Starting phenix.real_space_refine on Wed Aug 5 18:24:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mku_48338/08_2026/9mku_48338.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mku_48338/08_2026/9mku_48338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mku_48338/08_2026/9mku_48338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mku_48338/08_2026/9mku_48338.map" model { file = "/net/cci-nas-00/data/ceres_data/9mku_48338/08_2026/9mku_48338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mku_48338/08_2026/9mku_48338.cif" } resolution = 4.0 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 21 5.16 5 C 6766 2.51 5 N 1769 2.21 5 O 2143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10735 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 596 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 8, 'rna3p': 19} Chain: "C" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 161 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 9978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1207, 9978 Classifications: {'peptide': 1207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 1179} Chain breaks: 9 Time building chain proxies: 2.48, per 1000 atoms: 0.23 Number of scatterers: 10735 At special positions: 0 Unit cell: (98.04, 110.08, 135.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 36 15.00 O 2143 8.00 N 1769 7.00 C 6766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 483.8 milliseconds 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2320 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 11 sheets defined 51.8% alpha, 9.9% beta 12 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 35 through 66 removed outlier: 3.587A pdb=" N ASP A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 72 through 86 Processing helix chain 'A' and resid 91 through 116 removed outlier: 3.944A pdb=" N GLN A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 removed outlier: 3.594A pdb=" N LYS A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 121' Processing helix chain 'A' and resid 124 through 128 Processing helix chain 'A' and resid 136 through 148 Processing helix chain 'A' and resid 161 through 171 removed outlier: 3.824A pdb=" N ALA A 165 " --> pdb=" O ASP A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 178 Processing helix chain 'A' and resid 179 through 188 Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 206 through 225 removed outlier: 3.577A pdb=" N LYS A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 238 Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.589A pdb=" N GLU A 265 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 273 removed outlier: 3.996A pdb=" N ASN A 270 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 273 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 286 Processing helix chain 'A' and resid 299 through 311 Processing helix chain 'A' and resid 344 through 362 removed outlier: 4.395A pdb=" N VAL A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A 353 " --> pdb=" O VAL A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 383 Processing helix chain 'A' and resid 398 through 406 removed outlier: 3.917A pdb=" N LEU A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 Processing helix chain 'A' and resid 453 through 465 Processing helix chain 'A' and resid 474 through 484 removed outlier: 4.057A pdb=" N ILE A 478 " --> pdb=" O ARG A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 505 removed outlier: 3.915A pdb=" N PHE A 489 " --> pdb=" O ILE A 485 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN A 501 " --> pdb=" O ASP A 497 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE A 504 " --> pdb=" O ALA A 500 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS A 505 " --> pdb=" O GLN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 518 removed outlier: 3.978A pdb=" N LEU A 515 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ALA A 517 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N SER A 518 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 540 removed outlier: 3.594A pdb=" N GLN A 532 " --> pdb=" O ASP A 528 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 573 removed outlier: 3.742A pdb=" N CYS A 568 " --> pdb=" O VAL A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 586 removed outlier: 4.209A pdb=" N LEU A 578 " --> pdb=" O ASN A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 618 Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 667 through 674 removed outlier: 3.555A pdb=" N PHE A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 683 Processing helix chain 'A' and resid 685 through 694 Processing helix chain 'A' and resid 713 through 731 Processing helix chain 'A' and resid 732 through 736 removed outlier: 3.539A pdb=" N LYS A 735 " --> pdb=" O PRO A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 754 removed outlier: 3.633A pdb=" N PHE A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 781 removed outlier: 3.689A pdb=" N ILE A 774 " --> pdb=" O SER A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 812 removed outlier: 4.249A pdb=" N PHE A 812 " --> pdb=" O TRP A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 819 Processing helix chain 'A' and resid 870 through 875 removed outlier: 3.978A pdb=" N GLU A 875 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 907 Processing helix chain 'A' and resid 952 through 964 Processing helix chain 'A' and resid 977 through 1000 Processing helix chain 'A' and resid 1019 through 1036 Processing helix chain 'A' and resid 1101 through 1110 Processing helix chain 'A' and resid 1169 through 1181 Processing helix chain 'A' and resid 1191 through 1198 Processing helix chain 'A' and resid 1200 through 