Starting phenix.real_space_refine on Thu Jul 2 12:35:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7trp_26100/07_2026/7trp_26100.cif Found real_map, /net/cci-nas-00/data/ceres_data/7trp_26100/07_2026/7trp_26100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7trp_26100/07_2026/7trp_26100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7trp_26100/07_2026/7trp_26100.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7trp_26100/07_2026/7trp_26100.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7trp_26100/07_2026/7trp_26100.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7trp_26100/07_2026/7trp_26100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7trp_26100/07_2026/7trp_26100.map" } resolution = 2.4 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 64 5.16 5 Cl 1 4.86 5 C 5535 2.51 5 N 1461 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 8681 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2079 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 256} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2591 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 423 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1786 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1768 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "R" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'IUE': 1, 'IXO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.63, per 1000 atoms: 0.19 Number of scatterers: 8681 At special positions: 0 Unit cell: (93.79, 119.52, 123.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 64 16.00 O 1620 8.00 N 1461 7.00 C 5535 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 426 " - pdb=" SG CYS R 429 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 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: 0.49 Conformation dependent library (CDL) restraints added in 317.5 milliseconds 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 38.6% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'R' and resid 33 through 60 removed outlier: 3.624A pdb=" N ASN R 60 " --> pdb=" O SER R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 64 Processing helix chain 'R' and resid 66 through 84 removed outlier: 4.384A pdb=" N PHE R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU R 71 " --> pdb=" O ASN R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 96 Processing helix chain 'R' and resid 102 through 136 Processing helix chain 'R' and resid 145 through 175 Proline residue: R 166 - end of helix removed outlier: 5.184A pdb=" N GLN R 172 " --> pdb=" O ILE R 168 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N PHE R 173 " --> pdb=" O LEU R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 191 removed outlier: 3.564A pdb=" N LEU R 190 " --> pdb=" O ILE R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 204 Processing helix chain 'R' and resid 204 through 223 removed outlier: 3.906A pdb=" N ARG R 223 " --> pdb=" O SER R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 426 Proline residue: R 415 - end of helix removed outlier: 3.537A pdb=" N THR R 424 " --> pdb=" O VAL R 420 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE R 425 " --> pdb=" O LEU R 421 " (cutoff:3.500A) Processing helix chain 'R' and resid 431 through 448 removed outlier: 3.798A pdb=" N SER R 446 " --> pdb=" O CYS R 442 " (cutoff:3.500A) Processing helix chain 'R' and resid 448 through 454 Processing helix chain 'R' and resid 457 through 463 removed outlier: 3.625A pdb=" N LYS R 461 " --> pdb=" O ASN R 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.573A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.653A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 removed outlier: 4.355A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 220 through 224 removed outlier: 4.128A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.556A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.628A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.254A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.792A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.812A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 331 through 351 