Starting phenix.real_space_refine on Wed Aug 5 18:48:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8atw_15665/08_2026/8atw_15665.cif Found real_map, /net/cci-nas-00/data/ceres_data/8atw_15665/08_2026/8atw_15665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8atw_15665/08_2026/8atw_15665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8atw_15665/08_2026/8atw_15665.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8atw_15665/08_2026/8atw_15665.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8atw_15665/08_2026/8atw_15665.cif" model { file = "/net/cci-nas-00/data/ceres_data/8atw_15665/08_2026/8atw_15665.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8atw_15665/08_2026/8atw_15665.cif" } resolution = 3.62 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= 0.013 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 64 5.49 5 S 36 5.16 5 C 7024 2.51 5 N 1957 2.21 5 O 2202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 11283 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2758 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 316} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 7235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 922, 7235 Classifications: {'peptide': 922} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 44, 'TRANS': 877} Chain breaks: 2 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 6, 'ARG:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 80 Chain: "N" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 582 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "T" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 567 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "C" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 109 Classifications: {'RNAv2': 5} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.45, per 1000 atoms: 0.22 Number of scatterers: 11283 At special positions: 0 Unit cell: (106.7, 114.46, 118.34, 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 36 16.00 P 64 15.00 O 2202 8.00 N 1957 7.00 C 7024 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 518.5 milliseconds 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2380 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 10 sheets defined 59.3% alpha, 8.8% beta 23 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'B' and resid 7 through 12 Processing helix chain 'B' and resid 25 through 37 Processing helix chain 'B' and resid 44 through 47 Processing helix chain 'B' and resid 58 through 69 Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 104 through 114 removed outlier: 4.228A pdb=" N TYR B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER B 109 " --> pdb=" O TRP B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 157 removed outlier: 3.670A pdb=" N ILE B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.772A pdb=" N PHE B 163 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 210 through 215 Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 230 through 234 removed outlier: 4.028A pdb=" N GLU B 233 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE B 234 " --> pdb=" O ALA B 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 230 through 234' Processing helix chain 'B' and resid 255 through 267 Processing helix chain 'B' and resid 273 through 278 removed outlier: 3.602A pdb=" N VAL B 277 " --> pdb=" O PRO B 273 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N MET B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 273 through 278' Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 295 through 301 removed outlier: 3.793A pdb=" N LEU B 299 " --> pdb=" O ASP B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 Processing helix chain 'B' and resid 326 through 330 removed outlier: 3.659A pdb=" N MET B 329 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP B 330 " --> pdb=" O ILE B 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 326 through 330' Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 397 through 421 removed outlier: 3.747A pdb=" N GLN A 413 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASP A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 441 Processing helix chain 'A' and resid 446 through 477 Proline residue: A 463 - end of helix Processing helix chain 'A' and resid 488 through 501 removed outlier: 4.062A pdb=" N LEU A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY A 495 " --> pdb=" O THR A 491 " (cutoff:3.500A) Proline residue: A 498 - end of helix Processing helix chain 'A' and resid 504 through 519 Processing helix chain 'A' and resid 531 through 553 removed outlier: 3.646A pdb=" N ILE A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 612 Processing helix chain 