Starting phenix.real_space_refine on Wed Feb 4 01:47:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w4r_65642/02_2026/9w4r_65642.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w4r_65642/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9w4r_65642/02_2026/9w4r_65642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w4r_65642/02_2026/9w4r_65642.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w4r_65642/02_2026/9w4r_65642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w4r_65642/02_2026/9w4r_65642.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 1.71, 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: 0.60 Conformation dependent library (CDL) restraints added in 187.9 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: 0.82 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: 1.10 Time building geometry restraints manager: 0.85 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=" C HIS A 425 " pdb=" N PRO A 426 " ideal model delta sigma weight residual 1.335 1.352 -0.018 1.28e-02 6.10e+03 1.93e+00 bond pdb=" CB LEU A 341 " pdb=" CG LEU A 341 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.56e+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=" C LYS A 664 " pdb=" N ASN A 665 " pdb=" CA ASN A 665 " ideal model delta sigma weight residual 122.82 128.00 -5.18 1.42e+00 4.96e-01 1.33e+01 angle pdb=" C VAL A 563 " pdb=" N GLU A 564 " pdb=" CA GLU A 564 " ideal model delta sigma weight residual 122.61 128.08 -5.47 1.56e+00 4.11e-01 1.23e+01 angle pdb=" C VAL A 492 " pdb=" N PHE A 493 " pdb=" CA PHE A 493 " ideal model delta sigma weight residual 120.82 125.97 -5.15 1.50e+00 4.44e-01 1.18e+01 angle pdb=" C ILE A1209 " pdb=" N ARG A1210 " pdb=" CA ARG A1210 " ideal model delta sigma weight residual 121.54 127.51 -5.97 1.91e+00 2.74e-01 9.76e+00 angle pdb=" C GLU A 340 " pdb=" N LEU A 341 " pdb=" CA LEU A 341 " ideal model delta sigma weight residual 122.56 117.20 5.36 1.72e+00 3.38e-01 9.73e+00 ... (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: 0.110 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.800 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 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= 0.196 Angle : 0.766 8.358 11890 Z= 0.429 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 covalent geometry : bond 0.00384 ( 8607) covalent geometry : angle 0.75920 (11879) hydrogen bonds : bond 0.17410 ( 329) hydrogen bonds : angle 6.52873 ( 891) metal coordination : bond 0.00977 ( 16) metal coordination : angle 3.39377 ( 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 : 0.267 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: 0.1167 time to fit residues: 29.6514 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 : 0.223 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4172 r_free = 0.4172 target = 0.103836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.078337 restraints weight = 41472.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.080956 restraints weight = 25353.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.082650 restraints weight = 17832.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.083787 restraints weight = 13859.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.084551 restraints weight = 11470.902| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8623 Z= 0.255 Angle : 0.844 30.270 11890 Z= 0.401 Chirality : 0.045 0.209 1354 Planarity : 0.007 0.108 1302 Dihedral : 18.363 141.703 1853 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 26.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.57 % Allowed : 16.58 % Favored : 79.85 % 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 (0.28), residues: 867 helix: -0.03 (0.27), residues: 333 sheet: -1.68 (0.48), residues: 102 loop : -0.68 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1259 TYR 0.013 0.002 TYR A 695 PHE 0.024 0.002 PHE A 406 TRP 0.030 0.003 TRP A1189 HIS 0.006 0.002 HIS B 148 Details of bonding type rmsd covalent geometry : bond 0.00534 ( 8607) covalent geometry : angle 0.77896 (11879) hydrogen bonds : bond 0.06896 ( 329) hydrogen bonds : angle 5.74930 ( 891) metal coordination : bond 0.02039 ( 16) metal coordination : angle 10.72802 ( 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 168 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.299 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: 0.9436 (tp) cc_final: 0.9114 (tp) REVERT: A 284 LEU cc_start: 0.9433 (mm) cc_final: 0.8913 (tp) REVERT: A 329 LYS cc_start: 0.8152 (mttt) cc_final: 0.7751 (mmtt) REVERT: A 361 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8733 (pt0) REVERT: A 404 THR cc_start: 0.8765 (p) cc_final: 0.8343 (t) REVERT: A 414 ASN cc_start: 0.6454 (m110) cc_final: 0.5871 (m-40) REVERT: A 493 PHE cc_start: 0.7585 (t80) cc_final: 0.6808 (t80) REVERT: A 521 CYS cc_start: 0.8508 (m) cc_final: 0.8111 (m) REVERT: A 619 LEU cc_start: 0.5840 (OUTLIER) cc_final: 0.5391 (tt) REVERT: A 649 TYR cc_start: 0.8190 (m-80) cc_final: 0.7903 (m-80) REVERT: A 661 ARG cc_start: 0.6579 (mmm160) cc_final: 0.5344 (mmm160) REVERT: A 943 MET cc_start: 0.7391 (mmt) cc_final: 0.6980 (mmp) REVERT: A 960 ASP cc_start: 0.8985 (p0) cc_final: 0.8773 (p0) REVERT: A 968 GLU cc_start: 0.9553 (mm-30) cc_final: 0.8889 (tp30) REVERT: A 1187 GLU cc_start: 0.9363 (tp30) cc_final: 0.9083 (tp30) REVERT: A 1194 ARG cc_start: 0.9391 (ttp-110) cc_final: 0.8974 (ttm110) REVERT: A 1212 LYS cc_start: 0.9104 (pptt) cc_final: 0.8843 (ptmm) REVERT: A 1214 LEU cc_start: 0.9147 (mt) cc_final: 0.8943 (mt) REVERT: A 1222 TRP cc_start: 0.7666 (m100) cc_final: 0.7412 (m100) outliers start: 28 outliers final: 14 residues processed: 161 average time/residue: 0.1423 time to fit residues: 28.6466 Evaluate side-chains 136 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 670 ARG 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 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: 0.7980 chunk 73 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 46 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 85 optimal weight: 40.0000 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN A 377 GLN A 688 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.107973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.083074 restraints weight = 39823.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.085709 restraints weight = 23816.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.087448 restraints weight = 16518.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.088638 restraints weight = 12637.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.089435 restraints weight = 10418.288| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8623 Z= 0.147 Angle : 0.723 20.889 11890 Z= 0.355 Chirality : 0.043 0.187 1354 Planarity : 0.006 0.085 1302 Dihedral : 18.218 145.611 1833 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.44 % Allowed : 17.22 % 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: -0.76 (0.28), residues: 867 helix: 0.28 (0.28), residues: 330 sheet: -1.53 (0.48), residues: 104 loop : -0.76 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 699 TYR 0.015 0.001 TYR A 502 PHE 0.031 0.002 PHE A 406 TRP 0.017 0.002 TRP A 503 HIS 0.004 0.001 HIS B 148 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8607) covalent geometry : angle 0.68876 (11879) hydrogen bonds : bond 0.05558 ( 329) hydrogen bonds : angle 5.53058 ( 891) metal coordination : bond 0.01222 ( 16) metal coordination : angle 7.23215 ( 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 162 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.308 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 324 LYS cc_start: 0.9114 (tttp) cc_final: 0.8633 (tptt) REVERT: A 404 THR cc_start: 0.8831 (p) cc_final: 0.8490 (p) REVERT: A 414 ASN cc_start: 0.6201 (m110) cc_final: 0.5614 (m-40) REVERT: A 493 PHE cc_start: 0.7510 (t80) cc_final: 0.6749 (t80) REVERT: A 521 CYS cc_start: 0.8431 (m) cc_final: 0.8031 (m) REVERT: A 638 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8458 (ttmm) REVERT: A 661 ARG cc_start: 0.5986 (mmm160) cc_final: 0.5523 (mmm160) REVERT: A 668 LYS cc_start: 0.8789 (mptt) cc_final: 0.8537 (mptt) REVERT: A 679 VAL cc_start: 0.7387 (OUTLIER) cc_final: 0.7150 (t) REVERT: A 921 ASP cc_start: 0.8015 (p0) cc_final: 0.7586 (t0) REVERT: A 932 PHE cc_start: 0.8474 (m-80) cc_final: 0.8166 (m-10) REVERT: A 1187 GLU cc_start: 0.9217 (tp30) cc_final: 0.8824 (tm-30) REVERT: A 1189 TRP cc_start: 0.9033 (t-100) cc_final: 0.8805 (t-100) REVERT: A 1196 TYR cc_start: 0.8546 (m-80) cc_final: 0.8193 (m-80) REVERT: A 1212 LYS cc_start: 0.9155 (pptt) cc_final: 0.8901 (ptmm) REVERT: A 1250 PHE cc_start: 0.9241 (t80) cc_final: 0.8888 (m-80) REVERT: A 1252 MET cc_start: 0.9155 (mmm) cc_final: 0.8263 (mmm) outliers start: 27 outliers final: 16 residues processed: 156 average time/residue: 0.1522 time to fit residues: 29.3702 Evaluate side-chains 128 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 378 GLU 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 