Starting phenix.real_space_refine on Tue Feb 3 22:45:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zcj_39931/02_2026/8zcj_39931.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zcj_39931/02_2026/8zcj_39931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zcj_39931/02_2026/8zcj_39931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zcj_39931/02_2026/8zcj_39931.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zcj_39931/02_2026/8zcj_39931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zcj_39931/02_2026/8zcj_39931.map" } resolution = 3.09 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= 0.007 sd= 0.096 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 4945 2.51 5 N 1344 2.21 5 O 1478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7808 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1556 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 209 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 11, 'GLN:plan1': 2, 'ASP:plan': 6, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 145 Chain: "C" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2369 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 8, 'GLN:plan1': 7, 'ARG:plan': 9, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 131 Chain: "D" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 296 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "E" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1705 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "G" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 1818 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 418 Unresolved non-hydrogen dihedrals: 267 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'TYR:plan': 3, 'ARG:plan': 11, 'ASN:plan1': 4, 'PHE:plan': 9, 'TRP:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 186 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'004:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Classifications: {'peptide': 5} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.94, per 1000 atoms: 0.25 Number of scatterers: 7808 At special positions: 0 Unit cell: (85.6, 121.98, 121.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1478 8.00 N 1344 7.00 C 4945 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 103 " - pdb=" SG CYS C 114 " distance=2.04 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS G 112 " - pdb=" SG CYS G 186 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 228.2 milliseconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTR A 2 " Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 32.1% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.610A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.614A pdb=" N GLN B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET B 53 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 216 Processing helix chain 'B' and resid 243 through 255 Processing helix chain 'B' and resid 270 through 281 removed outlier: 3.708A pdb=" N GLU B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLU B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B 281 " --> pdb=" O LYS B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 removed outlier: 3.664A pdb=" N ALA B 299 " --> pdb=" O THR B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 310 Processing helix chain 'B' and resid 329 through 349 removed outlier: 4.233A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 24 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 34 through 44 removed outlier: 4.414A pdb=" N GLU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 191 through 193 No H-bonds generated for 'chain 'E' and resid 191 through 193' Processing helix chain 'G' and resid 44 through 66 Processing helix chain 'G' and resid 73 through 92 removed outlier: 3.973A pdb=" N GLY G 92 " --> pdb=" O LEU G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 98 removed outlier: 4.161A pdb=" N THR G 98 " --> pdb=" O PRO G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 142 removed outlier: 4.319A pdb=" N GLY G 120 " --> pdb=" O MET G 116 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL G 127 " --> pdb=" O GLN G 123 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL G 132 " --> pdb=" O PHE G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 151 Processing helix chain 'G' and