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.500A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.700A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.994A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.132A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.016A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.611A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.775A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.013A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.013A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.626A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.271A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1275 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: 1.40 Time building geometry restraints manager: 0.63 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: 1398 1.31 - 1.44: 2469 1.44 - 1.57: 4903 1.57 - 1.69: 1 1.69 - 1.82: 94 Bond restraints: 8865 Sorted by residual: bond pdb=" C10 IXO R 702 " pdb=" N11 IXO R 702 " ideal model delta sigma weight residual 1.270 1.475 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C10 IXO R 702 " pdb=" C14 IXO R 702 " ideal model delta sigma weight residual 1.492 1.331 0.161 2.00e-02 2.50e+03 6.50e+01 bond pdb=" C13 IXO R 702 " pdb=" O12 IXO R 702 " ideal model delta sigma weight residual 1.439 1.544 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C05 IXO R 702 " pdb=" C06 IXO R 702 " ideal model delta sigma weight residual 1.450 1.528 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C07 IXO R 702 " pdb=" C08 IXO R 702 " ideal model delta sigma weight residual 1.454 1.530 -0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 8860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 11627 2.00 - 4.00: 356 4.00 - 6.00: 41 6.00 - 8.00: 14 8.00 - 9.99: 3 Bond angle restraints: 12041 Sorted by residual: angle pdb=" N GLY H 209 " pdb=" CA GLY H 209 " pdb=" C GLY H 209 " ideal model delta sigma weight residual 113.18 121.40 -8.22 2.37e+00 1.78e-01 1.20e+01 angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 121.54 127.91 -6.37 1.91e+00 2.74e-01 1.11e+01 angle pdb=" N ALA R 165 " pdb=" CA ALA R 165 " pdb=" C ALA R 165 " ideal model delta sigma weight residual 112.75 117.28 -4.53 1.36e+00 5.41e-01 1.11e+01 angle pdb=" CA TRP R 440 " pdb=" CB TRP R 440 " pdb=" CG TRP R 440 " ideal model delta sigma weight residual 113.60 107.43 6.17 1.90e+00 2.77e-01 1.05e+01 angle pdb=" N CYS R 429 " pdb=" CA CYS R 429 " pdb=" C CYS R 429 " ideal model delta sigma weight residual 111.07 114.38 -3.31 1.07e+00 8.73e-01 9.54e+00 ... (remaining 12036 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 4903 16.99 - 33.98: 269 33.98 - 50.97: 45 50.97 - 67.96: 9 67.96 - 84.95: 4 Dihedral angle restraints: 5230 sinusoidal: 1970 harmonic: 3260 Sorted by residual: dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 160.91 19.09 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA PHE A 196 " pdb=" C PHE A 196 " pdb=" N LYS A 197 " pdb=" CA LYS A 197 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA HIS H 35 " pdb=" C HIS H 35 " pdb=" N TRP H 36 " pdb=" CA TRP H 36 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 5227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1099 0.064 - 0.127: 225 0.127 - 0.191: 53 0.191 - 0.255: 5 0.255 - 0.318: 3 Chirality restraints: 1385 Sorted by residual: chirality pdb=" CB VAL R 444 " pdb=" CA VAL R 444 " pdb=" CG1 VAL R 444 " pdb=" CG2 VAL R 444 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CB ILE A 184 " pdb=" CA ILE A 184 " pdb=" CG1 ILE A 184 " pdb=" CG2 ILE A 184 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CB THR R 90 " pdb=" CA THR R 90 " pdb=" OG1 THR R 90 " pdb=" CG2 THR R 90 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1382 not shown) Planarity restraints: 1511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N IUE R 701 " 0.035 2.00e-02 2.50e+03 3.45e-02 4.17e+01 pdb=" C IUE R 701 " -0.023 2.00e-02 2.50e+03 pdb=" O IUE R 701 " -0.039 2.00e-02 2.50e+03 pdb=" C1 IUE R 701 " 0.013 2.00e-02 2.50e+03 pdb=" C2 IUE R 701 " 0.029 2.00e-02 2.50e+03 pdb=" C3 IUE R 701 " 0.014 2.00e-02 2.50e+03 pdb=" C4 IUE R 701 " -0.012 2.00e-02 2.50e+03 pdb=" C5 IUE R 701 " 0.036 2.00e-02 2.50e+03 pdb=" C6 IUE R 701 " 0.004 2.00e-02 2.50e+03 pdb=" C7 IUE R 701 " -0.003 2.00e-02 2.50e+03 