1215 removed outlier: 3.645A pdb=" N LEU A1215 " --> pdb=" O LEU A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1275 removed outlier: 3.508A pdb=" N ASN A1275 " --> pdb=" O GLY A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1296 removed outlier: 3.805A pdb=" N GLN A1296 " --> pdb=" O PHE A1292 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 18 Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 18 removed outlier: 3.737A pdb=" N HIS A 881 " --> pdb=" O GLU A 829 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU A 829 " --> pdb=" O HIS A 881 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 21 through 23 removed outlier: 4.618A pdb=" N TYR A 628 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A 631 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 620 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 12.057A pdb=" N ALA A 619 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N TYR A 659 " --> pdb=" O ALA A 619 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU A 621 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE A 657 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE A 623 " --> pdb=" O LYS A 655 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 655 " --> pdb=" O ILE A 623 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 244 Processing sheet with id=AA5, first strand: chain 'A' and resid 287 through 288 removed outlier: 3.731A pdb=" N LYS A 288 " --> pdb=" O ARG A 297 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA7, first strand: chain 'A' and resid 848 through 850 Processing sheet with id=AA8, first strand: chain 'A' and resid 935 through 940 removed outlier: 6.839A pdb=" N HIS A 912 " --> pdb=" O ILE A1002 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N VAL A1004 " --> pdb=" O HIS A 912 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A 914 " --> pdb=" O VAL A1004 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N GLU A1006 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 9.604A pdb=" N ILE A 916 " --> pdb=" O GLU A1006 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1114 through 1118 Processing sheet with id=AB1, first strand: chain 'A' and resid 1150 through 1153 Processing sheet with id=AB2, first strand: chain 'A' and resid 1218 through 1219 450 hydrogen bonds defined for protein. 1290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 1.28 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: 3166 1.34 - 1.45: 1908 1.45 - 1.57: 5839 1.57 - 1.69: 70 1.69 - 1.81: 33 Bond restraints: 11016 Sorted by residual: bond pdb=" N GLU A1189 " pdb=" CA GLU A1189 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.88e+00 bond pdb=" N CYS A1190 " pdb=" CA CYS A1190 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.31e-02 5.83e+03 7.76e+00 bond pdb=" N ILE A 421 " pdb=" CA ILE A 421 " ideal model delta sigma weight residual 1.462 1.491 -0.029 1.18e-02 7.18e+03 6.14e+00 bond pdb=" N ILE A1191 " pdb=" CA ILE A1191 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.25e-02 6.40e+03 5.72e+00 bond pdb=" N ILE A 425 " pdb=" CA ILE A 425 " ideal model delta sigma weight residual 1.461 1.488 -0.027 1.17e-02 7.31e+03 5.37e+00 ... (remaining 11011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 14881 2.76 - 5.51: 73 5.51 - 8.27: 4 8.27 - 11.03: 1 11.03 - 13.78: 1 Bond angle restraints: 14960 Sorted by residual: angle pdb=" N GLN A 424 " pdb=" CA GLN A 424 " pdb=" C GLN A 424 " ideal model delta sigma weight residual 112.45 98.67 13.78 1.39e+00 5.18e-01 9.83e+01 angle pdb=" N GLN A 423 " pdb=" CA GLN A 423 " pdb=" C GLN A 423 " ideal model delta sigma weight residual 111.28 119.54 -8.26 1.09e+00 8.42e-01 5.74e+01 angle pdb=" C GLN A 423 " pdb=" CA GLN A 423 " pdb=" CB GLN A 423 " ideal model delta sigma weight residual 110.79 100.78 10.01 1.66e+00 3.63e-01 3.64e+01 angle pdb=" N3 DT C -1 " pdb=" C4 DT C -1 " pdb=" O4 DT C -1 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT C -8 " pdb=" C4 DT C -8 " pdb=" O4 DT C -8 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 14955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 5995 17.87 - 35.75: 501 35.75 - 53.62: 121 53.62 - 71.49: 71 71.49 - 89.36: 10 Dihedral angle restraints: 6698 sinusoidal: 3116 harmonic: 3582 Sorted by residual: dihedral pdb=" CA LYS A 973 " pdb=" C LYS A 973 " pdb=" N ILE A 974 " pdb=" CA ILE A 974 " ideal model delta harmonic sigma weight residual 180.00 159.57 20.43 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASP A 205 " pdb=" CB ASP A 205 " pdb=" CG ASP A 205 " pdb=" OD1 ASP A 205 " ideal model delta sinusoidal sigma weight residual -30.00 -86.98 56.98 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CB GLU A 829 " pdb=" CG GLU A 829 " pdb=" CD GLU A 829 " pdb=" OE1 GLU A 829 " ideal model delta sinusoidal sigma weight residual 0.00 89.36 -89.36 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 6695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1389 0.059 - 0.118: 202 0.118 - 0.177: 34 0.177 - 0.236: 4 0.236 - 0.295: 1 Chirality restraints: 1630 Sorted by residual: chirality pdb=" CA GLN A 424 " pdb=" N GLN A 424 " pdb=" C GLN A 424 " pdb=" CB GLN A 424 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA ILE A1191 " pdb=" N ILE A1191 " pdb=" C ILE A1191 " pdb=" CB ILE A1191 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ILE A 425 " pdb=" N ILE A 425 " pdb=" C ILE A 425 " pdb=" CB ILE A 425 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1627 not shown) Planarity restraints: 1786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A1188 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C GLY A1188 " -0.041 2.00e-02 2.50e+03 pdb=" O GLY A1188 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU A1189 