Starting phenix.real_space_refine on Fri Jul 3 00:57:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8atw_15665/07_2026/8atw_15665.cif Found real_map, /net/cci-nas-00/data/ceres_data/8atw_15665/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8atw_15665/07_2026/8atw_15665.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8atw_15665/07_2026/8atw_15665.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8atw_15665/07_2026/8atw_15665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8atw_15665/07_2026/8atw_15665.map" model { file = "/net/cci-nas-00/data/ceres_data/8atw_15665/07_2026/8atw_15665.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8atw_15665/07_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-dev-6108/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: {'RNA': 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: 0.97 Conformation dependent library (CDL) restraints added in 368.1 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: 1.33 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: 2.71 Time building geometry restraints manager: 1.27 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=" 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=" O3' DT N 109 " pdb=" P DA N 110 " ideal model delta sigma weight residual 1.607 1.436 0.171 1.50e-02 4.44e+03 1.30e+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: 15895 2.80 - 5.60: 167 5.60 - 8.40: 20 8.40 - 11.20: 8 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: 6049 21.65 - 43.30: 638 43.30 - 64.95: 166 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=" CA MET B 267 " pdb=" C MET B 267 " pdb=" N ILE B 268 " pdb=" CA ILE B 268 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 6875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1753 0.131 - 0.262: 20 0.262 - 0.393: 5 0.393 - 0.525: 2 0.525 - 0.656: 2 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=" C4' DT T 29 " pdb=" C5' DT T 29 " pdb=" O4' DT T 29 " pdb=" C3' DT T 29 " both_signs ideal model delta sigma weight residual False -2.53 -2.02 -0.51 2.00e-01 2.50e+01 6.57e+00 ... (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: 0.160 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.530 Find NCS groups from input model: 0.050 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.270 ------------------------------------------------------------------------------- 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= 0.382 Angle : 0.734 13.999 16094 Z= 0.469 Chirality : 0.055 0.656 1782 Planarity : 0.004 0.049 1838 Dihedral : 18.065 108.255 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 0.00489 / 0.37 (11677) covalent geometry : angle 0.73360 / 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 : 0.390 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: 0.0892 time to fit residues: 27.1572 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 : 0.391 ------------------------------------------------------------------------------- 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... B 265 HIS ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.143754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.112191 restraints weight = 18159.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.115792 restraints weight = 10155.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118136 restraints weight = 7120.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.119672 restraints weight = 5733.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.120680 restraints weight = 4992.162| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 11678 Z= 0.187 Angle : 0.631 9.645 16094 Z= 0.335 Chirality : 0.044 0.198 1782 Planarity : 0.005 0.048 1838 Dihedral : 18.558 98.445 2071 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.30 % Allowed : 9.23 % Favored : 89.47 % 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: 0.87 (0.24), residues: 1250 helix: 1.49 (0.20), residues: 710 sheet: 0.10 (0.44), residues: 129 loop : -0.83 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 827 TYR 0.016 0.002 TYR A1229 PHE 0.020 0.002 PHE A 754 TRP 0.008 0.001 TRP A1110 HIS 0.007 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (11677) covalent geometry : angle 0.63086 / 0.33 (16094) hydrogen bonds : bond 0.05257 / 3.30 ( 592) hydrogen bonds : angle 4.62505 / 3.27 ( 1667) Misc. bond : bond 0.00177 / 0.09 ( 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 175 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.355 Fit side-chains REVERT: B 60 GLN cc_start: 0.7104 (tm-30) cc_final: 0.6688 (tm-30) REVERT: A 922 PHE cc_start: 0.8484 (m-10) cc_final: 0.8149 (m-10) REVERT: A 1057 HIS cc_start: 0.7053 (m90) cc_final: 0.6593 (m90) outliers start: 14 outliers final: 12 residues processed: 171 average time/residue: 0.0847 time to fit residues: 21.8615 Evaluate side-chains 154 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 265 HIS 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: 3.9990 chunk 93 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 95 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1057 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.144474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.113582 restraints weight = 18044.