'A' and resid 652 through 661 removed outlier: 4.427A pdb=" N GLY A 661 " --> pdb=" O ARG A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 717 Processing helix chain 'A' and resid 719 through 732 removed outlier: 3.975A pdb=" N THR A 732 " --> pdb=" O VAL A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 751 removed outlier: 3.537A pdb=" N GLY A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 813 Processing helix chain 'A' and resid 842 through 848 Processing helix chain 'A' and resid 860 through 873 Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 890 through 900 Processing helix chain 'A' and resid 907 through 911 Processing helix chain 'A' and resid 913 through 930 Processing helix chain 'A' and resid 932 through 935 removed outlier: 3.560A pdb=" N GLU A 935 " --> pdb=" O ASN A 932 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 932 through 935' Processing helix chain 'A' and resid 948 through 959 Processing helix chain 'A' and resid 960 through 967 Processing helix chain 'A' and resid 977 through 994 Processing helix chain 'A' and resid 998 through 1005 Processing helix chain 'A' and resid 1009 through 1021 removed outlier: 4.285A pdb=" N VAL A1021 " --> pdb=" O VAL A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1038 Processing helix chain 'A' and resid 1047 through 1066 Processing helix chain 'A' and resid 1068 through 1085 Processing helix chain 'A' and resid 1090 through 1094 removed outlier: 3.656A pdb=" N LYS A1094 " --> pdb=" O VAL A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1181 Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1197 through 1214 Processing helix chain 'A' and resid 1216 through 1229 Processing helix chain 'A' and resid 1242 through 1260 removed outlier: 3.642A pdb=" N GLN A1246 " --> pdb=" O THR A1242 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS A1247 " --> pdb=" O ASP A1243 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A1259 " --> pdb=" O LEU A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1280 Processing helix chain 'A' and resid 1283 through 1293 Processing helix chain 'A' and resid 1295 through 1302 removed outlier: 3.984A pdb=" N ASP A1302 " --> pdb=" O SER A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1310 removed outlier: 4.212A pdb=" N LEU A1309 " --> pdb=" O ASP A1305 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A1310 " --> pdb=" O LEU A1306 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1305 through 1310' Processing helix chain 'A' and resid 1340 through 1346 removed outlier: 4.003A pdb=" N ASN A1345 " --> pdb=" O VAL A1342 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.277A pdb=" N TYR B 73 " --> pdb=" O GLN B 96 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU B 98 " --> pdb=" O TYR B 73 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LEU B 75 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER B 74 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 76 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LYS B 167 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 9.372A pdb=" N LYS B 131 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 13.135A pdb=" N LEU B 169 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 10.105A pdb=" N LEU B 133 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 12.528A pdb=" N TRP B 171 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N VAL B 135 " --> pdb=" O TRP B 171 " (cutoff:3.500A) removed outlier: 11.572A pdb=" N ASN B 137 " --> pdb=" O PRO B 173 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL B 166 " --> pdb=" O PRO B 249 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA B 206 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU B 246 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU B 204 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASP B 248 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N THR B 202 " --> pdb=" O ASP B 248 " (cutoff:3.500A) removed outlier: 9.616A pdb=" N ILE B 227 " --> pdb=" O LYS B 203 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ILE B 205 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 528 through 530 Processing sheet with id=AA3, first strand: chain 'A' and resid 613 through 619 removed outlier: 3.641A pdb=" N GLY A 629 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AA5, first strand: chain 'A' and resid 822 through 824 Processing sheet with id=AA6, first strand: chain 'A' and resid 855 through 856 Processing sheet with id=AA7, first strand: chain 'A' and resid 942 through 944 Processing sheet with id=AA8, first strand: chain 'A' and resid 1087 through 1088 removed outlier: 3.530A pdb=" N VAL A1323 " --> pdb=" O GLY A1236 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1109 through 1111 Processing sheet with id=AB1, first strand: chain 'A' and resid 1127 through 1131 removed outlier: 3.517A pdb=" N ILE A1139 " --> pdb=" O LYS A1128 " (cutoff:3.500A) 540 hydrogen bonds defined for protein. 