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 987 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C GLN A 987 " 0.034 2.00e-02 2.50e+03 pdb=" O GLN A 987 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL A 988 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 986 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" C SER A 986 " -0.034 2.00e-02 2.50e+03 pdb=" O SER A 986 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN A 987 " 0.011 2.00e-02 2.50e+03 ... (remaining 1783 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 981 2.74 - 3.28: 11591 3.28 - 3.82: 18608 3.82 - 4.36: 21694 4.36 - 4.90: 33838 Nonbonded interactions: 86712 Sorted by model distance: nonbonded pdb=" O PHE A1147 " pdb=" NH1 ARG A1150 " model vdw 2.201 3.120 nonbonded pdb=" NE2 GLN A1106 " pdb=" O CYS A1196 " model vdw 2.211 3.120 nonbonded pdb=" O GLY A 286 " pdb=" NZ LYS A 296 " model vdw 2.255 3.120 nonbonded pdb=" OH TYR A1181 " pdb=" OD2 ASP A1200 " model vdw 2.256 3.040 nonbonded pdb=" ND2 ASN A 156 " pdb=" OD1 ASP A 158 " model vdw 2.263 3.120 ... (remaining 86707 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.650 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 0.036 11016 Z= 0.187 Angle : 0.577 13.782 14960 Z= 0.393 Chirality : 0.044 0.295 1630 Planarity : 0.003 0.035 1786 Dihedral : 15.485 89.364 4378 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.39 % Favored : 94.52 % Rotamer: Outliers : 0.27 % Allowed : 1.00 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.24), residues: 1187 helix: 0.62 (0.22), residues: 555 sheet: -0.88 (0.48), residues: 122 loop : -0.79 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 583 TYR 0.015 0.001 TYR A 79 PHE 0.028 0.001 PHE A 720 TRP 0.007 0.001 TRP A1142 HIS 0.005 0.001 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.19 (11016) covalent geometry : angle 0.57738 / 0.39 (14960) hydrogen bonds : bond 0.16616 / 16.95 ( 476) hydrogen bonds : angle 6.03963 / 7.75 ( 1342) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 331 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.9214 (m-80) cc_final: 0.8292 (m-80) REVERT: A 46 ASP cc_start: 0.9462 (m-30) cc_final: 0.9185 (t0) REVERT: A 65 ILE cc_start: 0.9421 (tp) cc_final: 0.9187 (pt) REVERT: A 138 LEU cc_start: 0.9304 (mt) cc_final: 0.9030 (mt) REVERT: A 175 TRP cc_start: 0.8257 (m100) cc_final: 0.6790 (m-10) REVERT: A 312 ASN cc_start: 0.9164 (t0) cc_final: 0.8915 (m-40) REVERT: A 366 GLU cc_start: 0.9470 (mm-30) cc_final: 0.9034 (pm20) REVERT: A 378 PHE cc_start: 0.9331 (m-10) cc_final: 0.8938 (m-80) REVERT: A 389 SER cc_start: 0.9028 (p) cc_final: 0.8460 (p) REVERT: A 487 MET cc_start: 0.9362 (ptt) cc_final: 0.8682 (tpt) REVERT: A 536 LEU cc_start: 0.9736 (tp) cc_final: 0.9468 (mt) REVERT: A 595 LYS cc_start: 0.8723 (mtpp) cc_final: 0.8505 (mtpp) REVERT: A 647 LYS cc_start: 0.9485 (tppt) cc_final: 0.9281 (mmmt) REVERT: A 659 TYR cc_start: 0.9276 (t80) cc_final: 0.8821 (t80) REVERT: A 668 MET cc_start: 0.9537 (mmp) cc_final: 0.9282 (mmm) REVERT: A 746 ARG cc_start: 0.9204 (ttm170) cc_final: 0.8978 (mtm-85) REVERT: A 811 LEU cc_start: 0.9175 (mt) cc_final: 0.8921 (mt) REVERT: A 868 ILE cc_start: 0.9152 (mt) cc_final: 0.8901 (mm) REVERT: A 949 MET cc_start: 0.5977 (pmm) cc_final: 0.5776 (pmm) REVERT: A 971 TRP cc_start: 0.9446 (t60) cc_final: 0.9091 (t60) REVERT: A 1026 LYS cc_start: 0.9479 (tppt) cc_final: 0.9250 (tppt) REVERT: A 1067 MET cc_start: 0.8568 (mtm) cc_final: 0.8216 (mtt) REVERT: A 1100 GLU cc_start: 0.9715 (mt-10) cc_final: 0.9445 (mm-30) REVERT: A 1218 ARG cc_start: 0.8957 (ttm170) cc_final: 0.8134 (tpt170) REVERT: A 1250 MET cc_start: 0.8475 (mmm) cc_final: 0.7711 (mmm) outliers start: 3 outliers final: 1 residues processed: 334 average time/residue: 0.1379 time to fit residues: 61.1464 Evaluate side-chains 215 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1190 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.0470 chunk 97 optimal weight: 0.4980 chunk 113 optimal weight: 0.4980 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.0670 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 overall best weight: 1.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 ASN A 188 ASN A 214 ASN A 274 ASN ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN A 424 GLN A 508 ASN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN A 683 ASN A 835 GLN A 853 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.111047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.090218 restraints weight = 52422.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.092153 restraints weight = 40479.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.093420 restraints weight = 32816.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.094131 restraints weight = 28226.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.094987 restraints weight = 25601.468| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11016 Z= 0.167 Angle : 0.705 11.425 14960 Z= 0.374 Chirality : 0.043 0.225 1630 Planarity : 0.004 0.045 1786 Dihedral : 13.056 80.857 1798 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.73 % Favored : 94.19 % Rotamer: Outliers : 3.00 % Allowed : 12.92 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.24), residues: 1187 helix: 0.44 (0.21), residues: 566 sheet: -0.39 (0.54), residues: 104 loop : -0.84 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 921 TYR 0.024 0.002 TYR A 807 PHE 0.025 0.002 PHE A 880 TRP 0.017 0.003 TRP A 734 HIS 0.009 0.002 HIS A 731 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (11016) covalent geometry : angle 0.70450 / 0.37 (14960) hydrogen bonds : bond 0.05611 / 5.79 ( 476) hydrogen bonds : angle 5.15854 / 6.51 ( 