Starting phenix.real_space_refine on Wed Mar 4 23:36:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sqo_25389/03_2026/7sqo_25389_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sqo_25389/03_2026/7sqo_25389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sqo_25389/03_2026/7sqo_25389_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sqo_25389/03_2026/7sqo_25389_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sqo_25389/03_2026/7sqo_25389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sqo_25389/03_2026/7sqo_25389.map" } resolution = 3.17 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= 0.009 sd= 0.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 78 atoms to isotropic. 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 68 5.16 5 C 5528 2.51 5 N 1454 2.21 5 O 1568 1.98 5 H 8331 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16949 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 4304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 4304 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 8, 'TRANS': 261} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3294 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE%COO:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 5020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5020 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 26 Chain: "G" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 803 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3453 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 75 Unusual residues: {'A6F': 1, 'OLA': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'OLA:plan-2': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 3.23, per 1000 atoms: 0.19 Number of scatterers: 16949 At special positions: 0 Unit cell: (94.64, 117.52, 122.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 O 1568 8.00 N 1454 7.00 C 5528 6.00 H 8331 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 210 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 616.1 milliseconds 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 38.2% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'R' and resid 55 through 82 removed outlier: 4.319A pdb=" N ALA R 59 " --> pdb=" O TRP R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 117 removed outlier: 3.735A pdb=" N PHE R 92 " --> pdb=" O VAL R 88 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU R 108 " --> pdb=" O THR R 104 " (cutoff:3.500A) Proline residue: R 109 - end of helix Processing helix chain 'R' and resid 123 through 157 Proline residue: R 131 - end of helix Processing helix chain 'R' and resid 165 through 184 removed outlier: 4.062A pdb=" N MET R 184 " --> pdb=" O SER R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 190 removed outlier: 3.883A pdb=" N ILE R 189 " --> pdb=" O ILE R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 232 Processing helix chain 'R' and resid 232 through 253 Processing helix chain 'R' and resid 294 through 317 Processing helix chain 'R' and resid 317 through 328 Processing helix chain 'R' and resid 340 through 365 removed outlier: 3.789A pdb=" N ALA R 344 " --> pdb=" O GLU R 340 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 368 through 378 Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.592A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 213 removed outlier: 4.119A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.981A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.795A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.774A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.753A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 191 through 192 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 186 Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 186 removed outlier: 6.631A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.780A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 104 through 105 removed outlier: 5.746A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.527A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 191 removed outlier: 4.277A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 232 through 234 removed outlier: 6.859A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.687A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60 removed outlier: 5.159A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.527A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1227 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: 4.20 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8299 1.03 - 1.23: 32 1.23 - 1.42: 3709 1.42 - 1.62: 4990 1.62 - 1.81: 98 Bond restraints: 17128 Sorted by residual: bond pdb=" C10 OLA R 503 " pdb=" C9 OLA R 503 " ideal model delta sigma weight residual 1.332 1.470 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C10 OLA R 504 " pdb=" C9 OLA R 504 " ideal model delta sigma weight residual 1.332 1.470 -0.138 2.00e-02 2.50e+03 4.74e+01 bond pdb=" N25 A6F R 505 " pdb=" S26 A6F R 505 " ideal model delta sigma weight residual 1.647 1.696 -0.049 2.00e-02 2.50e+03 6.12e+00 bond pdb=" C7 A6F R 505 " pdb=" N1 A6F R 505 " ideal model delta sigma weight residual 1.356 1.400 -0.044 