Starting phenix.real_space_refine on Thu Jul 2 06:25:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w0o_65510/07_2026/9w0o_65510_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w0o_65510/07_2026/9w0o_65510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w0o_65510/07_2026/9w0o_65510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w0o_65510/07_2026/9w0o_65510.map" model { file = "/net/cci-nas-00/data/ceres_data/9w0o_65510/07_2026/9w0o_65510_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w0o_65510/07_2026/9w0o_65510_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 56 5.16 5 C 4479 2.51 5 N 1209 2.21 5 O 1280 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: 7024 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1752 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2548 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'ASP:plan': 2, 'ASN%COO:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 401 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2323 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 284} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.69, per 1000 atoms: 0.24 Number of scatterers: 7024 At special positions: 0 Unit cell: (118.085, 118.085, 86.735, 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 56 16.00 O 1280 8.00 N 1209 7.00 C 4479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 204 " - pdb=" SG CYS D 211 " distance=2.03 Simple disulfide: pdb=" SG CYS D 295 " - pdb=" SG CYS D 300 " 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: 0.59 Conformation dependent library (CDL) restraints added in 361.0 milliseconds 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1706 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 46.1% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 9 through 31 Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 46 through 51 removed outlier: 3.527A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.239A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.734A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.905A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.028A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 351 removed outlier: 4.459A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 26 removed outlier: 3.582A pdb=" N GLU B 10 " --> pdb=" O GLU B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.751A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 45 Processing helix chain 'D' and resid 42 through 51 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 65 through 94 removed outlier: 3.652A pdb=" N VAL D 70 " --> pdb=" O THR D 66 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 98 removed outlier: 3.608A pdb=" N ASN D 98 " --> pdb=" O LYS D 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 98' Processing helix chain 'D' and resid 99 through 125 removed outlier: 4.163A pdb=" N PHE D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE D 104 " --> pdb=" O MET D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 168 removed outlier: 3.625A pdb=" N TRP D 137 " --> pdb=" O SER D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 197 removed outlier: 4.405A pdb=" N VAL D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 201 removed outlier: 3.599A pdb=" N GLY D 201 " --> pdb=" O PRO D 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 198 through 201' Processing helix chain 'D' and resid 219 through 255 removed outlier: 3.602A pdb=" N LYS D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 295 removed outlier: 4.141A pdb=" N CYS D 281 " --> pdb=" O VAL D 277 " (cutoff:3.500A) Proline residue: D 284 - end of helix removed outlier: 3.723A pdb=" N PHE D 289 " --> pdb=" O LEU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 307 through 325 Proline residue: D 321 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 8.784A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.606A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.141A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.076A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.537A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 198 through 199 removed outlier: 