1342) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 233 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.9115 (m-80) cc_final: 0.8207 (m-80) REVERT: A 61 PHE cc_start: 0.9172 (t80) cc_final: 0.8961 (t80) REVERT: A 65 ILE cc_start: 0.9399 (tp) cc_final: 0.9118 (pt) REVERT: A 138 LEU cc_start: 0.9215 (mt) cc_final: 0.9002 (mt) REVERT: A 312 ASN cc_start: 0.9077 (t0) cc_final: 0.8848 (m-40) REVERT: A 366 GLU cc_start: 0.9390 (mm-30) cc_final: 0.9084 (pm20) REVERT: A 595 LYS cc_start: 0.8759 (mtpp) cc_final: 0.8547 (mtpp) REVERT: A 647 LYS cc_start: 0.9475 (tppt) cc_final: 0.9233 (mmmt) REVERT: A 659 TYR cc_start: 0.9148 (t80) cc_final: 0.8672 (t80) REVERT: A 668 MET cc_start: 0.9537 (mmp) cc_final: 0.9178 (mmm) REVERT: A 746 ARG cc_start: 0.9241 (ttm170) cc_final: 0.8854 (ptp-110) REVERT: A 811 LEU cc_start: 0.9094 (mt) cc_final: 0.8835 (mt) REVERT: A 831 PHE cc_start: 0.9380 (m-80) cc_final: 0.9167 (m-80) REVERT: A 868 ILE cc_start: 0.9046 (mt) cc_final: 0.8833 (mm) REVERT: A 949 MET cc_start: 0.6140 (pmm) cc_final: 0.5905 (pmm) REVERT: A 971 TRP cc_start: 0.9403 (t60) cc_final: 0.9077 (t60) REVERT: A 976 ASN cc_start: 0.8966 (m-40) cc_final: 0.7907 (t0) REVERT: A 980 MET cc_start: 0.8847 (mmp) cc_final: 0.8598 (mmp) REVERT: A 1007 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7033 (m-30) REVERT: A 1100 GLU cc_start: 0.9708 (mt-10) cc_final: 0.9362 (mm-30) REVERT: A 1250 MET cc_start: 0.8314 (mmm) cc_final: 0.7776 (mmm) outliers start: 33 outliers final: 20 residues processed: 249 average time/residue: 0.1223 time to fit residues: 41.6775 Evaluate side-chains 219 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1190 CYS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1283 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN A 305 ASN A 538 HIS ** A 588 GLN ** 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 = 0.4017 r_free = 0.4017 target = 0.110142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.089963 restraints weight = 53741.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.091803 restraints weight = 41115.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.093251 restraints weight = 33132.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.094199 restraints weight = 27994.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.094882 restraints weight = 24805.425| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11016 Z= 0.148 Angle : 0.674 11.864 14960 Z= 0.356 Chirality : 0.042 0.226 1630 Planarity : 0.004 0.052 1786 Dihedral : 12.951 80.126 1798 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.14 % Favored : 94.78 % Rotamer: Outliers : 3.18 % Allowed : 15.38 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.23), residues: 1187 helix: 0.34 (0.21), residues: 567 sheet: -0.39 (0.54), residues: 104 loop : -0.90 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 43 TYR 0.028 0.002 TYR A1024 PHE 0.031 0.002 PHE A 211 TRP 0.035 0.003 TRP A 175 HIS 0.006 0.001 HIS A 731 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (11016) covalent geometry : angle 0.67446 / 0.36 (14960) hydrogen bonds : bond 0.04990 / 5.18 ( 476) hydrogen bonds : angle 4.96696 / 6.30 ( 1342) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.9052 (m-80) cc_final: 0.8173 (m-80) REVERT: A 65 ILE cc_start: 0.9403 (tp) cc_final: 0.9092 (pt) REVERT: A 138 LEU cc_start: 0.9252 (mt) cc_final: 0.9044 (mt) REVERT: A 366 GLU cc_start: 0.9384 (mm-30) cc_final: 0.9100 (pm20) REVERT: A 595 LYS cc_start: 0.8759 (mtpp) cc_final: 0.8539 (mtpp) REVERT: A 647 LYS cc_start: 0.9492 (tppt) cc_final: 0.9285 (mmmt) REVERT: A 659 TYR cc_start: 0.9186 (t80) cc_final: 0.8872 (t80) REVERT: A 746 ARG cc_start: 0.9213 (ttm170) cc_final: 0.8837 (ptp-110) REVERT: A 811 LEU cc_start: 0.9052 (mt) cc_final: 0.8802 (mt) REVERT: A 831 PHE cc_start: 0.9374 (m-80) cc_final: 0.9103 (m-80) REVERT: A 870 ASP cc_start: 0.8841 (m-30) cc_final: 0.8408 (t0) REVERT: A 949 MET cc_start: 0.6133 (pmm) cc_final: 0.5879 (pmm) REVERT: A 965 ASP cc_start: 0.8258 (t70) cc_final: 0.7699 (m-30) REVERT: A 971 TRP cc_start: 0.9370 (t60) cc_final: 0.9065 (t60) REVERT: A 976 ASN cc_start: 0.9028 (m-40) cc_final: 0.7975 (t0) REVERT: A 1007 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7040 (m-30) REVERT: A 1067 MET cc_start: 0.7286 (mtt) cc_final: 0.6841 (mmt) REVERT: A 1100 GLU cc_start: 0.9717 (mt-10) cc_final: 0.9382 (mm-30) REVERT: A 1250 MET cc_start: 0.8411 (mmm) cc_final: 0.7918 (mmm) REVERT: A 1289 GLU cc_start: 0.9153 (mp0) cc_final: 0.8772 (mp0) outliers start: 35 outliers final: 23 residues processed: 229 average time/residue: 0.1056 time to fit residues: 33.4512 Evaluate side-chains 213 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 734 TRP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1283 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 0.0270 chunk 30 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.9842 ------------------------------------------------------------------------------- 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 = 0.4184 r_free = 0.4184 target = 0.114713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.094286 restraints weight = 52842.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.096534 restraints weight = 35328.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.098143 restraints weight = 27147.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.099213 restraints weight = 22289.