pdb=" C9 IUE R 701 " -0.086 2.00e-02 2.50e+03 pdb=" N2 IUE R 701 " 0.046 2.00e-02 2.50e+03 pdb=" S IUE R 701 " 0.016 2.00e-02 2.50e+03 pdb="CL IUE R 701 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 IUE R 701 " -0.057 2.00e-02 2.50e+03 4.82e-02 2.91e+01 pdb=" C4 IUE R 701 " -0.045 2.00e-02 2.50e+03 pdb=" C9 IUE R 701 " 0.021 2.00e-02 2.50e+03 pdb=" N1 IUE R 701 " 0.076 2.00e-02 2.50e+03 pdb=" O1 IUE R 701 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 113 " -0.019 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C TYR R 113 " 0.065 2.00e-02 2.50e+03 pdb=" O TYR R 113 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL R 114 " -0.022 2.00e-02 2.50e+03 ... (remaining 1508 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2315 2.81 - 3.33: 7729 3.33 - 3.85: 14628 3.85 - 4.38: 17643 4.38 - 4.90: 30339 Nonbonded interactions: 72654 Sorted by model distance: nonbonded pdb=" OH TYR R 113 " pdb=" OH TYR R 416 " model vdw 2.287 3.040 nonbonded pdb=" O THR R 433 " pdb=" OG SER R 436 " model vdw 2.311 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.320 3.040 nonbonded pdb=" OH TYR H 175 " pdb=" OE2 GLU A 8 " model vdw 2.324 3.040 nonbonded pdb=" O ASN R 87 " pdb=" OG1 THR R 90 " model vdw 2.329 3.040 ... (remaining 72649 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: 0.970 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.720 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 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 : 0.006 0.205 8869 Z= 0.277 Angle : 0.818 9.994 12049 Z= 0.464 Chirality : 0.056 0.318 1385 Planarity : 0.007 0.085 1511 Dihedral : 11.228 84.947 3114 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.21 % Allowed : 0.64 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.23), residues: 1106 helix: -0.02 (0.24), residues: 382 sheet: 0.22 (0.29), residues: 300 loop : -0.74 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 191 TYR 0.029 0.002 TYR R 215 PHE 0.035 0.003 PHE R 189 TRP 0.036 0.002 TRP R 440 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.28 ( 8865) covalent geometry : angle 0.81768 / 0.46 (12041) SS BOND : bond 0.00455 / 0.22 ( 4) SS BOND : angle 1.13729 / 0.60 ( 8) hydrogen bonds : bond 0.13106 / 9.16 ( 448) hydrogen bonds : angle 5.89039 / 4.40 ( 1275) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: R 210 ILE cc_start: 0.8052 (mm) cc_final: 0.7814 (mp) REVERT: R 223 ARG cc_start: 0.7963 (ttm110) cc_final: 0.7722 (ttm110) REVERT: B 270 ILE cc_start: 0.9015 (pt) cc_final: 0.8768 (tp) REVERT: H 186 GLN cc_start: 0.8733 (tt0) cc_final: 0.8461 (tt0) REVERT: H 220 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7958 (mm-30) REVERT: A 302 TYR cc_start: 0.8938 (t80) cc_final: 0.8697 (t80) REVERT: A 306 GLN cc_start: 0.8868 (mm110) cc_final: 0.8296 (mp10) REVERT: A 308 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8306 (mt-10) outliers start: 2 outliers final: 0 residues processed: 163 average time/residue: 0.7676 time to fit residues: 130.8898 Evaluate side-chains 123 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 117 ASN R 172 GLN B 268 ASN H 39 GLN H 194 ASN A 188 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.105949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.066911 restraints weight = 14773.738| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.69 r_work: 0.2730 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8869 Z= 0.155 Angle : 0.539 5.783 12049 Z= 0.295 Chirality : 0.042 0.134 1385 Planarity : 0.004 0.054 1511 Dihedral : 4.675 24.323 1221 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 1.93 % Allowed : 8.49 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.98 (0.25), residues: 1106 helix: 1.68 (0.26), residues: 393 sheet: 0.72 (0.30), residues: 282 loop : -0.28 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.015 0.001 TYR H 190 PHE 0.015 0.001 PHE R 189 TRP 0.016 0.001 TRP B 82 HIS 0.008 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 ( 8865) covalent geometry : angle 0.53931 / 0.30 (12041) SS BOND : bond 0.00377 / 0.18 ( 4) SS BOND : angle 0.73233 / 0.40 ( 8) hydrogen bonds : bond 0.04218 / 2.83 ( 448) hydrogen bonds : angle 4.49028 / 3.33 ( 1275) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.332 Fit side-chains REVERT: R 127 SER cc_start: 0.8843 (OUTLIER) cc_final: 0.8569 (p) REVERT: B 172 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8268 (tp30) REVERT: B 217 MET cc_start: 0.8601 (pmm) cc_final: 0.8326 (pmt) REVERT: B 254 ASP cc_start: 0.8651 (t70) cc_final: 0.8438 (t70) REVERT: B 266 HIS cc_start: 0.8806 (t-90) cc_final: 0.8557 (t-170) REVERT: G 15 LEU cc_start: 0.8252 (tt) cc_final: 0.7962 (tm) REVERT: H 186 GLN cc_start: 0.9217 (tt0) cc_final: 0.8892 (tt0) REVERT: A 306 GLN cc_start: 0.8927 (mm110) cc_final: 0.8343 (mp10) REVERT: A 308 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8401 (mt-10) outliers start: 18 outliers final: 4 residues processed: 137 average time/residue: 0.7776 time to fit residues: 111.6626 Evaluate side-chains 116 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 432 ASP Chi-restraints excluded: chain A residue 305 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 0.2980 chunk 56 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 172 GLN B 340 ASN A 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.103976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.064869 restraints weight = 14556.679| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.66 r_work: 0.2688 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8869 Z= 0.206 Angle : 0.548 5.453 12049 Z= 0.299 Chirality : 0.043 0.138 1385 Planarity : 0.004 0.049 1511 Dihedral : 4.556 21.325 1221 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.26 % Allowed : 9.99 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.25), residues: 1106 helix: 1.97 (0.26), residues: 395 sheet: 0.72 (0.30), residues: 281 loop : -0.09 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 313 TYR 0.017 0.002 TYR B 105 PHE 0.017 0.002 PHE R 189 TRP 0.016 0.001 TRP B 82 HIS 0.007 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 ( 8865) covalent geometry : angle 0.54767 / 0.30 (12041) SS BOND : bond 0.00419 / 0.20 ( 4) SS BOND : angle 0.84553 / 0.46 ( 8) hydrogen bonds : bond 0.04213 / 2.81 ( 448) hydrogen bonds : angle 4.47749 / 3.33 ( 1275) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.217 Fit side-chains REVERT: R 127 SER cc_start: 0.8895 (OUTLIER) cc_final: 0.8662 (p) REVERT: B 172 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8257 (tp30) REVERT: B 217 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8377 (pmt) REVERT: B 254 ASP cc_start: 0.8691 (t70) cc_final: 0.8462 (t70) REVERT: B 266 HIS cc_start: 0.8893 (t-90) cc_final: 0.8569 (t-170) REVERT: G 15 LEU cc_start: 0.8381 (tt) cc_final: 0.8091 (tm) REVERT: H 43 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8748 (mmmm) REVERT: H 186 GLN cc_start: 0.9234 (tt0) cc_final: 0.8901 (tt0) REVERT: A 33 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8360 (tt0) REVERT: A 205 ARG cc_start: 0.8604 (mmm160) cc_final: 0.8393 (mmp-170) REVERT: A 306 GLN cc_start: 0.8938 (mm110) cc_final: 0.8418 (mp10) REVERT: A 308 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8444 (mt-10) outliers start: 21 outliers final: 7 residues processed: 138 average time/residue: 0.6959 time to fit residues: 100.6984 Evaluate side-chains 118 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 432 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain A residue 33 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 68 ASN R 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.102802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.063778 restraints weight = 14885.226| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.68 r_work: 0.2662 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8869 Z= 0.230 Angle : 0.564 6.910 12049 Z= 0.307 Chirality : 0.043 0.138 1385 Planarity : 0.004 0.055 1511 Dihedral : 4.625 22.503 1221 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.69 % Allowed : 11.82 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.25), residues: 1106 helix: 1.93 (0.26), residues: 394 sheet: 0.73 (0.30), residues: 280 loop : -0.05 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 42 TYR 0.015 0.002 TYR R 89 PHE 0.019 0.002 PHE R 189 TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.23 ( 8865) covalent geometry : angle 0.56396 / 0.31 (12041) SS BOND : bond 0.00431 / 0.21 ( 4) SS BOND : angle 0.84545 / 0.45 ( 