Starting phenix.real_space_refine on Fri Sep 11 20:45:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s4s_54581/09_2026/9s4s_54581.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s4s_54581/09_2026/9s4s_54581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9s4s_54581/09_2026/9s4s_54581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s4s_54581/09_2026/9s4s_54581.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9s4s_54581/09_2026/9s4s_54581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s4s_54581/09_2026/9s4s_54581.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 60 5.16 5 Cl 2 4.86 5 C 7283 2.51 5 N 1800 2.21 5 O 1978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11129 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10660 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 1330, 10642 Classifications: {'peptide': 1330} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 1282} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 1330, 10642 Classifications: {'peptide': 1330} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 1282} Chain breaks: 6 bond proxies already assigned to first conformer: 10905 Conformer: "C" Number of residues, atoms: 1330, 10642 Classifications: {'peptide': 1330} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 1282} Chain breaks: 6 bond proxies already assigned to first conformer: 10905 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 460 Unusual residues: {' MG': 1, '1YN': 1, 'ADP': 1, 'ATP': 1, 'ERG': 12} Classifications: {'undetermined': 16, 'water': 4} Link IDs: {None: 19} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLU A 786 " occ=0.50 ... (25 atoms not shown) pdb=" OE2CGLU A 786 " occ=0.00 Time building chain proxies: 5.70, per 1000 atoms: 0.51 Number of scatterers: 11129 At special positions: 0 Unit cell: (85.512, 107.908, 150.664, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 2 17.00 S 60 16.00 P 5 15.00 Mg 1 11.99 O 1978 8.00 N 1800 7.00 C 7283 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 711 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A1399 " - pdb=" SG CYS A1443 " distance=2.03 Simple disulfide: pdb=" SG CYS A1415 " - pdb=" SG CYS A1440 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 1.5 seconds 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2502 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 9 sheets defined 62.4% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 31 through 51 removed outlier: 3.721A pdb=" N VAL A 35 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 100 Processing helix chain 'A' and resid 133 through 137 removed outlier: 4.039A pdb=" N ASN A 137 " --> pdb=" O ASN A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 265 through 280 Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 329 through 348 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 384 through 394 removed outlier: 4.546A pdb=" N GLU A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 411 removed outlier: 4.039A pdb=" N THR A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 426 Processing helix chain 'A' and resid 432 through 443 Processing helix chain 'A' and resid 443 through 458 Processing helix chain 'A' and resid 489 through 508 Processing helix chain 'A' and resid 510 through 530 removed outlier: 3.582A pdb=" N PHE A 514 " --> pdb=" O GLY A 510 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN A 519 " --> pdb=" O MET A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 535 Processing helix chain 'A' and resid 538 through 541 removed outlier: 3.567A pdb=" N THR A 541 " --> pdb=" O THR A 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 541' Processing helix chain 'A' and resid 542 through 556 Processing helix chain 'A' and resid 563 through 570 Processing helix chain 'A' and resid 570 through 580 Processing helix chain 'A' and resid 584 through 615 removed outlier: 3.702A pdb=" N ASP A 588 " --> pdb=" O HIS A 584 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 589 " --> pdb=" O PRO A 585 " (cutoff:3.500A) Proline residue: A 598 - end of helix Processing helix chain 'A' and resid 620 through 649 Processing helix chain 'A' and resid 651 through 669 removed outlier: 4.138A pdb=" N VAL A 657 " --> pdb=" O SER A 653 " (cutoff:3.500A) Proline residue: A 658 - end of helix Processing helix chain 'A' and resid 675 through 679 Processing helix chain 'A' and resid 680 through 682 No H-bonds generated for 'chain 'A' and resid 680 through 682' Processing helix chain 'A' and resid 683 through 690 Processing helix chain 'A' and resid 690 through 705 removed outlier: 3.968A pdb=" N TYR A 694 " --> pdb=" O ASN A 690 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 695 " --> pdb=" O PRO A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 