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.100043 restraints weight = 19351.821| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11016 Z= 0.141 Angle : 0.664 11.161 14960 Z= 0.349 Chirality : 0.042 0.272 1630 Planarity : 0.005 0.116 1786 Dihedral : 12.910 84.654 1797 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.39 % Favored : 94.52 % Rotamer: Outliers : 3.00 % Allowed : 16.92 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.24), residues: 1187 helix: 0.36 (0.21), residues: 565 sheet: -0.49 (0.52), residues: 106 loop : -0.92 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 583 TYR 0.023 0.002 TYR A 984 PHE 0.031 0.002 PHE A 880 TRP 0.042 0.003 TRP A 175 HIS 0.006 0.001 HIS A 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (11016) covalent geometry : angle 0.66367 / 0.35 (14960) hydrogen bonds : bond 0.04732 / 4.90 ( 476) hydrogen bonds : angle 4.85701 / 6.19 ( 1342) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.9174 (m-80) cc_final: 0.8309 (m-80) REVERT: A 65 ILE cc_start: 0.9441 (tp) cc_final: 0.9168 (pt) REVERT: A 138 LEU cc_start: 0.9306 (mt) cc_final: 0.9096 (mt) REVERT: A 166 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9079 (mt) REVERT: A 366 GLU cc_start: 0.9463 (mm-30) cc_final: 0.9210 (pm20) REVERT: A 498 ASN cc_start: 0.9508 (t0) cc_final: 0.9167 (m-40) REVERT: A 595 LYS cc_start: 0.8870 (mtpp) cc_final: 0.8635 (mtpp) REVERT: A 643 ASP cc_start: 0.9277 (p0) cc_final: 0.8845 (p0) REVERT: A 659 TYR cc_start: 0.9159 (t80) cc_final: 0.8687 (t80) REVERT: A 746 ARG cc_start: 0.9190 (ttm170) cc_final: 0.8844 (ptp-110) REVERT: A 811 LEU cc_start: 0.9088 (mt) cc_final: 0.8828 (mt) REVERT: A 870 ASP cc_start: 0.8809 (m-30) cc_final: 0.8380 (t0) REVERT: A 971 TRP cc_start: 0.9240 (t60) cc_final: 0.8926 (t60) REVERT: A 976 ASN cc_start: 0.9102 (m-40) cc_final: 0.8128 (t0) REVERT: A 980 MET cc_start: 0.8799 (mmp) cc_final: 0.8593 (mmp) REVERT: A 1007 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7202 (m-30) REVERT: A 1008 LEU cc_start: 0.4955 (mt) cc_final: 0.3696 (mm) REVERT: A 1100 GLU cc_start: 0.9636 (mt-10) cc_final: 0.9344 (mm-30) REVERT: A 1250 MET cc_start: 0.8423 (mmm) cc_final: 0.7927 (mmm) REVERT: A 1272 ARG cc_start: 0.9428 (OUTLIER) cc_final: 0.8999 (ptm160) outliers start: 33 outliers final: 17 residues processed: 225 average time/residue: 0.1036 time to fit residues: 32.5258 Evaluate side-chains 208 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1272 ARG Chi-restraints excluded: chain A residue 1283 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 74 optimal weight: 9.9990 chunk 46 optimal weight: 0.0370 chunk 78 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.110602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.090616 restraints weight = 54914.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.092330 restraints weight = 42551.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.093305 restraints weight = 34332.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.094389 restraints weight = 30046.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.095059 restraints weight = 26676.991| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11016 Z= 0.134 Angle : 0.660 15.702 14960 Z= 0.340 Chirality : 0.041 0.270 1630 Planarity : 0.004 0.073 1786 Dihedral : 12.872 83.536 1797 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.69 % Rotamer: Outliers : 2.37 % Allowed : 19.20 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.23), residues: 1187 helix: 0.42 (0.21), residues: 564 sheet: -0.47 (0.52), residues: 106 loop : -0.98 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 202 TYR 0.021 0.002 TYR A 773 PHE 0.032 0.002 PHE A 880 TRP 0.035 0.003 TRP A 175 HIS 0.004 0.001 HIS A 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (11016) covalent geometry : angle 0.66036 / 0.34 (14960) hydrogen bonds : bond 0.04579 / 4.72 ( 476) hydrogen bonds : angle 4.72665 / 6.00 ( 1342) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.9102 (m-80) cc_final: 0.8236 (m-80) REVERT: A 65 ILE cc_start: 0.9455 (tp) cc_final: 0.9162 (pt) REVERT: A 138 LEU cc_start: 0.9348 (mt) cc_final: 0.9144 (mt) REVERT: A 166 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9079 (mt) REVERT: A 366 GLU cc_start: 0.9415 (mm-30) cc_final: 0.9210 (pm20) REVERT: A 498 ASN cc_start: 0.9498 (t0) cc_final: 0.9172 (m-40) REVERT: A 538 HIS cc_start: 0.9563 (m-70) cc_final: 0.9195 (m-70) REVERT: A 595 LYS cc_start: 0.8973 (mtpp) cc_final: 0.8732 (mtpp) REVERT: A 627 LYS cc_start: 0.9368 (mtmm) cc_final: 0.9104 (pttm) REVERT: A 659 TYR cc_start: 0.9165 (t80) cc_final: 0.8734 (t80) REVERT: A 736 ASP cc_start: 0.9393 (m-30) cc_final: 0.9185 (p0) REVERT: A 746 ARG cc_start: 0.9232 (ttm170) cc_final: 0.8851 (ptp-110) REVERT: A 811 LEU cc_start: 0.9072 (mt) cc_final: 0.8797 (mt) REVERT: A 870 ASP cc_start: 0.8652 (m-30) cc_final: 0.8219 (t0) REVERT: A 971 TRP cc_start: 0.9288 (t60) cc_final: 0.8942 (t60) REVERT: A 976 ASN cc_start: 0.9097 (m-40) cc_final: 0.8080 (t0) REVERT: A 980 MET cc_start: 0.8786 (mmp) cc_final: 0.8485 (mmp) REVERT: A 1007 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7282 (m-30) REVERT: A 1008 LEU cc_start: 0.4597 (mt) cc_final: 0.4127 (mt) REVERT: A 1100 GLU cc_start: 0.9693 (mt-10) cc_final: 0.9394 (mm-30) REVERT: A 1250 MET cc_start: 0.8394 (mmm) cc_final: 0.7942 (mmm) outliers start: 26 outliers final: 17 residues processed: 222 average time/residue: 0.0964 time to fit residues: 30.3103 Evaluate side-chains 211 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain A residue 1207 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 50 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 99 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 85 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN A 423 GLN ** A 894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.106669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.087212 restraints weight = 56911.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.088943 restraints weight = 43504.