resid 152 through 172 removed outlier: 4.134A pdb=" N LEU G 168 " --> pdb=" O TRP G 164 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS G 169 " --> pdb=" O VAL G 165 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET G 170 " --> pdb=" O LEU G 166 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER G 171 " --> pdb=" O SER G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 210 removed outlier: 4.246A pdb=" N ALA G 199 " --> pdb=" O GLY G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 232 removed outlier: 3.616A pdb=" N TYR G 221 " --> pdb=" O ILE G 217 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU G 222 " --> pdb=" O CYS G 218 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE G 224 " --> pdb=" O CYS G 220 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL G 225 " --> pdb=" O TYR G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 262 removed outlier: 4.863A pdb=" N VAL G 252 " --> pdb=" O ARG G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 274 removed outlier: 3.693A pdb=" N ASN G 268 " --> pdb=" O PHE G 264 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU G 272 " --> pdb=" O ASN G 268 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA G 273 " --> pdb=" O ILE G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 304 removed outlier: 3.729A pdb=" N PHE G 288 " --> pdb=" O GLY G 284 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL G 290 " --> pdb=" O TYR G 286 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE G 291 " --> pdb=" O PHE G 287 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN G 296 " --> pdb=" O LEU G 292 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER G 297 " --> pdb=" O SER G 293 " (cutoff:3.500A) Proline residue: G 301 - end of helix Processing helix chain 'G' and resid 308 through 316 removed outlier: 4.357A pdb=" N SER G 314 " --> pdb=" O ASN G 310 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN G 316 " --> pdb=" O ARG G 312 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 187 removed outlier: 9.374A pdb=" N ALA B 220 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 51 removed outlier: 5.886A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 62 removed outlier: 4.015A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 103 Processing sheet with id=AA5, first strand: chain 'C' and resid 121 through 125 removed outlier: 6.292A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 148 through 149 removed outlier: 3.508A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 4.123A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 4.234A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.389A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS C 294 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 308 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.894A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR E 50 " --> pdb=" O TYR E 59 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 155 through 158 Processing sheet with id=AB4, first strand: chain 'E' and resid 185 through 187 Processing sheet with id=AB5, first strand: chain 'E' and resid 189 through 190 360 hydrogen bonds defined for protein. 1023 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: 1.31 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1313 1.31 - 1.44: 2166 1.44 - 1.56: 4431 1.56 - 1.69: 3 1.69 - 1.82: 55 Bond restraints: 7968 Sorted by residual: bond pdb=" C TYR A 4 " pdb=" N PHA A 5 " ideal model delta sigma weight residual 1.329 1.515 -0.186 1.40e-02 5.10e+03 1.77e+02 bond pdb=" C LYS A 3 " pdb=" N TYR A 4 " ideal model delta sigma weight residual 1.329 1.506 -0.177 1.40e-02 5.10e+03 1.61e+02 bond pdb=" C DTR A 2 " pdb=" N LYS A 3 " ideal model delta sigma weight residual 1.329 1.491 -0.162 1.40e-02 5.10e+03 1.35e+02 bond pdb=" N HYP A 6 " pdb=" CD HYP A 6 " ideal model delta sigma weight residual 1.473 1.321 0.152 1.40e-02 5.10e+03 1.18e+02 bond pdb=" C PHA A 5 " pdb=" N HYP A 6 " ideal model delta sigma weight residual 1.329 1.477 -0.148 1.40e-02 5.10e+03 1.12e+02 ... (remaining 7963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 10628 2.47 - 4.94: 208 4.94 - 7.41: 54 7.41 - 9.88: 16 9.88 - 12.35: 3 Bond angle restraints: 10909 Sorted by residual: angle pdb=" N LYS B 46 " pdb=" CA LYS B 46 " pdb=" C LYS B 