638 LYS Chi-restraints excluded: chain A residue 670 ARG 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 971 ASN Chi-restraints excluded: chain A residue 1006 ARG 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 81 MET Chi-restraints excluded: chain B residue 154 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 52 optimal weight: 5.9990 chunk 76 optimal weight: 30.0000 chunk 12 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 69 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 688 ASN A 969 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.103198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.076926 restraints weight = 41981.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.079476 restraints weight = 26112.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.081157 restraints weight = 18634.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.082257 restraints weight = 14622.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.082944 restraints weight = 12371.335| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 8623 Z= 0.266 Angle : 0.817 18.903 11890 Z= 0.407 Chirality : 0.044 0.205 1354 Planarity : 0.007 0.080 1302 Dihedral : 18.326 147.095 1833 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 29.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.21 % Allowed : 18.37 % Favored : 77.42 % 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: -0.02 (0.27), residues: 325 sheet: -1.55 (0.49), residues: 101 loop : -0.74 (0.32), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A1006 TYR 0.023 0.002 TYR A 649 PHE 0.020 0.002 PHE B 163 TRP 0.015 0.002 TRP A 503 HIS 0.008 0.002 HIS A 970 Details of bonding type rmsd covalent geometry : bond 0.00561 ( 8607) covalent geometry : angle 0.78776 (11879) hydrogen bonds : bond 0.06236 ( 329) hydrogen bonds : angle 5.80435 ( 891) metal coordination : bond 0.02146 ( 16) metal coordination : angle 7.11949 ( 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 156 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.291 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: symmetry clash REVERT: A 275 LEU cc_start: 0.9299 (tp) cc_final: 0.9057 (pp) REVERT: A 414 ASN cc_start: 0.6569 (m110) cc_final: 0.5964 (m-40) REVERT: A 493 PHE cc_start: 0.7468 (t80) cc_final: 0.6881 (t80) REVERT: A 521 CYS cc_start: 0.8334 (m) cc_final: 0.8008 (m) REVERT: A 565 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8738 (mm-30) REVERT: A 619 LEU cc_start: 0.5686 (OUTLIER) cc_final: 0.5229 (tt) REVERT: A 1045 ARG cc_start: 0.8610 (ptt90) cc_final: 0.8316 (ptt90) REVERT: A 1098 LEU cc_start: 0.9642 (mm) cc_final: 0.9298 (mm) REVERT: A 1102 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8828 (tmm) REVERT: A 1187 GLU cc_start: 0.9169 (tp30) cc_final: 0.8781 (tm-30) REVERT: A 1189 TRP cc_start: 0.9104 (t-100) cc_final: 0.8853 (t-100) REVERT: A 1196 TYR cc_start: 0.8740 (m-80) cc_final: 0.8180 (m-80) REVERT: A 1197 THR cc_start: 0.7473 (OUTLIER) cc_final: 0.7106 (p) REVERT: A 1252 MET cc_start: 0.9178 (mmm) cc_final: 0.8424 (mmm) REVERT: B 58 MET cc_start: 0.0931 (ttt) cc_final: -0.0036 (tpp) outliers start: 33 outliers final: 22 residues processed: 142 average time/residue: 0.1279 time to fit residues: 22.7271 Evaluate side-chains 135 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 361 GLU 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 568 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 971 ASN Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1197 THR Chi-restraints excluded: chain A residue 1226 CYS Chi-restraints excluded: chain A residue 1249 ASN Chi-restraints excluded: chain B residue 38 LEU 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 Chi-restraints excluded: chain B residue 170 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 52 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 86 optimal weight: 30.0000 chunk 13 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 0.0050 chunk 83 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 74 optimal weight: 50.0000 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4199 r_free = 0.4199 target = 0.105270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.079191 restraints weight = 40812.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.081861 restraints weight = 24903.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.083574 restraints weight = 17568.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.084727 restraints weight = 13642.