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.090132 restraints weight = 35407.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.091027 restraints weight = 30535.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.091592 restraints weight = 27216.399| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11016 Z= 0.190 Angle : 0.685 13.459 14960 Z= 0.357 Chirality : 0.043 0.338 1630 Planarity : 0.004 0.064 1786 Dihedral : 12.935 81.423 1797 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.98 % Favored : 93.93 % Rotamer: Outliers : 3.82 % Allowed : 18.93 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.23), residues: 1187 helix: 0.36 (0.21), residues: 563 sheet: -0.86 (0.48), residues: 117 loop : -0.99 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 467 TYR 0.019 0.002 TYR A 201 PHE 0.030 0.002 PHE A 880 TRP 0.030 0.003 TRP A 175 HIS 0.005 0.001 HIS A 881 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 (11016) covalent geometry : angle 0.68532 / 0.36 (14960) hydrogen bonds : bond 0.04632 / 4.78 ( 476) hydrogen bonds : angle 4.92260 / 6.27 ( 1342) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.9102 (m-80) cc_final: 0.8253 (m-80) REVERT: A 65 ILE cc_start: 0.9448 (tp) cc_final: 0.9123 (pt) REVERT: A 166 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9062 (mt) REVERT: A 175 TRP cc_start: 0.7570 (m-10) cc_final: 0.6991 (m-10) REVERT: A 366 GLU cc_start: 0.9422 (mm-30) cc_final: 0.9209 (pm20) REVERT: A 475 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7785 (m-10) REVERT: A 498 ASN cc_start: 0.9524 (t0) cc_final: 0.9206 (m-40) REVERT: A 538 HIS cc_start: 0.9560 (m-70) cc_final: 0.9198 (m-70) REVERT: A 627 LYS cc_start: 0.9350 (mtmm) cc_final: 0.9141 (pttm) REVERT: A 659 TYR cc_start: 0.9264 (t80) cc_final: 0.8795 (t80) REVERT: A 746 ARG cc_start: 0.9249 (ttm170) cc_final: 0.8886 (ptp-110) REVERT: A 811 LEU cc_start: 0.9108 (mt) cc_final: 0.8815 (mt) REVERT: A 870 ASP cc_start: 0.8681 (m-30) cc_final: 0.8229 (t0) REVERT: A 971 TRP cc_start: 0.9367 (t60) cc_final: 0.9037 (t60) REVERT: A 976 ASN cc_start: 0.9157 (m-40) cc_final: 0.8130 (t0) REVERT: A 1100 GLU cc_start: 0.9691 (mt-10) cc_final: 0.9387 (mm-30) REVERT: A 1250 MET cc_start: 0.8446 (mmm) cc_final: 0.7920 (mmm) outliers start: 42 outliers final: 37 residues processed: 215 average time/residue: 0.0896 time to fit residues: 27.3588 Evaluate side-chains 228 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1283 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 9 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.106721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.087591 restraints weight = 55324.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.089198 restraints weight = 42293.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.090411 restraints weight = 34522.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.091255 restraints weight = 29595.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.091912 restraints weight = 26437.269| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11016 Z= 0.169 Angle : 0.720 14.699 14960 Z= 0.374 Chirality : 0.042 0.291 1630 Planarity : 0.004 0.058 1786 Dihedral : 12.976 80.875 1797 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.98 % Favored : 93.93 % Rotamer: Outliers : 3.64 % Allowed : 20.20 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.23), residues: 1187 helix: 0.31 (0.21), residues: 563 sheet: -1.08 (0.48), residues: 121 loop : -1.04 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 467 TYR 0.027 0.002 TYR A 392 PHE 0.033 0.002 PHE A 831 TRP 0.024 0.003 TRP A 609 HIS 0.005 0.001 HIS A 881 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (11016) covalent geometry : angle 0.71989 / 0.37 (14960) hydrogen bonds : bond 0.04659 / 4.80 ( 476) hydrogen bonds : angle 4.89864 / 6.26 ( 1342) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.9112 (m-80) cc_final: 0.8270 (m-80) REVERT: A 65 ILE cc_start: 0.9389 (tp) cc_final: 0.9124 (pt) REVERT: A 166 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9069 (mt) REVERT: A 366 GLU cc_start: 0.9419 (mm-30) cc_final: 0.9219 (pm20) REVERT: A 392 TYR cc_start: 0.9673 (OUTLIER) cc_final: 0.9425 (t80) REVERT: A 475 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7773 (m-10) REVERT: A 498 ASN cc_start: 0.9524 (t0) cc_final: 0.9198 (m-40) REVERT: A 538 HIS cc_start: 0.9568 (m-70) cc_final: 0.9188 (m-70) REVERT: A 659 TYR cc_start: 0.9268 (t80) cc_final: 0.8788 (t80) REVERT: A 746 ARG cc_start: 0.9241 (ttm170) cc_final: 0.8899 (ptp-110) REVERT: A 811 LEU cc_start: 0.9172 (mt) cc_final: 0.8890 (mt) REVERT: A 870 ASP cc_start: 0.8678 (m-30) cc_final: 0.8221 (t0) REVERT: A 949 MET cc_start: 0.6340 (pmm) cc_final: 0.5929 (pmm) REVERT: A 971 TRP cc_start: 0.9383 (t60) cc_final: 0.9065 (t60) REVERT: A 976 ASN cc_start: 0.9150 (m-40) cc_final: 0.8085 (t0) REVERT: A 1100 GLU cc_start: 0.9681 (mt-10) cc_final: 0.9380 (mm-30) REVERT: A 1250 MET cc_start: 0.8480 (mmm) cc_final: 0.7921 (mmm) REVERT: A 1268 MET cc_start: 0.9150 (mpp) cc_final: 0.8804 (mpp) outliers start: 40 outliers final: 34 residues processed: 214 average time/residue: 0.0914 time to fit residues: 28.0079 Evaluate side-chains 220 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1070 GLN Chi-restraints excluded: chain A residue 1207 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 4 optimal weight: 0.0060 chunk 75 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 chunk 2 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.110367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.090085 restraints weight = 53014.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.091833 restraints weight = 40407.