Starting phenix.real_space_refine on Tue Mar 3 17:02:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tmw_26003/03_2026/7tmw_26003_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tmw_26003/03_2026/7tmw_26003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tmw_26003/03_2026/7tmw_26003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tmw_26003/03_2026/7tmw_26003.map" model { file = "/net/cci-nas-00/data/ceres_data/7tmw_26003/03_2026/7tmw_26003_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tmw_26003/03_2026/7tmw_26003_neut.cif" } resolution = 3.2 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= 0.001 sd= 0.936 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: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 4695 2.51 5 N 1242 2.21 5 O 1334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7320 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 4075 Classifications: {'peptide': 499} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 482} Chain breaks: 7 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2273 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 54 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 2, 'TRANS': 4} Chain: "N" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 918 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 1.76, per 1000 atoms: 0.24 Number of scatterers: 7320 At special positions: 0 Unit cell: (124.02, 95.4, 92.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 1334 8.00 N 1242 7.00 C 4695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 485 " - pdb=" SG CYS R 563 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 159 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 286.2 milliseconds 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1740 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 10 sheets defined 39.6% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'R' and resid 405 through 430 Processing helix chain 'R' and resid 437 through 468 Processing helix chain 'R' and resid 475 through 482 Processing helix chain 'R' and resid 482 through 515 removed outlier: 4.131A pdb=" N GLN R 486 " --> pdb=" O SER R 482 " (cutoff:3.500A) Processing helix chain 'R' and resid 524 through 549 Proline residue: R 546 - end of helix Processing helix chain 'R' and resid 549 through 554 Processing helix chain 'R' and resid 573 through 584 removed outlier: 4.622A pdb=" N TYR R 579 " --> pdb=" O GLY R 575 " (cutoff:3.500A) Processing helix chain 'R' and resid 587 through 608 Processing helix chain 'R' and resid 624 through 653 Proline residue: R 643 - end of helix Processing helix chain 'R' and resid 658 through 668 removed outlier: 3.836A pdb=" N THR R 662 " --> pdb=" O PRO R 658 " (cutoff:3.500A) Processing helix chain 'R' and resid 671 through 681 Proline residue: R 678 - end of helix Processing helix chain 'R' and resid 685 through 699 removed outlier: 3.514A pdb=" N LYS R 689 " --> pdb=" O THR R 685 " (cutoff:3.500A) Processing helix chain 'R' and resid 1008 through 1034 Processing helix chain 'R' and resid 1047 through 1058 removed outlier: 3.636A pdb=" N ILE R1051 " --> pdb=" O GLY R1047 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL R1052 " --> pdb=" O LYS R1048 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE R1057 " --> pdb=" O LYS R1053 " (cutoff:3.500A) Processing helix chain 'R' and resid 1229 through 1233 removed outlier: 3.601A pdb=" N CYS R1232 " --> pdb=" O TRP R1229 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE R1233 " --> pdb=" O ILE R1230 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 1229 through 1233' Processing helix chain 'R' and resid 1247 through 1264 Processing helix chain 'R' and resid 1278 through 1289 Processing helix chain 'R' and resid 1292 through 1297 removed outlier: 3.849A pdb=" N TYR R1296 " --> pdb=" O LYS R1292 " (cutoff:3.500A) Processing helix chain 'R' and resid 1298 through 1303 removed outlier: 3.771A pdb=" N TYR R1303 " --> pdb=" O PHE R1300 " (cutoff:3.500A) Processing helix chain 'R' and resid 1316 through 1336 removed outlier: 3.544A pdb=" N THR R1320 " --> pdb=" O ASP R1316 " (cutoff:3.500A) Processing helix chain 'R' and resid 1355 through 1376 Processing helix chain 'N' and resid 61 through 66 removed outlier: 4.515A pdb=" N GLY N 66 " --> pdb=" O GLY N 62 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 1206 through 1209 removed outlier: 6.476A pdb=" N HIS R1036 " --> pdb=" O HIS R1215 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N PHE R1217 " --> pdb=" O HIS R1036 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU R1038 " --> pdb=" O PHE R1217 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N ALA R1238 " --> pdb=" O THR R1035 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG R1037 " --> pdb=" O ALA R1238 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ILE R1240 " --> pdb=" O ARG R1037 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU R1039 " --> pdb=" O ILE R1240 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL R1242 " --> pdb=" O LEU R1039 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU R1041 " --> pdb=" O VAL R1242 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ASP