2.00e-02 2.50e+03 4.76e+00 bond pdb=" C1 OLA R 504 " pdb=" C2 OLA R 504 " ideal model delta sigma weight residual 1.542 1.510 0.032 2.00e-02 2.50e+03 2.63e+00 ... (remaining 17123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 30358 1.64 - 3.29: 345 3.29 - 4.93: 37 4.93 - 6.57: 8 6.57 - 8.22: 8 Bond angle restraints: 30756 Sorted by residual: angle pdb=" N ALA B 302 " pdb=" CA ALA B 302 " pdb=" CB ALA B 302 " ideal model delta sigma weight residual 114.17 110.93 3.24 1.14e+00 7.69e-01 8.08e+00 angle pdb=" C11 OLA R 504 " pdb=" C10 OLA R 504 " pdb=" C9 OLA R 504 " ideal model delta sigma weight residual 127.87 119.65 8.22 3.00e+00 1.11e-01 7.50e+00 angle pdb=" C11 OLA R 503 " pdb=" C10 OLA R 503 " pdb=" C9 OLA R 503 " ideal model delta sigma weight residual 127.87 120.07 7.80 3.00e+00 1.11e-01 6.76e+00 angle pdb=" C10 OLA R 504 " pdb=" C9 OLA R 504 " pdb=" C8 OLA R 504 " ideal model delta sigma weight residual 127.72 119.93 7.79 3.00e+00 1.11e-01 6.75e+00 angle pdb=" C10 OLA R 503 " pdb=" C9 OLA R 503 " pdb=" C8 OLA R 503 " ideal model delta sigma weight residual 127.72 119.93 7.79 3.00e+00 1.11e-01 6.74e+00 ... (remaining 30751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7446 17.95 - 35.90: 541 35.90 - 53.85: 153 53.85 - 71.80: 20 71.80 - 89.75: 1 Dihedral angle restraints: 8161 sinusoidal: 4296 harmonic: 3865 Sorted by residual: dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 157.20 22.80 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA ASP B 290 " pdb=" C ASP B 290 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " ideal model delta harmonic sigma weight residual 180.00 158.73 21.27 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 162.52 17.48 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 8158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1066 0.045 - 0.089: 238 0.089 - 0.133: 66 0.133 - 0.178: 3 0.178 - 0.222: 1 Chirality restraints: 1374 Sorted by residual: chirality pdb=" C3 A6F R 505 " pdb=" C2 A6F R 505 " pdb=" C4 A6F R 505 " pdb=" N25 A6F R 505 " both_signs ideal model delta sigma weight residual False 2.34 2.56 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C13 A6F R 505 " pdb=" C14 A6F R 505 " pdb=" C18 A6F R 505 " pdb=" O12 A6F R 505 " both_signs ideal model delta sigma weight residual False 2.50 2.65 -0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 1371 not shown) Planarity restraints: 2558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA R 504 " -0.162 2.00e-02 2.50e+03 1.27e-01 1.61e+02 pdb=" C11 OLA R 504 " 0.075 2.00e-02 2.50e+03 pdb=" C8 OLA R 504 " -0.076 2.00e-02 2.50e+03 pdb=" C9 OLA R 504 " 0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA R 503 " 0.148 2.00e-02 2.50e+03 1.16e-01 1.34e+02 pdb=" C11 OLA R 503 " -0.070 2.00e-02 2.50e+03 pdb=" C8 OLA R 503 " 0.069 2.00e-02 2.50e+03 pdb=" C9 OLA R 503 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 234 " 0.014 2.00e-02 2.50e+03 7.54e-03 1.71e+00 pdb=" CG PHE B 234 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE B 234 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE B 234 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 234 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 234 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 234 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE B 234 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE B 234 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE B 234 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE B 234 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE B 234 " -0.000 2.00e-02 2.50e+03 ... (remaining 2555 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1298 2.21 - 2.80: 35706 2.80 - 3.40: 46615 3.40 - 4.00: 61999 4.00 - 4.60: 95436 Nonbonded interactions: 241054 Sorted by model distance: nonbonded pdb=" HG1 THR B 274 " pdb=" O VAL B 315 " model vdw 1.608 2.450 nonbonded pdb=" O VAL R 113 " pdb=" HG1 THR R 117 " model vdw 1.618 2.450 nonbonded pdb=" O ALA R 359 " pdb=" H ILE R 363 " model vdw 1.625 2.450 nonbonded pdb="HD21 ASN R 72 " pdb=" OD2 ASP R 100 " model vdw 1.626 2.450 nonbonded pdb=" O PHE A 259 " pdb=" HZ2 LYS A 317 " model vdw 1.629 2.450 ... (remaining 241049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.100 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.980 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 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 : 0.004 0.138 8800 Z= 0.183 Angle : 0.589 8.217 11932 Z= 0.295 Chirality : 0.040 0.222 1374 Planarity : 0.005 0.127 1487 Dihedral : 13.249 89.751 3115 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.20 (0.27), residues: 1089 helix: 1.98 (0.28), residues: 375 sheet: -1.24 (0.31), residues: 290 loop : -1.19 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 38 TYR 0.021 0.001 TYR B 59 PHE 0.022 0.001 PHE B 234 TRP 0.010 0.001 TRP E 47 HIS 0.003 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 8797) covalent geometry : angle 0.58786 (11926) SS BOND : bond 0.00200 ( 3) SS BOND : angle 1.46317 ( 6) hydrogen bonds : bond 0.13110 ( 435) hydrogen bonds : angle 6.10232 ( 1227) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 85 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 