Starting phenix.real_space_refine on Wed Sep 17 13:55:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ixx_60980/09_2025/9ixx_60980_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ixx_60980/09_2025/9ixx_60980.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ixx_60980/09_2025/9ixx_60980_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ixx_60980/09_2025/9ixx_60980_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ixx_60980/09_2025/9ixx_60980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ixx_60980/09_2025/9ixx_60980.map" } resolution = 3.15 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= 0.003 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 57 5.16 5 C 5765 2.51 5 N 1545 2.21 5 O 1669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9036 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1908 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2597 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1768 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 407 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "R" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2322 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "R" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'LTD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.51, per 1000 atoms: 0.28 Number of scatterers: 9036 At special positions: 0 Unit cell: (121.128, 88.168, 125.248, 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 57 16.00 O 1669 8.00 N 1545 7.00 C 5765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 187 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 454.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 37.9% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.850A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 248 through 252 removed outlier: 4.470A pdb=" N THR A 251 " --> pdb=" O TRP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.839A pdb=" N TYR A 285 " --> pdb=" O PHE A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 318 Processing helix chain 'A' and resid 338 through 358 removed outlier: 3.621A pdb=" N ILE A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 30 Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.937A pdb=" N ILE B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 55 Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.563A pdb=" N THR E 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 28 through 43 removed outlier: 3.732A pdb=" N ALA G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 64 removed outlier: 3.771A pdb=" N GLU R 39 " --> pdb=" O ASN R 35 " (cutoff:3.500A) Proline residue: R 42 - end of helix removed outlier: 4.201A pdb=" N LEU R 58 " --> pdb=" O LEU R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 90 Processing helix chain 'R' and resid 90 through 100 removed outlier: 4.168A pdb=" N ARG R 94 " --> pdb=" O THR R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 142 removed outlier: 3.773A pdb=" N TYR R 119 " --> pdb=" O SER R 115 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET R 140 " --> pdb=" O ARG R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 171 removed outlier: 4.168A pdb=" N TRP R 156 " --> pdb=" O ILE R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 176 Processing helix chain 'R' and resid 191 through 193 No H-bonds generated for 'chain 'R' and resid 191 through 193' Processing helix chain 'R' and resid 194 through 209 removed outlier: 3.650A pdb=" N LEU R 198 " --> pdb=" O LYS R 194 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N THR R 200 " --> pdb=" O ALA R 196 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TYR R 203 " --> pdb=" O GLN R 199 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE R 204 " --> pdb=" O THR R 200 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA R 205 " --> pdb=" O MET R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 229 Processing helix chain 'R' and resid 240 through 258 removed outlier: 4.051A pdb=" N LYS R 244 " --> pdb=" O VAL R 240 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE R 250 " --> pdb=" O LEU R 246 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE R 251 " --> pdb=" O THR R 247 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR R 252 " --> pdb=" O THR R 248 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU R 258 " --> pdb=" O ILE R 254 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 272 Processing helix chain 'R' and resid 282 through 296 Processing helix chain 'R' and resid 296 through 306 Proline residue: R 302 - end of helix Processing helix chain 'R' and resid 309 through 321 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.560A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 