1563 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2617 1.33 - 1.45: 2671 1.45 - 1.57: 6212 1.57 - 1.69: 116 1.69 - 1.81: 61 Bond restraints: 11677 Sorted by residual: bond pdb=" C4' DT T 20 " pdb=" O4' DT T 20 " ideal model delta sigma weight residual 1.446 1.621 -0.175 1.00e-02 1.00e+04 3.07e+02 bond pdb=" O3' DT N 109 " pdb=" P DA N 110 " ideal model delta sigma weight residual 1.607 1.436 0.171 1.20e-02 6.94e+03 2.03e+02 bond pdb=" C4' DT T 21 " pdb=" O4' DT T 21 " ideal model delta sigma weight residual 1.446 1.568 -0.122 1.00e-02 1.00e+04 1.48e+02 bond pdb=" C4' DT T 19 " pdb=" O4' DT T 19 " ideal model delta sigma weight residual 1.446 1.528 -0.082 1.00e-02 1.00e+04 6.73e+01 bond pdb=" C4' DC T 22 " pdb=" O4' DC T 22 " ideal model delta sigma weight residual 1.446 1.525 -0.079 1.00e-02 1.00e+04 6.21e+01 ... (remaining 11672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 15888 2.80 - 5.60: 173 5.60 - 8.40: 20 8.40 - 11.20: 9 11.20 - 14.00: 4 Bond angle restraints: 16094 Sorted by residual: angle pdb=" O4' DT T 20 " pdb=" C4' DT T 20 " pdb=" C3' DT T 20 " ideal model delta sigma weight residual 106.00 95.72 10.28 6.00e-01 2.78e+00 2.94e+02 angle pdb=" O4' DT T 21 " pdb=" C4' DT T 21 " pdb=" C3' DT T 21 " ideal model delta sigma weight residual 106.00 97.85 8.15 6.00e-01 2.78e+00 1.84e+02 angle pdb=" O4' DC T 22 " pdb=" C4' DC T 22 " pdb=" C3' DC T 22 " ideal model delta sigma weight residual 106.00 100.11 5.89 6.00e-01 2.78e+00 9.62e+01 angle pdb=" O4' DT T 19 " pdb=" C4' DT T 19 " pdb=" C3' DT T 19 " ideal model delta sigma weight residual 106.00 100.40 5.60 6.00e-01 2.78e+00 8.72e+01 angle pdb=" C5' DA T 34 " pdb=" C4' DA T 34 " pdb=" O4' DA T 34 " ideal model delta sigma weight residual 109.30 123.30 -14.00 1.90e+00 2.77e-01 5.43e+01 ... (remaining 16089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.65: 6043 21.65 - 43.30: 643 43.30 - 64.95: 167 64.95 - 86.60: 20 86.60 - 108.26: 5 Dihedral angle restraints: 6878 sinusoidal: 3204 harmonic: 3674 Sorted by residual: dihedral pdb=" O5' GTP C 201 " pdb=" O3A GTP C 201 " pdb=" PA GTP C 201 " pdb=" PB GTP C 201 " ideal model delta sinusoidal sigma weight residual 274.12 165.87 108.26 1 2.00e+01 2.50e-03 3.15e+01 dihedral pdb=" C8 GTP C 201 " pdb=" C1' GTP C 201 " pdb=" N9 GTP C 201 " pdb=" O4' GTP C 201 " ideal model delta sinusoidal sigma weight residual 104.59 2.87 101.72 1 2.00e+01 2.50e-03 2.89e+01 dihedral pdb=" O5' G C 102 " pdb=" C5' G C 102 " pdb=" C4' G C 102 " pdb=" C3' G C 102 " ideal model delta sinusoidal sigma weight residual 60.00 34.05 25.95 3 6.40e+00 2.44e-02 2.06e+01 ... (remaining 6875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1749 0.131 - 0.262: 24 0.262 - 0.393: 5 0.393 - 0.525: 1 0.525 - 0.656: 3 Chirality restraints: 1782 Sorted by residual: chirality pdb=" P DG N 108 " pdb=" OP1 DG N 108 " pdb=" OP2 DG N 108 " pdb=" O5' DG N 108 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.66 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" C4' DT T 20 " pdb=" C5' DT T 20 " pdb=" O4' DT T 20 " pdb=" C3' DT T 20 " both_signs ideal model delta sigma weight residual False -2.53 -3.18 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" P G C 102 " pdb=" OP1 G C 102 " pdb=" OP2 G C 102 " pdb=" O5' G C 102 " both_signs ideal model delta sigma weight residual True 2.17 -2.81 -0.64 2.00e-01 2.50e+01 1.02e+01 ... (remaining 1779 not shown) Planarity restraints: 1838 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA T 28 " -0.022 2.00e-02 2.50e+03 1.21e-02 4.02e+00 pdb=" N9 DA T 28 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DA T 28 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA T 28 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DA T 28 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA T 28 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA T 28 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DA T 28 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DA T 28 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DA T 28 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DA T 28 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 272 " -0.033 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO B 273 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 273 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 273 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 119 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO B 120 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 120 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 120 " 0.020 5.00e-02 4.00e+02 ... (remaining 1835 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 828 2.74 - 3.28: 11157 3.28 - 3.82: 19479 3.82 - 4.36: 22248 4.36 - 4.90: 37648 Nonbonded interactions: 91360 Sorted by model distance: nonbonded pdb=" O LEU B 23 " pdb=" OH TYR B 29 " model vdw 2.199 3.040 nonbonded pdb=" OG1 THR A1132 " pdb=" O GLN A1135 " model vdw 2.210 3.040 nonbonded pdb=" NH2 ARG A1206 " pdb=" O SER A1346 " model vdw 2.260 3.120 nonbonded pdb=" OD2 ASP A 775 " pdb=" OG SER A 777 " model vdw 2.276 3.040 nonbonded pdb=" O PRO B 102 " pdb=" OH TYR B 108 " model vdw 2.283 3.040 ... (remaining 91355 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.130 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.210 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 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 : 0.005 0.175 11678 Z= 0.402 Angle : 0.742 13.999 16094 Z= 0.474 Chirality : 0.057 0.656 1782 Planarity : 0.004 0.049 1838 Dihedral : 18.111 108.255 4498 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: 1.06 (0.24), residues: 1250 helix: 1.59 (0.20), residues: 708 sheet: 0.27 (0.56), residues: 85 loop : -0.58 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 984 TYR 0.021 0.002 TYR A 979 PHE 0.020 0.001 PHE A1300 TRP 0.014 0.001 TRP B 159 HIS 0.004 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.39 (11677) covalent geometry : angle 0.74214 / 0.47 (16094) hydrogen bonds : bond 0.14427 / 9.33 ( 592) hydrogen bonds : angle 5.76474 / 4.08 ( 1667) Misc. bond : bond 0.09025 / 4.75 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.403 Fit side-chains REVERT: B 52 ASP cc_start: 0.6643 (t70) cc_final: 0.6442 (t70) REVERT: B 71 ARG cc_start: 0.7645 (ptp-110) cc_final: 0.7430 (ptt180) REVERT: B 247 MET cc_start: 0.8059 (mmt) cc_final: 0.7852 (mmp) REVERT: A 398 LEU cc_start: 0.8355 (mt) cc_final: 0.8045 (mt) REVERT: A 402 LYS cc_start: 0.8556 (mptt) cc_final: 0.8352 (mptt) REVERT: A 514 LEU cc_start: 0.8787 (mt) cc_final: 0.7974 (tp) REVERT: A 1057 HIS cc_start: 0.6975 (m90) cc_final: 0.6355 (m90) REVERT: A 1325 LEU cc_start: 0.8353 (mm) cc_final: 0.8106 (mt) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.0904 time to fit residues: 27.4045 Evaluate side-chains 153 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.143700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.112149 restraints weight = 18151.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.115714 restraints weight = 10145.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118077 restraints weight = 7121.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.119599 restraints weight = 5728.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.120456 restraints weight = 4993.583| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 11678 Z= 0.192 Angle : 0.645 10.022 16094 Z= 0.339 Chirality : 0.045 0.220 1782 Planarity : 0.005 0.047 1838 Dihedral : 18.652 98.470 2071 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.40 % Allowed : 9.51 % Favored : 89.10 % 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: 0.86 (0.24), residues: 1250 helix: 1.48 (0.20), residues: 710 sheet: 0.09 (0.44), residues: 129 loop : -0.84 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 827 TYR 0.018 0.002 TYR A1229 PHE 0.019 0.002 PHE A 754 TRP 0.008 0.001 TRP B 159 HIS 0.008 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (11677) covalent geometry : angle 0.64531 / 0.34 (16094) hydrogen bonds : bond 0.05119 / 3.21 ( 592) hydrogen bonds : angle 4.61510 / 3.26 ( 1667) Misc. bond : bond 0.00244 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.319 Fit side-chains REVERT: B 60 GLN cc_start: 0.7118 (tm-30) cc_final: 0.6700 (tm-30) REVERT: A 922 PHE cc_start: 0.8486 (m-10) cc_final: 0.8156 (m-10) REVERT: A 1057 HIS cc_start: 0.7059 (m90) cc_final: 0.6596 (m90) outliers start: 15 outliers final: 11 residues processed: 171 average time/residue: 0.0775 time to fit residues: 20.0632 Evaluate side-chains 156 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1332 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 63 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 95 optimal weight: 0.0270 chunk 64 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 265 HIS A1057 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.145765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.114603 restraints weight = 17991.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.118237 restraints weight = 9881.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.120653 restraints weight = 6878.