722 Processing helix chain 'A' and resid 725 through 729 Processing helix chain 'A' and resid 744 through 752 Processing helix chain 'A' and resid 756 through 758 No H-bonds generated for 'chain 'A' and resid 756 through 758' Processing helix chain 'A' and resid 759 through 784 removed outlier: 3.817A pdb=" N GLY A 763 " --> pdb=" O HIS A 759 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE A 764 " --> pdb=" O LYS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 803 removed outlier: 4.001A pdb=" N VAL A 802 " --> pdb=" O GLN A 799 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG A 803 " --> pdb=" O ASN A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 907 removed outlier: 3.576A pdb=" N LEU A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 961 Processing helix chain 'A' and resid 966 through 981 Processing helix chain 'A' and resid 999 through 1013 Processing helix chain 'A' and resid 1030 through 1048 Processing helix chain 'A' and resid 1060 through 1066 removed outlier: 3.713A pdb=" N PHE A1066 " --> pdb=" O LEU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1087 No H-bonds generated for 'chain 'A' and resid 1085 through 1087' Processing helix chain 'A' and resid 1088 through 1098 removed outlier: 3.551A pdb=" N ILE A1092 " --> pdb=" O CYS A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1118 Processing helix chain 'A' and resid 1128 through 1136 Processing helix chain 'A' and resid 1136 through 1157 removed outlier: 3.504A pdb=" N GLN A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) Proline residue: A1154 - end of helix Processing helix chain 'A' and resid 1171 through 1190 Processing helix chain 'A' and resid 1190 through 1212 removed outlier: 3.804A pdb=" N LEU A1194 " --> pdb=" O SER A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1233 Processing helix chain 'A' and resid 1235 through 1257 removed outlier: 3.958A pdb=" N LEU A1239 " --> pdb=" O ILE A1235 " (cutoff:3.500A) Proline residue: A1245 - end of helix Processing helix chain 'A' and resid 1265 through 1297 removed outlier: 3.578A pdb=" N GLU A1277 " --> pdb=" O GLN A1273 " (cutoff:3.500A) Proline residue: A1279 - end of helix removed outlier: 4.058A pdb=" N TYR A1294 " --> pdb=" O VAL A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1305 Processing helix chain 'A' and resid 1307 through 1337 removed outlier: 4.614A pdb=" N PHE A1336 " --> pdb=" O PHE A1332 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN A1337 " --> pdb=" O CYS A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1357 removed outlier: 3.697A pdb=" N ALA A1343 " --> pdb=" O VAL A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1378 Processing helix chain 'A' and resid 1378 through 1392 removed outlier: 4.227A pdb=" N TYR A1382 " --> pdb=" O SER A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1427 Proline residue: A1421 - end of helix Processing helix chain 'A' and resid 1447 through 1455 removed outlier: 3.851A pdb=" N PHE A1451 " --> pdb=" O HIS A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1460 No H-bonds generated for 'chain 'A' and resid 1458 through 1460' Processing helix chain 'A' and resid 1461 through 1488 Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 117 Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 232 removed outlier: 6.685A pdb=" N VAL A 229 " --> pdb=" O CYS A 320 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ASP A 322 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ASN A 231 " --> pdb=" O ASP A 322 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU A 177 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N CYS A 370 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL A 179 " --> pdb=" O CYS A 370 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LEU A 372 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU A 181 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 369 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE A 380 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL A 371 " --> pdb=" O ILE A 378 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 709 through 710 Processing sheet with id=AA4, first strand: chain 'A' and resid 714 through 715 Processing sheet with id=AA5, first strand: chain 'A' and resid 871 through 874 removed outlier: 5.907A pdb=" N HIS A 858 " --> pdb=" O VAL A 883 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL A 883 " --> pdb=" O HIS A 858 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ARG A 860 " --> pdb=" O GLY A 881 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N GLY A 881 " --> pdb=" O ARG A 860 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 871 through 874 removed outlier: 4.820A pdb=" N LEU A 862 " --> pdb=" O THR A 916 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR A 916 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR A 864 " --> pdb=" O VAL A 914 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL A 914 " --> pdb=" O TYR A 864 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 935 through 937 removed outlier: 6.989A pdb=" N THR A 889 " --> pdb=" O CYS A1053 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 992 through 993 Processing sheet with id=AA9, first strand: chain 'A' and resid 1430 through 1431 removed outlier: 3.806A pdb=" N TYR A1430 " --> pdb=" O CYS A1443 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1713 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.12 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3194 1.34 - 1.45: 1973 1.45 - 1.57: 6170 1.57 - 1.69: 9 1.69 - 1.81: 95 Bond restraints: 11441 Sorted by residual: bond pdb=" N SER A 89 " pdb=" CA SER A 89 " ideal model delta sigma weight residual 1.454 1.490 -0.037 1.23e-02 6.61e+03 8.93e+00 bond pdb=" N SER A 90 " pdb=" CA SER A 90 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.25e-02 6.40e+03 8.03e+00 bond pdb=" N VAL A 94 " pdb=" CA VAL A 94 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.88e+00 bond pdb=" C6 ERG A1616 " pdb=" C7 ERG A1616 " ideal model delta sigma weight residual 1.452 1.400 0.052 2.00e-02 2.50e+03 6.86e+00 bond pdb=" N MET A 97 " pdb=" CA MET A 97 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.73e+00 ... (remaining 11436 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 15283 2.13 - 4.25: 282 4.25 - 6.38: 33 6.38 - 8.50: 4 8.50 - 10.63: 1 Bond angle restraints: 15603 Sorted by residual: angle pdb=" N ILE A 263 " pdb=" CA ILE A 263 " pdb=" C ILE A 263 " ideal model delta sigma weight residual 112.43 108.35 4.08 9.20e-01 1.18e+00 1.97e+01 angle pdb=" N PRO A 962 " pdb=" CA PRO A 962 " pdb=" C PRO A 962 " ideal model delta sigma weight residual 111.11 117.28 -6.17 1.59e+00 3.96e-01 1.51e+01 angle pdb=" CA SER A 89 " pdb=" C SER A 89 " pdb=" O SER A 89 " ideal model delta sigma weight residual 121.46 117.11 4.35 1.17e+00 7.31e-01 1.38e+01 angle pdb=" C20 ERG A1613 " pdb=" C22 ERG A1613 " pdb=" C23 ERG A1613 " ideal model delta sigma weight residual 125.47 136.10 -10.63 3.00e+00 1.11e-01 1.25e+01 angle pdb=" CA LYS A1156 " pdb=" CB LYS A1156 " pdb=" CG LYS A1156 " ideal model delta sigma weight residual 114.10 121.00 -6.90 2.00e+00 2.50e-01 1.19e+01 ... (remaining 15598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.50: 6654 23.50 - 47.01: 554 47.01 - 70.51: 105 70.51 - 94.01: 16 94.01 - 117.52: 2 Dihedral angle restraints: 7331 sinusoidal: 3435 harmonic: 3896 Sorted by residual: dihedral pdb=" CB CYS A 711 " pdb=" SG CYS A 711 " pdb=" SG CYS A 731 " pdb=" CB CYS A 731 " ideal model delta sinusoidal sigma weight residual -86.00 -149.24 63.24 1 1.00e+01 1.00e-02 5.28e+01 dihedral pdb=" CB CYS A1399 " pdb=" SG CYS A1399 " pdb=" SG CYS A1443 " pdb=" CB CYS A1443 " ideal model delta sinusoidal sigma weight residual 93.00 50.72 42.28 1 1.00e+01 1.00e-02 2.50e+01 dihedral pdb=" C5' ADP A1604 " pdb=" O5' ADP A1604 " pdb=" PA ADP A1604 " pdb=" O2A ADP A1604 " ideal model delta sinusoidal sigma weight residual -60.00 -150.48 90.48 1 2.00e+01 2.50e-03 2.42e+01 ... (remaining 7328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1321 0.043 - 0.086: 319 0.086 - 0.128: 78 0.128 - 0.171: 7 0.171 - 0.214: 4 Chirality restraints: 1729 Sorted by residual: chirality pdb=" C20 ERG A1613 " pdb=" C17 ERG A1613 " pdb=" C21 ERG A1613 " pdb=" C22 ERG A1613 " both_signs ideal model delta sigma weight residual False 2.58 2.37 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C20 ERG A1606 " pdb=" C17 ERG A1606 " pdb=" C21 ERG A1606 " pdb=" C22 ERG A1606 " both_signs ideal model delta sigma weight residual False 2.58 2.37 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ILE A 100 " pdb=" N ILE A 100 " pdb=" C ILE A 100 " pdb=" CB ILE A 100 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1726 not shown) Planarity restraints: 1894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 ERG A1616 " 0.067 2.00e-02 2.50e+03 6.77e-02 4.59e+01 pdb=" C22 ERG A1616 " -0.065 2.00e-02 2.50e+03 pdb=" C23 ERG A1616 " -0.070 2.00e-02 2.50e+03 pdb=" C24 ERG A1616 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C03 1YN A1605 " -0.036 2.00e-02 2.50e+03 2.39e-02 1.14e+01 pdb=" C06 1YN A1605 " 0.009 2.00e-02 2.50e+03 pdb=" C09 1YN A1605 " 0.017 2.00e-02 2.50e+03 pdb=" C11 1YN A1605 " -0.043 2.00e-02 2.50e+03 pdb=" N05 1YN A1605 " 0.002 2.00e-02 2.50e+03 pdb=" N08 1YN A1605 " 0.016 2.00e-02 2.50e+03 pdb=" N10 1YN A1605 " 0.009 2.00e-02 2.50e+03 pdb=" O07 1YN A1605 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A1363 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO A1364 