6.597A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.587A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.919A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 1071 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: 1.14 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2274 1.34 - 1.46: 1655 1.46 - 1.58: 3149 1.58 - 1.70: 0 1.70 - 1.81: 79 Bond restraints: 7157 Sorted by residual: bond pdb=" CA GLU A 8 " pdb=" CB GLU A 8 " ideal model delta sigma weight residual 1.532 1.542 -0.010 1.51e-02 4.39e+03 4.65e-01 bond pdb=" N GLU A 8 " pdb=" CA GLU A 8 " ideal model delta sigma weight residual 1.462 1.472 -0.010 1.48e-02 4.57e+03 4.53e-01 bond pdb=" CB PRO C 60 " pdb=" CG PRO C 60 " ideal model delta sigma weight residual 1.492 1.525 -0.033 5.00e-02 4.00e+02 4.46e-01 bond pdb=" CA GLU D 63 " pdb=" CB GLU D 63 " ideal model delta sigma weight residual 1.530 1.541 -0.011 1.69e-02 3.50e+03 4.27e-01 bond pdb=" C PHE D 96 " pdb=" N HIS D 97 " ideal model delta sigma weight residual 1.330 1.338 -0.008 1.29e-02 6.01e+03 3.63e-01 ... (remaining 7152 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 9542 1.51 - 3.02: 114 3.02 - 4.53: 22 4.53 - 6.04: 4 6.04 - 7.55: 4 Bond angle restraints: 9686 Sorted by residual: angle pdb=" CB MET A 18 " pdb=" CG MET A 18 " pdb=" SD MET A 18 " ideal model delta sigma weight residual 112.70 119.23 -6.53 3.00e+00 1.11e-01 4.74e+00 angle pdb=" C SER D 62 " pdb=" N GLU D 63 " pdb=" CA GLU D 63 " ideal model delta sigma weight residual 121.54 125.69 -4.15 1.91e+00 2.74e-01 4.71e+00 angle pdb=" CA LEU D 326 " pdb=" CB LEU D 326 " pdb=" CG LEU D 326 " ideal model delta sigma weight residual 116.30 123.85 -7.55 3.50e+00 8.16e-02 4.65e+00 angle pdb=" CA GLU A 8 " pdb=" CB GLU A 8 " pdb=" CG GLU A 8 " ideal model delta sigma weight residual 114.10 117.97 -3.87 2.00e+00 2.50e-01 3.74e+00 angle pdb=" C ALA A 7 " pdb=" N GLU A 8 " pdb=" CA GLU A 8 " ideal model delta sigma weight residual 122.61 125.59 -2.98 1.56e+00 4.11e-01 3.66e+00 ... (remaining 9681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 3911 17.37 - 34.73: 302 34.73 - 52.10: 52 52.10 - 69.47: 8 69.47 - 86.83: 6 Dihedral angle restraints: 4279 sinusoidal: 1654 harmonic: 2625 Sorted by residual: dihedral pdb=" CB CYS D 204 " pdb=" SG CYS D 204 " pdb=" SG CYS D 211 " pdb=" CB CYS D 211 " ideal model delta sinusoidal sigma weight residual 93.00 41.12 51.88 1 1.00e+01 1.00e-02 3.67e+01 dihedral pdb=" CB GLU A 43 " pdb=" CG GLU A 43 " pdb=" CD GLU A 43 " pdb=" OE1 GLU A 43 " ideal model delta sinusoidal sigma weight residual 0.00 86.83 -86.83 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CA ARG B 304 " pdb=" C ARG B 304 " pdb=" N ALA B 305 " pdb=" CA ALA B 305 " ideal model delta harmonic sigma weight residual -180.00 -164.45 -15.55 0 5.00e+00 4.00e-02 9.67e+00 ... (remaining 4276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 680 0.029 - 0.058: 282 0.058 - 0.087: 112 0.087 - 0.115: 42 0.115 - 0.144: 7 Chirality restraints: 1123 Sorted by residual: chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA ILE A 221 " pdb=" N ILE A 221 " pdb=" C ILE A 221 " pdb=" CB ILE A 221 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 1120 not shown) Planarity restraints: 1216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 169 " 0.012 2.00e-02 2.50e+03 8.88e-03 1.97e+00 pdb=" CG TRP B 169 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP B 169 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP B 169 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 169 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 169 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 169 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 169 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 169 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 169 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO B 236 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER D 276 " -0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C SER D 276 " 0.023 2.00e-02 2.50e+03 pdb=" O SER D 276 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL D 277 " -0.008 2.00e-02 2.50e+03 ... (remaining 1213 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 324 2.73 - 