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.085447 restraints weight = 11435.126| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 8623 Z= 0.168 Angle : 0.747 18.593 11890 Z= 0.373 Chirality : 0.043 0.215 1354 Planarity : 0.006 0.064 1302 Dihedral : 18.346 144.912 1833 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 24.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.34 % Allowed : 19.64 % Favored : 76.02 % 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: -0.99 (0.29), residues: 867 helix: -0.08 (0.27), residues: 331 sheet: -1.54 (0.49), residues: 104 loop : -0.78 (0.33), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 327 TYR 0.016 0.002 TYR A 649 PHE 0.039 0.002 PHE A 406 TRP 0.016 0.002 TRP A 503 HIS 0.010 0.001 HIS B 148 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8607) covalent geometry : angle 0.71827 (11879) hydrogen bonds : bond 0.05448 ( 329) hydrogen bonds : angle 5.64194 ( 891) metal coordination : bond 0.01488 ( 16) metal coordination : angle 6.80297 ( 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 154 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.219 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 275 LEU cc_start: 0.9274 (tp) cc_final: 0.8984 (pp) REVERT: A 284 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.8883 (tp) REVERT: A 324 LYS cc_start: 0.9053 (tttp) cc_final: 0.8625 (tptt) REVERT: A 414 ASN cc_start: 0.6290 (m110) cc_final: 0.5696 (m-40) REVERT: A 493 PHE cc_start: 0.7261 (t80) cc_final: 0.6784 (t80) REVERT: A 521 CYS cc_start: 0.8378 (m) cc_final: 0.7963 (m) REVERT: A 619 LEU cc_start: 0.5615 (OUTLIER) cc_final: 0.5402 (tt) REVERT: A 638 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8413 (ttmm) REVERT: A 661 ARG cc_start: 0.7508 (mmt180) cc_final: 0.6261 (mmm160) REVERT: A 932 PHE cc_start: 0.8840 (m-10) cc_final: 0.8404 (m-10) REVERT: A 968 GLU cc_start: 0.8999 (mp0) cc_final: 0.8538 (mp0) REVERT: A 980 GLU cc_start: 0.9141 (tt0) cc_final: 0.8928 (tp30) REVERT: A 1006 ARG cc_start: 0.6656 (OUTLIER) cc_final: 0.6000 (tpm170) REVERT: A 1098 LEU cc_start: 0.9610 (mm) cc_final: 0.9280 (mm) REVERT: A 1102 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8706 (tmm) REVERT: A 1187 GLU cc_start: 0.9161 (tp30) cc_final: 0.8788 (tm-30) REVERT: A 1196 TYR cc_start: 0.8606 (m-80) cc_final: 0.8077 (m-80) REVERT: A 1252 MET cc_start: 0.9173 (mmm) cc_final: 0.8094 (mmm) outliers start: 34 outliers final: 21 residues processed: 140 average time/residue: 0.1181 time to fit residues: 20.5072 Evaluate side-chains 133 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 390 PHE 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 568 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 971 ASN Chi-restraints excluded: chain A residue 1006 ARG Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1102 MET 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 A residue 1249 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 9.9990 chunk 83 optimal weight: 0.0670 chunk 88 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4212 r_free = 0.4212 target = 0.106014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.080085 restraints weight = 40408.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.082775 restraints weight = 24450.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.084587 restraints weight = 17155.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.085674 restraints weight = 13257.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.086359 restraints weight = 11093.472| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8623 Z= 0.152 Angle : 0.736 16.814 11890 Z= 0.369 Chirality : 0.042 0.197 1354 Planarity : 0.005 0.057 1302 Dihedral : 18.334 144.569 1829 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 23.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.08 % Allowed : 19.52 % Favored : 76.40 % 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: -0.95 (0.29), residues: 867 helix: 0.01 (0.27), residues: 332 sheet: -1.47 (0.49), residues: 108 loop : -0.81 (0.33), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 699 TYR 0.013 0.001 TYR A 649 PHE 0.024 0.002 PHE B 163 TRP 0.016 0.002 TRP A 503 HIS 0.011 0.001 HIS B 148 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8607) covalent geometry : angle 0.71442 (11879) hydrogen bonds : bond 0.05364 ( 329) hydrogen bonds : angle 5.45856 ( 891) metal coordination : bond 0.01255 ( 16) metal coordination : angle 5.84553 ( 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 