R1244 " --> pdb=" O LEU R1041 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE R1239 " --> pdb=" O ILE R1273 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N PHE R1275 " --> pdb=" O ILE R1239 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE R1241 " --> pdb=" O PHE R1275 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASN R1277 " --> pdb=" O PHE R1241 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL R1243 " --> pdb=" O ASN R1277 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL R1272 " --> pdb=" O TYR R1345 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N HIS R1347 " --> pdb=" O VAL R1272 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU R1274 " --> pdb=" O HIS R1347 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 61 removed outlier: 3.719A pdb=" N ARG B 59 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 68 through 72 removed outlier: 7.010A pdb=" N ALA B 83 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET B 71 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL B 81 " --> pdb=" O MET B 71 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS B 88 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS B 101 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP B 93 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LYS B 99 " --> pdb=" O ASP B 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 115 removed outlier: 5.687A pdb=" N ASN B 135 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N VAL B 145 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 158 through 161 removed outlier: 3.660A pdb=" N CYS B 158 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP B 180 " --> pdb=" O GLN B 186 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLN B 186 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 197 through 202 Processing sheet with id=AA7, first strand: chain 'B' and resid 239 through 244 Processing sheet with id=AA8, first strand: chain 'B' and resid 283 through 288 removed outlier: 3.981A pdb=" N SER B 285 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASP B 308 " --> pdb=" O ARG B 314 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ARG B 314 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.700A pdb=" N THR N 69 " --> pdb=" O GLN N 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.611A pdb=" N GLU N 46 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.29 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2341 1.34 - 1.46: 1885 1.46 - 1.59: 3188 1.59 - 1.71: 0 1.71 - 1.83: 67 Bond restraints: 7481 Sorted by residual: bond pdb=" CG GLU R1329 " pdb=" CD GLU R1329 " ideal model delta sigma weight residual 1.516 1.470 0.046 2.50e-02 1.60e+03 3.43e+00 bond pdb=" C ILE R 642 " pdb=" N PRO R 643 " ideal model delta sigma weight residual 1.336 1.349 -0.013 1.23e-02 6.61e+03 1.18e+00 bond pdb=" CG PRO R 671 " pdb=" CD PRO R 671 " ideal model delta sigma weight residual 1.503 1.469 0.034 3.40e-02 8.65e+02 1.00e+00 bond pdb=" CB GLU R1329 " pdb=" CG GLU R1329 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.58e-01 bond pdb=" N GLU R1329 " pdb=" CA GLU R1329 " ideal model delta sigma weight residual 1.459 1.471 -0.012 1.28e-02 6.10e+03 8.79e-01 ... (remaining 7476 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 9923 2.04 - 4.09: 178 4.09 - 6.13: 30 6.13 - 8.17: 5 8.17 - 10.21: 3 Bond angle restraints: 10139 Sorted by residual: angle pdb=" N GLU R1329 " pdb=" CA GLU R1329 " pdb=" CB GLU R1329 " ideal model delta sigma weight residual 110.28 116.39 -6.11 1.55e+00 4.16e-01 1.56e+01 angle pdb=" CB ARG R1327 " pdb=" CG ARG R1327 " pdb=" CD ARG R1327 " ideal model delta sigma weight residual 111.30 119.93 -8.63 2.30e+00 1.89e-01 1.41e+01 angle pdb=" N VAL B 100 " pdb=" CA VAL B 100 " pdb=" C VAL B 100 " ideal model delta sigma weight residual 113.53 110.20 3.33 9.80e-01 1.04e+00 1.15e+01 angle pdb=" CA PRO R 546 " pdb=" N PRO R 546 " pdb=" CD PRO R 546 " ideal model delta sigma weight residual 112.00 107.34 4.66 1.40e+00 5.10e-01 1.11e+01 angle pdb=" CG ARG B 324 " pdb=" CD ARG B 324 " pdb=" NE ARG B 324 " ideal model delta sigma weight residual 112.00 118.76 -6.76 2.20e+00 2.07e-01 9.44e+00 ... (remaining 10134 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 3968 17.20 - 34.40: 359 34.40 - 51.60: 60 51.60 - 68.79: 5 68.79 - 85.99: 6 Dihedral angle restraints: 4398 sinusoidal: 1705 harmonic: 2693 Sorted by residual: dihedral pdb=" CB CYS R 485 " pdb=" SG CYS R 485 " pdb=" SG CYS R 563 " pdb=" CB CYS R 563 " ideal model delta sinusoidal sigma weight residual -86.00 -120.04 34.04 1 1.00e+01 1.00e-02 1.64e+01 dihedral pdb=" CA MET R1055 " pdb=" C MET R1055 " pdb=" N ARG R1056 " pdb=" CA ARG R1056 " ideal model delta harmonic sigma weight residual 180.00 161.93 18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA TRP B 92 " pdb=" C TRP B 92 " pdb=" N ASP B 93 " pdb=" CA ASP B 93 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 4395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 808 0.044 - 0.087: 237 0.087 - 0.131: 89 0.131 - 0.175: 9 0.175 - 0.219: 4 Chirality restraints: 1147 Sorted by residual: chirality pdb=" CA VAL N 37 " pdb=" N VAL N 37 " pdb=" C VAL N 37 " pdb=" CB