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.117159 restraints weight = 9889.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.119523 restraints weight = 6898.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.120872 restraints weight = 5516.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.122043 restraints weight = 4834.341| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11678 Z= 0.138 Angle : 0.575 10.321 16094 Z= 0.307 Chirality : 0.042 0.183 1782 Planarity : 0.004 0.053 1838 Dihedral : 18.469 99.260 2071 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.58 % Allowed : 12.21 % Favored : 86.21 % 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: 1.00 (0.24), residues: 1250 helix: 1.60 (0.20), residues: 703 sheet: 0.29 (0.45), residues: 124 loop : -0.79 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 493 TYR 0.018 0.002 TYR B 18 PHE 0.017 0.001 PHE B 17 TRP 0.012 0.001 TRP B 24 HIS 0.003 0.001 HIS A 939 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (11677) covalent geometry : angle 0.57540 / 0.31 (16094) hydrogen bonds : bond 0.04469 / 2.81 ( 592) hydrogen bonds : angle 4.34693 / 3.07 ( 1667) Misc. bond : bond 0.00101 / 0.05 ( 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 183 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.376 Fit side-chains REVERT: B 60 GLN cc_start: 0.7172 (tm-30) cc_final: 0.6929 (tm-30) REVERT: A 922 PHE cc_start: 0.8433 (m-10) cc_final: 0.8117 (m-10) REVERT: A 1057 HIS cc_start: 0.7249 (m-70) cc_final: 0.6852 (m90) REVERT: A 1096 PHE cc_start: 0.7550 (p90) cc_final: 0.7305 (p90) outliers start: 17 outliers final: 12 residues processed: 176 average time/residue: 0.0877 time to fit residues: 22.9892 Evaluate side-chains 158 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 437 GLU 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 1233 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1332 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 30 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 11 optimal weight: 30.0000 chunk 103 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 94 optimal weight: 0.2980 chunk 93 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 overall best weight: 3.6588 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.143722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.112219 restraints weight = 18293.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.115794 restraints weight = 10058.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118174 restraints weight = 7047.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.119701 restraints weight = 5644.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.120559 restraints weight = 4920.423| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11678 Z= 0.153 Angle : 0.573 8.075 16094 Z= 0.305 Chirality : 0.042 0.187 1782 Planarity : 0.004 0.039 1838 Dihedral : 18.491 101.011 2071 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.96 % Allowed : 13.61 % Favored : 84.44 % 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: 0.97 (0.24), residues: 1250 helix: 1.59 (0.20), residues: 699 sheet: 0.20 (0.45), residues: 126 loop : -0.77 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 827 TYR 0.015 0.001 TYR B 161 PHE 0.016 0.001 PHE A1300 TRP 0.014 0.001 TRP B 24 HIS 0.003 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (11677) covalent geometry : angle 0.57251 / 0.30 (16094) hydrogen bonds : bond 0.04423 / 2.79 ( 592) hydrogen bonds : angle 4.27912 / 3.03 ( 1667) Misc. bond : bond 0.00021 / 0.01 ( 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 175 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.324 Fit side-chains REVERT: B 60 GLN cc_start: 0.7231 (tm-30) cc_final: 0.6710 (tm-30) REVERT: A 1057 HIS cc_start: 0.7219 (m-70) cc_final: 0.6779 (m90) REVERT: A 1096 PHE cc_start: 0.7567 (p90) cc_final: 0.7287 (p90) outliers start: 21 outliers final: 16 residues processed: 168 average time/residue: 0.0848 time to fit residues: 21.6303 Evaluate side-chains 157 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 386 ILE Chi-restraints excluded: chain A residue 437 GLU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 21 optimal weight: 20.0000 chunk 53 optimal weight: 0.0060 chunk 50 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 121 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 57 optimal weight: 0.0770 overall best weight: 3.6160 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.143521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.111999 restraints weight = 18044.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.115571 restraints weight = 10046.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.117872 restraints weight = 7054.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.119422 restraints weight = 5683.