Starting phenix.real_space_refine on Mon Nov 17 15:28:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dnd_47036/11_2025/9dnd_47036.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dnd_47036/11_2025/9dnd_47036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dnd_47036/11_2025/9dnd_47036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dnd_47036/11_2025/9dnd_47036.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dnd_47036/11_2025/9dnd_47036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dnd_47036/11_2025/9dnd_47036.map" } resolution = 3.1 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= 0.001 sd= 0.152 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 39 5.16 5 C 3746 2.51 5 N 965 2.21 5 O 937 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5687 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1418 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 193} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 16, 'ASP:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 91 Chain: "C" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1428 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 192} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 18, 'ASN:plan1': 3, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "A" Number of atoms: 1423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1423 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 193} Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 16, 'ASN:plan1': 2, 'ASP:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 91 Chain: "B" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1418 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 192} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 18, 'ASP:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 88 Time building chain proxies: 1.54, per 1000 atoms: 0.27 Number of scatterers: 5687 At special positions: 0 Unit cell: (91, 114.4, 101.4, 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 39 16.00 O 937 8.00 N 965 7.00 C 3746 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 185 " - pdb=" SG CYS D 223 " distance=2.04 Simple disulfide: pdb=" SG CYS C 165 " - pdb=" SG CYS C 203 " distance=2.04 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 223 " distance=2.06 Simple disulfide: pdb=" SG CYS B 165 " - pdb=" SG CYS B 203 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 245.1 milliseconds 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1474 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 12 sheets defined 54.2% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'D' and resid 21 through 31 removed outlier: 3.840A pdb=" N GLU D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 54 Processing helix chain 'D' and resid 67 through 72 Processing helix chain 'D' and resid 75 through 80 removed outlier: 3.527A pdb=" N LYS D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 102 Processing helix chain 'D' and resid 113 through 124 Processing helix chain 'D' and resid 133 through 142 Processing helix chain 'D' and resid 183 through 189 removed outlier: 3.681A pdb=" N TRP D 187 " --> pdb=" O ASN D 183 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU D 189 " --> pdb=" O CYS D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 223 removed outlier: 3.539A pdb=" N CYS D 223 " --> pdb=" O LYS D 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 removed outlier: 3.676A pdb=" N LYS C 8 " --> pdb=" O GLU C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 35 Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.850A pdb=" N LYS C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 55 through 60' Processing helix chain 'C' and resid 72 through 83 Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 113 through 122 Processing helix chain 'C' and resid 132 through 137 removed outlier: 3.542A pdb=" N VAL C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 removed outlier: 4.085A pdb=" N VAL C 141 " --> pdb=" O GLY C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 171 removed outlier: 3.624A pdb=" N TRP C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE C 168 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 204 removed outlier: 4.191A pdb=" N GLU C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 31 removed outlier: 4.098A pdb=" N GLU A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 54 Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 92 through 102 Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 152 through 157 removed outlier: 3.549A pdb=" N VAL A 156 " --> pdb=" O PRO A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 164 removed outlier: 4.110A pdb=" N VAL A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 188 removed outlier: 3.564A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 223 removed outlier: 3.574A pdb=" N GLU A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 removed outlier: 3.994A pdb=" N GLU B 9 " --> pdb=" O GLU B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 