VAL N 37 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL N 37 " pdb=" CA VAL N 37 " pdb=" CG1 VAL N 37 " pdb=" CG2 VAL N 37 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.49e-01 chirality pdb=" CG LEU B 346 " pdb=" CB LEU B 346 " pdb=" CD1 LEU B 346 " pdb=" CD2 LEU B 346 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.69e-01 ... (remaining 1144 not shown) Planarity restraints: 1277 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 664 " -0.026 2.00e-02 2.50e+03 2.83e-02 2.01e+01 pdb=" CG TRP R 664 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP R 664 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP R 664 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 664 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 664 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 664 " -0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 664 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 664 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP R 664 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 545 " 0.075 5.00e-02 4.00e+02 1.11e-01 1.98e+01 pdb=" N PRO R 546 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO R 546 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO R 546 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 109 " 0.023 2.00e-02 2.50e+03 2.08e-02 1.08e+01 pdb=" CG TRP B 109 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP B 109 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 109 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 109 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 109 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 109 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 109 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 109 " 0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP B 109 " -0.001 2.00e-02 2.50e+03 ... (remaining 1274 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 450 2.73 - 3.28: 7442 3.28 - 3.82: 12428 3.82 - 4.36: 14502 4.36 - 4.90: 25054 Nonbonded interactions: 59876 Sorted by model distance: nonbonded pdb=" OG SER B 84 " pdb=" OD1 ASP B 86 " model vdw 2.193 3.040 nonbonded pdb=" O VAL R 542 " pdb=" OH TYR R 579 " model vdw 2.250 3.040 nonbonded pdb=" OG SER B 237 " pdb=" O PRO N 100 " model vdw 2.255 3.040 nonbonded pdb=" O ALA R 543 " pdb=" OH TYR R 557 " model vdw 2.262 3.040 nonbonded pdb=" O ILE B 133 " pdb=" OG SER B 146 " model vdw 2.266 3.040 ... (remaining 59871 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 0.020 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.150 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7485 Z= 0.157 Angle : 0.702 10.213 10147 Z= 0.382 Chirality : 0.048 0.219 1147 Planarity : 0.006 0.111 1277 Dihedral : 13.225 85.993 2646 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.28 (0.27), residues: 906 helix: 1.33 (0.29), residues: 326 sheet: -0.69 (0.34), residues: 210 loop : -1.22 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 160 TYR 0.016 0.002 TYR N 32 PHE 0.037 0.002 PHE R1325 TRP 0.076 0.003 TRP R 664 HIS 0.003 0.001 HIS R1342 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 7481) covalent geometry : angle 0.70120 (10139) SS BOND : bond 0.00601 ( 4) SS BOND : angle 1.51565 ( 8) hydrogen bonds : bond 0.11046 ( 369) hydrogen bonds : angle 5.60595 ( 1065) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: R 447 LEU cc_start: 0.7776 (tp) cc_final: 0.7549 (tp) REVERT: R 467 LYS cc_start: 0.7077 (tptm) cc_final: 0.6724 (mttt) REVERT: R 1019 LYS cc_start: 0.7276 (mtpp) cc_final: 0.7022 (mtpp) REVERT: R 1299 GLU cc_start: 0.7579 (mp0) cc_final: 0.7346 (mp0) REVERT: B 323 ASN cc_start: 0.7941 (m-40) cc_final: 0.7732 (m-40) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1159 time to fit residues: 23.7151 Evaluate side-chains 149 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 423 ASN R 608 GLN R1249 ASN B 305 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.165538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.150119 restraints weight = 11242.701| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 2.56 r_work: 0.4036 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 7485 Z= 0.198 Angle : 0.618 8.461 10147 Z= 0.330 Chirality : 0.045 0.173 1147 Planarity : 0.005 0.074 1277 Dihedral : 4.705 20.826 1003 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.02 % Allowed : 10.66 % Favored : 88.32 % 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: -0.23 (0.28), residues: 906 helix: 1.24 (0.28), residues: 346 sheet: -0.76 (0.34), residues: 209 loop : -1.10 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R1327 TYR 0.016 0.002 TYR R1296 PHE 0.022 0.002 PHE B 209 TRP 0.040 0.002 TRP R 664 HIS 0.004 0.001 HIS R1342 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 7481) covalent geometry : angle 0.61585 (10139) SS BOND : bond 0.00885 ( 4) SS BOND : angle 1.78467 ( 8) hydrogen bonds : bond 0.04591 ( 369) hydrogen bonds : angle 4.99094 ( 1065) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 447 LEU cc_start: 0.8055 (tp) cc_final: 0.7815 (tp) REVERT: R 648 LYS cc_start: 0.8118 (mmmt) cc_final: 0.7739 (tppt) REVERT: R 1019 LYS cc_start: 0.7520 (mtpp) cc_final: 