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.122186 restraints weight = 5498.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123128 restraints weight = 4781.993| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11678 Z= 0.124 Angle : 0.569 10.255 16094 Z= 0.302 Chirality : 0.042 0.194 1782 Planarity : 0.004 0.056 1838 Dihedral : 18.523 99.703 2071 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.77 % Allowed : 12.40 % Favored : 85.83 % 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: 1.08 (0.24), residues: 1250 helix: 1.67 (0.20), residues: 694 sheet: 0.29 (0.45), residues: 126 loop : -0.70 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 493 TYR 0.015 0.002 TYR B 18 PHE 0.017 0.001 PHE B 17 TRP 0.011 0.001 TRP B 24 HIS 0.006 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (11677) covalent geometry : angle 0.56906 / 0.30 (16094) hydrogen bonds : bond 0.04242 / 2.68 ( 592) hydrogen bonds : angle 4.28012 / 3.03 ( 1667) Misc. bond : bond 0.00155 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.261 Fit side-chains REVERT: B 60 GLN cc_start: 0.7171 (tm-30) cc_final: 0.6919 (tm-30) REVERT: A 514 LEU cc_start: 0.8743 (mt) cc_final: 0.8029 (tp) REVERT: A 1057 HIS cc_start: 0.7265 (m-70) cc_final: 0.6870 (m90) REVERT: A 1096 PHE cc_start: 0.7549 (p90) cc_final: 0.7308 (p90) outliers start: 19 outliers final: 12 residues processed: 180 average time/residue: 0.0855 time to fit residues: 23.0160 Evaluate side-chains 156 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1325 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 30 optimal weight: 0.0010 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 94 optimal weight: 20.0000 chunk 93 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 492 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.145398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.114037 restraints weight = 18204.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.117697 restraints weight = 9973.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.120115 restraints weight = 6927.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.121694 restraints weight = 5542.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.122581 restraints weight = 4810.858| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11678 Z= 0.125 Angle : 0.557 8.152 16094 Z= 0.294 Chirality : 0.041 0.180 1782 Planarity : 0.004 0.039 1838 Dihedral : 18.479 100.261 2071 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.68 % Allowed : 14.26 % Favored : 84.06 % 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: 1.11 (0.24), residues: 1250 helix: 1.70 (0.20), residues: 695 sheet: 0.27 (0.44), residues: 126 loop : -0.67 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 984 TYR 0.013 0.001 TYR B 73 PHE 0.013 0.001 PHE A 886 TRP 0.013 0.001 TRP B 24 HIS 0.005 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (11677) covalent geometry : angle 0.55659 / 0.29 (16094) hydrogen bonds : bond 0.04076 / 2.58 ( 592) hydrogen bonds : angle 4.17199 / 2.96 ( 1667) Misc. bond : bond 0.00065 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.402 Fit side-chains REVERT: B 60 GLN cc_start: 0.7214 (tm-30) cc_final: 0.6932 (tm-30) REVERT: A 461 MET cc_start: 0.7306 (ttm) cc_final: 0.7083 (ttm) REVERT: A 819 TYR cc_start: 0.8522 (m-10) cc_final: 0.8313 (m-10) REVERT: A 1057 HIS cc_start: 0.7234 (m-70) cc_final: 0.6797 (m90) REVERT: A 1096 PHE cc_start: 0.7549 (p90) cc_final: 0.7268 (p90) outliers start: 18 outliers final: 12 residues processed: 172 average time/residue: 0.0731 time to fit residues: 19.4780 Evaluate side-chains 155 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1325 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 21 optimal weight: 0.5980 chunk 53 optimal weight: 30.0000 chunk 50 optimal weight: 30.0000 chunk 31 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.142563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.110917 restraints weight = 18092.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.114429 restraints weight = 10096.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.116735 restraints weight = 7116.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118226 restraints weight = 5744.