34 Processing helix chain 'B' and resid 48 through 55 Processing helix chain 'B' and resid 56 through 62 removed outlier: 4.025A pdb=" N GLU B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA B 61 " --> pdb=" O PHE B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 93 through 104 Processing helix chain 'B' and resid 113 through 122 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.759A pdb=" N VAL B 141 " --> pdb=" O GLY B 137 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B 143 " --> pdb=" O GLN B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 171 removed outlier: 3.702A pdb=" N TRP B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE B 168 " --> pdb=" O VAL B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 202 removed outlier: 3.951A pdb=" N GLU B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 84 through 88 removed outlier: 4.277A pdb=" N LEU D 58 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL D 33 " --> pdb=" O VAL D 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 106 through 108 Processing sheet with id=AA3, first strand: chain 'D' and resid 130 through 131 Processing sheet with id=AA4, first strand: chain 'C' and resid 64 through 68 removed outlier: 6.680A pdb=" N ILE C 39 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N GLY C 68 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE C 41 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU C 38 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL C 13 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 86 through 88 Processing sheet with id=AA6, first strand: chain 'C' and resid 110 through 111 Processing sheet with id=AA7, first strand: chain 'A' and resid 84 through 88 removed outlier: 6.950A pdb=" N ILE A 32 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N GLU A 60 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA A 34 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR A 62 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU A 36 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A 33 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 106 through 108 Processing sheet with id=AA9, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB1, first strand: chain 'B' and resid 64 through 68 removed outlier: 7.133A pdb=" N ILE B 12 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N GLU B 40 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA B 14 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N THR B 42 " --> pdb=" O ALA B 14 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU B 16 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL B 13 " --> pdb=" O VAL B 177 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 86 through 88 Processing sheet with id=AB3, first strand: chain 'B' and resid 110 through 111 289 hydrogen bonds defined for protein. 867 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: 0.83 Time building geometry restraints manager: 0.62 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: 909 1.31 - 1.44: 1359 1.44 - 1.56: 3467 1.56 - 1.69: 6 1.69 - 1.81: 62 Bond restraints: 5803 Sorted by residual: bond pdb=" N PRO C 90 " pdb=" CD PRO C 90 " ideal model delta sigma weight residual 1.473 1.356 0.117 1.40e-02 5.10e+03 7.02e+01 bond pdb=" CA LYS B 145 " pdb=" C LYS B 145 " ideal model delta sigma weight residual 1.523 1.614 -0.091 1.35e-02 5.49e+03 4.57e+01 bond pdb=" CA LYS C 198 " pdb=" C LYS C 198 " ideal model delta sigma weight residual 1.524 1.604 -0.080 1.27e-02 6.20e+03 4.02e+01 bond pdb=" CA GLU B 81 " pdb=" C GLU B 81 " ideal model delta sigma weight residual 1.522 1.588 -0.065 1.38e-02 5.25e+03 2.25e+01 bond pdb=" C PRO B 109 " pdb=" O PRO B 109 " ideal model delta sigma weight residual 1.232 1.183 0.050 1.20e-02 6.94e+03 1.72e+01 ... (remaining 5798 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.89: 7728 4.89 - 9.78: 134 9.78 - 14.66: 14 14.66 - 19.55: 9 19.55 - 24.44: 5 Bond angle restraints: 7890 Sorted by residual: angle pdb=" N GLU B 183 " pdb=" CA GLU B 183 " pdb=" C GLU B 183 " ideal model delta sigma weight residual 110.53 133.65 -23.12 1.32e+00 5.74e-01 3.07e+02 angle pdb=" N VAL B 182 " pdb=" CA VAL B 182 " pdb=" C VAL B 182 " ideal model delta sigma weight residual 112.50 135.81 -23.31 1.39e+00 5.18e-01 2.81e+02 angle pdb=" N GLU B 183 " pdb=" CA GLU B 183 " pdb=" CB GLU B 183 " ideal model delta sigma weight residual 110.36 90.91 19.45 1.43e+00 4.89e-01 1.85e+02 angle pdb=" N PRO D 66 " pdb=" CA PRO D 66 " pdb=" C PRO D 66 " ideal model delta sigma weight residual 112.47 136.91 -24.44 2.06e+00 2.36e-01 1.41e+02 angle pdb=" CA VAL B 177 " pdb=" CB VAL B 177 " pdb=" CG2 VAL B 177 " ideal model delta sigma weight residual 110.40 128.12 -17.72 1.70e+00 3.46e-01 1.09e+02 ... (remaining 7885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.95: 3194 14.95 - 29.89: 153 29.89 - 44.84: 64 44.84 - 59.79: 19 59.79 - 74.73: 3 Dihedral angle restraints: 3433 sinusoidal: 1144 harmonic: 2289 Sorted by residual: dihedral