Starting phenix.real_space_refine on Thu Mar 6 09:25:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dnd_47036/03_2025/9dnd_47036.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dnd_47036/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9dnd_47036/03_2025/9dnd_47036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dnd_47036/03_2025/9dnd_47036.map" model { file = "/net/cci-nas-00/data/ceres_data/9dnd_47036/03_2025/9dnd_47036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dnd_47036/03_2025/9dnd_47036.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'GLU:plan': 16, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4} 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, 'ARG:plan': 1, 'ASP:plan': 4} 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: {'GLN:plan1': 1, 'GLU:plan': 16, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4} 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: {'GLN:plan1': 1, 'GLU:plan': 18, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 88 Time building chain proxies: 8.64, per 1000 atoms: 1.52 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: 1.35 Conformation dependent library (CDL) restraints added in 915.9 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: 0.75 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: 1.55 Time building geometry restraints manager: 1.62 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: 19.620 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 22.310 Find NCS groups from input model: 0.300 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.460 ------------------------------------------------------------------------------- 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 5803 Z= 0.660 Angle : 1.740 24.440 7890 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.020 0.005 TRP B 167 HIS 0.006 0.001 HIS B 91 PHE 0.024 0.002 PHE D 160 TYR 0.021 0.004 TYR D 127 ARG 0.004 0.001 ARG C 201 *********************** 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 : 0.611 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: 0.2068 time to fit residues: 35.4582 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 : 0.580 ------------------------------------------------------------------------------- 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 67 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 0.0020 chunk 38 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 183 ASN C 10 HIS A 180 ASN A 183 ASN B 10 HIS B 37 HIS B 91 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.122395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.100902 restraints weight = 6429.885| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.47 r_work: 0.2864 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5803 Z= 0.236 Angle : 0.567 6.604 7890 Z= 0.297 Chirality : 0.048 0.147 962 Planarity : 0.005 0.044 995 Dihedral : 6.271 67.008 853 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.96 % Allowed : 8.61 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.29), residues: 805 helix: 0.22 (0.25), residues: 436 sheet: 0.66 (0.40), residues: 161 loop : -0.23 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 187 HIS 0.004 0.001 HIS B 91 PHE 0.022 0.002 PHE A 77 TYR 0.008 0.001 TYR A 127 ARG 0.002 0.000 ARG A 97 *********************** 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 108 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.642 Fit side-chains REVERT: D 24 GLU cc_start: 0.7399 (tm-30) cc_final: 0.7007 (tm-30) REVERT: D 154 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8133 (pm20) REVERT: C 165 CYS cc_start: 0.7770 (m) cc_final: 0.7468 (m) REVERT: A 81 MET cc_start: 0.8200 (mtt) cc_final: 0.7769 (mtp) REVERT: A 128 MET cc_start: 0.9178 (ttp) cc_final: 0.8940 (ttp) REVERT: B 71 THR cc_start: 0.8816 (p) cc_final: 0.8553 (p) REVERT: B 129 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8479 (tmtm) REVERT: B 150 ASN cc_start: 0.8388 (p0) cc_final: 0.8111 (p0) outliers start: 10 outliers final: 5 residues processed: 101 average time/residue: 0.1994 time to fit residues: 25.8013 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 : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.5980 chunk 77 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 72 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.119834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.098472 restraints weight = 6505.372| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.46 r_work: 0.2840 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5803 Z= 0.233 Angle : 0.514 7.651 7890 Z= 0.266 Chirality : 0.047 0.141 962 Planarity : 0.005 0.047 995 Dihedral : 5.706 56.695 843 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.30), residues: 805 helix: 0.62 (0.25), residues: 439 sheet: 0.70 (0.39), residues: 159 loop : -0.22 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 187 HIS 0.003 0.001 HIS C 125 PHE 0.023 0.002 PHE A 119 TYR 0.007 0.001 TYR D 127 ARG 0.002 0.000 ARG D 37 *********************** 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 110 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: D 24 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7101 (tm-30) REVERT: D 154 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8287 (pm20) REVERT: C 7 PHE cc_start: 0.9240 (m-80) cc_final: 0.8829 (m-80) REVERT: C 194 ARG cc_start: 0.8121 (mmm160) cc_final: 0.7520 (mtp-110) REVERT: A 81 MET cc_start: 0.8244 (mtt) cc_final: 0.7856 (mtp) REVERT: A 128 MET cc_start: 0.9167 (ttp) cc_final: 0.8950 (ttp) REVERT: B 39 