327 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 6.936A pdb=" N ILE B 343 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR B 55 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU B 341 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 6.487A pdb=" N ALA B 78 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET B 66 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL B 76 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N TRP B 68 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N LEU B 74 " --> pdb=" O TRP B 68 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.889A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLY B 121 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 7.019A pdb=" N SER B 165 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N CYS B 154 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL B 163 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N PHE B 156 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N GLN B 161 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 7.408A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.986A pdb=" N SER B 250 " --> pdb=" O THR B 254 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N CYS B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR B 268 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 264 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.725A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 5.999A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 removed outlier: 5.999A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG E 97 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.297A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 180 through 181 445 hydrogen bonds defined for protein. 1245 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: 1.68 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1448 1.31 - 1.44: 2564 1.44 - 1.56: 5121 1.56 - 1.69: 4 1.69 - 1.81: 83 Bond restraints: 9220 Sorted by residual: bond pdb=" C SER R 241 " pdb=" O SER R 241 " ideal model delta sigma weight residual 1.236 1.302 -0.066 1.19e-02 7.06e+03 3.06e+01 bond pdb=" C10 LTD R 401 " pdb=" C11 LTD R 401 " ideal model delta sigma weight residual 1.447 1.537 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C22 LTD R 401 " pdb=" N3 LTD R 401 " ideal model delta sigma weight residual 1.332 1.421 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C21 LTD R 401 " pdb=" CA3 LTD R 401 " ideal model delta sigma weight residual 1.543 1.454 0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" N SER R 241 " pdb=" CA SER R 241 " ideal model delta sigma weight residual 1.459 1.512 -0.054 1.24e-02 6.50e+03 1.87e+01 ... (remaining 9215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.94: 12432 3.94 - 7.88: 31 7.88 - 11.83: 9 11.83 - 15.77: 3 15.77 - 19.71: 1 Bond angle restraints: 12476 Sorted by residual: angle pdb=" O VAL R 240 " pdb=" C VAL R 240 " pdb=" N SER R 241 " ideal model delta sigma weight residual 121.87 113.34 8.53 1.01e+00 9.80e-01 7.14e+01 angle pdb=" N ILE R 249 " pdb=" CA ILE R 249 " pdb=" C ILE R 249 " ideal model delta sigma weight residual 110.72 118.54 -7.82 1.01e+00 9.80e-01 5.99e+01 angle pdb=" C ASN R 301 " pdb=" CA ASN R 301 " pdb=" CB ASN R 301 " ideal model delta sigma weight residual 112.76 100.22 12.54 1.86e+00 2.89e-01 4.55e+01 angle pdb=" C3 LTD R 401 " pdb=" C4 LTD R 401 " pdb=" C5 LTD R 401 " ideal model delta sigma weight residual 113.85 133.56 -19.71 3.00e+00 1.11e-01 4.32e+01 angle pdb=" CA VAL R 240 " pdb=" C VAL R 240 " pdb=" N SER R 241 " ideal model delta sigma weight residual 117.53 124.81 -7.28 1.19e+00 7.06e-01 3.74e+01 ... (remaining 12471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.98: 5399 22.98 - 45.96: 69 45.96 - 68.95: 13 68.95 - 91.93: 5 91.93 - 114.91: 2 Dihedral angle restraints: 5488 sinusoidal: 2171 harmonic: 3317 Sorted by residual: dihedral pdb=" CB2 LTD R 401 " pdb=" C22 LTD R 401 " pdb=" CA2 LTD R 401 " pdb=" N3 LTD R 401 " ideal model delta sinusoidal sigma weight residual 87.84 -157.25 -114.91 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" N2 LTD R 401 " pdb=" C22 LTD R 401 " pdb=" CA2 LTD R 401 " pdb=" N3 LTD R 401 " ideal model delta sinusoidal sigma weight residual -150.23 -44.78 -105.45 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" C PHE R 307 " pdb=" N PHE R 307 " pdb=" CA PHE R 307 " pdb=" CB PHE R 307 " ideal model delta harmonic sigma weight residual -122.60 -130.72 8.12 0 2.50e+00 1.60e-01 1.05e+01 ... (remaining 5485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1314 0.079 - 0.158: 96 0.158 - 0.237: 4 0.237 - 0.316: 1 0.316 - 0.395: 2 