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A1364 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1364 " -0.028 5.00e-02 4.00e+02 ... (remaining 1891 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 544 2.73 - 3.27: 11689 3.27 - 3.82: 18935 3.82 - 4.36: 22548 4.36 - 4.90: 38398 Nonbonded interactions: 92114 Sorted by model distance: nonbonded pdb=" O LYS A 884 " pdb=" OG1 THR A 887 " model vdw 2.188 3.040 nonbonded pdb=" O SER A 560 " pdb=" OG SER A 560 " model vdw 2.196 3.040 nonbonded pdb=" O ILE A 263 " pdb=" OG1 THR A 267 " model vdw 2.242 3.040 nonbonded pdb=" O PHE A1095 " pdb=" OG SER A1100 " model vdw 2.249 3.040 nonbonded pdb=" OH TYR A 669 " pdb=" OG SER A 683 " model vdw 2.273 3.040 ... (remaining 92109 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.570 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: 0.410 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.580 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 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 : 0.003 0.052 11446 Z= 0.174 Angle : 0.668 10.627 15609 Z= 0.378 Chirality : 0.040 0.214 1729 Planarity : 0.005 0.068 1894 Dihedral : 16.723 117.518 4820 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.04 % Allowed : 19.60 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.46 (0.24), residues: 1318 helix: 1.60 (0.19), residues: 754 sheet: -0.97 (0.57), residues: 84 loop : -1.59 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 326 TYR 0.013 0.001 TYR A 958 PHE 0.024 0.001 PHE A 748 TRP 0.024 0.001 TRP A1148 HIS 0.010 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.17 (11441) covalent geometry : angle 0.66803 / 0.38 (15603) SS BOND : bond 0.00203 / 0.10 ( 3) SS BOND : angle 0.39994 / 0.22 ( 6) hydrogen bonds : bond 0.14962 / 9.86 ( 590) hydrogen bonds : angle 5.83912 / 4.03 ( 1713) Misc. bond : bond 0.00085 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7369 (mp0) REVERT: A 263 ILE cc_start: 0.7427 (mm) cc_final: 0.7164 (mm) REVERT: A 549 MET cc_start: 0.8490 (tpp) cc_final: 0.8085 (mmt) REVERT: A 687 TRP cc_start: 0.7995 (t-100) cc_final: 0.6838 (t-100) REVERT: A 688 TYR cc_start: 0.7643 (m-10) cc_final: 0.7395 (m-10) REVERT: A 1424 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7803 (pt0) REVERT: A 1459 TYR cc_start: 0.8115 (t80) cc_final: 0.7825 (t80) outliers start: 12 outliers final: 11 residues processed: 130 average time/residue: 0.1017 time to fit residues: 20.1375 Evaluate side-chains 126 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1126 ASN Chi-restraints excluded: chain A residue 1195 TRP Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1392 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 GLN A 343 GLN ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1127 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.152782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.118378 restraints weight = 34644.611| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.52 r_work: 0.3046 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11446 Z= 0.155 Angle : 0.620 10.334 15609 Z= 0.311 Chirality : 0.042 0.227 1729 Planarity : 0.005 0.050 1894 Dihedral : 11.177 95.355 2378 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.91 % Allowed : 19.25 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.52 (0.23), residues: 1318 helix: 1.61 (0.19), residues: 767 sheet: -1.05 (0.56), residues: 86 loop : -1.59 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 259 TYR 0.019 0.002 TYR A 958 PHE 0.020 0.002 PHE A1298 TRP 0.018 0.002 TRP A1148 HIS 0.008 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (11441) covalent geometry : angle 0.62046 / 0.31 (15603) SS BOND : bond 0.00277 / 0.14 ( 3) SS BOND : angle 0.60428 / 0.32 ( 6) hydrogen bonds : bond 0.04989 / 3.36 ( 590) hydrogen bonds : angle 4.61843 / 3.20 ( 1713) Misc. bond : bond 0.00087 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7697 (mp0) REVERT: A 263 ILE cc_start: 0.7362 (mm) cc_final: 0.7058 (mm) REVERT: A 687 TRP cc_start: 0.8228 (t-100) cc_final: 0.7135 (t-100) REVERT: A 688 TYR cc_start: 0.7741 (m-10) cc_final: 0.7494 (m-10) outliers start: 22 outliers final: 19 residues processed: 137 average time/residue: 0.1030 time to fit residues: 21.3041 Evaluate side-chains 132 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1064 GLN Chi-restraints excluded: chain A residue 1195 TRP Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1431 ILE Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 19 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 94 optimal weight: 0.0770 chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 20 optimal weight: 0.0980 chunk 106 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 GLN A 343 GLN A 420 GLN ** A 702 ASN ** 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 = 0.3737 r_free = 0.3737 target = 0.152094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.118972 restraints weight = 27516.842| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.91 r_work: 0.3121 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11446 Z= 0.140 Angle : 0.587 9.929 15609 Z= 0.292 Chirality : 0.041 0.229 1729 Planarity : 0.004 0.048 1894 Dihedral : 10.972 97.378 2369 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.08 % Allowed : 19.43 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.60 (0.23), residues: 1318 helix: 1.69 (0.19), residues: 765 sheet: -1.01 (0.56), residues: 86 loop : -1.57 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 425 TYR 0.017 0.001 TYR A 958 PHE 0.017 0.001 PHE A1298 TRP 0.019 0.001 TRP A1148 HIS 0.007 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (11441) covalent geometry : angle 0.58666 / 0.29 (15603) SS BOND : bond 0.00260 / 0.13 ( 3) SS BOND : angle 0.72691 / 0.36 ( 6) hydrogen bonds : bond 0.04788 / 3.23 ( 590) hydrogen bonds : angle 4.38903 / 3.04 ( 1713) Misc. bond : bond 0.00066 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 TRP cc_start: 0.7812 (t-100) cc_final: 0.7493 (t-100) REVERT: A 263 ILE cc_start: 0.7379 (mm) cc_final: 0.7052 (mm) REVERT: A 374 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7482 (m-30) REVERT: A 392 LYS cc_start: 0.8735 (mmtm) cc_final: 0.8462 (mmmt) REVERT: A 687 TRP cc_start: 0.8256 (t-100) cc_final: 0.7182 (t-100) REVERT: A 1272 SER cc_start: 0.8941 (m) cc_final: 0.8709 (p) REVERT: A 1459 TYR cc_start: 0.8628 (t80) cc_final: 0.8348 (t80) outliers start: 24 outliers final: 19 residues processed: 134 average time/residue: 0.1013 time to fit residues: 20.5026 Evaluate side-chains 130 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1064 GLN Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1431 ILE Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 71 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 3 optimal weight: 0.0060 chunk 132 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 GLN A 343 GLN ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.153602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.119673 restraints weight = 34988.723| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.48 r_work: 0.3036 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11446 Z= 0.121 Angle : 0.573 9.694 15609 Z= 0.284 Chirality : 0.041 0.232 1729 Planarity : 0.004 0.048 1894 Dihedral : 10.728 95.459 2367 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.82 % Allowed : 19.43 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.24), residues: 1318 helix: 1.82 (0.19), residues: 765 sheet: -1.07 (0.56), residues: 82 loop : -1.54 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 425 TYR 0.016 0.001 TYR A 439 PHE 0.015 0.001 PHE A1298 TRP 0.019 0.001 TRP A1148 HIS 0.006 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (11441) covalent geometry : angle 0.57347 / 0.28 (15603) SS BOND : bond 0.00214 / 0.11 ( 3) SS BOND : angle 0.62424 / 0.31 ( 6) hydrogen bonds : bond 0.04260 / 2.87 ( 590) hydrogen bonds : angle 4.24402 / 2.94 ( 1713) Misc. bond : bond 0.00061 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 TRP cc_start: 0.7793 (t-100) cc_final: 0.7488 (t-100) REVERT: A 263 ILE cc_start: 0.7402 (mm) cc_final: 0.7072 (mm) REVERT: A 374 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7516 (m-30) REVERT: A 392 LYS cc_start: 0.8657 (mmtm) cc_final: 0.8368 (mmmt) REVERT: A 687 TRP cc_start: 0.8266 (t-100) cc_final: 0.7217 (t-100) REVERT: A 875 ILE cc_start: 0.6344 (mm) cc_final: 0.6066 (mt) REVERT: A 1071 PHE cc_start: 0.7415 (t80) cc_final: 0.7204 (m-80) REVERT: A 1074 ARG cc_start: 0.8084 (ttp80) cc_final: 0.7440 (tmm-80) outliers start: 21 outliers final: 15 residues processed: 133 average time/residue: 0.1018 time to fit residues: 20.2616 Evaluate side-chains 123 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 805 MET Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1064 GLN Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1431 ILE Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 74 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 HIS A 319 GLN A 343 GLN ** A 702 ASN ** 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 = 0.3744 r_free = 0.3744 target = 0.153322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118852 restraints weight = 40435.868| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 4.05 r_work: 0.3017 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11446 Z= 0.122 Angle : 0.564 9.365 15609 Z= 0.280 Chirality : 0.041 0.234 1729 Planarity : 0.004 0.046 1894 Dihedral : 10.577 96.934 2367 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.99 % Allowed : 19.17 