46 " ideal model delta sigma weight residual 111.71 101.84 9.87 1.15e+00 7.56e-01 7.37e+01 angle pdb=" C HIS G 143 " pdb=" N PRO G 144 " pdb=" CA PRO G 144 " ideal model delta sigma weight residual 120.45 113.00 7.45 1.11e+00 8.12e-01 4.50e+01 angle pdb=" N ASP C 186 " pdb=" CA ASP C 186 " pdb=" C ASP C 186 " ideal model delta sigma weight residual 108.63 118.39 -9.76 1.60e+00 3.91e-01 3.72e+01 angle pdb=" N ASP C 118 " pdb=" CA ASP C 118 " pdb=" C ASP C 118 " ideal model delta sigma weight residual 113.20 105.99 7.21 1.21e+00 6.83e-01 3.55e+01 angle pdb=" N LEU B 39 " pdb=" CA LEU B 39 " pdb=" CB LEU B 39 " ideal model delta sigma weight residual 111.43 102.67 8.76 1.48e+00 4.57e-01 3.50e+01 ... (remaining 10904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 4079 17.66 - 35.32: 411 35.32 - 52.97: 112 52.97 - 70.63: 13 70.63 - 88.29: 7 Dihedral angle restraints: 4622 sinusoidal: 1375 harmonic: 3247 Sorted by residual: dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 146.42 -53.42 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CB CYS C 103 " pdb=" SG CYS C 103 " pdb=" SG CYS C 114 " pdb=" CB CYS C 114 " ideal model delta sinusoidal sigma weight residual -86.00 -42.30 -43.70 1 1.00e+01 1.00e-02 2.66e+01 dihedral pdb=" CB CYS G 112 " pdb=" SG CYS G 112 " pdb=" SG CYS G 186 " pdb=" CB CYS G 186 " ideal model delta sinusoidal sigma weight residual 93.00 127.92 -34.92 1 1.00e+01 1.00e-02 1.73e+01 ... (remaining 4619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1173 0.083 - 0.166: 111 0.166 - 0.249: 9 0.249 - 0.332: 3 0.332 - 0.414: 2 Chirality restraints: 1298 Sorted by residual: chirality pdb=" CA ASP B 193 " pdb=" N ASP B 193 " pdb=" C ASP B 193 " pdb=" CB ASP B 193 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" CA SER B 44 " pdb=" N SER B 44 " pdb=" C SER B 44 " pdb=" CB SER B 44 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CA ARG E 191 " pdb=" N ARG E 191 " pdb=" C ARG E 191 " pdb=" CB ARG E 191 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 1295 not shown) Planarity restraints: 1414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 150 " 0.060 5.00e-02 4.00e+02 8.97e-02 1.29e+01 pdb=" N PRO E 151 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO E 151 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 151 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 179 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" C GLN E 179 " 0.042 2.00e-02 2.50e+03 pdb=" O GLN E 179 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG E 180 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 38 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.68e+00 pdb=" C LEU B 38 " -0.041 2.00e-02 2.50e+03 pdb=" O LEU B 38 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU B 39 " 0.014 2.00e-02 2.50e+03 ... (remaining 1411 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2324 2.80 - 3.33: 7270 3.33 - 3.85: 13145 3.85 - 4.38: 14727 4.38 - 4.90: 25097 Nonbonded interactions: 62563 Sorted by model distance: nonbonded pdb=" O GLY E 112 " pdb=" OG SER E 184 " model vdw 2.279 3.040 nonbonded pdb=" OG1 THR C 86 " pdb=" OD1 ASN C 88 " model vdw 2.279 3.040 nonbonded pdb=" O ILE E 100 " pdb=" OG SER E 105 " model vdw 2.281 3.040 nonbonded pdb=" ND2 ASN G 81 " pdb=" OG SER G 160 " model vdw 2.342 3.120 nonbonded pdb=" O THR G 117 " pdb=" OG SER G 171 " model vdw 2.346 3.040 ... (remaining 62558 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.420 Find NCS groups from input model: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 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 : 0.007 0.186 7975 Z= 0.436 Angle : 0.931 12.354 10919 Z= 0.545 Chirality : 0.052 0.414 1298 Planarity : 0.005 0.090 1414 Dihedral : 16.041 88.290 2509 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.33 % Favored : 94.58 % Rotamer: Outliers : 0.44 % Allowed : 29.22 % Favored : 70.34 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.25), residues: 1107 helix: 0.30 (0.30), residues: 326 sheet: -0.55 (0.36), residues: 227 loop : -2.10 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 137 TYR 0.014 0.002 TYR C 111 PHE 0.029 0.001 PHE B 189 TRP 0.019 0.002 TRP C 211 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00692 ( 7968) covalent geometry : angle 0.92987 (10909) SS BOND : bond 0.00661 ( 5) SS BOND : angle 1.93207 ( 10) hydrogen bonds : bond 0.18811 ( 360) hydrogen bonds : angle 7.21621 ( 1023) Misc. bond : bond 0.04583 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 0.206 Fit side-chains REVERT: B 207 GLU cc_start: 0.7245 (tp30) cc_final: 0.5965 (pt0) REVERT: C 312 ASP cc_start: 0.7834 (t70) cc_final: 0.7555 (m-30) REVERT: E 75 PRO cc_start: 0.7505 (Cg_exo) cc_final: 0.7222 (Cg_endo) REVERT: G 249 MET cc_start: 0.6359 (mmt) cc_final: 0.5994 (tpp) outliers start: 3 outliers final: 1 residues processed: 147 average time/residue: 0.0751 time to fit residues: 15.4371 Evaluate side-chains 127 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 261 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.0770 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS B 333 GLN G 271 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.193899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.149827 restraints weight = 11023.782| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 2.67 r_work: 0.3978 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 7975 Z= 0.128 Angle : 0.594 8.798 10919 Z= 0.306 Chirality : 0.042 0.179 1298 Planarity : 0.005 0.066 1414 Dihedral : 4.823 49.966 1183 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.23 % Allowed : 28.34 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.25), residues: 1107 helix: 0.60 (0.30), residues: 329 sheet: -0.60 (0.34), residues: 238 loop : -1.90 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 180 TYR 0.018 0.001 TYR E 190 PHE 0.008 0.001 PHE B 189 TRP 0.014 0.002 TRP C 297 HIS 0.003 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7968) covalent geometry : angle 0.58813 (10909) SS BOND : bond 0.00362 ( 5) SS BOND : angle 2.85989 ( 10) hydrogen bonds : bond 0.03994 ( 360) hydrogen bonds : angle 5.68855 ( 1023) Misc. bond : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.290 Fit side-chains REVERT: B 9 ASP cc_start: 0.7683 (m-30) cc_final: 0.7343 (m-30) REVERT: B 46 LYS cc_start: 0.7018 (mtmm) cc_final: 0.6540 (mtpt) REVERT: B 207 GLU cc_start: 0.7169 (tp30) cc_final: 0.5954 (pt0) REVERT: C 52 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7850 (mtp85) REVERT: C 312 ASP cc_start: 0.8056 (t70) cc_final: 0.7575 (m-30) REVERT: G 145 LEU cc_start: 0.5280 (pt) cc_final: 0.5041 (pt) REVERT: G 261 TRP cc_start: 0.6734 (OUTLIER) cc_final: 0.6302 (t-100) outliers start: 22 outliers final: 7 residues processed: 158 average time/residue: 0.0668 time to fit residues: 15.1259 Evaluate side-chains 131 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain G residue 164 TRP Chi-restraints excluded: chain G residue 261 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 46 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 31 optimal weight: 0.1980 chunk 24 optimal weight: 30.0000 chunk 40 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 13 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.194301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.150394 restraints weight = 11075.674| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 2.70 r_work: 0.3984 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7975 Z= 0.115 Angle : 0.628 16.490 10919 Z= 0.315 Chirality : 0.042 0.199 1298 Planarity : 0.004 0.059 1414 Dihedral : 4.714 46.838 1183 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.67 % Allowed : 28.78 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.25), residues: 1107 helix: 0.57 (0.30), residues: 336 sheet: -0.59 (0.35), residues: 223 loop : -1.93 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 208 TYR 0.016 0.001 TYR E 190 PHE 0.019 0.001 PHE B 189 TRP 0.015 0.001 TRP C 82 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 7968) covalent geometry : angle 0.60744 (10909) SS BOND : bond 0.00479 ( 5) SS BOND : angle 5.28656 ( 10) hydrogen bonds : bond 0.03486 ( 360) hydrogen bonds : angle 5.41154 ( 1023) Misc. bond : bond 0.00028 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.288 Fit side-chains REVERT: B 9 ASP cc_start: 0.7738 (m-30) cc_final: 0.7400 (m-30) REVERT: B 46 LYS cc_start: 0.6941 (mtmm) cc_final: 0.6583 (mtpt) REVERT: B 216 GLU cc_start: 0.7776 (tt0) cc_final: 0.7505 (tt0) REVERT: C 234 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.7205 (m-80) REVERT: C 312 ASP cc_start: 