294 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue ILE 362 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue ALA 121 is missing expected H atoms. Skipping. Residue ALA 124 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8428 (m-30) cc_final: 0.8183 (m-30) REVERT: B 291 ASP cc_start: 0.7593 (m-30) cc_final: 0.7280 (m-30) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2547 time to fit residues: 62.4627 Evaluate side-chains 161 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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: 0.8980 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 324 ASN A 269 ASN ** B 340 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 = 0.3849 r_free = 0.3849 target = 0.136944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.104969 restraints weight = 36358.773| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.81 r_work: 0.3301 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8800 Z= 0.188 Angle : 0.536 6.109 11932 Z= 0.291 Chirality : 0.040 0.143 1374 Planarity : 0.003 0.032 1487 Dihedral : 6.042 56.466 1265 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.44 % Allowed : 8.19 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.40 (0.26), residues: 1089 helix: 1.67 (0.27), residues: 379 sheet: -1.25 (0.31), residues: 289 loop : -1.28 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.016 0.001 TYR B 59 PHE 0.018 0.001 PHE B 234 TRP 0.011 0.001 TRP E 47 HIS 0.006 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 8797) covalent geometry : angle 0.53329 (11926) SS BOND : bond 0.00179 ( 3) SS BOND : angle 2.25562 ( 6) hydrogen bonds : bond 0.04174 ( 435) hydrogen bonds : angle 5.09699 ( 1227) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 85 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 294 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue ILE 362 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue ALA 121 is missing expected H atoms. Skipping. Residue ALA 124 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 166 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8675 (m-30) cc_final: 0.8431 (m-30) REVERT: A 304 GLN cc_start: 0.8257 (tt0) cc_final: 0.7855 (mt0) outliers start: 4 outliers final: 4 residues processed: 169 average time/residue: 0.2476 time to fit residues: 55.4181 Evaluate side-chains 157 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 153 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 TRP Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 20 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 46 optimal weight: 0.8980 chunk 71 optimal weight: 0.0770 chunk 24 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 88 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.138423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.107151 restraints weight = 36144.667| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.71 r_work: 0.3342 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8800 Z= 0.113 Angle : 0.492 5.427 11932 Z= 0.264 Chirality : 0.039 0.137 1374 Planarity : 0.003 0.053 1487 Dihedral : 5.590 58.742 1265 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.66 % Allowed : 9.63 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.27), residues: 1089 helix: 1.74 (0.27), residues: 377 sheet: -1.25 (0.31), residues: 292 loop : -1.13 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 328 TYR 0.007 0.001 TYR E 103 PHE 0.016 0.001 PHE B 234 TRP 0.007 0.001 TRP B 339 HIS 0.006 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8797) covalent geometry : angle 0.49127 (11926) SS BOND : bond 0.00061 ( 3) SS BOND : angle 1.46256 ( 6) hydrogen bonds : bond 0.03636 ( 435) hydrogen bonds : angle 4.80663 ( 1227) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 85 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 294 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue ILE 362 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue ALA 121 is missing expected H atoms. Skipping. Residue ALA 124 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 164 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8710 (m-30) cc_final: 0.8458 (m-30) REVERT: A 20 ASP cc_start: 0.8668 (t0) cc_final: 0.8428 (t0) REVERT: A 297 GLU cc_start: 0.8780 (tp30) cc_final: 0.8578 (pm20) REVERT: B 76 ASP cc_start: 0.8138 (t0) cc_final: 0.7921 (t0) outliers start: 6 outliers final: 4 residues processed: 167 average time/residue: 0.2499 time to fit residues: 55.9939 Evaluate side-chains 157 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 153 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 TRP Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 20 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 67 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 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 = 0.3851 r_free = 0.3851 target = 0.136680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.105338 restraints weight = 36232.647| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.74 r_work: 0.3306 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8800 Z= 0.165 Angle : 0.507 5.466 11932 Z= 0.273 Chirality : 0.040 