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.119038 restraints weight = 5033.005| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11678 Z= 0.182 Angle : 0.591 9.481 16094 Z= 0.312 Chirality : 0.043 0.177 1782 Planarity : 0.004 0.041 1838 Dihedral : 18.595 102.399 2071 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.14 % Allowed : 16.03 % Favored : 81.83 % 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: 1.01 (0.24), residues: 1250 helix: 1.64 (0.20), residues: 692 sheet: 0.40 (0.45), residues: 120 loop : -0.81 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 493 TYR 0.016 0.002 TYR B 161 PHE 0.016 0.002 PHE A1138 TRP 0.018 0.001 TRP B 24 HIS 0.007 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (11677) covalent geometry : angle 0.59111 / 0.31 (16094) hydrogen bonds : bond 0.04568 / 2.87 ( 592) hydrogen bonds : angle 4.27323 / 3.03 ( 1667) Misc. bond : bond 0.00074 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.417 Fit side-chains REVERT: B 60 GLN cc_start: 0.7302 (tm-30) cc_final: 0.6692 (tm-30) REVERT: A 461 MET cc_start: 0.7233 (ttm) cc_final: 0.6910 (ttm) REVERT: A 529 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.7768 (ppp) REVERT: A 1057 HIS cc_start: 0.7063 (m-70) cc_final: 0.6709 (m90) REVERT: A 1096 PHE cc_start: 0.7517 (p90) cc_final: 0.7286 (p90) outliers start: 23 outliers final: 13 residues processed: 165 average time/residue: 0.0817 time to fit residues: 20.5119 Evaluate side-chains 153 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1332 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 79 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 38 optimal weight: 30.0000 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.140020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.109232 restraints weight = 17909.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.112665 restraints weight = 9838.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.114909 restraints weight = 6872.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.116374 restraints weight = 5517.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.117212 restraints weight = 4811.456| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11678 Z= 0.222 Angle : 0.626 8.265 16094 Z= 0.332 Chirality : 0.044 0.191 1782 Planarity : 0.004 0.044 1838 Dihedral : 18.706 105.563 2071 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.61 % Allowed : 16.78 % Favored : 80.62 % 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: 0.81 (0.24), residues: 1250 helix: 1.51 (0.20), residues: 692 sheet: 0.05 (0.46), residues: 118 loop : -0.86 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 493 TYR 0.032 0.002 TYR B 73 PHE 0.020 0.002 PHE A1300 TRP 0.020 0.002 TRP B 24 HIS 0.008 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (11677) covalent geometry : angle 0.62553 / 0.33 (16094) hydrogen bonds : bond 0.04874 / 3.08 ( 592) hydrogen bonds : angle 4.38892 / 3.11 ( 1667) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.307 Fit side-chains REVERT: B 60 GLN cc_start: 0.7263 (tm-30) cc_final: 0.6724 (tm-30) REVERT: A 461 MET cc_start: 0.7241 (ttm) cc_final: 0.6978 (ttm) REVERT: A 529 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.7881 (ppp) REVERT: A 930 MET cc_start: 0.7515 (ttm) cc_final: 0.7281 (ttt) REVERT: A 1057 HIS cc_start: 0.6960 (m-70) cc_final: 0.6624 (m90) REVERT: A 1096 PHE cc_start: 0.7527 (p90) cc_final: 0.7184 (p90) REVERT: A 1170 MET cc_start: 0.8286 (tmm) cc_final: 0.8029 (tmm) outliers start: 28 outliers final: 21 residues processed: 162 average time/residue: 0.0839 time to fit residues: 20.4817 Evaluate side-chains 157 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 754 PHE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1332 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 78 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 chunk 119 optimal weight: 50.0000 chunk 98 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.141139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110237 restraints weight = 17974.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.113818 restraints weight = 9881.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.116094 restraints weight = 6857.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.117573 restraints weight = 5521.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.118428 restraints weight = 4811.804| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 11678 Z= 0.214 Angle : 0.625 9.843 16094 Z= 0.330 Chirality : 0.043 0.186 1782 Planarity : 0.004 0.041 1838 Dihedral : 18.745 107.447 2071 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.52 % Allowed : 17.15 % Favored : 80.34 % 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: 0.71 (0.24), residues: 1250 helix: 1.46 (0.20), residues: 691 sheet: 0.01 (0.46), residues: 118 loop : -0.96 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 984 TYR 0.024 0.002 TYR B 73 PHE 0.019 0.002 PHE A1300 TRP 0.043 0.002 TRP B 235 HIS 0.007 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 (11677) covalent geometry : angle 0.62481 / 0.33 (16094) hydrogen bonds : bond 0.04877 / 3.09 ( 592) hydrogen