0.8067 (t70) cc_final: 0.7608 (m-30) REVERT: E 75 PRO cc_start: 0.7469 (Cg_exo) cc_final: 0.7152 (Cg_endo) REVERT: G 304 TYR cc_start: 0.6717 (OUTLIER) cc_final: 0.6061 (t80) outliers start: 25 outliers final: 13 residues processed: 158 average time/residue: 0.0733 time to fit residues: 16.5375 Evaluate side-chains 141 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 164 TRP Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 260 CYS Chi-restraints excluded: chain G residue 304 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 4 optimal weight: 4.9990 chunk 89 optimal weight: 0.0970 chunk 30 optimal weight: 0.7980 chunk 7 optimal weight: 0.0970 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 66 optimal weight: 0.1980 chunk 48 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS C 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.194391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.150750 restraints weight = 11280.115| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 2.75 r_work: 0.3967 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7975 Z= 0.106 Angle : 0.591 13.054 10919 Z= 0.298 Chirality : 0.041 0.200 1298 Planarity : 0.004 0.061 1414 Dihedral : 4.260 35.190 1181 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.85 % Allowed : 29.07 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.26), residues: 1107 helix: 0.70 (0.30), residues: 337 sheet: -0.78 (0.34), residues: 237 loop : -1.85 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 208 TYR 0.015 0.001 TYR E 190 PHE 0.014 0.001 PHE B 189 TRP 0.015 0.001 TRP C 82 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 7968) covalent geometry : angle 0.57478 (10909) SS BOND : bond 0.00344 ( 5) SS BOND : angle 4.57011 ( 10) hydrogen bonds : bond 0.03102 ( 360) hydrogen bonds : angle 5.11056 ( 1023) Misc. bond : bond 0.00022 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.295 Fit side-chains REVERT: B 9 ASP cc_start: 0.7687 (m-30) cc_final: 0.7380 (m-30) REVERT: B 216 GLU cc_start: 0.7868 (tt0) cc_final: 0.7634 (tt0) REVERT: C 52 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7712 (mtp85) REVERT: C 234 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.7192 (m-80) REVERT: C 312 ASP cc_start: 0.8053 (t70) cc_final: 0.7636 (m-30) REVERT: E 75 PRO cc_start: 0.7436 (Cg_exo) cc_final: 0.7137 (Cg_endo) REVERT: E 140 MET cc_start: 0.3518 (mmp) cc_final: 0.3186 (mmp) REVERT: G 304 TYR cc_start: 0.6801 (OUTLIER) cc_final: 0.6093 (t80) outliers start: 33 outliers final: 14 residues processed: 162 average time/residue: 0.0691 time to fit residues: 16.0413 Evaluate side-chains 143 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain G residue 164 TRP Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 260 CYS Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain G residue 304 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 107 optimal weight: 0.2980 chunk 16 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 46 optimal weight: 0.0060 chunk 5 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS G 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.195242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.151114 restraints weight = 11382.082| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 2.74 r_work: 0.4017 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7975 Z= 0.109 Angle : 0.584 11.008 10919 Z= 0.295 Chirality : 0.041 0.187 1298 Planarity : 0.004 0.058 1414 Dihedral : 4.187 34.692 1181 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.85 % Allowed : 29.81 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.26), residues: 1107 helix: 0.84 (0.30), residues: 331 sheet: -0.69 (0.34), residues: 237 loop : -1.91 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 180 TYR 0.013 0.001 TYR E 190 PHE 0.013 0.001 PHE B 189 TRP 0.014 0.001 TRP C 82 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 7968) covalent geometry : angle 0.57061 (10909) SS BOND : bond 0.00278 ( 5) SS BOND : angle 4.17946 ( 10) hydrogen bonds : bond 0.03020 ( 360) hydrogen bonds : angle 4.97873 ( 1023) Misc. bond : bond 0.00022 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.354 Fit side-chains REVERT: C 234 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7128 (m-80) REVERT: E 75 PRO cc_start: 0.7419 (Cg_exo) cc_final: 0.7128 (Cg_endo) REVERT: G 81 ASN cc_start: 0.7759 (OUTLIER) cc_final: 0.7511 (t0) REVERT: G 304 TYR cc_start: 0.6841 (OUTLIER) cc_final: 0.6156 (t80) outliers start: 33 outliers final: 20 residues processed: 156 average time/residue: 0.0784 time to fit residues: 17.4801 Evaluate side-chains 150 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 164 TRP Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 249 MET Chi-restraints excluded: chain G residue 304 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 34 optimal weight: 0.0070 chunk 63 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS G 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.194844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.151199 restraints weight = 11239.977| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 2.68 r_work: 0.4021 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7975 Z= 0.110 Angle : 0.599 12.212 10919 Z= 0.299 Chirality : 0.041 0.177 1298 Planarity : 0.004 0.056 1414 Dihedral : 4.171 34.422 1181 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.14 % Allowed : 29.96 % Favored : 64.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.26), residues: 1107 helix: 0.84 (0.30), residues: 327 sheet: -0.67 (0.34), residues: 237 loop : -1.87 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 180 TYR 0.012 0.001 TYR E 190 PHE 0.014 0.001 PHE B 189 TRP 0.031 0.002 TRP E 47 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 7968) covalent geometry : angle 0.58331 (10909) SS BOND : bond 0.00320 ( 5) SS BOND : angle 4.58516 ( 10) hydrogen bonds : bond 0.03035 ( 360) hydrogen bonds : angle 4.95076 ( 1023) Misc. bond : bond 0.00022 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.301 Fit side-chains REVERT: B 9 ASP cc_start: 0.7682 (m-30) cc_final: 0.7405 (m-30) REVERT: C 52 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7516 (mtp85) REVERT: C 234 PHE cc_start: 0.7778 (OUTLIER) cc_final: 0.7157 (m-80) REVERT: E 75 PRO cc_start: 0.7416 (Cg_exo) cc_final: 0.7131 (Cg_endo) REVERT: G 81 ASN cc_start: 0.7696 (OUTLIER) cc_final: 0.7477 (t0) REVERT: G 304 TYR cc_start: 0.6807 (OUTLIER) cc_final: 0.6110 (t80) outliers start: 35 outliers final: 24 residues processed: 155 average time/residue: 0.0763 time to fit residues: 16.6790 Evaluate side-chains 153 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 164 TRP Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 249 MET Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain G residue 304 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 30.0000 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 10 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS G 271 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.191816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.147197 restraints weight = 11174.107| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 2.66 r_work: 0.3958 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7975 Z= 0.142 Angle : 0.615 11.957 10919 Z= 0.310 Chirality : 0.042 0.192 1298 Planarity : 0.004 0.055 1414 Dihedral : 4.266 36.309 1181 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.85 % Allowed : 30.84 % Favored : 64.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.26), residues: 1107 helix: 0.80 (0.30), residues: 330 sheet: -0.64 (0.33), residues: 243 loop : -1.89 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 180 TYR 0.014 0.002 TYR E 50 PHE 0.011 0.001 PHE B 189 TRP 0.019 0.002 TRP E 47 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7968) covalent geometry : angle 0.59879 (10909) SS BOND : bond 0.00377 ( 5) SS BOND : angle 4.64629 ( 10) hydrogen bonds : bond 0.03252 ( 360) hydrogen bonds : angle 4.98066 ( 1023) Misc. bond : bond 0.00029 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.180 Fit side-chains REVERT: B 9 ASP cc_start: 0.7697 (m-30) cc_final: 0.7383 (m-30) REVERT: B 25 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7485 (tm-30) REVERT: C 52 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7809 (mtp85) REVERT: C 327 VAL cc_start: 0.7402 (OUTLIER) cc_final: 0.6955 (t) REVERT: G 271 ASN cc_start: 0.6055 (OUTLIER) cc_final: 0.5849 (p0) REVERT: G 304 TYR cc_start: 0.6810 (OUTLIER) cc_final: 0.5901 (t80) outliers start: 33 outliers final: 24 residues processed: 153 