149 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.298 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 275 LEU cc_start: 0.9219 (tp) cc_final: 0.8917 (pp) REVERT: A 284 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8718 (tp) REVERT: A 324 LYS cc_start: 0.9009 (tttp) cc_final: 0.8620 (tptt) REVERT: A 404 THR cc_start: 0.8986 (p) cc_final: 0.8720 (p) REVERT: A 414 ASN cc_start: 0.6265 (m110) cc_final: 0.5681 (m-40) REVERT: A 493 PHE cc_start: 0.7239 (t80) cc_final: 0.6976 (t80) REVERT: A 521 CYS cc_start: 0.8457 (m) cc_final: 0.8101 (m) REVERT: A 638 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8400 (ttmm) REVERT: A 661 ARG cc_start: 0.7370 (mmt180) cc_final: 0.4719 (mmm160) REVERT: A 679 VAL cc_start: 0.7491 (OUTLIER) cc_final: 0.7242 (t) REVERT: A 930 GLU cc_start: 0.8827 (pm20) cc_final: 0.8571 (pm20) REVERT: A 932 PHE cc_start: 0.8792 (m-10) cc_final: 0.8339 (m-10) REVERT: A 968 GLU cc_start: 0.8916 (mp0) cc_final: 0.8426 (mp0) REVERT: A 980 GLU cc_start: 0.9130 (tt0) cc_final: 0.8905 (tp30) REVERT: A 1006 ARG cc_start: 0.6621 (OUTLIER) cc_final: 0.6014 (tpm170) REVERT: A 1014 MET cc_start: 0.7764 (mmp) cc_final: 0.7314 (mmm) REVERT: A 1098 LEU cc_start: 0.9613 (mm) cc_final: 0.9292 (mm) REVERT: A 1187 GLU cc_start: 0.9104 (tp30) cc_final: 0.8844 (tm-30) REVERT: A 1196 TYR cc_start: 0.8623 (m-80) cc_final: 0.8263 (m-80) REVERT: A 1252 MET cc_start: 0.9301 (mmm) cc_final: 0.8504 (mmm) outliers start: 32 outliers final: 21 residues processed: 140 average time/residue: 0.1182 time to fit residues: 20.7344 Evaluate side-chains 138 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 466 LEU 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 623 THR Chi-restraints excluded: chain A residue 638 LYS 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 971 ASN Chi-restraints excluded: chain A residue 1006 ARG Chi-restraints excluded: chain A residue 1040 ARG 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 A residue 1249 ASN 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: 8.9990 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 15 optimal weight: 0.0030 chunk 71 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 GLN ** 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 = 0.4202 r_free = 0.4202 target = 0.105431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.079814 restraints weight = 40280.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.082500 restraints weight = 24197.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.084268 restraints weight = 16858.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.085454 restraints weight = 12944.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.086122 restraints weight = 10727.422| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8623 Z= 0.170 Angle : 0.771 15.225 11890 Z= 0.384 Chirality : 0.044 0.302 1354 Planarity : 0.006 0.076 1302 Dihedral : 18.359 144.272 1829 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 24.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.83 % Allowed : 20.15 % Favored : 76.02 % 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 (0.29), residues: 867 helix: 0.05 (0.27), residues: 333 sheet: -1.44 (0.49), residues: 108 loop : -0.88 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 699 TYR 0.016 0.002 TYR A1205 PHE 0.043 0.002 PHE A 406 TRP 0.015 0.002 TRP A 503 HIS 0.012 0.001 HIS B 148 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 8607) covalent geometry : angle 0.75256 (11879) hydrogen bonds : bond 0.05338 ( 329) hydrogen bonds : angle 5.52713 ( 891) metal coordination : bond 0.01379 ( 16) metal coordination : angle 5.57905 ( 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 148 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.213 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: 0.9211 (tp) cc_final: 0.8970 (pp) REVERT: A 284 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8732 (tp) REVERT: A 324 LYS cc_start: 0.8991 (tttp) cc_final: 0.8639 (tptt) REVERT: A 414 ASN cc_start: 0.6359 (m110) cc_final: 0.5775 (m-40) REVERT: A 493 PHE cc_start: 0.7236 (t80) cc_final: 0.6830 (t80) REVERT: A 521 CYS cc_start: 0.8497 (m) cc_final: 0.8129 (m) REVERT: A 638 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8400 (ttmm) REVERT: A 661 ARG cc_start: 0.7286 (mmt180) cc_final: 0.5553 (mmm160) REVERT: A 679 VAL cc_start: 0.7512 (OUTLIER) cc_final: 0.7251 (t) REVERT: A 930 GLU cc_start: 0.8777 (pm20) cc_final: 0.8509 (pm20) REVERT: A 932 PHE