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.120340 restraints weight = 4954.033| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11678 Z= 0.153 Angle : 0.568 9.423 16094 Z= 0.303 Chirality : 0.041 0.196 1782 Planarity : 0.004 0.044 1838 Dihedral : 18.476 102.291 2071 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.33 % Allowed : 15.10 % Favored : 82.57 % 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: 0.99 (0.24), residues: 1250 helix: 1.64 (0.20), residues: 692 sheet: 0.39 (0.45), residues: 120 loop : -0.84 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1275 TYR 0.014 0.001 TYR B 161 PHE 0.017 0.001 PHE A1300 TRP 0.013 0.001 TRP B 24 HIS 0.004 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (11677) covalent geometry : angle 0.56761 / 0.30 (16094) hydrogen bonds : bond 0.04351 / 2.74 ( 592) hydrogen bonds : angle 4.21904 / 2.99 ( 1667) Misc. bond : bond 0.00019 / 0.01 ( 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 171 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.363 Fit side-chains REVERT: B 33 PHE cc_start: 0.7743 (m-10) cc_final: 0.7487 (m-80) REVERT: B 60 GLN cc_start: 0.7276 (tm-30) cc_final: 0.6670 (tm-30) REVERT: A 529 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.7708 (ppp) REVERT: A 1057 HIS cc_start: 0.7098 (m-70) cc_final: 0.6755 (m90) REVERT: A 1096 PHE cc_start: 0.7512 (p90) cc_final: 0.7295 (p90) outliers start: 25 outliers final: 17 residues processed: 160 average time/residue: 0.0838 time to fit residues: 20.6993 Evaluate side-chains 159 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 437 GLU 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 755 LEU 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 1182 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 79 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 78 optimal weight: 0.0770 chunk 43 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 overall best weight: 5.4146 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.141632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.109938 restraints weight = 18054.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.113445 restraints weight = 10135.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.115714 restraints weight = 7167.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.117203 restraints weight = 5807.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.118002 restraints weight = 5082.929| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11678 Z= 0.196 Angle : 0.596 8.531 16094 Z= 0.318 Chirality : 0.042 0.177 1782 Planarity : 0.004 0.047 1838 Dihedral : 18.575 105.072 2071 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.24 % Allowed : 16.40 % Favored : 81.36 % 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: 0.83 (0.24), residues: 1250 helix: 1.52 (0.20), residues: 692 sheet: 0.22 (0.45), residues: 122 loop : -0.89 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1275 TYR 0.016 0.002 TYR B 161 PHE 0.017 0.002 PHE A1300 TRP 0.018 0.001 TRP B 24 HIS 0.006 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (11677) covalent geometry : angle 0.59567 / 0.32 (16094) hydrogen bonds : bond 0.04719 / 2.97 ( 592) hydrogen bonds : angle 4.33299 / 3.07 ( 1667) Misc. bond : bond 0.00026 / 0.01 ( 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 171 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.305 Fit side-chains REVERT: A 529 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.7790 (ppp) REVERT: A 930 MET cc_start: 0.7458 (ttm) cc_final: 0.7222 (ttt) REVERT: A 1057 HIS cc_start: 0.6966 (m-70) cc_final: 0.6620 (m90) REVERT: A 1096 PHE cc_start: 0.7546 (p90) cc_final: 0.7232 (p90) outliers start: 24 outliers final: 20 residues processed: 163 average time/residue: 0.0913 time to fit residues: 22.4851 Evaluate side-chains 156 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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 755 LEU Chi-restraints excluded: chain A residue 867 ILE 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 1182 LEU 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: 40.0000 chunk 98 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 102 optimal weight: 0.0470 chunk 2 optimal weight: 0.9990 overall best weight: 4.0086 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.142386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.110657 restraints weight = 18039.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.114191 restraints weight = 10143.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.116479 restraints weight = 7158.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.117986 restraints weight = 5790.