8) hydrogen bonds : bond 0.04237 / 2.81 ( 448) hydrogen bonds : angle 4.51691 / 3.35 ( 1275) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.337 Fit side-chains REVERT: R 127 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8661 (p) REVERT: R 395 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7151 (tt0) REVERT: B 172 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8251 (tm-30) REVERT: B 217 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8408 (pmt) REVERT: B 254 ASP cc_start: 0.8660 (t70) cc_final: 0.8398 (t70) REVERT: B 266 HIS cc_start: 0.8950 (OUTLIER) cc_final: 0.8671 (t-170) REVERT: G 15 LEU cc_start: 0.8439 (tt) cc_final: 0.8183 (tm) REVERT: G 18 GLN cc_start: 0.8240 (tp40) cc_final: 0.7951 (tp40) REVERT: H 43 LYS cc_start: 0.9005 (mmtt) cc_final: 0.8744 (mmmm) REVERT: H 186 GLN cc_start: 0.9222 (tt0) cc_final: 0.8874 (tt0) REVERT: A 306 GLN cc_start: 0.8985 (mm110) cc_final: 0.8445 (mp10) outliers start: 25 outliers final: 8 residues processed: 135 average time/residue: 0.6517 time to fit residues: 92.2912 Evaluate side-chains 126 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 395 GLU Chi-restraints excluded: chain R residue 432 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain H residue 234 GLU Chi-restraints excluded: chain A residue 305 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 44 optimal weight: 0.0010 chunk 78 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.105044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.066754 restraints weight = 14794.756| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.67 r_work: 0.2730 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8869 Z= 0.112 Angle : 0.518 7.865 12049 Z= 0.278 Chirality : 0.041 0.133 1385 Planarity : 0.004 0.054 1511 Dihedral : 4.277 20.728 1221 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.50 % Allowed : 14.50 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.26), residues: 1106 helix: 2.13 (0.27), residues: 395 sheet: 0.79 (0.30), residues: 280 loop : 0.03 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 19 TYR 0.015 0.001 TYR H 190 PHE 0.021 0.001 PHE R 84 TRP 0.019 0.001 TRP B 82 HIS 0.002 0.000 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 8865) covalent geometry : angle 0.51760 / 0.28 (12041) SS BOND : bond 0.00248 / 0.12 ( 4) SS BOND : angle 0.46391 / 0.26 ( 8) hydrogen bonds : bond 0.03519 / 2.34 ( 448) hydrogen bonds : angle 4.21599 / 3.14 ( 1275) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.276 Fit side-chains REVERT: R 148 MET cc_start: 0.6820 (mmp) cc_final: 0.6599 (mmm) REVERT: B 172 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8329 (tp30) REVERT: B 217 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8469 (pmt) REVERT: B 254 ASP cc_start: 0.8601 (t70) cc_final: 0.8372 (t70) REVERT: B 266 HIS cc_start: 0.8938 (OUTLIER) cc_final: 0.8616 (t-170) REVERT: G 15 LEU cc_start: 0.8375 (tt) cc_final: 0.8133 (tm) REVERT: H 43 LYS cc_start: 0.9023 (mmtt) cc_final: 0.8757 (mmmm) REVERT: H 186 GLN cc_start: 0.9173 (tt0) cc_final: 0.8903 (tt0) REVERT: A 33 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8345 (tp30) REVERT: A 306 GLN cc_start: 0.8968 (mm110) cc_final: 0.8440 (mp10) outliers start: 14 outliers final: 5 residues processed: 133 average time/residue: 0.7095 time to fit residues: 99.0857 Evaluate side-chains 135 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 305 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.103670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.065067 restraints weight = 14786.221| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.68 r_work: 0.2691 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8869 Z= 0.165 Angle : 0.549 8.926 12049 Z= 0.291 Chirality : 0.042 0.131 1385 Planarity : 0.004 0.054 1511 Dihedral : 4.366 20.380 1221 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.04 % Allowed : 15.47 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.26), residues: 1106 helix: 2.13 (0.27), residues: 397 sheet: 0.74 (0.30), residues: 280 loop : 0.11 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 24 TYR 0.021 0.001 TYR A 296 PHE 0.016 0.001 PHE R 189 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 8865) covalent geometry : angle 