3.27: 7089 3.27 - 3.82: 11893 3.82 - 4.36: 13479 4.36 - 4.90: 23719 Nonbonded interactions: 56504 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.191 3.040 nonbonded pdb=" OD1 ASP D 111 " pdb=" OG SER D 317 " model vdw 2.267 3.040 nonbonded pdb=" OE2 GLU A 289 " pdb=" OH TYR A 302 " model vdw 2.286 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.296 3.040 nonbonded pdb=" O ASN D 121 " pdb=" OG SER D 125 " model vdw 2.304 3.040 ... (remaining 56499 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: 1.250 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.480 Find NCS groups from input model: 0.040 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:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 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 : 0.002 0.033 7159 Z= 0.089 Angle : 0.464 7.546 9690 Z= 0.242 Chirality : 0.039 0.144 1123 Planarity : 0.002 0.035 1216 Dihedral : 12.831 86.833 2567 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.99 (0.28), residues: 888 helix: 2.54 (0.27), residues: 378 sheet: 0.25 (0.45), residues: 128 loop : -1.21 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 48 TYR 0.009 0.001 TYR A 230 PHE 0.015 0.001 PHE D 138 TRP 0.024 0.001 TRP B 169 HIS 0.002 0.000 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00174 / 0.09 ( 7157) covalent geometry : angle 0.46316 / 0.24 ( 9686) SS BOND : bond 0.00076 / 0.04 ( 2) SS BOND : angle 1.50497 / 0.81 ( 4) hydrogen bonds : bond 0.12206 / 8.39 ( 370) hydrogen bonds : angle 4.90584 / 3.50 ( 1071) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 134 ARG cc_start: 0.4186 (tpm170) cc_final: 0.3896 (ttt90) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.3900 time to fit residues: 60.9099 Evaluate side-chains 103 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 HIS D 83 ASN D 259 ASN ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.172480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.131016 restraints weight = 7834.351| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.52 r_work: 0.3608 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 7159 Z= 0.256 Angle : 0.679 7.855 9690 Z= 0.348 Chirality : 0.047 0.254 1123 Planarity : 0.004 0.044 1216 Dihedral : 4.529 21.053 967 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.44 % Allowed : 11.64 % Favored : 84.92 % 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: 0.47 (0.28), residues: 888 helix: 1.69 (0.26), residues: 376 sheet: -0.25 (0.40), residues: 158 loop : -0.91 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 96 TYR 0.019 0.002 TYR D 324 PHE 0.017 0.002 PHE A 196 TRP 0.030 0.003 TRP B 211 HIS 0.007 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.26 ( 7157) covalent geometry : angle 0.67735 / 0.35 ( 9686) SS BOND : bond 0.00443 / 0.23 ( 2) SS BOND : angle 2.64408 / 1.44 ( 4) hydrogen bonds : bond 0.04043 / 2.78 ( 370) hydrogen bonds : angle 4.59938 / 3.20 ( 1071) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.281 Fit side-chains REVERT: A 25 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6942 (mt-10) REVERT: A 193 ASP cc_start: 0.7751 (t0) cc_final: 0.7360 (t0) REVERT: A 197 LYS cc_start: 0.8585 (mtmt) cc_final: 0.8187 (mttt) REVERT: A 229 ASP cc_start: 0.7518 (t0) cc_final: 0.6811 (t70) REVERT: B 59 TYR cc_start: 0.8949 (m-80) cc_final: 0.8735 (m-80) REVERT: B 134 ARG cc_start: 0.5736 (tpm170) cc_final: 0.4633 (ttt180) REVERT: B 267 ASP cc_start: 0.7951 (m-30) cc_final: 0.7723 (m-30) REVERT: B 270 ILE cc_start: 0.7196 (OUTLIER) cc_final: 0.6994 (pp) REVERT: C 32 LYS cc_start: 0.8220 (tttt) cc_final: 0.7946 (tttp) REVERT: D 101 TYR cc_start: 0.7962 (m-10) cc_final: 0.7568 (m-80) REVERT: D 296 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6808 (mmt90) REVERT: D 305 LYS cc_start: 0.7551 (tptp) cc_final: 0.6354 (pmtt) outliers start: 26 outliers final: 11 residues processed: 142 average time/residue: 0.4151 time to fit residues: 63.2439 Evaluate side-chains 112 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 296 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 77 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN B 230 ASN ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.174455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.133593 