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.118818 restraints weight = 5063.121| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11678 Z= 0.163 Angle : 0.584 9.965 16094 Z= 0.311 Chirality : 0.041 0.180 1782 Planarity : 0.004 0.046 1838 Dihedral : 18.549 106.471 2071 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.14 % Allowed : 17.52 % 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: 0.90 (0.24), residues: 1250 helix: 1.57 (0.20), residues: 691 sheet: 0.22 (0.45), residues: 122 loop : -0.84 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 984 TYR 0.016 0.002 TYR A1229 PHE 0.016 0.001 PHE A1300 TRP 0.021 0.001 TRP B 24 HIS 0.005 0.001 HIS B 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (11677) covalent geometry : angle 0.58419 / 0.31 (16094) hydrogen bonds : bond 0.04502 / 2.85 ( 592) hydrogen bonds : angle 4.28485 / 3.05 ( 1667) Misc. bond : bond 0.00024 / 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 172 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.409 Fit side-chains REVERT: B 329 MET cc_start: 0.6846 (mtm) cc_final: 0.6306 (mmm) REVERT: A 529 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.7809 (ppp) REVERT: A 930 MET cc_start: 0.7428 (ttm) cc_final: 0.7214 (ttt) REVERT: A 1057 HIS cc_start: 0.6949 (m-70) cc_final: 0.6608 (m90) REVERT: A 1096 PHE cc_start: 0.7503 (p90) cc_final: 0.7133 (p90) outliers start: 23 outliers final: 19 residues processed: 165 average time/residue: 0.0779 time to fit residues: 20.0350 Evaluate side-chains 156 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 754 PHE Chi-restraints excluded: chain A residue 755 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 85 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.140396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.108674 restraints weight = 18030.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112082 restraints weight = 10217.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.114352 restraints weight = 7274.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.115770 restraints weight = 5894.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.116551 restraints weight = 5172.085| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11678 Z= 0.213 Angle : 0.634 9.042 16094 Z= 0.336 Chirality : 0.044 0.345 1782 Planarity : 0.004 0.047 1838 Dihedral : 18.669 109.242 2071 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.52 % Allowed : 17.80 % Favored : 79.68 % 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 (0.23), residues: 1250 helix: 1.44 (0.20), residues: 691 sheet: 0.00 (0.45), residues: 118 loop : -0.98 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 984 TYR 0.028 0.002 TYR B 73 PHE 0.018 0.002 PHE A1300 TRP 0.025 0.002 TRP B 24 HIS 0.007 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (11677) covalent geometry : angle 0.63398 / 0.34 (16094) hydrogen bonds : bond 0.04956 / 3.14 ( 592) hydrogen bonds : angle 4.38658 / 3.11 ( 1667) Misc. bond : bond 0.00029 / 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 167 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.396 Fit side-chains REVERT: A 529 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.7898 (ppp) REVERT: A 694 GLN cc_start: 0.7659 (mp10) cc_final: 0.7451 (mp10) REVERT: A 926 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7397 (mm-30) REVERT: A 930 MET cc_start: 0.7529 (ttm) cc_final: 0.7321 (ttt) REVERT: A 1057 HIS cc_start: 0.6992 (m-70) cc_final: 0.6679 (m-70) REVERT: A 1096 PHE cc_start: 0.7492 (p90) cc_final: 0.7112 (p90) outliers start: 27 outliers final: 21 residues processed: 160 average time/residue: 0.0783 time to fit residues: 19.4829 Evaluate side-chains 154 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 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 927 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 1296 THR 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: 6.9990 chunk 56 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 88 optimal weight: 0.4980 chunk 64 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN A 952 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.140966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.110289 restraints weight = 17821.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.113756 restraints weight = 9763.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.116039 restraints weight = 6805.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.117526 restraints weight = 5452.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.118503 restraints weight = 4741.675| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11678 Z= 0.170 Angle : 0.615 9.032 16094 Z= 0.326 Chirality : 0.042 0.248 1782 Planarity : 0.004 0.048 1838 Dihedral : 18.636 110.332 2071 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.14 % Allowed : 18.92 % Favored : 78.94 % 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: 1250 helix: 1.45 (0.20), residues: 697 sheet: 0.01 (0.45), residues: 118 loop : -1.05 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 984 TYR 0.031 0.002 TYR B 335 PHE 0.017 0.001 PHE A1300 TRP 0.056 0.002 TRP B 235 HIS 0.005 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (11677) covalent geometry : angle 0.61474 / 0.33 (16094) hydrogen bonds : bond 0.04654 / 2.95 ( 592) hydrogen bonds : angle 4.31530 / 3.07 ( 1667) Misc. bond : bond 0.00031 / 0.02 ( 