0.54922 / 0.29 (12041) SS BOND : bond 0.00324 / 0.16 ( 4) SS BOND : angle 0.78131 / 0.40 ( 8) hydrogen bonds : bond 0.03775 / 2.50 ( 448) hydrogen bonds : angle 4.32857 / 3.22 ( 1275) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.319 Fit side-chains REVERT: R 148 MET cc_start: 0.6828 (mmp) cc_final: 0.6611 (mmm) REVERT: R 184 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7431 (mp10) REVERT: R 395 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.7047 (tt0) REVERT: B 172 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8353 (tp30) REVERT: B 217 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8508 (pmt) REVERT: B 254 ASP cc_start: 0.8627 (t70) cc_final: 0.8353 (t70) REVERT: B 266 HIS cc_start: 0.8992 (t-90) cc_final: 0.8680 (t-170) REVERT: H 43 LYS cc_start: 0.9048 (mmtt) cc_final: 0.8773 (mmmm) REVERT: H 186 GLN cc_start: 0.9189 (tt0) cc_final: 0.8849 (tt0) REVERT: A 306 GLN cc_start: 0.8972 (mm110) cc_final: 0.8430 (mp10) REVERT: A 308 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8324 (mt-10) outliers start: 19 outliers final: 7 residues processed: 144 average time/residue: 0.7508 time to fit residues: 113.2422 Evaluate side-chains 127 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 84 PHE Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 184 GLN Chi-restraints excluded: chain R residue 395 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain A residue 315 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 50 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.103770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.065223 restraints weight = 14923.902| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.70 r_work: 0.2696 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8869 Z= 0.156 Angle : 0.564 8.525 12049 Z= 0.301 Chirality : 0.042 0.134 1385 Planarity : 0.004 0.053 1511 Dihedral : 4.338 20.060 1221 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.61 % Allowed : 16.97 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.26), residues: 1106 helix: 2.15 (0.27), residues: 397 sheet: 0.71 (0.30), residues: 280 loop : 0.18 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 19 TYR 0.026 0.001 TYR A 296 PHE 0.016 0.001 PHE R 189 TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 8865) covalent geometry : angle 0.56430 / 0.30 (12041) SS BOND : bond 0.00317 / 0.15 ( 4) SS BOND : angle 0.75636 / 0.39 ( 8) hydrogen bonds : bond 0.03741 / 2.49 ( 448) hydrogen bonds : angle 4.32790 / 3.23 ( 1275) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.335 Fit side-chains REVERT: R 395 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.7043 (tt0) REVERT: B 172 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8391 (tp30) REVERT: B 217 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8520 (pmt) REVERT: B 254 ASP cc_start: 0.8616 (t70) cc_final: 0.8387 (t70) REVERT: H 43 LYS cc_start: 0.9047 (mmtt) cc_final: 0.8766 (mmmm) REVERT: H 186 GLN cc_start: 0.9170 (tt0) cc_final: 0.8861 (tt0) REVERT: A 33 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8324 (tp30) REVERT: A 207 GLU cc_start: 0.8468 (tp30) cc_final: 0.8212 (tp30) REVERT: A 306 GLN cc_start: 0.8969 (mm110) cc_final: 0.8414 (mp10) REVERT: A 308 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8476 (mt-10) outliers start: 15 outliers final: 6 residues processed: 138 average time/residue: 0.7404 time to fit residues: 107.1675 Evaluate side-chains 126 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 395 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 315 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 28 optimal weight: 6.9990 chunk 82 optimal weight: 0.0980 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 0.0980 chunk 79 optimal weight: 0.0570 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 172 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.106356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.068609 restraints weight = 14706.206| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.68 r_work: 0.2772 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8869 Z= 0.105 Angle : 0.555 10.915 12049 Z= 0.291 Chirality : 0.041 0.141 1385 Planarity : 0.004 0.050 1511 Dihedral : 4.073 22.507 1221 