restraints weight = 7781.521| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.35 r_work: 0.3659 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7159 Z= 0.146 Angle : 0.551 6.492 9690 Z= 0.283 Chirality : 0.042 0.171 1123 Planarity : 0.003 0.027 1216 Dihedral : 4.253 19.268 967 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.17 % Allowed : 17.06 % Favored : 79.76 % 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: 0.60 (0.28), residues: 888 helix: 1.88 (0.26), residues: 377 sheet: -0.17 (0.40), residues: 156 loop : -0.95 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.013 0.001 TYR A 230 PHE 0.017 0.001 PHE B 199 TRP 0.025 0.002 TRP B 169 HIS 0.003 0.000 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 7157) covalent geometry : angle 0.54955 / 0.28 ( 9686) SS BOND : bond 0.00172 / 0.09 ( 2) SS BOND : angle 1.93721 / 1.06 ( 4) hydrogen bonds : bond 0.03475 / 2.38 ( 370) hydrogen bonds : angle 4.42038 / 3.07 ( 1071) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6827 (mt-10) REVERT: A 330 LYS cc_start: 0.8002 (ttmm) cc_final: 0.7613 (mtpp) REVERT: B 127 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7184 (mmpt) REVERT: B 134 ARG cc_start: 0.5711 (tpm170) cc_final: 0.4781 (ttt180) REVERT: B 234 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.6746 (m-80) REVERT: B 267 ASP cc_start: 0.7784 (m-30) cc_final: 0.7556 (m-30) REVERT: C 32 LYS cc_start: 0.8293 (tttt) cc_final: 0.8061 (tttp) REVERT: D 208 LEU cc_start: 0.7134 (mm) cc_final: 0.6920 (mm) REVERT: D 305 LYS cc_start: 0.7559 (tptp) cc_final: 0.6415 (pmtt) outliers start: 24 outliers final: 10 residues processed: 123 average time/residue: 0.4424 time to fit residues: 58.1246 Evaluate side-chains 112 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain D residue 213 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 59 optimal weight: 0.0770 chunk 55 optimal weight: 6.9990 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 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 = 0.4183 r_free = 0.4183 target = 0.169407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.128413 restraints weight = 7953.293| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.38 r_work: 0.3572 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7159 Z= 0.190 Angle : 0.593 11.521 9690 Z= 0.304 Chirality : 0.043 0.147 1123 Planarity : 0.003 0.029 1216 Dihedral : 4.445 20.565 967 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.37 % Allowed : 17.99 % Favored : 77.65 % 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: 0.24 (0.27), residues: 888 helix: 1.60 (0.26), residues: 379 sheet: -0.56 (0.36), residues: 174 loop : -1.09 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.012 0.002 TYR D 324 PHE 0.025 0.002 PHE B 199 TRP 0.028 0.002 TRP B 169 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 ( 7157) covalent geometry : angle 0.59129 / 0.30 ( 9686) SS BOND : bond 0.00246 / 0.13 ( 2) SS BOND : angle 2.11730 / 1.17 ( 4) hydrogen bonds : bond 0.03649 / 2.52 ( 370) hydrogen bonds : angle 4.60642 / 3.20 ( 1071) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.326 Fit side-chains REVERT: A 20 ASP cc_start: 0.7394 (m-30) cc_final: 0.7139 (m-30) REVERT: A 25 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6821 (mt-10) REVERT: A 193 ASP cc_start: 0.7628 (t0) cc_final: 0.7327 (t0) REVERT: A 229 ASP cc_start: 0.7596 (t0) cc_final: 0.6777 (t70) REVERT: B 127 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7236 (mmpt) REVERT: B 134 ARG cc_start: 0.5991 (tpm170) cc_final: 0.5069 (ttt180) REVERT: B 220 GLN cc_start: 0.6103 (OUTLIER) cc_final: 0.5796 (mt0) REVERT: B 234 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.6823 (m-80) REVERT: B 270 ILE cc_start: 0.6908 (OUTLIER) cc_final: 0.6567 (pp) REVERT: C 32 LYS cc_start: 0.8460 (tttt) cc_final: 0.8165 (tttp) REVERT: D 101 TYR cc_start: 0.7586 (m-80) cc_final: 0.7370 (m-80) REVERT: D 124 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.6800 (ppp) REVERT: D 208 LEU cc_start: 0.7125 (mm) cc_final: 0.6870 (mm) REVERT: D 257 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7881 (p0) REVERT: D 296 ARG cc_start: 0.7142 (mtp85) cc_final: 