cc_start: 0.8769 (m-10) cc_final: 0.8312 (m-10) REVERT: A 968 GLU cc_start: 0.8971 (mp0) cc_final: 0.8460 (mp0) REVERT: A 980 GLU cc_start: 0.9139 (tt0) cc_final: 0.8554 (tp30) REVERT: A 984 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7406 (mm-40) REVERT: A 1006 ARG cc_start: 0.6590 (OUTLIER) cc_final: 0.5939 (tpm170) REVERT: A 1014 MET cc_start: 0.7944 (mmp) cc_final: 0.7450 (mmp) REVERT: A 1187 GLU cc_start: 0.9097 (tp30) cc_final: 0.8821 (tm-30) REVERT: A 1196 TYR cc_start: 0.8666 (m-80) cc_final: 0.8363 (m-80) REVERT: A 1252 MET cc_start: 0.9375 (mmm) cc_final: 0.8674 (mmm) outliers start: 30 outliers final: 20 residues processed: 140 average time/residue: 0.1186 time to fit residues: 20.9213 Evaluate side-chains 134 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 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 638 LYS 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 971 ASN Chi-restraints excluded: chain A residue 1006 ARG Chi-restraints excluded: chain A residue 1040 ARG 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 A residue 1249 ASN Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 GLU 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: 2.9990 chunk 22 optimal weight: 0.9990 chunk 76 optimal weight: 40.0000 chunk 11 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 0.1980 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 GLN ** 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 = 0.4212 r_free = 0.4212 target = 0.105964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.080183 restraints weight = 41515.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.082907 restraints weight = 25132.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.084656 restraints weight = 17639.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.085825 restraints weight = 13682.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.086439 restraints weight = 11426.767| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8623 Z= 0.159 Angle : 0.776 14.654 11890 Z= 0.390 Chirality : 0.045 0.364 1354 Planarity : 0.006 0.072 1302 Dihedral : 18.324 143.317 1829 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 24.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.44 % Allowed : 20.92 % Favored : 75.64 % 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: -0.95 (0.29), residues: 867 helix: 0.11 (0.27), residues: 332 sheet: -1.34 (0.50), residues: 108 loop : -0.96 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 699 TYR 0.022 0.002 TYR A 649 PHE 0.067 0.002 PHE A1250 TRP 0.017 0.002 TRP A1189 HIS 0.012 0.001 HIS B 148 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8607) covalent geometry : angle 0.75742 (11879) hydrogen bonds : bond 0.05224 ( 329) hydrogen bonds : angle 5.47711 ( 891) metal coordination : bond 0.01375 ( 16) metal coordination : angle 5.54933 ( 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 141 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.253 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 275 LEU cc_start: 0.9199 (tp) cc_final: 0.8997 (pp) REVERT: A 284 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8779 (tp) REVERT: A 324 LYS cc_start: 0.8928 (tttp) cc_final: 0.8634 (tptt) REVERT: A 404 THR cc_start: 0.8954 (p) cc_final: 0.8710 (p) REVERT: A 414 ASN cc_start: 0.6332 (m110) cc_final: 0.5756 (m-40) REVERT: A 521 CYS cc_start: 0.8281 (m) cc_final: 0.7917 (m) REVERT: A 638 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8393 (ttmm) REVERT: A 661 ARG cc_start: 0.7175 (mmt180) cc_final: 0.5863 (mmm160) REVERT: A 679 VAL cc_start: 0.7492 (OUTLIER) cc_final: 0.7247 (t) REVERT: A 932 PHE cc_start: 0.8773 (m-10) cc_final: 0.8334 (m-10) REVERT: A 968 GLU cc_start: 0.8977 (mp0) cc_final: 0.8443 (mp0) REVERT: A 980 GLU cc_start: 0.9109 (tt0) cc_final: 0.8759 (tp30) REVERT: A 1006 ARG cc_start: 0.6528 (OUTLIER) cc_final: 0.5844 (tpm170) REVERT: A 1187 GLU cc_start: 0.9065 (tp30) cc_final: 0.8831 (tm-30) REVERT: A 1196 TYR cc_start: 0.8539 (m-80) cc_final: 0.8241 (m-80) REVERT: A 1252 MET cc_start: 0.9329 (mmm) cc_final: 0.8629 (mmm) REVERT: B 58 MET cc_start: 0.4393 (ttt) cc_final: 0.2667 (tpp) outliers start: 27 outliers final: 19 residues processed: 134 average time/residue: 0.1272 time to fit residues: 21.1789 Evaluate side-chains 131 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 341 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 623 THR Chi-restraints excluded: chain A residue 638 LYS 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 