pdb=" N PRO D 66 " pdb=" C PRO D 66 " pdb=" CA PRO D 66 " pdb=" CB PRO D 66 " ideal model delta harmonic sigma weight residual 115.10 154.91 -39.81 0 2.50e+00 1.60e-01 2.54e+02 dihedral pdb=" C PRO D 66 " pdb=" N PRO D 66 " pdb=" CA PRO D 66 " pdb=" CB PRO D 66 " ideal model delta harmonic sigma weight residual -120.70 -157.30 36.60 0 2.50e+00 1.60e-01 2.14e+02 dihedral pdb=" C VAL B 182 " pdb=" N VAL B 182 " pdb=" CA VAL B 182 " pdb=" CB VAL B 182 " ideal model delta harmonic sigma weight residual -122.00 -151.84 29.84 0 2.50e+00 1.60e-01 1.42e+02 ... (remaining 3430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.370: 948 0.370 - 0.740: 12 0.740 - 1.110: 0 1.110 - 1.480: 1 1.480 - 1.850: 1 Chirality restraints: 962 Sorted by residual: chirality pdb=" CA PRO D 66 " pdb=" N PRO D 66 " pdb=" C PRO D 66 " pdb=" CB PRO D 66 " both_signs ideal model delta sigma weight residual False 2.72 0.87 1.85 2.00e-01 2.50e+01 8.55e+01 chirality pdb=" CA VAL B 182 " pdb=" N VAL B 182 " pdb=" C VAL B 182 " pdb=" CB VAL B 182 " both_signs ideal model delta sigma weight residual False 2.44 1.07 1.37 2.00e-01 2.50e+01 4.67e+01 chirality pdb=" CA ASP D 67 " pdb=" N ASP D 67 " pdb=" C ASP D 67 " pdb=" CB ASP D 67 " both_signs ideal model delta sigma weight residual False 2.51 3.15 -0.64 2.00e-01 2.50e+01 1.01e+01 ... (remaining 959 not shown) Planarity restraints: 995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 34 " -0.031 2.00e-02 2.50e+03 6.01e-02 3.61e+01 pdb=" C GLY C 34 " 0.104 2.00e-02 2.50e+03 pdb=" O GLY C 34 " -0.038 2.00e-02 2.50e+03 pdb=" N GLY C 35 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 193 " -0.020 2.00e-02 2.50e+03 3.84e-02 1.48e+01 pdb=" C ALA B 193 " 0.067 2.00e-02 2.50e+03 pdb=" O ALA B 193 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE B 194 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 198 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.09e+00 pdb=" C LYS C 198 " -0.043 2.00e-02 2.50e+03 pdb=" O LYS C 198 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS C 199 " 0.014 2.00e-02 2.50e+03 ... (remaining 992 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 463 2.74 - 3.28: 5500 3.28 - 3.82: 8818 3.82 - 4.36: 11350 4.36 - 4.90: 19184 Nonbonded interactions: 45315 Sorted by model distance: nonbonded pdb=" O ASN D 183 " pdb=" N CYS D 185 " model vdw 2.202 3.120 nonbonded pdb=" O ASN D 183 " pdb=" N GLU D 186 " model vdw 2.296 3.120 nonbonded pdb=" O ASN A 183 " pdb=" N GLU A 186 " model vdw 2.361 3.120 nonbonded pdb=" O ASN A 183 " pdb=" N CYS A 185 " model vdw 2.365 3.120 nonbonded pdb=" OG1 THR B 71 " pdb=" OE1 GLN B 75 " model vdw 2.392 3.040 ... (remaining 45310 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 40 or resid 42 through 44 or resid \ 48 through 52 or resid 54 through 64 or (resid 65 and (name N or name CA or nam \ e C or name O or name CB )) or resid 66 through 69 or resid 71 through 73 or res \ id 75 or resid 78 through 79 or resid 82 through 108 or (resid 109 and (name N o \ r name CA or name C or name O or name CB )) or resid 111 through 121 or (resid 1 \ 22 through 123 and (name N or name CA or name C or name O or name CB )) or resid \ 124 or (resid 125 and (name N or name CA or name C or name O or name CB )) or r \ esid 126 through 137 or resid 139 through 150 or resid 152 through 161 or (resid \ 162 through 163 and (name N or name CA or name C or name O or name CB )) or res \ id 164 through 171 or (resid 172 and (name N or name CA or name C or name O or n \ ame CB )) or resid 173 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB )) or resid 177 through 179 or (resid 180 and (name N or \ name CA or name C or name O or name CB )) or resid 181 through 185 or (resid 186 \ and (name N or name CA or name C or name O or name CB )) or resid 187 through 2 \ 04 or resid 206 or resid 208 through 211 or resid 213 or resid 216 through 217 o \ r resid 219 through 220 or resid 222 through 223)) selection = (chain 'B' and (resid 2 through 3 or (resid 4 through 5 and (name N or name CA o \ r name C or name O or name CB )) or resid 6 through 18 or (resid 19 through 20 a \ nd (name N or name CA or name C or name O or name CB )) or resid 22 through 24 o \ r resid 28 through 32 or resid 34 through 49 or resid 51 through 53 or resid 55 \ or resid 58 through 59 or resid 62 through 68 or (resid 69 and (name N or name C \ A or name C or name O or name CB )) or resid 70 or (resid 71 through 72 and (nam \ e N or name CA or name C or name O or name CB )) or resid 73 through 77 or (resi \ d 78 through 79 and (name N or name CA or name C or name O or name CB )) or resi \ d 80 or (resid 81 through 82 and (name N or name CA or name C or name O or name \ CB )) or resid 83 through 88 or (resid 89 and (name N or name CA or name C or na \ me O or name CB )) or resid 91 through 101 or (resid 102 through 103 and (name N \ or name CA or name C or name O or name CB )) or resid 104 or (resid 105 and (na \ me N or name CA or name C or name O or name CB )) or resid 106 through 