0.6835 (mmt90) REVERT: D 305 LYS cc_start: 0.7477 (tptp) cc_final: 0.6426 (pmtt) outliers start: 33 outliers final: 12 residues processed: 138 average time/residue: 0.4153 time to fit residues: 61.5615 Evaluate side-chains 129 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain D residue 187 CYS Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 257 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 61 optimal weight: 0.0980 chunk 74 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN B 75 GLN B 125 ASN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.171573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.131484 restraints weight = 7813.869| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.34 r_work: 0.3628 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7159 Z= 0.150 Angle : 0.563 11.020 9690 Z= 0.290 Chirality : 0.042 0.138 1123 Planarity : 0.003 0.026 1216 Dihedral : 4.287 19.941 967 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.44 % Allowed : 21.43 % Favored : 75.13 % 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: 0.31 (0.27), residues: 888 helix: 1.76 (0.26), residues: 372 sheet: -0.53 (0.36), residues: 173 loop : -1.11 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.010 0.001 TYR D 245 PHE 0.020 0.001 PHE B 199 TRP 0.022 0.002 TRP B 169 HIS 0.002 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 7157) covalent geometry : angle 0.56259 / 0.29 ( 9686) SS BOND : bond 0.00153 / 0.08 ( 2) SS BOND : angle 1.67004 / 0.92 ( 4) hydrogen bonds : bond 0.03489 / 2.40 ( 370) hydrogen bonds : angle 4.56237 / 3.17 ( 1071) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.320 Fit side-chains REVERT: A 25 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6942 (mt-10) REVERT: A 193 ASP cc_start: 0.7636 (t0) cc_final: 0.7369 (t0) REVERT: A 229 ASP cc_start: 0.7595 (t0) cc_final: 0.6684 (t70) REVERT: B 134 ARG cc_start: 0.5958 (tpm170) cc_final: 0.5120 (ttt180) REVERT: B 200 VAL cc_start: 0.7575 (m) cc_final: 0.7255 (m) REVERT: B 217 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7295 (pmt) REVERT: B 220 GLN cc_start: 0.6091 (OUTLIER) cc_final: 0.5755 (mt0) REVERT: B 234 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.6829 (m-80) REVERT: C 32 LYS cc_start: 0.8472 (tttt) cc_final: 0.8179 (tttp) REVERT: D 100 MET cc_start: 0.6488 (tpp) cc_final: 0.5944 (pmt) REVERT: D 138 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7492 (t80) REVERT: D 208 LEU cc_start: 0.7098 (mm) cc_final: 0.6834 (mm) REVERT: D 305 LYS cc_start: 0.7535 (tptp) cc_final: 0.6393 (pmtt) outliers start: 26 outliers final: 10 residues processed: 134 average time/residue: 0.4305 time to fit residues: 61.5623 Evaluate side-chains 123 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 311 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 320 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 = 0.4186 r_free = 0.4186 target = 0.169854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.129412 restraints weight = 8006.619| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.46 r_work: 0.3623 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7159 Z= 0.161 Angle : 0.582 10.163 9690 Z= 0.301 Chirality : 0.043 0.140 1123 Planarity : 0.003 0.027 1216 Dihedral : 4.366 20.713 967 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.84 % Allowed : 21.43 % Favored : 74.74 % 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: 0.30 (0.27), residues: 888 helix: 1.78 (0.26), residues: 366 sheet: -0.62 (0.37), residues: 172 loop : -1.06 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.010 0.001 TYR D 245 PHE 0.024 0.002 PHE D 78 TRP 0.021 0.002 TRP B 169 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 7157) covalent geometry : angle 0.58132 / 0.30 ( 9686) SS BOND : bond 0.00147 / 0.08 ( 2) SS BOND : angle 1.73720 / 0.96 ( 4) hydrogen bonds : bond 0.03519 / 2.40 ( 370) hydrogen bonds : angle 4.59703 / 3.20 ( 1071) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.271 Fit side-chains REVERT: A 25 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6957 (mt-10) REVERT: A 193 ASP cc_start: 0.7532 (t0) cc_final: 0.7231 (t0) REVERT: A 229 ASP cc_start: 0.7646 (t0) cc_final: 0.7214 (t70) REVERT: B 134 ARG cc_start: 0.6008 (tpm170) cc_final: 0.5035 (ttt180) REVERT: B 175 GLN cc_start: 0.7550 (pm20) cc_final: 0.7333 (pm20) REVERT: B 200 VAL cc_start: 0.7739 (m) cc_final: 0.7398 (m) REVERT: B 212 ASP cc_start: 0.7947 (m-30) cc_final: 0.7684 (m-30) REVERT: B 220 GLN cc_start: 0.6057 (OUTLIER) cc_final: 0.5679 (mt0) REVERT: B 234 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.6805 (m-80) REVERT: C 32 LYS cc_start: 0.8516 (tttt) cc_final: 0.8209 (tttp) REVERT: D 101 TYR cc_start: 0.7701 (m-80) cc_final: 0.7247 (m-80) REVERT: D 124 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.6853 (ppp) REVERT: D 208 LEU cc_start: 0.7106 (mm) cc_final: 0.6839 (mm) REVERT: D 305 LYS cc_start: 0.7579 (tptp) cc_final: 0.6377 (pmtt) outliers start: 29 outliers final: 18 residues processed: 133 average time/residue: 0.4178 time to fit residues: 59.4342 Evaluate side-chains 128 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain D residue 187 CYS Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 311 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 chunk 44 optimal weight: 0.0970 chunk 11 optimal weight: 0.0770 chunk 60 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 320 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 = 0.4228 r_free = 0.4228 target = 0.174106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.134644 restraints weight = 7883.024| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.41 r_work: 0.3662 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7159 Z= 0.124 Angle : 0.581 13.347 9690 Z= 0.293 Chirality : 0.042 0.273 1123 Planarity : 0.003 0.028 1216 Dihedral : 4.202 19.855 967 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.97 % Allowed : 22.62 % Favored : 73.41 % 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: 0.41 (0.27), residues: 888 helix: 1.88 (0.26), residues: 366 sheet: -0.40 (0.38), residues: 167 loop : -1.10 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 162 TYR 0.009 0.001 TYR D 324 PHE 0.026 0.001 PHE D 225 TRP 0.019 0.001 TRP B 169 HIS 0.002 0.000 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 7157) covalent geometry : angle 0.58069 / 0.29 ( 9686) SS BOND : bond 0.00101 / 0.05 ( 2) SS BOND : angle 1.50724 / 0.81 ( 4) hydrogen bonds : bond 0.03351 / 2.28 ( 370) hydrogen bonds : angle 4.48399 / 3.13 ( 1071) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.167 Fit side-chains REVERT: A 25 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6948 (mt-10) REVERT: A 198 MET cc_start: 0.8083 (mpt) cc_final: 0.7883 (mpt) REVERT: A 207 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7218 (mt-10) REVERT: A 229 ASP cc_start: 0.7601 (t0) cc_final: 0.7151 (t70) REVERT: A 247 MET cc_start: 0.7166 (mtm) cc_final: 0.6921 (mtm) REVERT: B 118 ASP cc_start: 0.6838 (OUTLIER) cc_final: 0.6614 (p0) REVERT: B 127 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7101 (mmpt) REVERT: B 134 ARG cc_start: 0.5921 (tpm170) cc_final: 0.4948 (ttt180) REVERT: B 212 ASP cc_start: 0.7989 (m-30) cc_final: 0.7727 (m-30) REVERT: B 217 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7244 (pmt) REVERT: C 32 LYS cc_start: 0.8479 (tttt) cc_final: 0.8192 (tttp) REVERT: D 124 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6705 (ppp) REVERT: D 160 ILE cc_start: 0.8194 (mm) cc_final: 0.7984 (mt) REVERT: D 169 MET cc_start: 0.7881 (tpp) cc_final: 0.7663 (mmm) REVERT: D 208 LEU cc_start: 0.7033 (mm) cc_final: 0.6764 (mm) REVERT: D 296 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6760 (mmt90) REVERT: D 305 LYS cc_start: 0.7525 (tptp) cc_final: 0.6335 (pmtt) outliers start: 30 outliers final: 17 residues processed: 135 average time/residue: 0.3716 time to fit residues: 53.9307 Evaluate side-chains 131 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 187 CYS Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 296 ARG Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 311 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.166389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.125795 restraints weight = 7959.944| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.35 r_work: 0.3550 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7159 Z= 0.214 