971 ASN Chi-restraints excluded: chain A residue 1006 ARG Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1094 ARG Chi-restraints excluded: chain A residue 1226 CYS Chi-restraints excluded: chain A residue 1249 ASN 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: 7.9990 chunk 84 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 74 optimal weight: 50.0000 chunk 27 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 57 optimal weight: 40.0000 chunk 51 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 GLN ** 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 = 0.4151 r_free = 0.4151 target = 0.102919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.076819 restraints weight = 41233.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.079396 restraints weight = 25458.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.081045 restraints weight = 18162.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.082164 restraints weight = 14262.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.082827 restraints weight = 12024.102| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 8623 Z= 0.244 Angle : 0.839 15.614 11890 Z= 0.422 Chirality : 0.048 0.292 1354 Planarity : 0.006 0.079 1302 Dihedral : 18.475 143.169 1829 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 31.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.70 % Allowed : 21.81 % Favored : 74.49 % 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: -1.06 (0.29), residues: 867 helix: -0.10 (0.27), residues: 338 sheet: -1.52 (0.51), residues: 96 loop : -0.91 (0.33), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 699 TYR 0.022 0.002 TYR A1205 PHE 0.056 0.003 PHE B 163 TRP 0.014 0.002 TRP A 503 HIS 0.014 0.002 HIS B 148 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 8607) covalent geometry : angle 0.81588 (11879) hydrogen bonds : bond 0.05778 ( 329) hydrogen bonds : angle 5.77272 ( 891) metal coordination : bond 0.02491 ( 16) metal coordination : angle 6.43744 ( 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 137 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.181 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 275 LEU cc_start: 0.9183 (tp) cc_final: 0.8976 (pp) REVERT: A 324 LYS cc_start: 0.8968 (tttp) cc_final: 0.8691 (tptt) REVERT: A 414 ASN cc_start: 0.6508 (m110) cc_final: 0.5908 (m-40) REVERT: A 429 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8573 (mp) REVERT: A 493 PHE cc_start: 0.7076 (t80) cc_final: 0.6419 (t80) REVERT: A 506 LEU cc_start: 0.9109 (pp) cc_final: 0.8903 (pp) REVERT: A 521 CYS cc_start: 0.8269 (m) cc_final: 0.7934 (m) REVERT: A 565 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8784 (mm-30) REVERT: A 638 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8403 (ttmm) REVERT: A 661 ARG cc_start: 0.7515 (mmt180) cc_final: 0.6259 (mmm160) REVERT: A 670 ARG cc_start: 0.7627 (mpp-170) cc_final: 0.7376 (mpp-170) REVERT: A 679 VAL cc_start: 0.7539 (OUTLIER) cc_final: 0.7254 (t) REVERT: A 932 PHE cc_start: 0.8915 (m-10) cc_final: 0.8435 (m-10) REVERT: A 968 GLU cc_start: 0.8980 (mp0) cc_final: 0.8450 (mp0) REVERT: A 980 GLU cc_start: 0.9111 (tt0) cc_final: 0.8487 (tp30) REVERT: A 1006 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.6027 (tpm170) REVERT: A 1187 GLU cc_start: 0.9090 (tp30) cc_final: 0.8849 (tm-30) REVERT: A 1196 TYR cc_start: 0.8680 (m-80) cc_final: 0.8377 (m-80) REVERT: A 1252 MET cc_start: 0.9384 (mmm) cc_final: 0.8650 (mmm) REVERT: B 58 MET cc_start: 0.1183 (ttt) cc_final: -0.0306 (tpp) outliers start: 29 outliers final: 22 residues processed: 128 average time/residue: 0.1498 time to fit residues: 23.4962 Evaluate side-chains 127 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 390 PHE Chi-restraints excluded: chain A residue 429 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 634 LEU Chi-restraints excluded: chain A residue 638 LYS 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 971 ASN Chi-restraints excluded: chain A residue 1006 ARG Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1094 ARG Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1226 CYS Chi-restraints excluded: chain A residue 1249 ASN 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: 3.9990 chunk 57 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 GLN ** 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 = 0.4155 r_free = 0.4155 target = 0.103157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.077302 restraints weight = 40586.