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.093059 restraints weight = 32900.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.093912 restraints weight = 28331.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.094394 restraints weight = 25358.797| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11016 Z= 0.137 Angle : 0.710 15.117 14960 Z= 0.368 Chirality : 0.042 0.270 1630 Planarity : 0.004 0.059 1786 Dihedral : 12.951 81.153 1797 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.69 % Rotamer: Outliers : 2.82 % Allowed : 20.66 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.24), residues: 1187 helix: 0.36 (0.21), residues: 565 sheet: -0.80 (0.49), residues: 118 loop : -0.97 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 467 TYR 0.038 0.002 TYR A 450 PHE 0.029 0.002 PHE A 61 TRP 0.032 0.003 TRP A 609 HIS 0.004 0.001 HIS A 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (11016) covalent geometry : angle 0.71011 / 0.37 (14960) hydrogen bonds : bond 0.04474 / 4.57 ( 476) hydrogen bonds : angle 4.73936 / 6.03 ( 1342) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.9094 (m-80) cc_final: 0.8237 (m-80) REVERT: A 32 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8218 (mmtt) REVERT: A 65 ILE cc_start: 0.9388 (tp) cc_final: 0.9117 (pt) REVERT: A 138 LEU cc_start: 0.9313 (mt) cc_final: 0.9096 (mt) REVERT: A 166 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9037 (mt) REVERT: A 366 GLU cc_start: 0.9427 (mm-30) cc_final: 0.9225 (pm20) REVERT: A 392 TYR cc_start: 0.9691 (OUTLIER) cc_final: 0.9459 (t80) REVERT: A 475 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7576 (m-10) REVERT: A 494 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6976 (pm20) REVERT: A 498 ASN cc_start: 0.9509 (t0) cc_final: 0.9190 (m-40) REVERT: A 538 HIS cc_start: 0.9574 (m-70) cc_final: 0.9210 (m-70) REVERT: A 659 TYR cc_start: 0.9208 (t80) cc_final: 0.8681 (t80) REVERT: A 746 ARG cc_start: 0.9215 (ttm170) cc_final: 0.8883 (ptp-110) REVERT: A 811 LEU cc_start: 0.9105 (mt) cc_final: 0.8846 (mt) REVERT: A 870 ASP cc_start: 0.8573 (m-30) cc_final: 0.8116 (t0) REVERT: A 949 MET cc_start: 0.6411 (pmm) cc_final: 0.6044 (pmm) REVERT: A 971 TRP cc_start: 0.9341 (t60) cc_final: 0.9007 (t60) REVERT: A 976 ASN cc_start: 0.9129 (m-40) cc_final: 0.8147 (t0) REVERT: A 1100 GLU cc_start: 0.9682 (mt-10) cc_final: 0.9379 (mm-30) REVERT: A 1250 MET cc_start: 0.8459 (mmm) cc_final: 0.7890 (mmm) REVERT: A 1268 MET cc_start: 0.9081 (mpp) cc_final: 0.8875 (mpp) outliers start: 31 outliers final: 25 residues processed: 213 average time/residue: 0.1125 time to fit residues: 33.8467 Evaluate side-chains 216 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 1024 TYR Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1207 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 65 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 117 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.108289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.088823 restraints weight = 55699.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.090504 restraints weight = 43404.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.091335 restraints weight = 35039.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.092310 restraints weight = 30918.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.092981 restraints weight = 27832.022| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11016 Z= 0.152 Angle : 0.702 14.578 14960 Z= 0.366 Chirality : 0.043 0.296 1630 Planarity : 0.004 0.062 1786 Dihedral : 12.971 79.868 1797 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.64 % Favored : 94.27 % Rotamer: Outliers : 3.00 % Allowed : 20.93 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.24), residues: 1187 helix: 0.33 (0.21), residues: 562 sheet: -0.92 (0.49), residues: 120 loop : -0.99 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 202 TYR 0.025 0.002 TYR A 984 PHE 0.036 0.002 PHE A 880 TRP 0.032 0.002 TRP A 609 HIS 0.004 0.001 HIS A 881 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (11016) covalent geometry : angle 0.70178 / 0.37 (14960) hydrogen bonds : bond 0.04502 / 4.57 ( 476) hydrogen bonds : angle 4.81020 / 6.08 ( 1342) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.9128 (m-80) cc_final: 0.8279 (m-80) REVERT: A 32 LYS cc_start: 0.9000 (mmtt) cc_final: 0.8242 (mmtt) REVERT: A 65 ILE cc_start: 0.9391 (tp) cc_final: 0.9123 (pt) REVERT: A 166 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9053 (mt) REVERT: A 275 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8376 (mm-40) REVERT: A 366 GLU cc_start: 0.9403 (mm-30) cc_final: 0.9185 (pm20) REVERT: A 392 TYR cc_start: 0.9704 (OUTLIER) cc_final: 0.9465 (t80) REVERT: A 475 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7597 (m-10) REVERT: A 494 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6970 (pm20) REVERT: A 498 ASN cc_start: 0.9518 (t0) cc_final: 0.9209 (m-40) REVERT: A 536 LEU cc_start: 0.9492 (tp) cc_final: 0.9108 (mt) REVERT: A 538 HIS cc_start: 0.9552 (m-70) cc_final: 0.9175 (m-70) REVERT: A 602 ASN cc_start: 0.7983 (t0) cc_final: 0.7659 (t0) REVERT: A 659 TYR cc_start: 0.9228 (t80) cc_final: 0.8816 (t80) REVERT: A 746 ARG cc_start: 0.9247 (ttm170) cc_final: 0.8905 (ptp-110) REVERT: A 811 LEU cc_start: 0.9148 (mt) cc_final: 0.8875 (mt) REVERT: A 870 ASP cc_start: 0.8624 (m-30) cc_final: 0.8147 (t0) REVERT: A 964 ARG cc_start: 0.7852 (mmt180) cc_final: 0.6765 (mmt180) REVERT: A 971 TRP cc_start: 0.9366 (t60) cc_final: 0.9032 (t60) REVERT: A 975 ASN cc_start: 0.9206 (t0) cc_final: 0.8467 (m-40) REVERT: A 976 ASN cc_start: 0.9121 (m-40) cc_final: 0.7945 (t0) REVERT: A 1007 ASP cc_start: 0.8954 (t0) cc_final: 0.8296 (m-30) REVERT: A 