0.7238 (mtpp) REVERT: R 1044 ASP cc_start: 0.7751 (m-30) cc_final: 0.7491 (m-30) REVERT: R 1228 LYS cc_start: 0.7487 (mptt) cc_final: 0.7285 (mmtm) REVERT: B 242 ILE cc_start: 0.8170 (tt) cc_final: 0.7538 (tp) REVERT: B 272 MET cc_start: 0.6642 (tpp) cc_final: 0.6280 (tpp) REVERT: B 323 ASN cc_start: 0.8176 (m-40) cc_final: 0.7818 (m-40) outliers start: 8 outliers final: 3 residues processed: 156 average time/residue: 0.1072 time to fit residues: 21.1714 Evaluate side-chains 148 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 145 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 529 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain N residue 30 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 37 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 62 optimal weight: 0.6980 chunk 82 optimal weight: 0.0020 chunk 79 optimal weight: 4.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 608 GLN B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.165032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.149938 restraints weight = 11130.322| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 2.51 r_work: 0.4041 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7485 Z= 0.156 Angle : 0.570 7.948 10147 Z= 0.306 Chirality : 0.043 0.159 1147 Planarity : 0.004 0.059 1277 Dihedral : 4.557 16.877 1003 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.16 % Allowed : 13.45 % Favored : 84.39 % 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: -0.07 (0.28), residues: 906 helix: 1.40 (0.28), residues: 344 sheet: -0.69 (0.35), residues: 210 loop : -1.03 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R1327 TYR 0.017 0.002 TYR R1032 PHE 0.025 0.002 PHE R 459 TRP 0.024 0.002 TRP R 664 HIS 0.003 0.001 HIS R1342 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 7481) covalent geometry : angle 0.56886 (10139) SS BOND : bond 0.00620 ( 4) SS BOND : angle 1.38591 ( 8) hydrogen bonds : bond 0.04203 ( 369) hydrogen bonds : angle 4.82847 ( 1065) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 447 LEU cc_start: 0.8023 (tp) cc_final: 0.7799 (tp) REVERT: R 595 ILE cc_start: 0.5536 (OUTLIER) cc_final: 0.5022 (mm) REVERT: R 599 TYR cc_start: 0.7610 (OUTLIER) cc_final: 0.6086 (m-80) REVERT: R 1019 LYS cc_start: 0.7386 (mtpp) cc_final: 0.7128 (mtpp) REVERT: R 1044 ASP cc_start: 0.7617 (m-30) cc_final: 0.7401 (m-30) REVERT: R 1299 GLU cc_start: 0.7672 (mp0) cc_final: 0.7471 (mp0) REVERT: R 1369 GLN cc_start: 0.6556 (mm110) cc_final: 0.6343 (mm-40) REVERT: B 78 ARG cc_start: 0.7635 (mtp180) cc_final: 0.7159 (mtp180) REVERT: B 242 ILE cc_start: 0.8161 (tt) cc_final: 0.7553 (tp) REVERT: B 272 MET cc_start: 0.6603 (tpp) cc_final: 0.6389 (tpp) REVERT: B 323 ASN cc_start: 0.8046 (m-40) cc_final: 0.7672 (m-40) outliers start: 17 outliers final: 9 residues processed: 157 average time/residue: 0.1090 time to fit residues: 21.8513 Evaluate side-chains 153 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 467 LYS Chi-restraints excluded: chain R residue 513 CYS Chi-restraints excluded: chain R residue 529 ILE Chi-restraints excluded: chain R residue 595 ILE Chi-restraints excluded: chain R residue 599 TYR Chi-restraints excluded: chain R residue 1055 MET Chi-restraints excluded: chain R residue 1219 VAL Chi-restraints excluded: chain R residue 1249 ASN Chi-restraints excluded: chain R residue 1366 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain N residue 30 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 0.0570 chunk 79 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 423 ASN R 677 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.163679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.148640 restraints weight = 11361.224| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 2.51 r_work: 0.4014 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7485 Z= 0.177 Angle : 0.566 8.117 10147 Z= 0.304 Chirality : 0.043 0.139 1147 Planarity : 0.004 0.053 1277 Dihedral : 4.589 17.285 1003 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.55 % Allowed : 13.71 % Favored : 82.74 % 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: -0.02 (0.28), residues: 906 helix: 1.45 (0.28), residues: 344 sheet: -0.68 (0.35), residues: 211 loop : -0.98 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 160 TYR 0.018 0.002 TYR R1032 PHE 0.020 0.002 PHE R 597 TRP 0.016 0.002 TRP R 664 HIS 0.003 0.001 HIS R1342 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 7481) covalent geometry : angle 0.56493 (10139) SS BOND : bond 0.00707 ( 4) SS BOND : angle 1.53228 ( 8) hydrogen bonds : bond 0.04283 ( 369) hydrogen bonds : angle 4.80162 ( 1065) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 447 LEU cc_start: 0.8053 (tp) cc_final: 0.7842 (tp) REVERT: R 467 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6783 (mtmm) REVERT: R 599 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.7281 (m-80) REVERT: R 648 LYS cc_start: 0.8126 (mmmt) cc_final: 0.7792 (mmmt) REVERT: R 1019 LYS cc_start: 0.7360 (mtpp) cc_final: 0.7104 (mtpp) REVERT: R 1299 GLU cc_start: 0.7685 (mp0) cc_final: 0.7396 (mp0) REVERT: B 58 ARG cc_start: 0.6388 (ttt180) cc_final: 0.6149 (ttt-90) REVERT: B 242 ILE cc_start: 0.8142 (tt) cc_final: 0.7644 (tp) REVERT: B 323 ASN cc_start: 0.8051 (m-40) cc_final: 0.7667 (m-40) outliers start: 28 outliers final: 16 residues processed: 166 average time/residue: 0.0913 time to fit residues: 19.8127 Evaluate side-chains 164 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 467 LYS Chi-restraints excluded: chain R residue 513 CYS Chi-restraints excluded: chain R residue 525 LYS Chi-restraints excluded: chain R residue 529 ILE Chi-restraints excluded: chain R residue 599 TYR Chi-restraints excluded: chain R residue 1055 MET Chi-restraints excluded: chain R residue 1216 MET Chi-restraints excluded: chain R residue 1219 VAL Chi-restraints excluded: chain R residue 1225 GLU Chi-restraints excluded: chain R residue 1249 ASN Chi-restraints excluded: chain R residue 1305 THR Chi-restraints excluded: chain R residue 1366 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 72 optimal weight: 0.0870 chunk 54 optimal weight: 0.0980 chunk 62 optimal weight: 0.0570 chunk 66 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1256 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 = 0.4322 r_free = 0.4322 target = 0.165911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.150950 restraints weight = 11204.478| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 2.50 r_work: 0.4044 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7485 Z= 0.127 Angle : 0.531 7.424 10147 Z= 0.287 Chirality : 0.043 0.232 1147 Planarity : 0.004 0.047 1277 Dihedral : 4.400 17.005 1003 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.81 % Allowed : 14.34 % Favored : 81.85 % 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: 0.13 (0.28), residues: 906 helix: 1.66 (0.28), residues: 344 sheet: -0.57 (0.35), residues: 217 loop : -1.04 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 324 TYR 0.022 0.001 TYR R1032 PHE 0.020 0.001 PHE R 597 TRP 0.017 0.002 TRP R 664 HIS 0.003 0.001 HIS R1342 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 7481) covalent geometry : angle 0.53100 (10139) SS BOND : bond 0.00717 ( 4) SS BOND : angle 0.66067 ( 8) hydrogen bonds : bond 0.03888 ( 369) hydrogen bonds : angle 4.68410 ( 1065) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 447 LEU cc_start: 0.7968 (tp) cc_final: 0.7756 (tp) REVERT: R 599 TYR cc_start: 0.7603 (OUTLIER) cc_final: 0.7090 (m-80) REVERT: R 648 LYS cc_start: 0.8106 (mmmt) cc_final: 0.7736 (tppt) REVERT: R 1019 LYS cc_start: 0.7444 (mtpp) cc_final: 0.7193 (mtpp) REVERT: R 1280 ASP cc_start: 0.5823 (p0) cc_final: 0.4848 (m-30) REVERT: R 1299 GLU cc_start: 0.7652 (mp0) cc_final: 0.7400 (mp0) REVERT: B 109 TRP cc_start: 0.7720 (OUTLIER) cc_final: 0.6665 (p-90) REVERT: B 323 ASN cc_start: 0.8016 (m-40) cc_final: 0.7623 (m-40) outliers start: 30 outliers final: 16 residues processed: 171 average time/residue: 0.1118 time to fit residues: 24.4447 Evaluate side-chains 168 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 407 ILE Chi-restraints excluded: chain R residue 467 LYS Chi-restraints excluded: chain R residue 513 CYS Chi-restraints excluded: chain R residue 529 ILE Chi-restraints excluded: chain R residue 599 TYR Chi-restraints excluded: chain R residue 1052 VAL Chi-restraints excluded: chain R residue 1055 MET Chi-restraints excluded: chain R residue 1219 VAL Chi-restraints excluded: chain R residue 1249 ASN Chi-restraints excluded: chain R residue 1354 THR Chi-restraints excluded: chain R residue 1366 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 109 TRP Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain N residue 30 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 84 optimal weight: 0.0770 chunk 70 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 423 ASN ** R1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.163512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.148495 restraints weight = 11199.627| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 2.50 r_work: 0.4013 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7485 Z= 0.177 Angle : 0.580 11.590 10147 Z= 0.310 Chirality : 0.044 0.265 1147 Planarity : 0.004 0.063 1277 Dihedral : 4.539 18.937 1003 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.57 % Allowed : 15.10 % Favored : 80.33 % 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: 0.08 (0.28), residues: 906 helix: 1.58 (0.28), residues: 344 sheet: -0.53 (0.35), residues: 218 loop : -1.07 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R1037 TYR 0.021 0.002 TYR R1032 PHE 0.021 0.002 PHE R 597 TRP 0.015 0.002 TRP R1229 HIS 0.009 0.001 HIS R1215 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 7481) covalent geometry : angle 0.57933 (10139) SS BOND : bond 0.00907 ( 4) SS BOND : angle 1.15405 ( 8) hydrogen bonds : bond 0.04226 ( 369) hydrogen bonds : angle 4.74019 ( 1065) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 447 LEU cc_start: 0.8027 (tp) cc_final: 0.7782 (tp) REVERT: R 448 CYS cc_start: 0.5301 (OUTLIER) cc_final: 0.4652 (t) REVERT: R 486 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6891 (mp10) REVERT: R 599 TYR cc_start: 0.7630 (OUTLIER) cc_final: 0.7262 (m-80) REVERT: R 648 LYS cc_start: 0.8150 (mmmt) cc_final: 