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.079856 restraints weight = 24923.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.081485 restraints weight = 17749.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.082596 restraints weight = 13865.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.083245 restraints weight = 11639.841| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8623 Z= 0.222 Angle : 0.855 14.482 11890 Z= 0.435 Chirality : 0.048 0.230 1354 Planarity : 0.007 0.113 1302 Dihedral : 18.521 142.056 1829 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 30.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.06 % Allowed : 23.09 % Favored : 73.85 % 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: -1.22 (0.29), residues: 867 helix: -0.31 (0.26), residues: 339 sheet: -1.52 (0.52), residues: 96 loop : -0.95 (0.33), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG A1045 TYR 0.023 0.002 TYR A1205 PHE 0.059 0.003 PHE B 163 TRP 0.089 0.005 TRP A1189 HIS 0.016 0.002 HIS B 148 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 8607) covalent geometry : angle 0.83463 (11879) hydrogen bonds : bond 0.05794 ( 329) hydrogen bonds : angle 5.87519 ( 891) metal coordination : bond 0.02178 ( 16) metal coordination : angle 6.08399 ( 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 127 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.359 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: A 307 LYS cc_start: 0.9215 (mtmm) cc_final: 0.8961 (mtmt) REVERT: A 324 LYS cc_start: 0.8992 (tttp) cc_final: 0.8720 (tptt) REVERT: A 381 GLU cc_start: 0.9087 (pt0) cc_final: 0.8702 (mp0) REVERT: A 414 ASN cc_start: 0.6216 (m110) cc_final: 0.5663 (m-40) REVERT: A 521 CYS cc_start: 0.8194 (m) cc_final: 0.7836 (m) REVERT: A 638 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8419 (ttmm) REVERT: A 669 ARG cc_start: 0.7673 (mtt-85) cc_final: 0.7271 (mmt90) REVERT: A 679 VAL cc_start: 0.7521 (OUTLIER) cc_final: 0.7247 (t) REVERT: A 930 GLU cc_start: 0.8837 (pm20) cc_final: 0.8549 (pm20) REVERT: A 932 PHE cc_start: 0.8900 (m-10) cc_final: 0.8445 (m-10) REVERT: A 968 GLU cc_start: 0.9061 (mp0) cc_final: 0.8850 (mp0) REVERT: A 1187 GLU cc_start: 0.9093 (tp30) cc_final: 0.8823 (tm-30) REVERT: A 1196 TYR cc_start: 0.8657 (m-80) cc_final: 0.8405 (m-80) REVERT: A 1252 MET cc_start: 0.9384 (mmm) cc_final: 0.8659 (mmm) outliers start: 24 outliers final: 19 residues processed: 121 average time/residue: 0.1196 time to fit residues: 18.0867 Evaluate side-chains 118 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 390 PHE 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 638 LYS 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 971 ASN Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1226 CYS Chi-restraints excluded: chain A residue 1249 ASN 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: 0.0070 chunk 21 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 GLN ** 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 = 0.4199 r_free = 0.4199 target = 0.105337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.079547 restraints weight = 39639.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.082170 restraints weight = 24176.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.083927 restraints weight = 17060.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.085125 restraints weight = 13243.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.085769 restraints weight = 11051.052| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 8623 Z= 0.165 Angle : 0.832 16.292 11890 Z= 0.421 Chirality : 0.046 0.236 1354 Planarity : 0.008 0.137 1302 Dihedral : 18.435 140.896 1829 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 26.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.93 % Allowed : 23.21 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.15 (0.29), residues: 867 helix: -0.13 (0.27), residues: 332 sheet: -1.61 (0.52), residues: 98 loop : -0.96 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A1045 TYR 0.014 0.002 TYR A1205 PHE 0.067 0.003 PHE A 406 TRP 0.070 0.004 TRP A1189 HIS 0.014 0.002 HIS B 148 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8607) covalent geometry : angle 0.81535 (11879) hydrogen bonds : bond 0.05764 ( 329) hydrogen bonds : angle 5.75758 ( 891) metal coordination : bond 0.01574 ( 16) metal coordination : angle 5.50562 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2170.67 seconds wall clock time: 37 minutes 58.81 seconds (2278.81 seconds total)