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8713 (mp) REVERT: B 71 THR cc_start: 0.8765 (p) cc_final: 0.8516 (p) REVERT: B 129 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8389 (tmtm) REVERT: B 150 ASN cc_start: 0.8315 (p0) cc_final: 0.8053 (p0) outliers start: 15 outliers final: 9 residues processed: 101 average time/residue: 0.2026 time to fit residues: 26.1199 Evaluate side-chains 105 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 A residue 154 GLU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 188 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 56 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3198 r_free = 0.3198 target = 0.118072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.095707 restraints weight = 6635.204| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.56 r_work: 0.2749 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5803 Z= 0.285 Angle : 0.540 8.561 7890 Z= 0.277 Chirality : 0.048 0.143 962 Planarity : 0.005 0.049 995 Dihedral : 5.692 57.681 843 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.94 % Allowed : 12.52 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.30), residues: 805 helix: 0.62 (0.25), residues: 440 sheet: 0.58 (0.37), residues: 178 loop : -0.36 (0.47), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 187 HIS 0.003 0.001 HIS C 125 PHE 0.025 0.002 PHE A 119 TYR 0.005 0.001 TYR D 127 ARG 0.003 0.000 ARG D 37 *********************** 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 102 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 24 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7110 (tm-30) REVERT: D 154 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8340 (pm20) REVERT: C 57 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.6447 (pp-130) REVERT: C 194 ARG cc_start: 0.8115 (mmm160) cc_final: 0.7648 (mtp-110) REVERT: A 81 MET cc_start: 0.8170 (mtt) cc_final: 0.7743 (mtp) REVERT: A 128 MET cc_start: 0.9204 (ttp) cc_final: 0.8994 (ttp) REVERT: B 39 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8730 (mp) REVERT: B 129 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8390 (tmtm) REVERT: B 134 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8423 (pm20) REVERT: B 188 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7935 (mt-10) outliers start: 15 outliers final: 7 residues processed: 93 average time/residue: 0.2055 time to fit residues: 24.2863 Evaluate side-chains 97 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 57 MET 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 134 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 188 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 70 optimal weight: 0.0270 chunk 13 optimal weight: 0.7980 chunk 77 optimal weight: 0.0980 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 chunk 55 optimal weight: 0.0980 overall best weight: 0.2638 ------------------------------------------------------------------------------- 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 = 0.3247 r_free = 0.3247 target = 0.121155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.098454 restraints weight = 6550.901| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.60 r_work: 0.2827 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5803 Z= 0.145 Angle : 0.451 7.581 7890 Z= 0.230 Chirality : 0.046 0.134 962 Planarity : 0.005 0.044 995 Dihedral : 4.789 59.466 840 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.54 % Allowed : 13.50 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.30), residues: 805 helix: 1.07 (0.26), residues: 433 sheet: 0.79 (0.38), residues: 172 loop : -0.30 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 167 HIS 0.002 0.001 HIS B 10 PHE 0.026 0.001 PHE A 119 TYR 0.004 0.001 TYR A 127 ARG 0.003 0.000 ARG A 97 *********************** 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 106 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: D 24 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7164 (tm-30) REVERT: D 25 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7565 (mm-30) REVERT: C 7 PHE cc_start: 0.9145 (m-80) cc_final: 0.8754 (m-80) REVERT: C 134 GLU cc_start: 0.8876 (pt0) cc_final: 0.8663 (pt0) REVERT: C 194 ARG cc_start: 0.8058 (mmm160) cc_final: 0.7616 (mtp-110) REVERT: A 63 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.7366 (m-80) REVERT: A 81 MET cc_start: 0.8193 (mtt) cc_final: 0.7778 (mtp) REVERT: A 128 MET cc_start: 0.9167 (ttp) cc_final: 0.8927 (ttp) REVERT: B 188 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7927 (mt-10) outliers start: 13 outliers final: 5 residues processed: 101 average time/residue: 0.2036 time to fit residues: 26.1856 Evaluate side-chains 97 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 188 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 55 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 0.0010 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 17 optimal weight: 0.0050 overall best weight: 0.4200 ------------------------------------------------------------------------------- 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 = 0.3226 r_free = 0.3226 target = 0.120174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.099213 restraints weight = 6431.743| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.42 r_work: 0.2831 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5803 Z= 0.187 Angle : 0.470 8.289 7890 Z= 0.240 Chirality : 0.047 0.182 962 Planarity : 0.005 0.044 995 Dihedral : 3.610 24.228 830 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.54 % Allowed : 14.48 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.30), residues: 805 helix: 1.13 (0.26), residues: 434 sheet: 0.79 (0.37), residues: 178 loop : -0.29 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 167 HIS 0.002 0.000 HIS C 125 PHE 0.023 0.001 PHE B 99 TYR 0.003 0.001 TYR A 127 ARG 0.003 0.000 ARG A 97 *********************** 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 104 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: D 24 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7221 (tm-30) REVERT: D 25 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7593 (mm-30) REVERT: C 7 PHE cc_start: 0.9102 (m-80) cc_final: 0.8707 (m-10) REVERT: C 57 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.6184 (pp-130) REVERT: C 134 GLU cc_start: 0.8883 (pt0) cc_final: 0.8648 (pt0) REVERT: C 194 ARG cc_start: 0.8122 (mmm160) cc_final: 0.7797 (mtp-110) REVERT: A 63 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.7390 (m-80) REVERT: A 81 MET cc_start: 0.8230 (mtt) cc_final: 0.7807 (mtp) REVERT: A 128 MET cc_start: 0.9137 (ttp) cc_final: 0.8900 (ttp) REVERT: B 188 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7935 (mt-10) outliers start: 13 outliers final: 10 residues processed: 99 average time/residue: 0.1909 time to fit residues: 24.3858 Evaluate side-chains 102 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 156 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 165 CYS 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 B residue 81 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 188 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 19 optimal weight: 0.0970 chunk 26 optimal weight: 0.0770 chunk 41 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 0.0770 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 14 optimal weight: 0.0030 overall best weight: 0.1704 ------------------------------------------------------------------------------- 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 = 0.3261 r_free = 0.3261 target = 0.122905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.101780 restraints weight = 6526.251| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.45 r_work: 0.2881 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5803 Z= 0.120 Angle : 0.424 7.216 7890 Z= 0.216 Chirality : 0.045 0.140 962 Planarity : 0.004 0.041 995 Dihedral : 3.319 21.369 830 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.15 % Allowed : 15.66 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.30), residues: 805 helix: 1.43 (0.26), residues: 430 sheet: 1.00 (0.38), residues: 179 loop : -0.28 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 167 HIS 0.001 0.000 HIS B 10 PHE 0.026 0.001 PHE B 99 TYR 0.004 0.001 TYR A 127 ARG 0.003 0.000 ARG A 97 *********************** 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 106 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.623 Fit side-chains REVERT: D 24 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7157 (tm-30) REVERT: D 25 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7643 (mm-30) REVERT: C 7 PHE cc_start: 0.9023 (m-80) cc_final: 0.8710 (m-10) REVERT: C 134 GLU cc_start: 0.8884 (pt0) cc_final: 0.8621 (pt0) REVERT: C 194 ARG cc_start: 0.8133 (mmm160) cc_final: 0.7381 (ttp-110) REVERT: A 63 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.7397 (m-80) REVERT: A 81 MET cc_start: 0.8175 (mtt) cc_final: 0.7748 (mtp) REVERT: A 121 LYS cc_start: 0.8343 (ttpt) cc_final: 0.7886 (ttpp) REVERT: A 128 MET cc_start: 0.9107 (ttp) cc_final: 0.8883 (ttp) outliers start: 11 outliers final: 8 residues processed: 101 average time/residue: 0.2203 time to fit residues: 28.7387 Evaluate side-chains 100 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain B residue 81 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 29 optimal weight: 0.0670 chunk 73 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.3220 r_free = 0.3220 target = 0.119720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.097527 restraints weight = 6475.100| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.53 r_work: 0.2816 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5803 Z= 0.229 Angle : 0.493 8.779 7890 Z= 0.252 Chirality : 0.047 0.151 962 Planarity : 0.005 0.044 995 Dihedral : 3.618 23.161 830 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.94 % Allowed : 15.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.30), residues: 805 helix: 1.32 (0.26), residues: 432 sheet: 0.87 (0.38), residues: 178 loop : -0.41 (0.46), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 167 HIS 0.002 0.001 HIS C 125 PHE 0.025 0.002 PHE B 99 TYR 0.004 0.001 TYR D 127 ARG 0.002 0.000 ARG A 97 *********************** 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 106 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.620 Fit side-chains REVERT: D 24 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7062 (tm-30) REVERT: C 7 PHE cc_start: 0.9085 (m-80) cc_final: 0.8714 (m-10) REVERT: C 57 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.6366 (pp-130) REVERT: C 134 GLU cc_start: 0.8948 (pt0) cc_final: 0.8698 (pt0) REVERT: C 194 ARG cc_start: 0.8130 (mmm160) cc_final: 0.7792 (mtp-110) REVERT: A 63 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.7420 (m-80) REVERT: A 81 MET cc_start: 0.8176 (mtt) cc_final: 0.7738 (mtp) REVERT: A 128 MET cc_start: 0.9157 (ttp) cc_final: 0.8946 (ttp) REVERT: B 188 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7836 (mt-10) outliers start: 15 outliers final: 12 residues processed: 98 average