bonds : angle 4.40705 / 3.13 ( 1667) Misc. bond : bond 0.00020 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.394 Fit side-chains REVERT: B 60 GLN cc_start: 0.7282 (tm-30) cc_final: 0.7065 (tm-30) REVERT: A 461 MET cc_start: 0.7330 (ttm) cc_final: 0.7031 (ttm) REVERT: A 529 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.7873 (ppp) REVERT: A 926 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7375 (mm-30) REVERT: A 930 MET cc_start: 0.7485 (ttm) cc_final: 0.7258 (ttt) REVERT: A 1057 HIS cc_start: 0.6946 (m-70) cc_final: 0.6671 (m-70) REVERT: A 1096 PHE cc_start: 0.7527 (p90) cc_final: 0.7160 (p90) REVERT: A 1170 MET cc_start: 0.8277 (tmm) cc_final: 0.8031 (tmm) outliers start: 27 outliers final: 21 residues processed: 160 average time/residue: 0.0790 time to fit residues: 19.0296 Evaluate side-chains 159 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 754 PHE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1332 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 85 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 122 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.143440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.112747 restraints weight = 17850.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.116388 restraints weight = 9842.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.118693 restraints weight = 6822.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.120195 restraints weight = 5489.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.120858 restraints weight = 4777.598| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11678 Z= 0.149 Angle : 0.597 9.287 16094 Z= 0.313 Chirality : 0.042 0.168 1782 Planarity : 0.004 0.046 1838 Dihedral : 18.655 107.909 2071 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.05 % Allowed : 18.45 % Favored : 79.50 % 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: 0.85 (0.24), residues: 1250 helix: 1.58 (0.20), residues: 690 sheet: 0.02 (0.46), residues: 118 loop : -0.89 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 984 TYR 0.020 0.002 TYR A 819 PHE 0.018 0.001 PHE B 85 TRP 0.028 0.001 TRP B 235 HIS 0.004 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (11677) covalent geometry : angle 0.59737 / 0.31 (16094) hydrogen bonds : bond 0.04438 / 2.82 ( 592) hydrogen bonds : angle 4.28069 / 3.05 ( 1667) Misc. bond : bond 0.00047 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.420 Fit side-chains REVERT: A 529 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.7809 (ppp) REVERT: A 926 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7343 (mm-30) REVERT: A 930 MET cc_start: 0.7412 (ttm) cc_final: 0.7206 (ttt) REVERT: A 1057 HIS cc_start: 0.6917 (m-70) cc_final: 0.6594 (m90) REVERT: A 1096 PHE cc_start: 0.7457 (p90) cc_final: 0.7002 (p90) outliers start: 22 outliers final: 18 residues processed: 161 average time/residue: 0.0854 time to fit residues: 20.9024 Evaluate side-chains 155 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 754 PHE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1332 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 116 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 88 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 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 = 0.3776 r_free = 0.3776 target = 0.144304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.113946 restraints weight = 17866.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.117507 restraints weight = 9863.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.119815 restraints weight = 6887.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.121299 restraints weight = 5528.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.122260 restraints weight = 4811.539| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 11678 Z= 0.137 Angle : 0.588 8.924 16094 Z= 0.309 Chirality : 0.041 0.276 1782 Planarity : 0.004 0.045 1838 Dihedral : 18.576 107.918 2071 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.96 % Allowed : 19.01 % Favored : 79.03 % 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: 0.91 (0.24), residues: 1250 helix: 1.64 (0.20), residues: 690 sheet: 0.05 (0.46), residues: 118 loop : -0.89 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 984 TYR 0.015 0.002 TYR B 29 PHE 0.016 0.001 PHE B 85 TRP 0.024 0.001 TRP B 24 HIS 0.004 0.001 HIS B 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (11677) covalent geometry : angle 0.58791 / 0.31 (16094) hydrogen bonds : bond 0.04244 / 2.69 ( 592) hydrogen bonds : angle 4.21986 / 3.02 ( 1667) Misc. bond : bond 0.00053 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.354 Fit side-chains REVERT: B 116 