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 161 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.375 Fit side-chains REVERT: B 329 MET cc_start: 0.6845 (mtm) cc_final: 0.6303 (mmm) REVERT: A 529 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.7861 (ppp) REVERT: A 694 GLN cc_start: 0.7651 (mp10) cc_final: 0.7435 (mp10) REVERT: A 926 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7356 (mm-30) REVERT: A 930 MET cc_start: 0.7495 (ttm) cc_final: 0.7273 (ttt) REVERT: A 1057 HIS cc_start: 0.6948 (m-70) cc_final: 0.6660 (m-70) REVERT: A 1096 PHE cc_start: 0.7464 (p90) cc_final: 0.7006 (p90) outliers start: 23 outliers final: 20 residues processed: 155 average time/residue: 0.0781 time to fit residues: 18.4341 Evaluate side-chains 155 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 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 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 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: 10.0000 chunk 21 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.141029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.110374 restraints weight = 17840.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.113907 restraints weight = 9749.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.116203 restraints weight = 6764.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.117593 restraints weight = 5411.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.118609 restraints weight = 4727.927| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11678 Z= 0.166 Angle : 0.608 8.581 16094 Z= 0.322 Chirality : 0.041 0.181 1782 Planarity : 0.004 0.052 1838 Dihedral : 18.595 111.542 2071 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.14 % Allowed : 18.64 % Favored : 79.22 % 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: 0.69 (0.24), residues: 1250 helix: 1.46 (0.20), residues: 699 sheet: -0.00 (0.45), residues: 118 loop : -1.04 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1275 TYR 0.023 0.002 TYR B 73 PHE 0.020 0.002 PHE B 85 TRP 0.030 0.002 TRP B 24 HIS 0.004 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (11677) covalent geometry : angle 0.60799 / 0.32 (16094) hydrogen bonds : bond 0.04567 / 2.89 ( 592) hydrogen bonds : angle 4.29110 / 3.07 ( 1667) Misc. bond : bond 0.00044 / 0.02 ( 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: 23 poor density : 141 time to evaluate : 0.404 Fit side-chains REVERT: B 116 ARG cc_start: 0.7352 (mmp80) cc_final: 0.6879 (mmp-170) REVERT: B 329 MET cc_start: 0.6855 (mtm) cc_final: 0.6314 (mmm) REVERT: A 529 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.7860 (ppp) REVERT: A 694 GLN cc_start: 0.7665 (mp10) cc_final: 0.7436 (mp10) REVERT: A 926 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7337 (mm-30) REVERT: A 930 MET cc_start: 0.7469 (ttm) cc_final: 0.7250 (ttt) REVERT: A 1018 MET cc_start: 0.8673 (ttp) cc_final: 0.8395 (ttp) REVERT: A 1057 HIS cc_start: 0.6967 (m-70) cc_final: 0.6666 (m-70) REVERT: A 1096 PHE cc_start: 0.7425 (p90) cc_final: 0.6955 (p90) outliers start: 23 outliers final: 20 residues processed: 158 average time/residue: 0.0894 time to fit residues: 21.2328 Evaluate side-chains 155 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 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 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 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: 2.9990 chunk 124 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 chunk 61 optimal weight: 0.7980 chunk 120 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 127 optimal weight: 50.0000 chunk 66 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.144072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.112995 restraints weight = 17828.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.116637 restraints weight = 9770.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.119066 restraints weight = 6805.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.120574 restraints weight = 5417.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.121297 restraints weight = 4718.930| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11678 Z= 0.128 Angle : 0.592 8.812 16094 Z= 0.313 Chirality : 0.040 0.175 1782 Planarity : 0.004 0.054 1838 Dihedral : 18.463 111.442 2071 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.77 % Allowed : 19.11 % Favored : 79.12 % 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: 1.62 (0.20), residues: 691 sheet: 0.21 (0.44), residues: 124 loop : -0.95 (0.29), residues: 435 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 0.015 0.001 PHE B 85 TRP 0.030 0.001 TRP B 235 HIS 0.004 0.001 HIS B 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (11677) covalent geometry : angle 0.59159 / 0.31 (16094) hydrogen bonds : bond 0.04173 / 2.64 ( 592) hydrogen bonds : angle 4.16282 / 3.00 ( 1667) Misc. bond : bond 0.00047 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1629.11 seconds wall clock time: 29 minutes 2.94 seconds (1742.94 seconds total)