Angle : 0.680 16.192 9690 Z= 0.342 Chirality : 0.045 0.269 1123 Planarity : 0.003 0.033 1216 Dihedral : 4.608 20.759 967 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.76 % Allowed : 22.09 % Favored : 73.15 % 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 (0.27), residues: 888 helix: 1.62 (0.26), residues: 366 sheet: -0.78 (0.37), residues: 174 loop : -1.06 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.012 0.002 TYR D 245 PHE 0.021 0.002 PHE D 225 TRP 0.020 0.002 TRP B 169 HIS 0.004 0.001 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.21 ( 7157) covalent geometry : angle 0.67888 / 0.34 ( 9686) SS BOND : bond 0.00157 / 0.08 ( 2) SS BOND : angle 1.94559 / 1.07 ( 4) hydrogen bonds : bond 0.03736 / 2.55 ( 370) hydrogen bonds : angle 4.76031 / 3.33 ( 1071) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7180 (mt-10) REVERT: A 229 ASP cc_start: 0.7878 (t0) cc_final: 0.7379 (t70) REVERT: A 247 MET cc_start: 0.7339 (mtm) cc_final: 0.7071 (mtm) REVERT: B 127 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7190 (mmpt) REVERT: B 134 ARG cc_start: 0.6356 (tpm170) cc_final: 0.5448 (ttt180) REVERT: B 176 GLN cc_start: 0.8205 (mt0) cc_final: 0.7962 (tt0) REVERT: B 217 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7192 (pmt) REVERT: B 220 GLN cc_start: 0.6295 (OUTLIER) cc_final: 0.5915 (mt0) REVERT: B 234 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.6733 (m-80) REVERT: C 32 LYS cc_start: 0.8571 (tttt) cc_final: 0.8290 (tttp) REVERT: D 124 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.7036 (ppp) REVERT: D 296 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6744 (mmt90) REVERT: D 305 LYS cc_start: 0.7658 (tptp) cc_final: 0.6671 (pptt) outliers start: 36 outliers final: 20 residues processed: 129 average time/residue: 0.4118 time to fit residues: 56.9769 Evaluate side-chains 128 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 187 CYS Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 296 ARG Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 311 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 22 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 0.4980 chunk 4 optimal weight: 0.0670 chunk 78 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.4195 r_free = 0.4195 target = 0.170654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.131214 restraints weight = 7909.590| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.37 r_work: 0.3624 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7159 Z= 0.145 Angle : 0.646 15.784 9690 Z= 0.319 Chirality : 0.043 0.267 1123 Planarity : 0.003 0.027 1216 Dihedral : 4.366 20.270 967 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.50 % Allowed : 22.22 % Favored : 73.28 % 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: 0.33 (0.27), residues: 888 helix: 1.78 (0.26), residues: 365 sheet: -0.42 (0.39), residues: 158 loop : -1.09 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.010 0.001 TYR B 59 PHE 0.018 0.001 PHE D 225 TRP 0.021 0.002 TRP B 169 HIS 0.002 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 ( 7157) covalent geometry : angle 0.64508 / 0.32 ( 9686) SS BOND : bond 0.00137 / 0.07 ( 2) SS BOND : angle 1.60255 / 0.87 ( 4) hydrogen bonds : bond 0.03470 / 2.36 ( 370) hydrogen bonds : angle 4.55844 / 3.19 ( 1071) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7278 (mt-10) REVERT: A 229 ASP cc_start: 0.7828 (t0) cc_final: 0.7384 (t70) REVERT: A 247 MET cc_start: 0.7187 (mtm) cc_final: 0.6957 (mtm) REVERT: B 127 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7125 (mmpt) REVERT: B 134 ARG cc_start: 0.6157 (tpm170) cc_final: 0.5175 (ttt180) REVERT: B 176 GLN cc_start: 0.7771 (mt0) cc_final: 0.7564 (tt0) REVERT: B 217 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7071 (pmt) REVERT: B 220 GLN cc_start: 0.6325 (OUTLIER) cc_final: 0.5862 (mt0) REVERT: C 32 LYS cc_start: 0.8543 (tttt) cc_final: 0.8231 (tttp) REVERT: D 85 MET cc_start: 0.7459 (ptm) cc_final: 0.6286 (pp-130) REVERT: D 124 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6838 (ppp) REVERT: D 172 TYR cc_start: 0.8550 (m-80) cc_final: 0.8278 (m-80) REVERT: D 208 LEU cc_start: 0.7079 (mm) cc_final: 0.6802 (mm) REVERT: D 296 