0.017 0.002 TRP A 503 HIS 0.011 0.001 HIS B 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 8607) covalent geometry : angle 0.73977 / 0.38 (11879) hydrogen bonds : bond 0.05360 / 3.71 ( 329) hydrogen bonds : angle 5.46725 / 3.97 ( 891) metal coordination : bond 0.01090 / 0.77 ( 16) metal coordination : angle 5.22383 / 3.99 ( 11) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 ARG cc_start: 0.8593 (ttm-80) cc_final: 0.8246 (mtm-85) REVERT: A 324 LYS cc_start: 0.8942 (tttp) cc_final: 0.8555 (tptt) REVERT: A 414 ASN cc_start: 0.6352 (m110) cc_final: 0.5764 (m-40) REVERT: A 423 MET cc_start: 0.8036 (pmm) cc_final: 0.7718 (pmm) REVERT: A 459 ARG cc_start: 0.8545 (tpp80) cc_final: 0.8335 (tpp80) REVERT: A 521 CYS cc_start: 0.8571 (m) cc_final: 0.8104 (m) REVERT: A 565 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8647 (mm-30) REVERT: A 656 GLN cc_start: 0.8464 (tm-30) cc_final: 0.7927 (tm-30) REVERT: A 661 ARG cc_start: 0.5987 (mmm160) cc_final: 0.5121 (mmm160) REVERT: A 668 LYS cc_start: 0.8785 (mptt) cc_final: 0.8529 (mptt) REVERT: A 932 PHE cc_start: 0.8859 (m-80) cc_final: 0.8427 (m-10) REVERT: A 1014 MET cc_start: 0.7885 (mmp) cc_final: 0.7517 (mmp) REVERT: A 1073 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6581 (pt) REVERT: A 1102 MET cc_start: 0.8825 (ptm) cc_final: 0.8603 (ptm) REVERT: A 1187 GLU cc_start: 0.9099 (tp30) cc_final: 0.8851 (tm-30) REVERT: A 1196 TYR cc_start: 0.8382 (m-80) cc_final: 0.8064 (m-80) REVERT: A 1212 LYS cc_start: 0.9124 (pptt) cc_final: 0.8919 (ptmm) REVERT: A 1250 PHE cc_start: 0.9291 (t80) cc_final: 0.8950 (m-80) REVERT: A 1252 MET cc_start: 0.9270 (mmm) cc_final: 0.8512 (mmm) REVERT: B 159 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7603 (tptp) outliers start: 17 outliers final: 14 residues processed: 115 average time/residue: 0.1209 time to fit residues: 17.6610 Evaluate side-chains 117 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1127 MET Chi-restraints excluded: chain A residue 1226 CYS Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 170 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 88 optimal weight: 30.0000 chunk 13 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 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 = 0.4213 r_free = 0.4213 target = 0.106650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.081472 restraints weight = 39839.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.084070 restraints weight = 24208.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.085761 restraints weight = 17043.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.086831 restraints weight = 13263.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.087586 restraints weight = 11033.393| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8623 Z= 0.153 Angle : 0.753 12.446 11890 Z= 0.384 Chirality : 0.045 0.291 1354 Planarity : 0.005 0.052 1302 Dihedral : 18.030 141.112 1829 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 25.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.30 % Allowed : 22.83 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.28), residues: 867 helix: 0.16 (0.27), residues: 332 sheet: -1.44 (0.52), residues: 94 loop : -0.82 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 699 TYR 0.038 0.002 TYR A1205 PHE 0.053 0.002 PHE B 163 TRP 0.016 0.002 TRP A1189 HIS 0.012 0.001 HIS B 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 8607) covalent geometry : angle 0.73868 / 0.38 (11879) hydrogen bonds : bond 0.05362 / 3.73 ( 329) hydrogen bonds : angle 5.43762 / 3.93 ( 891) metal coordination : bond 0.01262 / 0.86 ( 16) metal coordination : angle 4.80413 / 3.62 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2036.23 seconds wall clock time: 35 minutes 42.32 seconds (2142.32 seconds total)