ARG cc_start: 0.7178 (mmp80) cc_final: 0.6746 (mmp-170) REVERT: A 503 ILE cc_start: 0.8415 (mp) cc_final: 0.8157 (mt) REVERT: A 529 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.7724 (ppp) REVERT: A 926 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7309 (mm-30) REVERT: A 930 MET cc_start: 0.7463 (ttm) cc_final: 0.7254 (ttt) REVERT: A 1018 MET cc_start: 0.8720 (ttp) cc_final: 0.8480 (ttp) REVERT: A 1057 HIS cc_start: 0.6887 (m-70) cc_final: 0.6583 (m90) REVERT: A 1096 PHE cc_start: 0.7417 (p90) cc_final: 0.6998 (p90) outliers start: 21 outliers final: 19 residues processed: 166 average time/residue: 0.0811 time to fit residues: 20.6838 Evaluate side-chains 155 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 754 PHE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1332 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 77 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 1 optimal weight: 0.3980 chunk 14 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.145084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.114661 restraints weight = 17831.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.118233 restraints weight = 9848.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.120576 restraints weight = 6885.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.121912 restraints weight = 5513.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.122979 restraints weight = 4830.908| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 11678 Z= 0.131 Angle : 0.586 8.851 16094 Z= 0.308 Chirality : 0.041 0.181 1782 Planarity : 0.004 0.053 1838 Dihedral : 18.527 107.896 2071 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.86 % Allowed : 19.57 % Favored : 78.56 % 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: 0.93 (0.24), residues: 1250 helix: 1.65 (0.20), residues: 691 sheet: 0.12 (0.46), residues: 118 loop : -0.87 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 984 TYR 0.013 0.002 TYR B 29 PHE 0.014 0.001 PHE A1300 TRP 0.029 0.001 TRP B 24 HIS 0.004 0.001 HIS B 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (11677) covalent geometry : angle 0.58589 / 0.31 (16094) hydrogen bonds : bond 0.04130 / 2.61 ( 592) hydrogen bonds : angle 4.16646 / 2.99 ( 1667) Misc. bond : bond 0.00056 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.378 Fit side-chains REVERT: B 329 MET cc_start: 0.6833 (mtm) cc_final: 0.6341 (mmm) REVERT: A 503 ILE cc_start: 0.8294 (mp) cc_final: 0.8041 (mt) REVERT: A 926 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7286 (mm-30) REVERT: A 1018 MET cc_start: 0.8715 (ttp) cc_final: 0.8500 (ttp) REVERT: A 1057 HIS cc_start: 0.6837 (m-70) cc_final: 0.6598 (m-70) REVERT: A 1096 PHE cc_start: 0.7397 (p90) cc_final: 0.6966 (p90) outliers start: 20 outliers final: 19 residues processed: 161 average time/residue: 0.0795 time to fit residues: 19.6380 Evaluate side-chains 156 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 754 PHE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1332 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 43 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 50 optimal weight: 0.0000 chunk 61 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 127 optimal weight: 50.0000 chunk 66 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.144227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.113724 restraints weight = 17963.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.117248 restraints weight = 9905.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.119577 restraints weight = 6933.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.121077 restraints weight = 5562.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.121994 restraints weight = 4843.820| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 11678 Z= 0.151 Angle : 0.598 8.542 16094 Z= 0.314 Chirality : 0.041 0.171 1782 Planarity : 0.004 0.050 1838 Dihedral : 18.564 108.354 2071 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.05 % Allowed : 19.76 % Favored : 78.19 % 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: 0.89 (0.24), residues: 1250 helix: 1.61 (0.20), residues: 690 sheet: 0.13 (0.46), residues: 118 loop : -0.89 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1275 TYR 0.013 0.002 TYR B 161 PHE 0.014 0.001 PHE A1300 TRP 0.031 0.002 TRP A 685 HIS 0.004 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (11677) covalent geometry : angle 0.59766 / 0.31 (16094) hydrogen bonds : bond 0.04276 / 2.70 ( 592) hydrogen bonds : angle 4.19686 / 3.00 ( 1667) Misc. bond : bond 0.00053 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1565.70 seconds wall clock time: 27 minutes 43.99 seconds (1663.99 seconds total)