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6707 (mmt90) REVERT: D 305 LYS cc_start: 0.7625 (tptp) cc_final: 0.6640 (pptt) outliers start: 34 outliers final: 17 residues processed: 131 average time/residue: 0.3994 time to fit residues: 56.2412 Evaluate side-chains 127 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 187 CYS Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 296 ARG Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 311 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 38 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 23 optimal weight: 0.0970 chunk 78 optimal weight: 0.7980 chunk 75 optimal weight: 0.0470 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.174161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.134841 restraints weight = 7870.697| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.35 r_work: 0.3699 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7159 Z= 0.134 Angle : 0.658 14.788 9690 Z= 0.321 Chirality : 0.043 0.260 1123 Planarity : 0.003 0.029 1216 Dihedral : 4.278 19.904 967 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.57 % Allowed : 23.94 % Favored : 72.49 % 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: 0.43 (0.27), residues: 888 helix: 1.89 (0.26), residues: 366 sheet: -0.29 (0.40), residues: 148 loop : -1.11 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.016 0.001 TYR A 287 PHE 0.020 0.001 PHE D 78 TRP 0.020 0.002 TRP B 169 HIS 0.002 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 7157) covalent geometry : angle 0.65742 / 0.32 ( 9686) SS BOND : bond 0.00128 / 0.06 ( 2) SS BOND : angle 1.53133 / 0.82 ( 4) hydrogen bonds : bond 0.03429 / 2.32 ( 370) hydrogen bonds : angle 4.41103 / 3.09 ( 1071) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7337 (mt-10) REVERT: A 229 ASP cc_start: 0.7818 (t0) cc_final: 0.7380 (t70) REVERT: A 247 MET cc_start: 0.7081 (mtm) cc_final: 0.6858 (mtm) REVERT: B 127 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7113 (mmpt) REVERT: B 134 ARG cc_start: 0.6046 (tpm170) cc_final: 0.5224 (ttt180) REVERT: B 220 GLN cc_start: 0.6036 (OUTLIER) cc_final: 0.5633 (mt0) REVERT: C 32 LYS cc_start: 0.8480 (tttt) cc_final: 0.8182 (tttp) REVERT: D 85 MET cc_start: 0.7423 (ptm) cc_final: 0.6259 (pp-130) REVERT: D 208 LEU cc_start: 0.7023 (mm) cc_final: 0.6742 (mm) REVERT: D 296 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.6742 (mmt90) REVERT: D 305 LYS cc_start: 0.7526 (tptp) cc_final: 0.6518 (pptt) outliers start: 27 outliers final: 16 residues processed: 127 average time/residue: 0.3588 time to fit residues: 48.7616 Evaluate side-chains 126 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 187 CYS Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 296 ARG Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 311 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 4.9990 chunk 39 optimal weight: 0.3980 chunk 3 optimal weight: 0.0570 chunk 58 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.0870 chunk 24 optimal weight: 0.8980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.174934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.135838 restraints weight = 7833.628| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.34 r_work: 0.3683 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7159 Z= 0.134 Angle : 0.650 14.916 9690 Z= 0.319 Chirality : 0.043 0.293 1123 Planarity : 0.003 0.028 1216 Dihedral : 4.231 19.467 967 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.17 % Allowed : 24.21 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.27), residues: 888 helix: 1.89 (0.26), residues: 366 sheet: -0.19 (0.40), residues: 148 loop : -1.11 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.017 0.001 TYR A 287 PHE 0.018 0.001 PHE D 225 TRP 0.020 0.002 TRP B 169 HIS 0.002 0.000 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 7157) covalent geometry : angle 0.64975 / 0.32 ( 9686) SS BOND : bond 0.00123 / 0.06 ( 2) SS BOND : angle 1.56424 / 0.84 ( 4) hydrogen bonds : bond 0.03373 / 2.30 ( 370) hydrogen bonds : angle 4.39596 / 3.08 ( 1071) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3633.48 seconds wall clock time: 62 minutes 30.11 seconds (3750.11 seconds total)