time/residue: 0.1819 time to fit residues: 23.1531 Evaluate side-chains 105 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 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 82 SER Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 113 THR 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 52 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3199 r_free = 0.3199 target = 0.118041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.096057 restraints weight = 6500.894| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.52 r_work: 0.2800 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5803 Z= 0.285 Angle : 0.529 8.864 7890 Z= 0.272 Chirality : 0.049 0.166 962 Planarity : 0.005 0.048 995 Dihedral : 3.836 24.759 830 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.72 % Allowed : 14.48 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.30), residues: 805 helix: 1.15 (0.25), residues: 433 sheet: 0.66 (0.38), residues: 179 loop : -0.42 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 167 HIS 0.003 0.001 HIS C 125 PHE 0.025 0.002 PHE A 119 TYR 0.004 0.001 TYR D 127 ARG 0.003 0.000 ARG A 97 *********************** 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 109 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.779 Fit side-chains REVERT: D 24 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7302 (tm-30) REVERT: C 7 PHE cc_start: 0.9094 (m-80) cc_final: 0.8722 (m-10) REVERT: C 57 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.6471 (pp-130) REVERT: C 134 GLU cc_start: 0.8951 (pt0) cc_final: 0.8701 (pt0) REVERT: C 194 ARG cc_start: 0.8160 (mmm160) cc_final: 0.7798 (mtp-110) REVERT: A 63 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.7482 (m-80) REVERT: A 81 MET cc_start: 0.8141 (mtt) cc_final: 0.7670 (mtp) REVERT: A 128 MET cc_start: 0.9168 (ttp) cc_final: 0.8936 (ttp) outliers start: 19 outliers final: 12 residues processed: 100 average time/residue: 0.2235 time to fit residues: 28.9570 Evaluate side-chains 103 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.460 ------------------------------------------------------------------------------- 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 165 CYS Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 139 GLN 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 21 optimal weight: 0.0980 chunk 13 optimal weight: 0.1980 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 30 optimal weight: 0.0060 chunk 7 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- 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 = 0.3236 r_free = 0.3236 target = 0.120663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.098706 restraints weight = 6534.663| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.52 r_work: 0.2832 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5803 Z= 0.161 Angle : 0.461 8.315 7890 Z= 0.236 Chirality : 0.046 0.143 962 Planarity : 0.005 0.045 995 Dihedral : 3.543 22.544 830 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.35 % Allowed : 15.85 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.30), residues: 805 helix: 1.37 (0.25), residues: 432 sheet: 0.71 (0.40), residues: 161 loop : -0.29 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 167 HIS 0.002 0.001 HIS A 30 PHE 0.027 0.002 PHE B 99 TYR 0.003 0.001 TYR A 127 ARG 0.003 0.000 ARG A 97 ********************** 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 103 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.580 Fit side-chains REVERT: D 24 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7150 (tm-30) REVERT: D 25 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7518 (mm-30) REVERT: C 7 PHE cc_start: 0.9020 (m-80) cc_final: 0.8697 (m-10) REVERT: C 57 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.6342 (pp-130) REVERT: C 134 GLU cc_start: 0.8917 (pt0) cc_final: 0.8661 (pt0) REVERT: C 194 ARG cc_start: 0.8118 (mmm160) cc_final: 0.7310 (ttp-110) REVERT: A 63 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.7482 (m-80) REVERT: A 81 MET cc_start: 0.8156 (mtt) cc_final: 0.7709 (mtp) REVERT: A 128 MET cc_start: 0.9151 (ttp) cc_final: 0.8921 (ttp) outliers start: 12 outliers final: 9 residues processed: 95 average time/residue: 0.1841 time to fit residues: 22.5539 Evaluate side-chains 103 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 154 GLU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 113 THR 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 18 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 chunk 35 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 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 = 0.3211 r_free = 0.3211 target = 0.118899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.097300 restraints weight = 6588.478| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.49 r_work: 0.2801 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5803 Z= 0.230 Angle : 0.496 8.735 7890 Z= 0.254 Chirality : 0.047 0.153 962 Planarity : 0.005 0.046 995 Dihedral : 3.656 23.536 830 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.96 % Allowed : 16.44 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.30), residues: 805 helix: 1.30 (0.25), residues: 432 sheet: 0.72 (0.38), residues: 172 loop : -0.42 (0.46), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 167 HIS 0.002 0.001 HIS C 125 PHE 0.027 0.002 PHE A 119 TYR 0.004 0.001 TYR D 127 ARG 0.002 0.000 ARG B 195 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4970.14 seconds wall clock time: 87 minutes 34.99 seconds (5254.99 seconds total)