average time/residue: 0.0688 time to fit residues: 14.5458 Evaluate side-chains 152 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 164 TRP Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 249 MET Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 271 ASN Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain G residue 304 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 46 optimal weight: 0.0770 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS G 271 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.191135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.146548 restraints weight = 11172.580| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 2.64 r_work: 0.3949 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7975 Z= 0.142 Angle : 0.630 12.247 10919 Z= 0.316 Chirality : 0.042 0.189 1298 Planarity : 0.004 0.054 1414 Dihedral : 4.294 37.095 1181 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 5.43 % Allowed : 31.13 % Favored : 63.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.26), residues: 1107 helix: 0.86 (0.30), residues: 333 sheet: -0.63 (0.34), residues: 232 loop : -1.82 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 180 TYR 0.013 0.002 TYR E 50 PHE 0.011 0.001 PHE C 199 TRP 0.019 0.002 TRP E 47 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7968) covalent geometry : angle 0.61417 (10909) SS BOND : bond 0.00535 ( 5) SS BOND : angle 4.70354 ( 10) hydrogen bonds : bond 0.03223 ( 360) hydrogen bonds : angle 4.95390 ( 1023) Misc. bond : bond 0.00063 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.299 Fit side-chains REVERT: B 25 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7476 (tm-30) REVERT: C 52 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7811 (mtp85) REVERT: C 234 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.7367 (m-80) REVERT: C 327 VAL cc_start: 0.7382 (OUTLIER) cc_final: 0.6945 (t) REVERT: G 221 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.5825 (m-80) REVERT: G 271 ASN cc_start: 0.5715 (OUTLIER) cc_final: 0.5429 (p0) REVERT: G 304 TYR cc_start: 0.6815 (OUTLIER) cc_final: 0.5877 (t80) outliers start: 37 outliers final: 25 residues processed: 150 average time/residue: 0.0730 time to fit residues: 15.3335 Evaluate side-chains 156 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 164 TRP Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain G residue 249 MET Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 271 ASN Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain G residue 304 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 59 optimal weight: 6.9990 chunk 93 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 27 optimal weight: 0.0020 chunk 89 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS ** G 271 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 = 0.4561 r_free = 0.4561 target = 0.193493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.149085 restraints weight = 11144.826| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 2.72 r_work: 0.3980 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 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 : 0.003 0.042 7975 Z= 0.112 Angle : 0.614 12.651 10919 Z= 0.306 Chirality : 0.041 0.179 1298 Planarity : 0.004 0.054 1414 Dihedral : 4.170 35.430 1181 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.85 % Allowed : 31.42 % Favored : 63.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.26), residues: 1107 helix: 0.90 (0.30), residues: 329 sheet: -0.57 (0.35), residues: 224 loop : -1.78 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 180 TYR 0.013 0.001 TYR E 190 PHE 0.012 0.001 PHE B 189 TRP 0.019 0.002 TRP E 47 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 7968) covalent geometry : angle 0.59926 (10909) SS BOND : bond 0.00239 ( 5) SS BOND : angle 4.46822 ( 10) hydrogen bonds : bond 0.02970 ( 360) hydrogen bonds : angle 4.83318 ( 1023) Misc. bond : bond 0.00037 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.298 Fit side-chains REVERT: B 9 ASP cc_start: 0.7690 (m-30) cc_final: 0.7451 (m-30) REVERT: B 25 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7399 (tm-30) REVERT: C 52 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7811 (mtp85) REVERT: C 234 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7332 (m-80) REVERT: C 327 VAL cc_start: 0.7323 (OUTLIER) cc_final: 0.6930 (t) REVERT: G 221 TYR cc_start: 0.6998 (OUTLIER) cc_final: 0.5702 (m-80) REVERT: G 304 TYR cc_start: 0.6786 (OUTLIER) cc_final: 0.6024 (t80) outliers start: 33 outliers final: 24 residues processed: 149 average time/residue: 0.0729 time to fit residues: 15.3096 Evaluate side-chains 147 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 164 TRP Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain G residue 249 MET Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 271 ASN Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain G residue 304 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 97 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 62 optimal weight: 20.0000 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 0.1980 chunk 78 optimal weight: 5.9990 chunk 56 optimal weight: 0.0980 chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.193658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.157003 restraints weight = 11157.915| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.56 r_work: 0.3967 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7975 Z= 0.112 Angle : 0.618 12.041 10919 Z= 0.307 Chirality : 0.041 0.169 1298 Planarity : 0.004 0.053 1414 Dihedral : 4.125 35.213 1181 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.55 % Allowed : 31.57 % Favored : 63.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.26), residues: 1107 helix: 0.91 (0.30), residues: 333 sheet: -0.52 (0.34), residues: 226 loop : -1.85 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 180 TYR 0.012 0.001 TYR E 190 PHE 0.012 0.001 PHE B 189 TRP 0.022 0.002 TRP G 261 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 7968) covalent geometry : angle 0.60358 (10909) SS BOND : bond 0.00346 ( 5) SS BOND : angle 4.42115 ( 10) hydrogen bonds : bond 0.02932 ( 360) hydrogen bonds : angle 4.80336 ( 1023) Misc. bond : bond 0.00027 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.304 Fit side-chains REVERT: B 9 ASP cc_start: 0.7743 (m-30) cc_final: 0.7516 (m-30) REVERT: B 25 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7425 (tm-30) REVERT: C 52 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7776 (mtp85) REVERT: C 234 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7287 (m-80) REVERT: C 327 VAL cc_start: 0.7296 (OUTLIER) cc_final: 0.6889 (t) REVERT: E 231 GLN cc_start: 0.5877 (tp40) cc_final: 0.5660 (tp40) REVERT: G 123 GLN cc_start: 0.7256 (tm-30) cc_final: 0.7049 (tp40) REVERT: G 221 TYR cc_start: 0.7041 (OUTLIER) cc_final: 0.5778 (m-80) REVERT: G 304 TYR cc_start: 0.6853 (OUTLIER) cc_final: 0.6077 (t80) outliers start: 31 outliers final: 23 residues processed: 146 average time/residue: 0.0829 time to fit residues: 16.7898 Evaluate side-chains 146 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 164 TRP Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain G residue 249 MET Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain G residue 304 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS ** E 231 GLN ** 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 = 0.4532 r_free = 0.4532 target = 0.190491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.145188 restraints weight = 11149.977| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.74 r_work: 0.3932 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7975 Z= 0.151 Angle : 0.656 13.815 10919 Z= 0.329 Chirality : 0.042 0.200 1298 Planarity : 0.004 0.053 1414 Dihedral : 4.315 38.442 1181 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.26 % Allowed : 32.31 % Favored : 63.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.26), residues: 1107 helix: 0.87 (0.30), residues: 338 sheet: -0.68 (0.33), residues: 239 loop : -1.89 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 180 TYR 0.015 0.002 TYR E 50 PHE 0.011 0.001 PHE E 239 TRP 0.025 0.002 TRP G 261 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 7968) covalent geometry : angle 0.63977 (10909) SS BOND : bond 0.00546 ( 5) SS BOND : angle 4.83834 ( 10) hydrogen bonds : bond 0.03236 ( 360) hydrogen bonds : angle 4.90703 ( 1023) Misc. bond : bond 0.00034 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2482.31 seconds wall clock time: 43 minutes 1.93 seconds (2581.93 seconds total)