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.24), residues: 1318 helix: 1.85 (0.19), residues: 766 sheet: -0.95 (0.55), residues: 85 loop : -1.49 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 259 TYR 0.015 0.001 TYR A 958 PHE 0.015 0.001 PHE A1298 TRP 0.021 0.001 TRP A1148 HIS 0.006 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (11441) covalent geometry : angle 0.56369 / 0.28 (15603) SS BOND : bond 0.00203 / 0.10 ( 3) SS BOND : angle 0.62037 / 0.30 ( 6) hydrogen bonds : bond 0.04233 / 2.85 ( 590) hydrogen bonds : angle 4.15933 / 2.89 ( 1713) Misc. bond : bond 0.00059 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 93 TRP cc_start: 0.7738 (t-100) cc_final: 0.7412 (t-100) REVERT: A 236 ILE cc_start: 0.8349 (mm) cc_final: 0.8069 (mt) REVERT: A 263 ILE cc_start: 0.7433 (mm) cc_final: 0.7077 (mm) REVERT: A 392 LYS cc_start: 0.8520 (mmtm) cc_final: 0.8228 (mmmt) REVERT: A 687 TRP cc_start: 0.8287 (t-100) cc_final: 0.7206 (t-100) REVERT: A 875 ILE cc_start: 0.6285 (mm) cc_final: 0.6010 (mt) REVERT: A 1011 GLU cc_start: 0.7424 (mm-30) cc_final: 0.6624 (mm-30) REVERT: A 1074 ARG cc_start: 0.8054 (ttp80) cc_final: 0.7348 (tmm-80) outliers start: 23 outliers final: 18 residues processed: 131 average time/residue: 0.1053 time to fit residues: 20.6963 Evaluate side-chains 126 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 805 MET Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1064 GLN Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1431 ILE Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 42 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 37 optimal weight: 0.1980 chunk 73 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 319 GLN A 343 GLN A 702 ASN A1394 ASN A1412 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.152678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.118028 restraints weight = 43428.897| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.88 r_work: 0.3070 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (14 function evaluations) r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11446 Z= 0.124 Angle : 0.567 9.023 15609 Z= 0.282 Chirality : 0.041 0.235 1729 Planarity : 0.004 0.046 1894 Dihedral : 10.457 97.052 2366 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.08 % Allowed : 18.99 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.84 (0.24), residues: 1318 helix: 1.89 (0.19), residues: 764 sheet: -0.93 (0.55), residues: 85 loop : -1.45 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 296 TYR 0.015 0.001 TYR A 958 PHE 0.015 0.001 PHE A1298 TRP 0.021 0.001 TRP A1148 HIS 0.004 0.001 HIS A1098 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (11441) covalent geometry : angle 0.56653 / 0.28 (15603) SS BOND : bond 0.00211 / 0.11 ( 3) SS BOND : angle 0.62472 / 0.30 ( 6) hydrogen bonds : bond 0.04218 / 2.85 ( 590) hydrogen bonds : angle 4.13053 / 2.87 ( 1713) Misc. bond : bond 0.00068 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 31 PHE cc_start: 0.6220 (OUTLIER) cc_final: 0.5068 (m-80) REVERT: A 93 TRP cc_start: 0.7874 (t-100) cc_final: 0.7580 (t-100) REVERT: A 236 ILE cc_start: 0.8454 (mm) cc_final: 0.8169 (mt) REVERT: A 263 ILE cc_start: 0.7446 (mm) cc_final: 0.7081 (mm) REVERT: A 392 LYS cc_start: 0.8517 (mmtm) cc_final: 0.8244 (mmmt) REVERT: A 687 TRP cc_start: 0.8313 (t-100) cc_final: 0.7278 (t-100) REVERT: A 875 ILE cc_start: 0.6487 (mm) cc_final: 0.6206 (mt) REVERT: A 1074 ARG cc_start: 0.8100 (ttp80) cc_final: 0.7414 (tmm-80) outliers start: 24 outliers final: 20 residues processed: 137 average time/residue: 0.1019 time to fit residues: 20.9751 Evaluate side-chains 134 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 805 MET Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1064 GLN Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1431 ILE Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 114 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 0.2980 chunk 120 optimal weight: 0.0870 chunk 128 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 29 optimal weight: 0.4980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 GLN A1073 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.154268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.119961 restraints weight = 43314.904| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 4.22 r_work: 0.3026 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11446 Z= 0.112 Angle : 0.560 8.760 15609 Z= 0.279 Chirality : 0.040 0.234 1729 Planarity : 0.004 0.045 1894 Dihedral : 10.297 96.529 2366 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.82 % Allowed : 19.17 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.24), residues: 1318 helix: 1.98 (0.19), residues: 766 sheet: -0.87 (0.57), residues: 83 loop : -1.44 