Chirality restraints: 1417 Sorted by residual: chirality pdb=" C6 LTD R 401 " pdb=" SG2 LTD R 401 " pdb=" C5 LTD R 401 " pdb=" C7 LTD R 401 " both_signs ideal model delta sigma weight residual False -3.17 -2.77 -0.40 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CA PHE R 307 " pdb=" N PHE R 307 " pdb=" C PHE R 307 " pdb=" CB PHE R 307 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CA TYR R 305 " pdb=" N TYR R 305 " pdb=" C TYR R 305 " pdb=" CB TYR R 305 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1414 not shown) Planarity restraints: 1574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 240 " -0.017 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C VAL R 240 " 0.055 2.00e-02 2.50e+03 pdb=" O VAL R 240 " -0.019 2.00e-02 2.50e+03 pdb=" N SER R 241 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 302 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" C PRO R 302 " -0.055 2.00e-02 2.50e+03 pdb=" O PRO R 302 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU R 303 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS R 142 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.63e+00 pdb=" N PRO R 143 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO R 143 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO R 143 " 0.023 5.00e-02 4.00e+02 ... (remaining 1571 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 82 2.56 - 3.15: 7783 3.15 - 3.73: 13864 3.73 - 4.32: 19901 4.32 - 4.90: 33288 Nonbonded interactions: 74918 Sorted by model distance: nonbonded pdb=" O ILE B 128 " pdb=" OG SER B 141 " model vdw 1.977 3.040 nonbonded pdb=" NH1 ARG A 323 " pdb=" CE1 HIS A 324 " model vdw 2.077 3.340 nonbonded pdb=" OG SER B 79 " pdb=" OD1 ASP B 81 " model vdw 2.129 3.040 nonbonded pdb=" O ALA A 41 " pdb=" OG SER A 44 " model vdw 2.151 3.040 nonbonded pdb=" OG1 THR B 226 " pdb=" OE2 GLU G 21 " model vdw 2.170 3.040 ... (remaining 74913 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: 1.730 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.360 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5364 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 : 0.008 0.661 9222 Z= 0.725 Angle : 0.651 19.711 12478 Z= 0.368 Chirality : 0.042 0.395 1417 Planarity : 0.003 0.041 1574 Dihedral : 9.060 114.909 3345 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.30 % Allowed : 3.05 % Favored : 96.65 % 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 aren not related in a simple way. whole: -1.89 (0.23), residues: 1123 helix: -0.21 (0.25), residues: 383 sheet: -1.45 (0.30), residues: 250 loop : -1.93 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 243 TYR 0.023 0.001 TYR R 306 PHE 0.010 0.001 PHE R 300 TRP 0.007 0.001 TRP B 87 HIS 0.002 0.000 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9220) covalent geometry : angle 0.65070 (12476) SS BOND : bond 0.00424 ( 1) SS BOND : angle 2.47896 ( 2) hydrogen bonds : bond 0.12717 ( 441) hydrogen bonds : angle 5.60993 ( 1245) Misc. bond : bond 0.66143 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 197 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 ASP cc_start: 0.6610 (p0) cc_final: 0.5897 (t0) REVERT: B 144 LEU cc_start: 0.6111 (pp) cc_final: 0.5420 (mt) REVERT: B 227 PHE cc_start: 0.6149 (m-80) cc_final: 0.5934 (m-80) REVERT: B 282 SER cc_start: 0.5861 (t) cc_final: 0.5593 (p) REVERT: R 170 SER cc_start: 0.5590 (p) cc_final: 0.5315 (p) REVERT: R 243 ARG cc_start: 0.7254 (ttm-80) cc_final: 0.6819 (ttp-170) outliers start: 3 outliers final: 2 residues processed: 200 average time/residue: 0.1168 time to fit residues: 30.7174 Evaluate side-chains 133 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain R residue 306 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.0070 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.2980 chunk 106 optimal weight: 2.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN B 300 ASN E 34 HIS R 148 HIS R 242 HIS ** R 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.269824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.238899 restraints weight = 8858.051| |-----------------------------------------------------------------------------| r_work (start): 0.4532 rms_B_bonded: 1.32 r_work: 0.4376 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4253 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.4253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9222 Z= 0.124 Angle : 0.537 8.215 12478 Z= 0.280 Chirality : 0.041 0.177 1417 Planarity : 0.004 0.034 1574 Dihedral : 7.548 89.777 1279 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.54 % Allowed : 8.63 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.25), residues: 1123 helix: 1.38 (0.26), residues: 374 sheet: -0.93 (0.30), residues: 262 loop : -1.37 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 71 TYR 0.019 0.002 TYR R 116 PHE 0.015 0.001 PHE B 283 TRP 0.011 0.001 TRP B 87 HIS 0.006 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9220) covalent geometry : angle 0.53677 (12476) SS BOND : bond 0.00033 ( 1) SS BOND : angle 0.61491 ( 2) hydrogen bonds : bond 0.03261 ( 441) hydrogen bonds : angle 4.24357 ( 1245) Misc. bond : bond 0.00077 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 144 LEU cc_start: 0.7096 (pp) cc_final: 0.6413 (mt) REVERT: B 230 HIS cc_start: 0.5443 (OUTLIER) cc_final: 0.4693 (t-90) REVERT: R 170 SER cc_start: 0.6559 (p) cc_final: 0.6264 (p) outliers start: 25 outliers final: 12 residues processed: 157 average time/residue: 0.1157 time to fit residues: 24.3264 Evaluate side-chains 139 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 148 HIS Chi-restraints excluded: chain R residue 306 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 22 optimal weight: 0.0270 chunk 18 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 overall best weight: 1.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN E 194 ASN R 148 HIS ** R 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.240696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.206652 restraints weight = 8602.625| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 1.42 r_work: 0.4053 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3915 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9222 Z= 0.161 Angle : 0.601 11.048 12478 Z= 0.313 Chirality : 0.043 0.178 1417 Planarity : 0.004 0.037 1574 Dihedral : 7.406 84.917 1279 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.64 % Allowed : 10.56 % Favored : 86.80 % 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 aren not related in a simple way. whole: -0.20 (0.25), residues: 1123 helix: 1.59 (0.26), residues: 385 sheet: -0.79 (0.30), residues: 261 loop : -1.14 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 57 TYR 0.019 0.002 TYR E 190 PHE 0.013 0.002 PHE E 26 TRP 0.016 0.002 TRP E 46 HIS 0.032 0.002 HIS R 148 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9220) covalent geometry : angle 0.60082 (12476) SS BOND : bond 0.00029 ( 1) SS BOND : angle 0.44254 ( 2) hydrogen bonds : bond 0.03814 ( 441) hydrogen bonds : angle 4.49415 ( 1245) Misc. bond : bond 0.00210 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7912 (tttt) cc_final: 0.7372 (tptt) REVERT: B 134 ARG cc_start: 0.7965 (mmm160) cc_final: 0.7576 (mtp180) REVERT: B 279 THR cc_start: 0.8639 (m) cc_final: 0.8289 (p) REVERT: E 140 MET cc_start: 0.7188 (mtp) cc_final: 0.6364 (mmm) REVERT: R 170 SER cc_start: 0.7022 (p) cc_final: 0.6727 (p) outliers start: 26 outliers final: 15 residues processed: 162 average time/residue: 0.1129 time to fit residues: 24.7271 Evaluate side-chains 135 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 141 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 87 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 0.1980 chunk 18 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS ** R 301 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 = 0.4564 r_free = 0.4564 target = 0.242012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.210862 restraints weight = 8814.818| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 1.39 r_work: 0.4057 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3915 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9222 Z= 0.110 Angle : 0.505 6.964 12478 Z= 0.265 Chirality : 0.040 0.165 1417 Planarity : 0.003 0.039 1574 Dihedral : 6.871 82.229 1275 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.34 % Allowed : 11.57 % Favored : 86.09 % 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 aren not related in a simple way. whole: 0.00 (0.25), residues: 1123 helix: 1.75 (0.26), residues: 391 sheet: -0.64 (0.30), residues: 260 loop : -1.08 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 35 TYR 0.018 0.001 TYR R 116 PHE 0.010 0.001 PHE R 93 TRP 0.013 0.001 TRP B 87 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9220) covalent geometry : angle 0.50526 (12476) SS BOND : bond 0.00033 ( 1) SS BOND : angle 0.62378 ( 2) hydrogen bonds : bond 0.03261 ( 441) hydrogen bonds : angle 4.16484 ( 1245) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7947 (tttt) cc_final: 0.7420 (tptt) REVERT: B 64 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.7608 (m-80) REVERT: B 134 ARG cc_start: 0.8062 (mmm160) cc_final: 0.7691 (mtp180) REVERT: B 330 MET cc_start: 0.7814 (mmt) cc_final: 0.7544 (tpt) REVERT: E 140 MET cc_start: 0.7320 (mtp) cc_final: 0.6364 (mmm) REVERT: R 104 TRP