0.7875 (mmtt) REVERT: R 1019 LYS cc_start: 0.7413 (mtpp) cc_final: 0.7165 (mtpp) REVERT: R 1228 LYS cc_start: 0.7448 (mptt) cc_final: 0.7189 (mptt) REVERT: B 109 TRP cc_start: 0.7831 (OUTLIER) cc_final: 0.6742 (p-90) REVERT: B 242 ILE cc_start: 0.8147 (tt) cc_final: 0.7712 (tp) REVERT: B 323 ASN cc_start: 0.8041 (m-40) cc_final: 0.7660 (m-40) outliers start: 36 outliers final: 26 residues processed: 177 average time/residue: 0.1139 time to fit residues: 25.5157 Evaluate side-chains 180 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 407 ILE Chi-restraints excluded: chain R residue 448 CYS Chi-restraints excluded: chain R residue 467 LYS Chi-restraints excluded: chain R residue 486 GLN Chi-restraints excluded: chain R residue 500 VAL Chi-restraints excluded: chain R residue 513 CYS Chi-restraints excluded: chain R residue 529 ILE Chi-restraints excluded: chain R residue 599 TYR Chi-restraints excluded: chain R residue 665 VAL Chi-restraints excluded: chain R residue 1052 VAL Chi-restraints excluded: chain R residue 1055 MET Chi-restraints excluded: chain R residue 1219 VAL Chi-restraints excluded: chain R residue 1225 GLU Chi-restraints excluded: chain R residue 1249 ASN Chi-restraints excluded: chain R residue 1305 THR Chi-restraints excluded: chain R residue 1354 THR Chi-restraints excluded: chain R residue 1366 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 109 TRP Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 50 optimal weight: 0.0670 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 89 optimal weight: 0.0970 chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1256 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 = 0.4303 r_free = 0.4303 target = 0.164465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.149492 restraints weight = 11209.442| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 2.49 r_work: 0.4020 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7485 Z= 0.149 Angle : 0.562 10.547 10147 Z= 0.301 Chirality : 0.043 0.237 1147 Planarity : 0.004 0.043 1277 Dihedral : 4.496 19.737 1003 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.57 % Allowed : 16.88 % Favored : 78.55 % 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: 0.12 (0.28), residues: 906 helix: 1.61 (0.28), residues: 344 sheet: -0.49 (0.35), residues: 217 loop : -1.05 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R1037 TYR 0.025 0.001 TYR R1032 PHE 0.029 0.002 PHE R 411 TRP 0.014 0.002 TRP R 664 HIS 0.004 0.001 HIS R1215 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 7481) covalent geometry : angle 0.56108 (10139) SS BOND : bond 0.00690 ( 4) SS BOND : angle 1.05318 ( 8) hydrogen bonds : bond 0.04069 ( 369) hydrogen bonds : angle 4.70566 ( 1065) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 412 VAL cc_start: 0.6812 (OUTLIER) cc_final: 0.6063 (m) REVERT: R 447 LEU cc_start: 0.8026 (tp) cc_final: 0.7772 (tp) REVERT: R 595 ILE cc_start: 0.5480 (OUTLIER) cc_final: 0.5159 (tp) REVERT: R 1019 LYS cc_start: 0.7441 (mtpp) cc_final: 0.7195 (mtpp) REVERT: R 1280 ASP cc_start: 0.5841 (p0) cc_final: 0.4936 (m-30) REVERT: B 62 ARG cc_start: 0.6869 (mtt-85) cc_final: 0.6177 (mtt-85) REVERT: B 109 TRP cc_start: 0.7787 (OUTLIER) cc_final: 0.6593 (p-90) REVERT: B 242 ILE cc_start: 0.8152 (tt) cc_final: 0.7687 (tp) REVERT: B 323 ASN cc_start: 0.7920 (m-40) cc_final: 0.7553 (m-40) REVERT: B 345 PHE cc_start: 0.7927 (m-10) cc_final: 0.7055 (m-10) outliers start: 36 outliers final: 24 residues processed: 175 average time/residue: 0.1071 time to fit residues: 24.0202 Evaluate side-chains 177 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 407 ILE Chi-restraints excluded: chain R residue 412 VAL Chi-restraints excluded: chain R residue 467 LYS Chi-restraints excluded: chain R residue 500 VAL Chi-restraints excluded: chain R residue 513 CYS Chi-restraints excluded: chain R residue 595 ILE Chi-restraints excluded: chain R residue 599 TYR Chi-restraints excluded: chain R residue 665 VAL Chi-restraints excluded: chain R residue 1055 MET Chi-restraints excluded: chain R residue 1219 VAL Chi-restraints excluded: chain R residue 1225 GLU Chi-restraints excluded: chain R residue 1249 ASN Chi-restraints excluded: chain R residue 1305 THR Chi-restraints excluded: chain R residue 1354 THR Chi-restraints excluded: chain R residue 1366 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 109 TRP Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 49 optimal weight: 0.0050 chunk 76 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 26 optimal weight: 0.0570 chunk 31 optimal weight: 0.8980 overall best weight: 0.4712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1256 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 = 0.4298 r_free = 0.4298 target = 0.163847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.148929 restraints weight = 11252.345| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 2.49 r_work: 0.4018 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7485 Z= 0.154 Angle : 0.579 10.493 10147 Z= 0.307 Chirality : 0.043 0.203 1147 Planarity : 0.004 0.056 1277 Dihedral : 4.529 20.400 1003 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.57 % Allowed : 17.26 % Favored : 78.17 % 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: 0.12 (0.28), residues: 906 helix: 1.62 (0.28), residues: 344 sheet: -0.48 (0.35), residues: 217 loop : -1.09 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 324 TYR 0.024 0.002 TYR R1032 PHE 0.042 0.002 PHE R 411 TRP 0.015 0.002 TRP R1229 HIS 0.003 0.001 HIS R1342 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 7481) covalent geometry : angle 0.57870 (10139) SS BOND : bond 0.00747 ( 4) SS BOND : angle 1.11610 ( 8) hydrogen bonds : bond 0.04101 ( 369) hydrogen bonds : angle 4.71575 ( 1065) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 408 GLN cc_start: 0.6623 (mm110) cc_final: 0.6397 (mm-40) REVERT: R 412 VAL cc_start: 0.6729 (OUTLIER) cc_final: 0.5937 (m) REVERT: R 447 LEU cc_start: 0.8018 (tp) cc_final: 0.7754 (tp) REVERT: R 449 CYS cc_start: 0.5864 (m) cc_final: 0.5499 (m) REVERT: R 599 TYR cc_start: 0.7613 (OUTLIER) cc_final: 0.7151 (m-80) REVERT: R 648 LYS cc_start: 0.8141 (mmmt) cc_final: 0.7830 (mmmt) REVERT: R 1019 LYS cc_start: 0.7408 (mtpp) cc_final: 0.7163 (mtpp) REVERT: R 1216 MET cc_start: 0.6885 (ttm) cc_final: 0.6391 (ptm) REVERT: R 1285 LYS cc_start: 0.5587 (ttmt) cc_final: 0.4991 (tttt) REVERT: R 1369 GLN cc_start: 0.6559 (mm110) cc_final: 0.6303 (mm110) REVERT: B 62 ARG cc_start: 0.6936 (mtt-85) cc_final: 0.6300 (mtt-85) REVERT: B 109 TRP cc_start: 0.7772 (OUTLIER) cc_final: 0.6465 (p-90) REVERT: B 242 ILE cc_start: 0.8153 (tt) cc_final: 0.7705 (tp) REVERT: B 323 ASN cc_start: 0.7935 (m-40) cc_final: 0.7559 (m-40) REVERT: B 345 PHE cc_start: 0.7913 (m-10) cc_final: 0.6775 (m-10) outliers start: 36 outliers final: 27 residues processed: 176 average time/residue: 0.1053 time to fit residues: 23.7520 Evaluate side-chains 184 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 407 ILE Chi-restraints excluded: chain R residue 412 VAL Chi-restraints excluded: chain R residue 416 SER Chi-restraints excluded: chain R residue 467 LYS Chi-restraints excluded: chain R residue 500 VAL Chi-restraints excluded: chain R residue 513 CYS Chi-restraints excluded: chain R residue 525 LYS Chi-restraints excluded: chain R residue 599 TYR Chi-restraints excluded: chain R residue 665 VAL Chi-restraints excluded: chain R residue 1055 MET Chi-restraints excluded: chain R residue 1203 PHE Chi-restraints excluded: chain R residue 1219 VAL Chi-restraints excluded: chain R residue 1249 ASN Chi-restraints excluded: chain R residue 1305 THR Chi-restraints excluded: chain R residue 1354 THR Chi-restraints excluded: chain R residue 1366 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 109 TRP Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 6 optimal weight: 0.0980 chunk 69 optimal weight: 3.9990 chunk 39 optimal weight: 0.0670 chunk 7 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 54 optimal weight: 0.0070 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1256 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 = 0.4315 r_free = 0.4315 target = 0.165370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.150731 restraints weight = 11080.454| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 2.46 r_work: 0.4042 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7485 Z= 0.127 Angle : 0.560 10.042 10147 Z= 0.298 Chirality : 0.042 0.173 1147 Planarity : 0.004 0.040 1277 Dihedral : 4.424 20.127 1003 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.43 % Allowed : 18.91 % Favored : 77.66 % 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: 0.25 (0.29), residues: 906 helix: 1.76 (0.28), residues: 345 sheet: -0.43 (0.36), residues: 217 loop : -1.04 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 324 TYR 0.023 0.001 TYR R1032 PHE 0.030 0.001 PHE R 411 TRP 0.015 0.002 TRP N 47 HIS 0.003 0.001 HIS R1342 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7481) covalent geometry : angle 0.55979 (10139) SS BOND : bond 0.00579 ( 4) SS BOND : angle 0.92124 ( 8) hydrogen bonds : bond 0.03813 ( 369) hydrogen bonds : angle 4.64443 ( 1065) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 412 VAL cc_start: 0.6696 (OUTLIER) cc_final: 0.5865 (m) REVERT: R 447 LEU cc_start: 0.7919 (tp) cc_final: 0.7683 (tp) REVERT: R 449 CYS cc_start: 0.5830 (m) cc_final: 0.5452 (m) REVERT: R 599 TYR cc_start: 0.7568 (OUTLIER) cc_final: 0.7070 (m-80) REVERT: R 648 LYS cc_start: 0.8129 (mmmt) cc_final: 0.7796 (mmmt) REVERT: R 1019 LYS cc_start: 0.7382 (mtpp) cc_final: 0.7137 (mtpp) REVERT: R 1216 MET cc_start: 0.6818 (ttm) cc_final: 0.6473 (ptm) REVERT: R 1228 LYS cc_start: 0.7703 (mmmm) cc_final: 0.7431 (mmmm) REVERT: R 1285 LYS cc_start: 0.5447 (ttmt) cc_final: 0.4734 (ttmt) REVERT: R 1332 ARG cc_start: 0.7855 (ptm-80) cc_final: 0.7581 (ttp80) REVERT: B 62 ARG cc_start: 0.6914 (mtt-85) cc_final: 0.6293 (mtt-85) REVERT: B 69 TYR cc_start: 0.8071 (m-80) cc_final: 0.7856 (m-80) REVERT: B 109 TRP cc_start: 0.7694 (OUTLIER) cc_final: 0.6444 (p-90) REVERT: B 323 ASN cc_start: 0.7877 (m-40) cc_final: 0.7517 (m-40) outliers start: 27 outliers final: 20 residues processed: 171 average time/residue: 0.1088 time to fit residues: 23.7956 Evaluate side-chains 173 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 