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 425 TYR 0.018 0.001 TYR A 986 PHE 0.014 0.001 PHE A1298 TRP 0.022 0.001 TRP A1148 HIS 0.004 0.001 HIS A1098 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (11441) covalent geometry : angle 0.55954 / 0.28 (15603) SS BOND : bond 0.00194 / 0.10 ( 3) SS BOND : angle 0.57341 / 0.28 ( 6) hydrogen bonds : bond 0.03932 / 2.66 ( 590) hydrogen bonds : angle 4.07462 / 2.82 ( 1713) Misc. bond : bond 0.00051 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 PHE cc_start: 0.6202 (OUTLIER) cc_final: 0.4996 (m-80) REVERT: A 93 TRP cc_start: 0.7752 (t-100) cc_final: 0.7441 (t-100) REVERT: A 236 ILE cc_start: 0.8317 (mm) cc_final: 0.8045 (mt) REVERT: A 263 ILE cc_start: 0.7483 (mm) cc_final: 0.7121 (mm) REVERT: A 392 LYS cc_start: 0.8396 (mmtm) cc_final: 0.8122 (mmmt) REVERT: A 687 TRP cc_start: 0.8273 (t-100) cc_final: 0.7251 (t-100) REVERT: A 875 ILE cc_start: 0.6366 (mm) cc_final: 0.6100 (mt) REVERT: A 1002 GLN cc_start: 0.8130 (mt0) cc_final: 0.7774 (mm-40) outliers start: 21 outliers final: 17 residues processed: 132 average time/residue: 0.1021 time to fit residues: 20.2789 Evaluate side-chains 135 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 805 MET Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1431 ILE Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 75 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.151794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.118178 restraints weight = 31574.299| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.23 r_work: 0.3069 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11446 Z= 0.134 Angle : 0.577 8.413 15609 Z= 0.290 Chirality : 0.041 0.231 1729 Planarity : 0.004 0.045 1894 Dihedral : 10.384 98.905 2366 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.82 % Allowed : 19.17 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.24), residues: 1318 helix: 1.93 (0.19), residues: 767 sheet: -0.81 (0.57), residues: 82 loop : -1.46 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1074 TYR 0.034 0.001 TYR A 986 PHE 0.016 0.001 PHE A1071 TRP 0.023 0.001 TRP A1148 HIS 0.004 0.001 HIS A1098 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (11441) covalent geometry : angle 0.57691 / 0.29 (15603) SS BOND : bond 0.00214 / 0.11 ( 3) SS BOND : angle 0.66212 / 0.32 ( 6) hydrogen bonds : bond 0.04299 / 2.91 ( 590) hydrogen bonds : angle 4.10409 / 2.84 ( 1713) Misc. bond : bond 0.00074 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 PHE cc_start: 0.6242 (OUTLIER) cc_final: 0.4997 (m-80) REVERT: A 93 TRP cc_start: 0.7822 (t-100) cc_final: 0.7526 (t-100) REVERT: A 236 ILE cc_start: 0.8365 (mm) cc_final: 0.8095 (mt) REVERT: A 263 ILE cc_start: 0.7476 (mm) cc_final: 0.7117 (mm) REVERT: A 392 LYS cc_start: 0.8374 (mmtm) cc_final: 0.8114 (mmmt) REVERT: A 687 TRP cc_start: 0.8317 (t-100) cc_final: 0.7232 (t-100) REVERT: A 875 ILE cc_start: 0.6440 (mm) cc_final: 0.6179 (mt) REVERT: A 986 TYR cc_start: 0.6998 (p90) cc_final: 0.6652 (p90) REVERT: A 1002 GLN cc_start: 0.8158 (mt0) cc_final: 0.7642 (mm-40) outliers start: 21 outliers final: 17 residues processed: 131 average time/residue: 0.0999 time to fit residues: 19.7041 Evaluate side-chains 131 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 805 MET Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1431 ILE Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 127 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 chunk 31 optimal weight: 0.9980 chunk 4 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.153354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.117441 restraints weight = 49504.370| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 4.38 r_work: 0.3011 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11446 Z= 0.115 Angle : 0.559 8.172 15609 Z= 0.280 Chirality : 0.040 0.229 1729 Planarity : 0.004 0.045 1894 Dihedral : 10.324 97.786 2366 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.65 % Allowed : 19.17 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.24), residues: 1318 helix: 1.97 (0.19), residues: 764 sheet: -0.83 (0.56), residues: 82 loop : -1.44 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1074 TYR 0.027 0.001 TYR A 986 PHE 0.016 0.001 PHE A1071 TRP 0.023 0.001 TRP A1148 HIS 0.007 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (11441) covalent geometry : angle 0.55875 / 0.28 (15603) SS BOND : bond 0.00197 / 0.10 ( 3) SS BOND : angle 0.60726 / 0.30 ( 6) hydrogen bonds : bond 0.04016 / 2.73 ( 590) hydrogen bonds : angle 4.07591 / 2.82 ( 1713) Misc. bond : bond 0.00066 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 PHE cc_start: 0.6255 (OUTLIER) cc_final: 0.4277 (m-80) REVERT: A 93 TRP cc_start: 0.7803 (t-100) cc_final: 0.7515 (t-100) REVERT: A 236 ILE cc_start: 0.8336 (mm) cc_final: 0.8069 (mt) REVERT: A 263 ILE cc_start: 0.7514 (mm) cc_final: 0.7186 (mm) REVERT: A 392 LYS cc_start: 0.8317 (mmtm) cc_final: 0.8041 (mmmt) REVERT: A 687 TRP cc_start: 0.8332 (t-100) cc_final: 0.7285 (t-100) REVERT: A 875 ILE cc_start: 0.6371 (mm) cc_final: 0.6111 (mt) REVERT: A 986 TYR cc_start: 0.7024 (p90) cc_final: 0.6742 (p90) REVERT: A 1002 GLN cc_start: 0.8154 (mt0) cc_final: 0.7608 (mm-40) REVERT: A 1071 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.7099 (m-80) outliers start: 19 outliers final: 16 residues processed: 134 average time/residue: 0.0948 time to fit residues: 19.1719 Evaluate side-chains 135 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 805 MET Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1071 PHE Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1431 ILE Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 131 optimal weight: 0.8980 chunk 78 optimal weight: 0.0570 chunk 49 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.153919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119747 restraints weight = 40990.150| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.89 r_work: 0.3040 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11446 Z= 0.115 Angle : 0.557 7.864 15609 Z= 0.279 Chirality : 0.040 0.226 1729 Planarity : 0.004 0.045 1894 Dihedral : 10.322 98.576 2366 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.65 % Allowed : 19.51 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.00 (0.24), residues: 1318 helix: 2.01 (0.19), residues: 767 sheet: -0.81 (0.56), residues: 82 loop : -1.40 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1074 TYR 0.026 0.001 TYR A 986 PHE 0.014 0.001 PHE A1071 TRP 0.024 0.001 TRP A1148 HIS 0.008 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (11441) covalent geometry : angle 0.55662 / 0.28 (15603) SS BOND : bond 0.00202 / 0.10 ( 3) SS BOND : angle 0.56967 / 0.28 ( 6) hydrogen bonds : bond 0.03948 / 2.68 ( 590) hydrogen bonds : angle 4.04754 / 2.80 ( 1713) Misc. bond : bond 0.00057 / 0.03 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 PHE cc_start: 0.5814 (OUTLIER) cc_final: 0.4293 (m-80) REVERT: A 93 TRP cc_start: 0.7807 (t-100) cc_final: 0.7575 (t-100) REVERT: A 209 THR cc_start: 0.7847 (p) cc_final: 0.7094 (t) REVERT: A 236 ILE cc_start: 0.8336 (mm) cc_final: 0.8070 (mt) REVERT: A 263 ILE cc_start: 0.7498 (mm) cc_final: 0.7190 (mm) REVERT: A 392 LYS cc_start: 0.8275 (mmtm) cc_final: 0.8001 (mmmt) REVERT: A 549 MET cc_start: 0.8642 (tpp) cc_final: 0.8352 (mmt) REVERT: A 687 TRP cc_start: 0.8334 (t-100) cc_final: 0.7273 (t-100) REVERT: A 875 ILE cc_start: 0.6386 (mm) cc_final: 0.6131 (mt) REVERT: A 986 TYR cc_start: 0.7018 (p90) cc_final: 0.6735 (p90) REVERT: A 1002 GLN cc_start: 0.8157 (mt0) cc_final: 0.7573 (mm-40) REVERT: A 1401 ASN cc_start: 0.7762 (t0) cc_final: 0.7333 (t0) outliers start: 19 outliers final: 16 residues processed: 136 average time/residue: 0.1004 time to fit residues: 20.7984 Evaluate side-chains 138 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 805 MET Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1001 GLU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1431 ILE Chi-restraints excluded: chain A residue 1442 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 63 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 76 optimal weight: 0.4980 chunk 74 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 121 optimal weight: 0.0000 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.154630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.120835 restraints weight = 37114.306| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.67 r_work: 0.3078 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (12 function evaluations) r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11446 Z= 0.112 Angle : 0.566 13.205 15609 Z= 0.285 Chirality : 0.040 0.223 1729 Planarity : 0.004 0.045 1894 Dihedral : 10.312 98.584 2366 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.39 % Allowed : 19.77 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.05 (0.24), residues: 1318 helix: 2.04 (0.19), residues: 767 sheet: -0.84 (0.56), residues: 82 loop : -1.36 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1074 TYR 0.024 0.001 TYR A 986 PHE 0.019 0.001 PHE A1071 TRP 0.023 0.001 TRP A1148 HIS 0.006 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (11441) covalent geometry : angle 0.56647 / 0.28 (15603) SS BOND : bond 0.00192 / 0.10 ( 3) SS BOND : angle 0.54945 / 0.28 ( 6) hydrogen bonds : bond 0.03858 / 2.62 ( 590) hydrogen bonds : angle 4.02491 / 2.79 ( 1713) Misc. bond : bond 0.00071 / 0.03 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3067.47 seconds wall clock time: 53 minutes 36.61 seconds (3216.61 seconds total)