cc_start: 0.7245 (t-100) cc_final: 0.6929 (t-100) REVERT: R 170 SER cc_start: 0.7306 (p) cc_final: 0.6985 (p) REVERT: R 291 LEU cc_start: 0.7990 (tp) cc_final: 0.7731 (tt) outliers start: 23 outliers final: 12 residues processed: 148 average time/residue: 0.1109 time to fit residues: 22.2803 Evaluate side-chains 134 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 8.9990 chunk 63 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 92 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN ** R 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 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 = 0.4541 r_free = 0.4541 target = 0.239227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.205515 restraints weight = 8660.741| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 1.47 r_work: 0.4033 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3890 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.5799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9222 Z= 0.108 Angle : 0.512 6.673 12478 Z= 0.266 Chirality : 0.040 0.166 1417 Planarity : 0.003 0.036 1574 Dihedral : 6.612 83.797 1275 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.23 % Allowed : 13.20 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.25), residues: 1123 helix: 1.87 (0.26), residues: 389 sheet: -0.53 (0.30), residues: 266 loop : -0.92 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 224 TYR 0.016 0.001 TYR R 116 PHE 0.010 0.001 PHE E 67 TRP 0.013 0.001 TRP B 87 HIS 0.008 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9220) covalent geometry : angle 0.51180 (12476) SS BOND : bond 0.00025 ( 1) SS BOND : angle 0.53841 ( 2) hydrogen bonds : bond 0.03320 ( 441) hydrogen bonds : angle 4.13707 ( 1245) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7887 (tttt) cc_final: 0.7369 (tptt) REVERT: B 64 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.7727 (m-80) REVERT: B 134 ARG cc_start: 0.8075 (mmm160) cc_final: 0.7729 (mtp180) REVERT: B 230 HIS cc_start: 0.7084 (OUTLIER) cc_final: 0.6577 (t-90) REVERT: B 330 MET cc_start: 0.7810 (mmt) cc_final: 0.7541 (tpt) REVERT: E 140 MET cc_start: 0.7456 (mtp) cc_final: 0.6982 (mmm) REVERT: G 47 ASP cc_start: 0.7286 (t0) cc_final: 0.6737 (t0) REVERT: R 104 TRP cc_start: 0.7274 (t-100) cc_final: 0.6922 (t-100) REVERT: R 170 SER cc_start: 0.7289 (p) cc_final: 0.6960 (p) REVERT: R 291 LEU cc_start: 0.8016 (tp) cc_final: 0.7754 (tt) outliers start: 22 outliers final: 15 residues processed: 143 average time/residue: 0.1066 time to fit residues: 21.0194 Evaluate side-chains 139 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN B 230 HIS E 38 GLN ** R 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.235644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.205745 restraints weight = 8806.060| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 1.32 r_work: 0.4007 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3864 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.6192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9222 Z= 0.108 Angle : 0.503 6.669 12478 Z= 0.262 Chirality : 0.040 0.166 1417 Planarity : 0.003 0.036 1574 Dihedral : 6.211 84.425 1275 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.74 % Allowed : 13.40 % Favored : 83.86 % 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 aren not related in a simple way. whole: 0.28 (0.25), residues: 1123 helix: 1.89 (0.26), residues: 391 sheet: -0.36 (0.30), residues: 259 loop : -0.92 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 232 TYR 0.020 0.001 TYR R 116 PHE 0.009 0.001 PHE B 156 TRP 0.017 0.001 TRP B 302 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9220) covalent geometry : angle 0.50270 (12476) SS BOND : bond 0.00035 ( 1) SS BOND : angle 0.43801 ( 2) hydrogen bonds : bond 0.03255 ( 441) hydrogen bonds : angle 4.10170 ( 1245) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 238 ASN cc_start: 0.7258 (m110) cc_final: 0.6984 (m-40) REVERT: B 64 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7809 (m-80) REVERT: B 134 ARG cc_start: 0.8062 (mmm160) cc_final: 0.7739 (mtp180) REVERT: B 279 THR cc_start: 0.8557 (m) cc_final: 0.8153 (p) REVERT: E 140 MET cc_start: 0.7560 (mtp) cc_final: 0.6956 (mmm) REVERT: G 47 ASP cc_start: 0.7355 (t0) cc_final: 0.6989 (t0) REVERT: R 170 SER cc_start: 0.7321 (p) cc_final: 0.6994 (p) REVERT: R 291 LEU cc_start: 0.8026 (tp) cc_final: 0.7777 (tt) outliers start: 27 outliers final: 22 residues processed: 146 average time/residue: 0.0996 time to fit residues: 20.2061 Evaluate side-chains 139 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN ** R 301 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 = 0.4458 r_free = 0.4458 