117 or re \ sid 119 through 121 or (resid 122 and (name N or name CA or name C or name O or \ name CB )) or resid 123 through 130 or resid 132 through 149 or (resid 150 and ( \ name N or name CA or name C or name O or name CB )) or resid 151 or (resid 152 a \ nd (name N or name CA or name C or name O or name CB )) or resid 153 through 159 \ or (resid 160 and (name N or name CA or name C or name O or name CB )) or resid \ 161 through 184 or resid 186 or (resid 188 and (name N or name CA or name C or \ name O or name CB )) or resid 189 through 191 or resid 193 or resid 196 through \ 197 or resid 199 through 200 or resid 202 through 203)) selection = (chain 'C' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 20 or (resid 22 through 24 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 32 or resid 34 through 44 or (resid \ 45 and (name N or name CA or name C or name O or name CB )) or resid 46 through \ 49 or resid 51 through 53 or resid 55 or resid 58 through 59 or resid 62 throug \ h 70 or (resid 71 through 72 and (name N or name CA or name C or name O or name \ CB )) or resid 73 or (resid 74 and (name N or name CA or name C or name O or nam \ e CB )) or resid 75 through 77 or (resid 78 through 79 and (name N or name CA or \ name C or name O or name CB )) or resid 80 through 81 or (resid 82 and (name N \ or name CA or name C or name O or name CB )) or resid 83 through 88 or (resid 89 \ and (name N or name CA or name C or name O or name CB )) or resid 91 through 97 \ or (resid 98 and (name N or name CA or name C or name O or name CB )) or resid \ 99 through 117 or resid 119 through 121 or (resid 122 and (name N or name CA or \ name C or name O or name CB )) or resid 123 through 130 or resid 132 through 151 \ or (resid 152 and (name N or name CA or name C or name O or name CB )) or resid \ 153 through 155 or (resid 156 and (name N or name CA or name C or name O or nam \ e CB )) or resid 157 through 184 or resid 186 or resid 188 through 191 or resid \ 193 or resid 196 through 197 or resid 199 through 200 or resid 202 through 203)) \ selection = (chain 'D' and (resid 22 through 23 or (resid 24 through 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26 through 27 or (resid 28 through \ 29 and (name N or name CA or name C or name O or name CB )) or resid 30 through \ 40 or (resid 42 through 44 and (name N or name CA or name C or name O or name C \ B )) or resid 48 through 52 or resid 54 through 64 or (resid 65 and (name N or n \ ame CA or name C or name O or name CB )) or resid 66 through 69 or resid 71 thro \ ugh 73 or resid 75 or resid 78 through 79 or resid 82 through 88 or (resid 89 an \ d (name N or name CA or name C or name O or name CB )) or resid 90 through 109 o \ r resid 111 through 124 or (resid 125 and (name N or name CA or name C or name O \ or name CB )) or resid 126 through 137 or resid 139 through 150 or resid 152 th \ rough 179 or (resid 180 and (name N or name CA or name C or name O or name CB )) \ or resid 181 through 185 or (resid 186 and (name N or name CA or name C or name \ O or name CB )) or resid 187 through 204 or resid 206 or resid 208 through 211 \ or resid 213 or resid 216 through 217 or resid 219 through 220 or resid 222 thro \ ugh 223)) } 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: 28.140 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.010 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 : 0.010 0.117 5807 Z= 0.624 Angle : 1.740 24.440 7898 Z= 1.188 Chirality : 0.123 1.850 962 Planarity : 0.006 0.060 995 Dihedral : 11.431 74.734 1947 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.11 % Favored : 96.52 % Rotamer: Outliers : 3.33 % Allowed : 3.52 % Favored : 93.15 % Cbeta Deviations : 1.09 % Peptide Plane: Cis-proline : 10.26 % 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 (0.28), residues: 805 helix: -1.33 (0.21), residues: 430 sheet: 0.31 (0.39), residues: 173 loop : -0.18 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 201 TYR 0.021 0.004 TYR D 127 PHE 0.024 0.002 PHE D 160 TRP 0.020 0.005 TRP B 167 HIS 0.006 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00970 ( 5803) covalent geometry : angle 1.73986 ( 7890) SS BOND : bond 0.01536 ( 4) SS BOND : angle 1.98162 ( 8) hydrogen bonds : bond 0.22173 ( 289) hydrogen bonds : angle 7.76226 ( 867) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.159 Fit side-chains REVERT: C 78 GLU cc_start: 0.7255 (tt0) cc_final: 0.7029 (tt0) REVERT: C 165 CYS cc_start: 0.6735 (m) cc_final: 0.6508 (m) REVERT: A 81 MET cc_start: 0.8314 (mtt) cc_final: 0.7972 (mtp) REVERT: A 128 MET cc_start: 0.8836 (ttp) cc_final: 0.8581 (ttp) REVERT: B 129 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8184 (tmtm) REVERT: B 144 MET cc_start: 0.8698 (mmp) cc_final: 0.8490 (mmm) REVERT: B 199 LYS cc_start: 0.8776 (tttm) cc_final: 0.8496 (tttt) outliers start: 17 outliers final: 9 residues processed: 138 average time/residue: 0.0963 time to fit residues: 16.5605 Evaluate side-chains 97 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 