0.155 1374 Planarity : 0.003 0.031 1487 Dihedral : 5.364 53.817 1265 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.55 % Allowed : 10.30 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.27), residues: 1089 helix: 1.72 (0.27), residues: 380 sheet: -1.21 (0.32), residues: 285 loop : -1.23 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 328 TYR 0.008 0.001 TYR B 59 PHE 0.019 0.001 PHE B 234 TRP 0.008 0.001 TRP E 47 HIS 0.005 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8797) covalent geometry : angle 0.50587 (11926) SS BOND : bond 0.00080 ( 3) SS BOND : angle 1.85779 ( 6) hydrogen bonds : bond 0.03526 ( 435) hydrogen bonds : angle 4.70664 ( 1227) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 85 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 294 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue ILE 362 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue ALA 121 is missing expected H atoms. Skipping. Residue ALA 124 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Evaluate side-chains 168 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 163 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8757 (m-30) cc_final: 0.8522 (m-30) REVERT: B 76 ASP cc_start: 0.8353 (t0) cc_final: 0.8152 (t0) outliers start: 5 outliers final: 5 residues processed: 166 average time/residue: 0.2410 time to fit residues: 53.9218 Evaluate side-chains 159 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 154 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 TRP Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 103 optimal weight: 0.0870 chunk 12 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN ** B 340 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 = 0.3846 r_free = 0.3846 target = 0.136304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.105106 restraints weight = 36105.404| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.73 r_work: 0.3295 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8800 Z= 0.166 Angle : 0.510 5.496 11932 Z= 0.274 Chirality : 0.040 0.138 1374 Planarity : 0.003 0.030 1487 Dihedral : 5.263 50.059 1265 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.89 % Allowed : 12.07 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.27), residues: 1089 helix: 1.76 (0.27), residues: 377 sheet: -1.25 (0.32), residues: 285 loop : -1.23 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 328 TYR 0.009 0.001 TYR B 59 PHE 0.020 0.001 PHE B 234 TRP 0.007 0.001 TRP B 99 HIS 0.004 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8797) covalent geometry : angle 0.50820 (11926) SS BOND : bond 0.00083 ( 3) SS BOND : angle 1.88145 ( 6) hydrogen bonds : bond 0.03459 ( 435) hydrogen bonds : angle 4.64080 ( 1227) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 85 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 294 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue ILE 362 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue ALA 121 is missing expected H atoms. Skipping. Residue ALA 124 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 165 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8734 (m-30) cc_final: 0.8500 (m-30) REVERT: A 20 ASP cc_start: 0.8719 (t0) cc_final: 0.8482 (t70) outliers start: 8 outliers final: 6 residues processed: 170 average time/residue: 0.2491 time to fit residues: 56.3109 Evaluate side-chains 163 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 157 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 TRP Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 343 TYR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** B 340 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 = 0.3828 r_free = 0.3828 target = 0.134398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.103295 restraints weight = 35784.694| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.71 r_work: 0.3285 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 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 : 0.004 0.036 8800 Z= 0.162 Angle : 0.512 6.889 11932 Z= 0.274 Chirality : 0.040 0.139 1374 Planarity : 0.003 0.030 1487 Dihedral : 5.201 51.897 1265 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.89 % Allowed : 12.96 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.35 (0.27), residues: 1089 helix: 1.75 (0.27), residues: 377 sheet: -1.36 (0.31), residues: 294 loop : -1.14 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 328 TYR 0.010 0.001 TYR B 59 PHE 0.020 0.001 PHE B 234 TRP 0.007 0.001 TRP B 99 HIS 0.004 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8797) covalent geometry : angle 0.51056 (11926) SS BOND : bond 0.00077 ( 3) SS BOND : angle 1.58355 ( 6) hydrogen bonds : bond 0.03425 ( 435) hydrogen bonds : angle 4.60151 ( 1227) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 85 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 294 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue ILE 362 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue ALA 121 is missing expected H atoms. Skipping. Residue ALA 124 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8741 (m-30) cc_final: 0.8502 (m-30) REVERT: A 297 GLU cc_start: 0.8897 (tp30) cc_final: 0.8627 (pm20) REVERT: B 289 TYR cc_start: 0.8891 (m-80) cc_final: 0.8618 (m-80) outliers start: 8 outliers final: 7 residues processed: 169 average time/residue: 0.2501 time to fit residues: 56.4239 Evaluate side-chains 163 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 156 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 TRP Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 343 TYR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 40 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 74 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 269 ASN ** B 340 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 = 0.3858 r_free = 0.3858 target = 0.137433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.106039 restraints weight = 35853.434| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.77 r_work: 0.3300 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8800 Z= 0.121 Angle : 0.499 5.492 11932 Z= 0.266 Chirality : 0.040 0.191 1374 Planarity : 0.003 0.029 1487 Dihedral : 5.134 59.676 1265 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.11 % Allowed : 12.96 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.29 (0.27), residues: 1089 helix: 1.77 (0.27), residues: 377 sheet: -1.30 (0.31), residues: 293 loop : -1.10 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 328 TYR 0.010 0.001 TYR A 302 PHE 0.016 0.001 PHE B 234 TRP 0.006 0.001 TRP B 99 HIS 0.004 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8797) covalent geometry : angle 0.49744 (11926) SS BOND : bond 0.00106 ( 3) SS BOND : angle 1.75078 ( 6) hydrogen bonds : bond 0.03297 ( 435) hydrogen bonds : angle 4.52775 ( 1227) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 85 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 294 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue ILE 362 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue ALA 121 is missing expected H atoms. Skipping. Residue ALA 124 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8705 (m-30) cc_final: 0.8472 (m-30) REVERT: A 20 ASP cc_start: 0.8638 (t0) cc_final: 0.8422 (t70) REVERT: A 297 GLU cc_start: 0.8854 (tp30) cc_final: 0.8618 (pm20) REVERT: A 304 GLN cc_start: 0.8084 (tt0) cc_final: 0.7804 (tt0) REVERT: B 289 TYR cc_start: 0.8868 (m-80) cc_final: 0.8598 (m-80) outliers start: 10 outliers final: 9 residues processed: 172 average time/residue: 0.2620 time to fit residues: 59.4837 Evaluate side-chains 174 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 TRP Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 343 TYR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 103 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.137618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.106544 restraints weight = 36133.643| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.72 r_work: 0.3316 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8800 Z= 0.123 Angle : 0.498 5.483 11932 Z= 0.265 Chirality : 0.039 0.152 1374 Planarity : 0.003 0.058 1487 Dihedral : 4.914 46.560 1265 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.11 % Allowed : 13.07 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.27), residues: 1089 helix: 1.77 (0.27), residues: 378 sheet: -1.32 (0.31), residues: 295 loop : -1.07 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 148 TYR 0.012 0.001 TYR A 302 PHE 0.017 0.001 PHE B 234 TRP 0.006 0.001 TRP B 99 HIS 0.004 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8797) covalent geometry : angle 0.49639 (11926) SS BOND : bond 0.00080 ( 3) SS BOND : angle 1.91777 ( 6) hydrogen bonds : bond 0.03264 ( 435) hydrogen bonds : angle 4.47819 ( 1227) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 85 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 294 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue ILE 362 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue ALA 121 is missing expected H atoms. Skipping. Residue ALA 124 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 168 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8757 (m-30) cc_final: 0.8539 (m-30) REVERT: A 18 MET cc_start: 0.8070 (tpp) cc_final: 0.7483 (tmm) REVERT: A 20 ASP cc_start: 0.8720 (t0) cc_final: 0.8499 (t70) REVERT: A 294 ASN cc_start: 0.8786 (m-40) cc_final: 0.8248 (t0) REVERT: A 297 GLU cc_start: 0.8884 (tp30) cc_final: 0.8639 (pm20) REVERT: A 304 GLN cc_start: 0.8084 (tt0) cc_final: 0.7809 (tt0) REVERT: A 337 ASP cc_start: 0.7836 (p0) cc_final: 0.7584 (p0) outliers start: 10 outliers final: 10 residues processed: 174 average time/residue: 0.2476 time to fit residues: 57.2636 Evaluate side-chains 172 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 TRP Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 343 TYR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 160 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 269 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.135122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.104579 restraints weight = 36000.838| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.65 r_work: 0.3315 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8800 Z= 0.143 Angle : 0.509 5.501 11932 Z= 0.272 Chirality : 0.040 0.138 1374 