target = 0.228705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.196658 restraints weight = 8770.056| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 1.40 r_work: 0.3922 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.6656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9222 Z= 0.151 Angle : 0.563 7.113 12478 Z= 0.297 Chirality : 0.042 0.251 1417 Planarity : 0.004 0.036 1574 Dihedral : 6.389 84.905 1275 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.94 % Allowed : 12.89 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.25), residues: 1123 helix: 1.72 (0.26), residues: 387 sheet: -0.39 (0.31), residues: 266 loop : -0.85 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 145 TYR 0.016 0.002 TYR R 116 PHE 0.013 0.001 PHE B 156 TRP 0.015 0.002 TRP B 302 HIS 0.009 0.002 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9220) covalent geometry : angle 0.56285 (12476) SS BOND : bond 0.00123 ( 1) SS BOND : angle 0.45739 ( 2) hydrogen bonds : bond 0.03760 ( 441) hydrogen bonds : angle 4.35393 ( 1245) Misc. bond : bond 0.00052 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 226 ASP cc_start: 0.5863 (t0) cc_final: 0.5369 (t0) REVERT: A 238 ASN cc_start: 0.6980 (m110) cc_final: 0.6588 (m110) REVERT: B 64 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: B 134 ARG cc_start: 0.8169 (mmm160) cc_final: 0.7749 (mtp180) REVERT: B 230 HIS cc_start: 0.7049 (OUTLIER) cc_final: 0.6778 (t-90) REVERT: E 140 MET cc_start: 0.7654 (mtp) cc_final: 0.6989 (mmm) REVERT: G 47 ASP cc_start: 0.7642 (t0) cc_final: 0.7329 (t0) REVERT: R 170 SER cc_start: 0.7374 (p) cc_final: 0.7034 (p) REVERT: R 291 LEU cc_start: 0.8131 (tp) cc_final: 0.7897 (tt) outliers start: 29 outliers final: 21 residues processed: 138 average time/residue: 0.0933 time to fit residues: 18.3622 Evaluate side-chains 137 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 144 PHE Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 299 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN B 230 HIS E 38 GLN R 191 ASN ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.217057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.185756 restraints weight = 8900.863| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 1.42 r_work: 0.3807 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.7730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9222 Z= 0.256 Angle : 0.731 8.530 12478 Z= 0.385 Chirality : 0.049 0.314 1417 Planarity : 0.005 0.051 1574 Dihedral : 7.197 91.944 1275 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.35 % Allowed : 13.30 % Favored : 83.35 % 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 aren not related in a simple way. whole: -0.35 (0.25), residues: 1123 helix: 0.96 (0.26), residues: 388 sheet: -0.48 (0.31), residues: 259 loop : -1.01 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 315 TYR 0.021 0.003 TYR R 263 PHE 0.022 0.002 PHE B 156 TRP 0.022 0.002 TRP E 46 HIS 0.011 0.002 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00619 ( 9220) covalent geometry : angle 0.73072 (12476) SS BOND : bond 0.00157 ( 1) SS BOND : angle 0.30634 ( 2) hydrogen bonds : bond 0.04961 ( 441) hydrogen bonds : angle 5.04584 ( 1245) Misc. bond : bond 0.00095 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.7807 (m) cc_final: 0.7366 (m) REVERT: A 336 THR cc_start: 0.7545 (m) cc_final: 0.7188 (p) REVERT: B 134 ARG cc_start: 0.8232 (mmm160) cc_final: 0.7852 (mtp180) REVERT: B 239 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.6844 (m-80) REVERT: R 170 SER cc_start: 0.7418 (p) cc_final: 0.7081 (p) outliers start: 33 outliers final: 23 residues processed: 150 average time/residue: 0.0995 time to fit residues: 20.9017 Evaluate side-chains 128 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 144 PHE Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 299 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS E 171 ASN R 79 ASN ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.227397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.193899 restraints weight = 8625.810| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 1.51 r_work: 0.3889 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.7641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9222 Z= 0.133 Angle : 0.566 6.991 12478 Z= 0.295 Chirality : 0.042 0.232 1417 Planarity : 0.004 0.047 1574 Dihedral : 6.631 87.967 1275 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.54 % Allowed : 14.42 % Favored : 83.05 % 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 aren not related in a simple way. whole: 0.01 (0.25), residues: 1123 helix: 1.43 (0.27), residues: 386 sheet: -0.38 (0.31), residues: 265 loop : -0.92 