183 ASN Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain B residue 129 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 183 ASN A 180 ASN A 183 ASN B 10 HIS B 37 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.124228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.101752 restraints weight = 6577.885| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.58 r_work: 0.2875 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5807 Z= 0.129 Angle : 0.553 6.761 7898 Z= 0.289 Chirality : 0.047 0.142 962 Planarity : 0.005 0.044 995 Dihedral : 6.239 66.906 853 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.57 % Allowed : 8.81 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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 (0.29), residues: 805 helix: 0.33 (0.25), residues: 429 sheet: 0.70 (0.40), residues: 161 loop : -0.19 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 97 TYR 0.007 0.001 TYR A 127 PHE 0.020 0.002 PHE A 77 TRP 0.008 0.001 TRP A 187 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 5803) covalent geometry : angle 0.55191 ( 7890) SS BOND : bond 0.00146 ( 4) SS BOND : angle 1.20304 ( 8) hydrogen bonds : bond 0.03268 ( 289) hydrogen bonds : angle 4.82694 ( 867) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.238 Fit side-chains REVERT: D 24 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7040 (tm-30) REVERT: D 154 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8254 (pm20) REVERT: C 165 CYS cc_start: 0.7716 (m) cc_final: 0.7419 (m) REVERT: A 81 MET cc_start: 0.8227 (mtt) cc_final: 0.7804 (mtp) REVERT: A 128 MET cc_start: 0.9201 (ttp) cc_final: 0.8977 (ttp) REVERT: B 71 THR cc_start: 0.8798 (p) cc_final: 0.8526 (p) REVERT: B 129 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8482 (tmtm) REVERT: B 144 MET cc_start: 0.9179 (mmp) cc_final: 0.8924 (mmp) REVERT: B 150 ASN cc_start: 0.8304 (p0) cc_final: 0.8024 (p0) outliers start: 8 outliers final: 5 residues processed: 102 average time/residue: 0.0908 time to fit residues: 11.8442 Evaluate side-chains 98 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain B residue 129 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 33 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 70 optimal weight: 0.0020 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 HIS C 37 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.120422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.099030 restraints weight = 6515.552| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.46 r_work: 0.2827 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5807 Z= 0.130 Angle : 0.506 7.233 7898 Z= 0.263 Chirality : 0.047 0.139 962 Planarity : 0.005 0.047 995 Dihedral : 5.636 56.058 843 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.94 % Allowed : 10.57 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.59 (0.30), residues: 805 helix: 0.65 (0.25), residues: 439 sheet: 0.76 (0.40), residues: 159 loop : -0.20 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 97 TYR 0.005 0.001 TYR D 127 PHE 0.023 0.002 PHE A 119 TRP 0.007 0.002 TRP A 187 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 5803) covalent geometry : angle 0.50546 ( 7890) SS BOND : bond 0.00270 ( 4) SS BOND : angle 0.97018 ( 8) hydrogen bonds : bond 0.03187 ( 289) hydrogen bonds : angle 4.38013 ( 867) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: D 24 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7062 (tm-30) REVERT: D 154 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8248 (pm20) REVERT: C 7 PHE cc_start: 0.9198 (m-80) cc_final: 0.8775 (m-80) REVERT: C 194 ARG cc_start: 0.8177 (mmm160) cc_final: 0.7614 (mtp-110) REVERT: A 81 MET cc_start: 0.8227 (mtt) cc_final: 0.7852 (mtp) REVERT: A 128 MET cc_start: 0.9177 (ttp) cc_final: 0.8958 (ttp) REVERT: B 39 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8726 (mp) REVERT: B 71 THR cc_start: 0.8748 (p) cc_final: 0.8474 (p) REVERT: B 129 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8374 (tmtm) REVERT: B 150 ASN cc_start: 0.8318 (p0) cc_final: 0.8043 (p0) outliers start: 15 outliers final: 7 residues processed: 101 average time/residue: 0.0935 time to fit residues: 12.0091 Evaluate side-chains 103 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 159 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 76 optimal weight: 0.0570 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 56 optimal weight: 0.3980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.3229 r_free = 0.3229 target = 0.120064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.097700 restraints weight = 6528.201| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.55 r_work: 0.2832 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5807 Z= 0.133 Angle : 0.502 8.403 7898 Z= 0.258 Chirality : 0.047 0.141 962 Planarity : 0.005 0.047 995 Dihedral : 4.993 57.728 840 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.74 % Allowed : 13.11 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.70 (0.30), residues: 805 helix: 0.75 (0.25), residues: 441 sheet: 0.84 (0.38), residues: 171 loop : -0.27 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 37 TYR 0.004 0.001 TYR D 127 PHE 0.025 0.002 PHE A 119 TRP 0.005 0.001 TRP A 187 HIS 0.003 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 5803) covalent geometry : angle 0.50170 ( 7890) SS BOND : bond 0.00241 ( 4) SS BOND : angle 0.84841 ( 8) hydrogen bonds : bond 0.02925 ( 289) hydrogen bonds : angle 4.24652 ( 867) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 24 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7302 (tm-30) REVERT: D 154 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8305 (pm20) REVERT: C 7 PHE cc_start: 0.9202 (m-80) cc_final: 0.8784 (m-80) REVERT: C 194 ARG cc_start: 0.8080 (mmm160) cc_final: 0.7561 (mtp-110) REVERT: A 81 MET cc_start: 0.8204 (mtt) cc_final: 0.7792 (mtp) REVERT: A 128 MET cc_start: 0.9175 (ttp) cc_final: 0.8959 (ttp) REVERT: B 39 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8738 (mp) REVERT: B 71 THR cc_start: 0.8758 (p) cc_final: 0.8549 (p) outliers start: 14 outliers final: 7 residues processed: 100 average time/residue: 0.1006 time to fit residues: 12.7761 Evaluate side-chains 102 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 159 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3169 r_free = 0.3169 target = 0.115894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.095800 restraints weight = 6762.167| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.41 r_work: 0.2780 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5807 Z= 0.183 Angle : 0.556 8.885 7898 Z= 0.284 Chirality : 0.049 0.152 962 Planarity : 0.005 0.051 995 Dihedral : 4.399 43.603 833 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.13 % Allowed : 13.31 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.48 (0.30), residues: 805 helix: 0.65 (0.25), residues: 440 sheet: 0.57 (0.37), residues: 178 loop : -0.43 (0.46), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 37 TYR 0.005 0.001 TYR D 127 PHE 0.025 0.002 PHE A 119 TRP 0.006 0.002 TRP A 187 HIS 0.003 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 5803) covalent geometry : angle 0.55556 ( 7890) SS BOND : bond 0.00315 ( 4) SS BOND : angle 0.85982 ( 8) hydrogen bonds : bond 0.03583 ( 289) hydrogen bonds : angle 4.36245 ( 867) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 24 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7158 (tm-30) REVERT: D 154 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8402 (pm20) REVERT: C 7 PHE cc_start: 0.9241 (m-80) cc_final: 0.8823 (m-10) REVERT: C 57 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.6554 (pp-130) REVERT: C 194 ARG cc_start: 0.8198 (mmm160) cc_final: 0.7852 (mtp-110) REVERT: A 63 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.7406 (m-80) REVERT: A 81 MET cc_start: 0.8209 (mtt) cc_final: 0.7787 (mtp) REVERT: A 128 MET cc_start: 0.9180 (ttp) cc_final: 0.8969 (ttp) REVERT: B 39 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8724 (mp) REVERT: B 71 THR cc_start: 0.8779 (p) cc_final: 0.8574 (p) REVERT: B 134 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8403 (pm20) outliers start: 16 outliers final: 10 residues processed: 98 average time/residue: 0.0879 time to fit residues: 11.1576 Evaluate side-chains 104 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 159 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 77 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3171 r_free = 0.3171 target = 0.115822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.096328 restraints weight = 6712.388| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.37 r_work: 0.2790 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5807 Z= 0.177 Angle : 0.539 9.044 7898 Z= 0.275 Chirality : 0.049 0.154 962 Planarity : 0.005 0.051 995 Dihedral : 4.376 42.912 833 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.52 % Allowed : 12.92 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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 (0.30), residues: 805 helix: 0.64 (0.25), residues: 440 sheet: 0.47 (0.37), residues: 172 loop : -0.49 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 37 TYR 0.004 0.001 TYR D 127 PHE 0.022 0.002 PHE B 99 TRP 0.006 0.002 TRP B 167 HIS 0.003 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 5803) covalent geometry : angle 0.53862 ( 7890) SS BOND : bond 0.00288 ( 4) SS BOND : angle 0.77389 ( 8) hydrogen bonds : bond 0.03364 ( 289) hydrogen bonds : angle 4.33679 ( 867) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 24 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7151 (tm-30) REVERT: D 154 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8407 (pm20) REVERT: C 7 PHE cc_start: 0.9201 (m-80) cc_final: 0.8784 (m-10) REVERT: C 57 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.6467 (pp-130) REVERT: C 194 ARG cc_start: 0.8203 (mmm160) cc_final: 0.7847 (mtp-110) REVERT: A 63 