407 ILE Chi-restraints excluded: chain R residue 412 VAL Chi-restraints excluded: chain R residue 467 LYS Chi-restraints excluded: chain R residue 599 TYR Chi-restraints excluded: chain R residue 665 VAL Chi-restraints excluded: chain R residue 1055 MET Chi-restraints excluded: chain R residue 1219 VAL Chi-restraints excluded: chain R residue 1225 GLU Chi-restraints excluded: chain R residue 1249 ASN Chi-restraints excluded: chain R residue 1305 THR Chi-restraints excluded: chain R residue 1354 THR Chi-restraints excluded: chain R residue 1366 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 109 TRP Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 82 optimal weight: 0.0980 chunk 4 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1256 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 = 0.4268 r_free = 0.4268 target = 0.161374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.146526 restraints weight = 11237.417| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 2.50 r_work: 0.3990 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 7485 Z= 0.210 Angle : 0.643 12.214 10147 Z= 0.337 Chirality : 0.045 0.190 1147 Planarity : 0.004 0.039 1277 Dihedral : 4.719 21.987 1003 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.17 % Allowed : 19.92 % Favored : 76.90 % 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: 0.07 (0.28), residues: 906 helix: 1.54 (0.28), residues: 344 sheet: -0.48 (0.36), residues: 211 loop : -1.06 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 324 TYR 0.022 0.002 TYR R1032 PHE 0.026 0.002 PHE R 411 TRP 0.018 0.002 TRP R1229 HIS 0.004 0.001 HIS R1342 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 7481) covalent geometry : angle 0.64211 (10139) SS BOND : bond 0.00965 ( 4) SS BOND : angle 1.42664 ( 8) hydrogen bonds : bond 0.04481 ( 369) hydrogen bonds : angle 4.86035 ( 1065) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 412 VAL cc_start: 0.6775 (OUTLIER) cc_final: 0.5886 (m) REVERT: R 447 LEU cc_start: 0.8078 (tp) cc_final: 0.7819 (tp) REVERT: R 449 CYS cc_start: 0.5978 (m) cc_final: 0.5566 (m) REVERT: R 599 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.7242 (m-80) REVERT: R 632 PHE cc_start: 0.5333 (m-10) cc_final: 0.4726 (m-80) REVERT: R 648 LYS cc_start: 0.8160 (mmmt) cc_final: 0.7822 (mmmt) REVERT: R 1019 LYS cc_start: 0.7298 (mtpp) cc_final: 0.7065 (mtpp) REVERT: R 1203 PHE cc_start: 0.5756 (OUTLIER) cc_final: 0.4173 (m-10) REVERT: R 1206 LYS cc_start: 0.7831 (mmtt) cc_final: 0.7525 (mmtt) REVERT: R 1228 LYS cc_start: 0.7764 (mmmm) cc_final: 0.7503 (mmmm) REVERT: R 1285 LYS cc_start: 0.5569 (ttmt) cc_final: 0.4859 (ttmt) REVERT: B 109 TRP cc_start: 0.7808 (OUTLIER) cc_final: 0.6486 (p-90) REVERT: B 223 VAL cc_start: 0.7701 (t) cc_final: 0.7339 (m) REVERT: B 242 ILE cc_start: 0.8161 (tt) cc_final: 0.7766 (tp) REVERT: B 323 ASN cc_start: 0.7842 (m-40) cc_final: 0.7522 (m-40) outliers start: 25 outliers final: 18 residues processed: 171 average time/residue: 0.1116 time to fit residues: 24.3002 Evaluate side-chains 176 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 407 ILE Chi-restraints excluded: chain R residue 412 VAL Chi-restraints excluded: chain R residue 467 LYS Chi-restraints excluded: chain R residue 599 TYR Chi-restraints excluded: chain R residue 665 VAL Chi-restraints excluded: chain R residue 1055 MET Chi-restraints excluded: chain R residue 1203 PHE Chi-restraints excluded: chain R residue 1219 VAL Chi-restraints excluded: chain R residue 1249 ASN Chi-restraints excluded: chain R residue 1305 THR Chi-restraints excluded: chain R residue 1354 THR Chi-restraints excluded: chain R residue 1366 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 109 TRP Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 56 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 25 optimal weight: 0.0770 chunk 53 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 chunk 48 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 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 = 0.4298 r_free = 0.4298 target = 0.163939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.149398 restraints weight = 11211.004| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 2.48 r_work: 0.4020 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7485 Z= 0.145 Angle : 0.587 10.550 10147 Z= 0.312 Chirality : 0.043 0.163 1147 Planarity : 0.004 0.047 1277 Dihedral : 4.584 21.918 1003 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.66 % Allowed : 20.81 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.28), residues: 906 helix: 1.68 (0.28), residues: 345 sheet: -0.45 (0.36), residues: 211 loop : -1.04 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 62 TYR 0.025 0.002 TYR R1032 PHE 0.030 0.002 PHE R 411 TRP 0.015 0.002 TRP N 47 HIS 0.004 0.001 HIS R1342 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 7481) covalent geometry : angle 0.58692 (10139) SS BOND : bond 0.00614 ( 4) SS BOND : angle 1.08357 ( 8) hydrogen bonds : bond 0.04035 ( 369) hydrogen bonds : angle 4.79022 ( 1065) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2054.68 seconds wall clock time: 35 minutes 54.40 seconds (2154.40 seconds total)