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.07 % Allowed : 17.62 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.26), residues: 1106 helix: 2.33 (0.27), residues: 396 sheet: 0.85 (0.30), residues: 285 loop : 0.20 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 24 TYR 0.015 0.001 TYR H 190 PHE 0.013 0.001 PHE R 189 TRP 0.020 0.001 TRP B 82 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 8865) covalent geometry : angle 0.55538 / 0.29 (12041) SS BOND : bond 0.00249 / 0.12 ( 4) SS BOND : angle 0.55416 / 0.29 ( 8) hydrogen bonds : bond 0.03259 / 2.18 ( 448) hydrogen bonds : angle 4.05671 / 3.02 ( 1275) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.334 Fit side-chains REVERT: R 129 ASP cc_start: 0.8517 (t70) cc_final: 0.8267 (t70) REVERT: R 395 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.7000 (tt0) REVERT: B 188 MET cc_start: 0.9165 (mmm) cc_final: 0.8820 (mmm) REVERT: B 217 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8599 (pmt) REVERT: B 254 ASP cc_start: 0.8557 (t70) cc_final: 0.8313 (t70) REVERT: G 46 LYS cc_start: 0.9205 (ptpp) cc_final: 0.8993 (pmtt) REVERT: G 52 THR cc_start: 0.8036 (p) cc_final: 0.7797 (t) REVERT: G 58 GLU cc_start: 0.8426 (mp0) cc_final: 0.7997 (pm20) REVERT: H 43 LYS cc_start: 0.8984 (mmtt) cc_final: 0.8749 (mmmm) REVERT: H 180 ARG cc_start: 0.8807 (mtt90) cc_final: 0.8459 (mtt90) REVERT: H 186 GLN cc_start: 0.9043 (tt0) cc_final: 0.8716 (pt0) REVERT: H 222 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7763 (tm-30) REVERT: A 21 ARG cc_start: 0.8202 (ttp-110) cc_final: 0.7988 (ttp-110) REVERT: A 33 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8328 (tp30) REVERT: A 242 ARG cc_start: 0.8483 (mtm-85) cc_final: 0.7996 (mtt90) REVERT: A 306 GLN cc_start: 0.8943 (mm110) cc_final: 0.8363 (mp10) REVERT: A 308 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8303 (mt-10) outliers start: 10 outliers final: 6 residues processed: 141 average time/residue: 0.7340 time to fit residues: 108.5610 Evaluate side-chains 132 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 PHE Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 395 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 315 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 14 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 172 GLN ** A 294 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 = 0.3568 r_free = 0.3568 target = 0.104664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.066416 restraints weight = 14711.569| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.68 r_work: 0.2724 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8869 Z= 0.137 Angle : 0.575 9.606 12049 Z= 0.302 Chirality : 0.041 0.140 1385 Planarity : 0.004 0.052 1511 Dihedral : 4.158 20.892 1221 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.18 % Allowed : 18.37 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.26), residues: 1106 helix: 2.37 (0.27), residues: 391 sheet: 0.74 (0.30), residues: 281 loop : 0.21 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.027 0.001 TYR A 296 PHE 0.014 0.001 PHE R 189 TRP 0.017 0.001 TRP R 440 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 8865) covalent geometry : angle 0.57514 / 0.30 (12041) SS BOND : bond 0.00279 / 0.13 ( 4) SS BOND : angle 0.62319 / 0.32 ( 8) hydrogen bonds : bond 0.03555 / 2.36 ( 448) hydrogen bonds : angle 4.16887 / 3.12 ( 1275) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.404 Fit side-chains REVERT: R 148 MET cc_start: 0.6834 (mmp) cc_final: 0.6599 (mmm) REVERT: R 395 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.7021 (tt0) REVERT: B 19 ARG cc_start: 0.8547 (ttp80) cc_final: 0.8058 (ttp80) REVERT: B 217 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8562 (pmt) REVERT: B 254 ASP cc_start: 0.8593 (t70) cc_final: 0.8353 (t70) REVERT: G 46 LYS cc_start: 0.9211 (ptpp) cc_final: 0.8997 (pmtt) REVERT: G 58 GLU cc_start: 0.8453 (mp0) cc_final: 0.7954 (pm20) REVERT: H 43 LYS cc_start: 0.9005 (mmtt) cc_final: 0.8763 (mmmm) REVERT: H 180 ARG cc_start: 0.8859 (mtt90) cc_final: 0.8418 (mtt90) REVERT: H 186 GLN cc_start: 0.9111 (tt0) cc_final: 0.8696 (pt0) REVERT: H 222 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7746 (tm-30) REVERT: A 242 ARG cc_start: 0.8484 (mtm-85) cc_final: 0.8006 (mtt90) REVERT: A 306 GLN cc_start: 0.8946 (mm110) cc_final: 0.8394 (mp10) REVERT: A 308 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8346 (mt-10) outliers start: 11 outliers final: 6 residues processed: 136 average time/residue: 0.7582 time to fit residues: 107.9772 Evaluate side-chains 139 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 PHE Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 395 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain A residue 315 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 76 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.105392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.067287 restraints weight = 14781.750| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.68 r_work: 0.2744 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8869 Z= 0.120 Angle : 0.577 10.095 12049 Z= 0.300 Chirality : 0.041 0.145 1385 Planarity : 0.004 0.048 1511 Dihedral : 4.090 20.652 1221 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.07 % Allowed : 18.58 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.26), residues: 1106 helix: 2.43 (0.27), residues: 390 sheet: 0.77 (0.30), residues: 280 loop : 0.23 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 42 TYR 0.013 0.001 TYR H 190 PHE 0.013 0.001 PHE R 189 TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 8865) covalent geometry : angle 0.57708 / 0.30 (12041) SS BOND : bond 0.00289 / 0.13 ( 4) SS BOND : angle 0.56703 / 0.30 ( 8) hydrogen bonds : bond 0.03358 / 2.24 ( 448) hydrogen bonds : angle 4.08743 / 3.06 ( 1275) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.347 Fit side-chains REVERT: R 148 MET cc_start: 0.6824 (mmp) cc_final: 0.6611 (mmm) REVERT: R 395 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.7021 (tt0) REVERT: B 19 ARG cc_start: 0.8554 (ttp80) cc_final: 0.8053 (ttp80) REVERT: B 217 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8583 (pmt) REVERT: G 58 GLU cc_start: 0.8441 (mp0) cc_final: 0.7981 (pm20) REVERT: H 43 LYS cc_start: 0.8990 (mmtt) cc_final: 0.8753 (mmmm) REVERT: H 180 ARG cc_start: 0.8843 (mtt90) cc_final: 0.8429 (mtt90) REVERT: H 186 GLN cc_start: 0.9107 (tt0) cc_final: 0.8722 (pt0) REVERT: H 222 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7745 (tm-30) REVERT: A 205 ARG cc_start: 0.8187 (mmm160) cc_final: 0.7736 (mmp-170) REVERT: A 207 GLU cc_start: 0.8914 (tp30) cc_final: 0.8469 (tp30) REVERT: A 242 ARG cc_start: 0.8505 (mtm-85) cc_final: 0.8016 (mtt90) REVERT: A 306 GLN cc_start: 0.8938 (mm110) cc_final: 0.8362 (mp10) REVERT: A 308 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8330 (mt-10) outliers start: 10 outliers final: 6 residues processed: 137 average time/residue: 0.7015 time to fit residues: 100.7597 Evaluate side-chains 137 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 PHE Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 395 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain A residue 315 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 172 GLN ** A 294 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 = 0.3582 r_free = 0.3582 target = 0.105411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.067348 restraints weight = 14663.490| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.66 r_work: 0.2744 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8869 Z= 0.120 Angle : 0.579 9.979 12049 Z= 0.302 Chirality : 0.041 0.147 1385 Planarity : 0.004 0.054 1511 Dihedral : 4.101 20.644 1221 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.07 % Allowed : 18.15 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.26), residues: 1106 helix: 2.29 (0.27), residues: 397 sheet: 0.76 (0.30), residues: 280 loop : 0.11 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 24 TYR 0.028 0.001 TYR A 296 PHE 0.013 0.001 PHE R 189 TRP 0.016 0.001 TRP R 440 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 8865) covalent geometry : angle 0.57947 / 0.30 (12041) SS BOND : bond 0.00273 / 0.13 ( 4) SS BOND : angle 0.55062 / 0.29 ( 8) hydrogen bonds : bond 0.03354 / 2.24 ( 448) hydrogen bonds : angle 4.07711 / 3.05 ( 1275) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4643.29 seconds wall clock time: 79 minutes 45.07 seconds (4785.07 seconds total)