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.7475 (m-80) REVERT: A 81 MET cc_start: 0.8100 (mtt) cc_final: 0.7701 (mtp) REVERT: A 128 MET cc_start: 0.9167 (ttp) cc_final: 0.8952 (ttp) REVERT: B 39 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8746 (mp) REVERT: B 134 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8367 (pm20) outliers start: 18 outliers final: 11 residues processed: 101 average time/residue: 0.0906 time to fit residues: 11.7701 Evaluate side-chains 107 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 159 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 50 optimal weight: 0.0010 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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 = 0.3192 r_free = 0.3192 target = 0.117443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.096388 restraints weight = 6588.222| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.45 r_work: 0.2804 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5807 Z= 0.144 Angle : 0.511 8.991 7898 Z= 0.260 Chirality : 0.048 0.150 962 Planarity : 0.005 0.049 995 Dihedral : 4.306 41.615 833 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.72 % Allowed : 13.11 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.59 (0.30), residues: 805 helix: 0.87 (0.25), residues: 434 sheet: 0.60 (0.38), residues: 161 loop : -0.55 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 97 TYR 0.003 0.001 TYR D 127 PHE 0.026 0.002 PHE A 119 TRP 0.006 0.001 TRP B 167 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 5803) covalent geometry : angle 0.51094 ( 7890) SS BOND : bond 0.00258 ( 4) SS BOND : angle 0.68637 ( 8) hydrogen bonds : bond 0.03040 ( 289) hydrogen bonds : angle 4.24677 ( 867) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 24 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7156 (tm-30) REVERT: C 7 PHE cc_start: 0.9168 (m-80) cc_final: 0.8798 (m-80) REVERT: C 57 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.6444 (pp-130) REVERT: C 194 ARG cc_start: 0.8189 (mmm160) cc_final: 0.7826 (mtp-110) REVERT: A 63 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: A 81 MET cc_start: 0.8095 (mtt) cc_final: 0.7676 (mtp) REVERT: A 128 MET cc_start: 0.9155 (ttp) cc_final: 0.8937 (ttp) REVERT: B 39 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8743 (mp) REVERT: B 78 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6659 (mt-10) REVERT: B 134 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8446 (pm20) outliers start: 19 outliers final: 12 residues processed: 102 average time/residue: 0.0900 time to fit residues: 11.7538 Evaluate side-chains 109 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 159 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 57 optimal weight: 0.0370 chunk 71 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.3196 r_free = 0.3196 target = 0.117719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.096783 restraints weight = 6546.219| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.44 r_work: 0.2809 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5807 Z= 0.134 Angle : 0.496 9.014 7898 Z= 0.252 Chirality : 0.047 0.152 962 Planarity : 0.005 0.048 995 Dihedral : 3.734 19.109 830 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.13 % Allowed : 13.70 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.69 (0.30), residues: 805 helix: 0.96 (0.25), residues: 434 sheet: 0.63 (0.38), residues: 161 loop : -0.54 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 97 TYR 0.003 0.001 TYR D 127 PHE 0.025 0.002 PHE B 99 TRP 0.006 0.001 TRP B 167 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 5803) covalent geometry : angle 0.49612 ( 7890) SS BOND : bond 0.00241 ( 4) SS BOND : angle 0.64460 ( 8) hydrogen bonds : bond 0.02885 ( 289) hydrogen bonds : angle 4.19612 ( 867) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: D 24 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7165 (tm-30) REVERT: C 7 PHE cc_start: 0.9128 (m-80) cc_final: 0.8705 (m-10) REVERT: C 57 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.6488 (pp-130) REVERT: C 194 ARG cc_start: 0.8151 (mmm160) cc_final: 0.7795 (mtp-110) REVERT: A 63 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.7492 (m-80) REVERT: A 81 MET cc_start: 0.8076 (mtt) cc_final: 0.7653 (mtp) REVERT: A 128 MET cc_start: 0.9146 (ttp) cc_final: 0.8926 (ttp) REVERT: B 39 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8748 (mp) REVERT: B 78 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6624 (mt-10) REVERT: B 134 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8409 (pm20) outliers start: 16 outliers final: 12 residues processed: 98 average time/residue: 0.0964 time to fit residues: 12.2026 Evaluate side-chains 107 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 159 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 0.0980 chunk 61 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3200 r_free = 0.3200 target = 0.118052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.097119 