1100 GLU cc_start: 0.9697 (mt-10) cc_final: 0.9381 (mm-30) REVERT: A 1250 MET cc_start: 0.8458 (mmm) cc_final: 0.7948 (mmm) REVERT: A 1268 MET cc_start: 0.9045 (mpp) cc_final: 0.8648 (mpp) outliers start: 33 outliers final: 28 residues processed: 204 average time/residue: 0.1092 time to fit residues: 31.8621 Evaluate side-chains 215 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 1024 TYR Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1172 LYS Chi-restraints excluded: chain A residue 1207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 49 optimal weight: 0.0670 chunk 35 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 72 optimal weight: 0.4980 chunk 112 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 45 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.2120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.112503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.092248 restraints weight = 51994.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.094382 restraints weight = 36539.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.095881 restraints weight = 28271.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.096911 restraints weight = 23340.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.097708 restraints weight = 20288.650| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11016 Z= 0.135 Angle : 0.721 15.055 14960 Z= 0.372 Chirality : 0.043 0.276 1630 Planarity : 0.004 0.060 1786 Dihedral : 12.965 79.841 1797 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 2.46 % Allowed : 21.93 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.24), residues: 1187 helix: 0.38 (0.21), residues: 560 sheet: -0.62 (0.50), residues: 113 loop : -1.07 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 202 TYR 0.027 0.002 TYR A 201 PHE 0.033 0.002 PHE A 880 TRP 0.045 0.003 TRP A 609 HIS 0.004 0.001 HIS A 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (11016) covalent geometry : angle 0.72146 / 0.37 (14960) hydrogen bonds : bond 0.04418 / 4.47 ( 476) hydrogen bonds : angle 4.71675 / 5.98 ( 1342) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.9366 (mmmt) cc_final: 0.9095 (mmmt) REVERT: A 19 PHE cc_start: 0.9201 (m-80) cc_final: 0.8329 (m-80) REVERT: A 32 LYS cc_start: 0.9022 (mmtt) cc_final: 0.8270 (mmtt) REVERT: A 65 ILE cc_start: 0.9383 (tp) cc_final: 0.9120 (pt) REVERT: A 166 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9079 (mt) REVERT: A 275 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8246 (mm-40) REVERT: A 366 GLU cc_start: 0.9417 (mm-30) cc_final: 0.9204 (pm20) REVERT: A 392 TYR cc_start: 0.9692 (OUTLIER) cc_final: 0.9444 (t80) REVERT: A 463 PHE cc_start: 0.9745 (t80) cc_final: 0.9504 (m-80) REVERT: A 475 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7516 (m-10) REVERT: A 494 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6922 (pm20) REVERT: A 498 ASN cc_start: 0.9506 (t0) cc_final: 0.9182 (m-40) REVERT: A 536 LEU cc_start: 0.9482 (tp) cc_final: 0.9098 (mt) REVERT: A 538 HIS cc_start: 0.9562 (m-70) cc_final: 0.9183 (m-70) REVERT: A 602 ASN cc_start: 0.7884 (t0) cc_final: 0.7531 (t0) REVERT: A 659 TYR cc_start: 0.9174 (t80) cc_final: 0.8679 (t80) REVERT: A 746 ARG cc_start: 0.9212 (ttm170) cc_final: 0.8874 (ptp-110) REVERT: A 811 LEU cc_start: 0.9155 (mt) cc_final: 0.8888 (mt) REVERT: A 870 ASP cc_start: 0.8773 (m-30) cc_final: 0.8320 (t0) REVERT: A 964 ARG cc_start: 0.7673 (mmt180) cc_final: 0.6328 (mmt180) REVERT: A 971 TRP cc_start: 0.9289 (t60) cc_final: 0.8961 (t60) REVERT: A 976 ASN cc_start: 0.9088 (m-40) cc_final: 0.8047 (t0) REVERT: A 1007 ASP cc_start: 0.8959 (t0) cc_final: 0.8326 (m-30) REVERT: A 1100 GLU cc_start: 0.9656 (mt-10) cc_final: 0.9362 (mm-30) REVERT: A 1250 MET cc_start: 0.8433 (mmm) cc_final: 0.7890 (mmm) REVERT: A 1268 MET cc_start: 0.8982 (mpp) cc_final: 0.8551 (mpp) outliers start: 27 outliers final: 23 residues processed: 205 average time/residue: 0.1107 time to fit residues: 32.2964 Evaluate side-chains 211 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 1024 TYR Chi-restraints excluded: chain A residue 1172 LYS Chi-restraints excluded: chain A residue 1207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 99 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 86 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.111689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.092119 restraints weight = 54180.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.094162 restraints weight = 38622.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.095590 restraints weight = 29889.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.096562 restraints weight = 24795.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.097114 restraints weight = 21588.596| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11016 Z= 0.157 Angle : 0.734 14.607 14960 Z= 0.384 Chirality : 0.043 0.262 1630 Planarity : 0.004 0.060 1786 Dihedral : 13.009 79.191 1797 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.56 % Favored : 94.36 % Rotamer: Outliers : 2.73 % Allowed : 22.11 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.24), residues: 1187 helix: 0.28 (0.21), residues: 565 sheet: -1.04 (0.48), residues: 122 loop : -1.04 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 467 TYR 0.025 0.002 TYR A 201 PHE 0.047 0.002 PHE A 753 TRP 0.041 0.003 TRP A 609 HIS 0.004 0.001 HIS A 731 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (11016) covalent geometry : angle 0.73448 / 0.38 (14960) hydrogen bonds : bond 0.04451 / 4.52 ( 476) hydrogen bonds : angle 4.83232 / 6.12 ( 1342) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2039.32 seconds wall clock time: 36 minutes 6.43 seconds (2166.43 seconds total)