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 57 TYR 0.015 0.001 TYR B 64 PHE 0.012 0.001 PHE B 156 TRP 0.014 0.001 TRP B 87 HIS 0.008 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9220) covalent geometry : angle 0.56598 (12476) SS BOND : bond 0.00115 ( 1) SS BOND : angle 0.60100 ( 2) hydrogen bonds : bond 0.03845 ( 441) hydrogen bonds : angle 4.47698 ( 1245) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7452 (m-30) REVERT: A 336 THR cc_start: 0.7516 (m) cc_final: 0.7202 (p) REVERT: B 134 ARG cc_start: 0.7965 (mmm160) cc_final: 0.7729 (mtp180) REVERT: R 93 PHE cc_start: 0.6475 (m-10) cc_final: 0.6247 (m-10) REVERT: R 170 SER cc_start: 0.7038 (p) cc_final: 0.6696 (p) REVERT: R 291 LEU cc_start: 0.8010 (tp) cc_final: 0.7780 (tt) outliers start: 25 outliers final: 23 residues processed: 138 average time/residue: 0.0921 time to fit residues: 18.2216 Evaluate side-chains 135 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 299 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 69 optimal weight: 0.0570 chunk 102 optimal weight: 0.8980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN B 230 HIS R 79 ASN ** R 301 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 = 0.4468 r_free = 0.4468 target = 0.230606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.197073 restraints weight = 8601.285| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 1.53 r_work: 0.3924 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.7631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9222 Z= 0.109 Angle : 0.532 7.103 12478 Z= 0.278 Chirality : 0.041 0.189 1417 Planarity : 0.004 0.042 1574 Dihedral : 6.385 85.720 1275 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.23 % Allowed : 14.92 % Favored : 82.84 % 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 aren not related in a simple way. whole: 0.23 (0.25), residues: 1123 helix: 1.65 (0.27), residues: 387 sheet: -0.18 (0.32), residues: 255 loop : -0.88 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 57 TYR 0.014 0.001 TYR R 116 PHE 0.012 0.001 PHE R 76 TRP 0.016 0.001 TRP B 87 HIS 0.006 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9220) covalent geometry : angle 0.53184 (12476) SS BOND : bond 0.00117 ( 1) SS BOND : angle 0.60038 ( 2) hydrogen bonds : bond 0.03546 ( 441) hydrogen bonds : angle 4.29037 ( 1245) Misc. bond : bond 0.00004 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 192 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7600 (m-30) REVERT: A 336 THR cc_start: 0.7396 (m) cc_final: 0.7118 (p) REVERT: B 134 ARG cc_start: 0.8056 (mmm160) cc_final: 0.7724 (mtp180) REVERT: B 168 ASP cc_start: 0.7743 (p0) cc_final: 0.7502 (p0) REVERT: B 230 HIS cc_start: 0.6739 (OUTLIER) cc_final: 0.6264 (t70) REVERT: E 6 SER cc_start: 0.7756 (p) cc_final: 0.7047 (m) REVERT: R 93 PHE cc_start: 0.6337 (m-10) cc_final: 0.5975 (m-10) REVERT: R 170 SER cc_start: 0.7278 (p) cc_final: 0.6927 (p) REVERT: R 291 LEU cc_start: 0.7999 (tp) cc_final: 0.7761 (tt) outliers start: 22 outliers final: 18 residues processed: 132 average time/residue: 0.0875 time to fit residues: 16.8596 Evaluate side-chains 128 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 299 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 15 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN B 230 HIS R 79 ASN ** R 301 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 = 0.4428 r_free = 0.4428 target = 0.225723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.192000 restraints weight = 8433.621| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 1.56 r_work: 0.3863 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.7797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9222 Z= 0.157 Angle : 0.589 7.248 12478 Z= 0.308 Chirality : 0.043 0.237 1417 Planarity : 0.004 0.043 1574 Dihedral : 6.534 84.269 1275 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.74 % Allowed : 15.13 % Favored : 82.13 % 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 aren not related in a simple way. whole: 0.13 (0.25), residues: 1123 helix: 1.50 (0.26), residues: 390 sheet: -0.22 (0.32), residues: 261 loop : -0.89 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 57 TYR 0.015 0.002 TYR R 116 PHE 0.016 0.002 PHE B 156 TRP 0.014 0.002 TRP B 87 HIS 0.009 0.002 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 9220) covalent geometry : angle 0.58858 (12476) SS BOND : bond 0.00125 ( 1) SS BOND : angle 0.53807 ( 2) hydrogen bonds : bond 0.03972 ( 441) hydrogen bonds : angle 4.48712 ( 1245) Misc. bond : bond 0.00050 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2746.18 seconds wall clock time: 47 minutes 48.59 seconds (2868.59 seconds total)