restraints weight = 6575.186| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.44 r_work: 0.2814 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5807 Z= 0.126 Angle : 0.488 8.953 7898 Z= 0.248 Chirality : 0.047 0.150 962 Planarity : 0.005 0.048 995 Dihedral : 3.680 20.013 830 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.72 % Allowed : 13.50 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.78 (0.30), residues: 805 helix: 1.06 (0.25), residues: 434 sheet: 0.64 (0.40), residues: 150 loop : -0.49 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 97 TYR 0.003 0.001 TYR D 127 PHE 0.027 0.002 PHE D 119 TRP 0.005 0.001 TRP B 167 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 5803) covalent geometry : angle 0.48765 ( 7890) SS BOND : bond 0.00219 ( 4) SS BOND : angle 0.83205 ( 8) hydrogen bonds : bond 0.02775 ( 289) hydrogen bonds : angle 4.15707 ( 867) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: C 7 PHE cc_start: 0.9104 (m-80) cc_final: 0.8728 (m-10) REVERT: C 57 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.6335 (pp-130) REVERT: C 194 ARG cc_start: 0.8136 (mmm160) cc_final: 0.7776 (mtp-110) REVERT: A 63 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.7498 (m-80) REVERT: A 81 MET cc_start: 0.8178 (mtt) cc_final: 0.7730 (mtp) REVERT: A 128 MET cc_start: 0.9138 (ttp) cc_final: 0.8914 (ttp) REVERT: B 39 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8735 (mp) REVERT: B 78 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6657 (mt-10) REVERT: B 134 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8428 (pm20) outliers start: 19 outliers final: 13 residues processed: 100 average time/residue: 0.0858 time to fit residues: 11.0706 Evaluate side-chains 108 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3170 r_free = 0.3170 target = 0.115821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.096336 restraints weight = 6754.080| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.37 r_work: 0.2792 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5807 Z= 0.180 Angle : 0.542 9.169 7898 Z= 0.277 Chirality : 0.049 0.165 962 Planarity : 0.005 0.050 995 Dihedral : 3.881 21.266 830 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.33 % Allowed : 14.29 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.62 (0.30), residues: 805 helix: 0.91 (0.25), residues: 434 sheet: 0.56 (0.38), residues: 167 loop : -0.59 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 37 TYR 0.004 0.001 TYR D 127 PHE 0.025 0.002 PHE A 119 TRP 0.005 0.002 TRP B 167 HIS 0.003 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 5803) covalent geometry : angle 0.54118 ( 7890) SS BOND : bond 0.00286 ( 4) SS BOND : angle 0.97027 ( 8) hydrogen bonds : bond 0.03380 ( 289) hydrogen bonds : angle 4.29312 ( 867) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: D 24 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7274 (tm-30) REVERT: C 7 PHE cc_start: 0.9122 (m-80) cc_final: 0.8764 (m-10) REVERT: C 57 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.6481 (pp-130) REVERT: C 194 ARG cc_start: 0.8313 (mmm160) cc_final: 0.7880 (mtp-110) REVERT: A 63 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.7530 (m-80) REVERT: A 81 MET cc_start: 0.8097 (mtt) cc_final: 0.7708 (mtp) REVERT: A 128 MET cc_start: 0.9166 (ttp) cc_final: 0.8948 (ttp) REVERT: B 39 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8708 (mp) REVERT: B 78 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6683 (mt-10) REVERT: B 134 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8354 (pm20) outliers start: 17 outliers final: 11 residues processed: 97 average time/residue: 0.0884 time to fit residues: 10.8720 Evaluate side-chains 106 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 11 optimal weight: 0.9990 chunk 72 optimal weight: 0.1980 chunk 75 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3197 r_free = 0.3197 target = 0.117765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.095774 restraints weight = 6559.654| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.54 r_work: 0.2805 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5807 Z= 0.137 Angle : 0.503 9.017 7898 Z= 0.256 Chirality : 0.048 0.154 962 Planarity : 0.005 0.049 995 Dihedral : 3.749 20.133 830 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.33 % Allowed : 14.68 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.77 (0.30), residues: 805 helix: 1.06 (0.25), residues: 434 sheet: 0.66 (0.41), residues: 150 loop : -0.54 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 195 TYR 0.003 0.001 TYR D 127 PHE 0.026 0.002 PHE A 119 TRP 0.005 0.001 TRP C 167 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 5803) covalent geometry : angle 0.50212 ( 7890) SS BOND : bond 0.00249 ( 4) SS BOND : angle 0.79452 ( 8) hydrogen bonds : bond 0.02906 ( 289) hydrogen bonds : angle 4.19959 ( 867) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2293.38 seconds wall clock time: 39 minutes 57.66 seconds (2397.66 seconds total)