Planarity : 0.003 0.029 1487 Dihedral : 4.765 41.465 1265 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.22 % Allowed : 13.62 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.32 (0.27), residues: 1089 helix: 1.74 (0.27), residues: 378 sheet: -1.39 (0.31), residues: 299 loop : -1.05 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 148 TYR 0.013 0.001 TYR A 302 PHE 0.017 0.001 PHE B 234 TRP 0.007 0.001 TRP B 99 HIS 0.004 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8797) covalent geometry : angle 0.50776 (11926) SS BOND : bond 0.00123 ( 3) SS BOND : angle 1.76231 ( 6) hydrogen bonds : bond 0.03287 ( 435) hydrogen bonds : angle 4.48816 ( 1227) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 85 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 294 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue ILE 362 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue ALA 121 is missing expected H atoms. Skipping. Residue ALA 124 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8762 (m-30) cc_final: 0.8550 (m-30) REVERT: A 18 MET cc_start: 0.8095 (tpp) cc_final: 0.7525 (tmm) REVERT: A 20 ASP cc_start: 0.8701 (t0) cc_final: 0.8477 (t70) REVERT: A 294 ASN cc_start: 0.8796 (m-40) cc_final: 0.8292 (t0) REVERT: A 297 GLU cc_start: 0.8871 (tp30) cc_final: 0.8645 (pm20) REVERT: A 304 GLN cc_start: 0.8105 (tt0) cc_final: 0.7777 (tt0) REVERT: B 289 TYR cc_start: 0.8916 (m-80) cc_final: 0.8646 (m-80) outliers start: 11 outliers final: 11 residues processed: 171 average time/residue: 0.2445 time to fit residues: 55.4325 Evaluate side-chains 170 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 TRP Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 343 TYR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 160 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 104 optimal weight: 0.2980 chunk 69 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.136123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.105243 restraints weight = 35724.934| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.71 r_work: 0.3320 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8800 Z= 0.116 Angle : 0.508 7.317 11932 Z= 0.269 Chirality : 0.039 0.136 1374 Planarity : 0.003 0.044 1487 Dihedral : 4.704 42.490 1265 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.22 % Allowed : 14.06 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.27), residues: 1089 helix: 1.80 (0.27), residues: 377 sheet: -1.28 (0.31), residues: 295 loop : -1.04 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 148 TYR 0.013 0.001 TYR A 302 PHE 0.015 0.001 PHE B 234 TRP 0.006 0.001 TRP B 99 HIS 0.004 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8797) covalent geometry : angle 0.50633 (11926) SS BOND : bond 0.00071 ( 3) SS BOND : angle 1.65822 ( 6) hydrogen bonds : bond 0.03209 ( 435) hydrogen bonds : angle 4.43967 ( 1227) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 85 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 294 is missing expected H atoms. Skipping. Residue VAL 308 is missing expected H atoms. Skipping. Residue ILE 362 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue ALA 121 is missing expected H atoms. Skipping. Residue ALA 124 is missing expected H atoms. Skipping. Residue THR 198 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8717 (m-30) cc_final: 0.8479 (m-30) REVERT: A 18 MET cc_start: 0.7995 (tpp) cc_final: 0.7399 (tmm) REVERT: A 294 ASN cc_start: 0.8831 (m-40) cc_final: 0.8303 (t0) REVERT: A 297 GLU cc_start: 0.8871 (tp30) cc_final: 0.8604 (pm20) REVERT: A 304 GLN cc_start: 0.8077 (tt0) cc_final: 0.7771 (tt0) outliers start: 11 outliers final: 11 residues processed: 168 average time/residue: 0.2583 time to fit residues: 57.2284 Evaluate side-chains 173 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 TRP Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 343 TYR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 160 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 55 optimal weight: 0.2980 chunk 13 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.135577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.104766 restraints weight = 35825.960| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.70 r_work: 0.3315 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8800 Z= 0.137 Angle : 0.516 6.651 11932 Z= 0.273 Chirality : 0.039 0.142 1374 Planarity : 0.003 0.036 1487 Dihedral : 4.666 44.185 1265 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.22 % Allowed : 14.51 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.26 (0.27), residues: 1089 helix: 1.76 (0.27), residues: 379 sheet: -1.36 (0.31), residues: 299 loop : -0.98 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 148 TYR 0.013 0.001 TYR A 302 PHE 0.016 0.001 PHE B 234 TRP 0.007 0.001 TRP B 99 HIS 0.004 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8797) covalent geometry : angle 0.51437 (11926) SS BOND : bond 0.00080 ( 3) SS BOND : angle 1.71172 ( 6) hydrogen bonds : bond 0.03244 ( 435) hydrogen bonds : angle 4.46297 ( 1227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5072.05 seconds wall clock time: 86 minutes 45.94 seconds (5205.94 seconds total)