Starting phenix.real_space_refine on Thu Jul 24 08:03:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dnd_47036/07_2025/9dnd_47036.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dnd_47036/07_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_47036/07_2025/9dnd_47036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dnd_47036/07_2025/9dnd_47036.map" model { file = "/net/cci-nas-00/data/ceres_data/9dnd_47036/07_2025/9dnd_47036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dnd_47036/07_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-5711/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: 12.23, per 1000 atoms: 2.15 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: 1.43 Conformation dependent library (CDL) restraints added in 947.4 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: 0.80 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: 1.54 Time building geometry restraints manager: 1.65 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: 110.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 26.140 Find NCS groups from input model: 0.270 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.460 ------------------------------------------------------------------------------- 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 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.22173 ( 289) hydrogen bonds : angle 7.76226 ( 867) SS BOND : bond 0.01536 ( 4) SS BOND : angle 1.98162 ( 8) covalent geometry : bond 0.00970 ( 5803) covalent geometry : angle 1.73986 ( 7890) *********************** 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 : 0.669 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: 0.2071 time to fit residues: 35.6645 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 : 0.591 ------------------------------------------------------------------------------- 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 5807 Z= 0.147 Angle : 0.568 6.604 7898 Z= 0.298 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 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 289) hydrogen bonds : angle 4.82617 ( 867) SS BOND : bond 0.00172 ( 4) SS BOND : angle 1.20694 ( 8) covalent geometry : bond 0.00355 ( 5803) covalent geometry : angle 0.56702 ( 7890) *********************** 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 : 0.693 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: 0.2349 time to fit residues: 30.5776 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 : 0.682 ------------------------------------------------------------------------------- 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 5807 Z= 0.139 Angle : 0.515 7.651 7898 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 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 289) hydrogen bonds : angle 4.40821 ( 867) SS BOND : bond 0.00159 ( 4) SS BOND : angle 0.77016 ( 8) covalent geometry : bond 0.00346 ( 5803) covalent geometry : angle 0.51435 ( 7890) *********************** 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 : 0.591 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: 0.1937 time to fit residues: 24.9148 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 : 0.588 ------------------------------------------------------------------------------- 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 5807 Z= 0.166 Angle : 0.540 8.561 7898 Z= 0.278 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 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 289) hydrogen bonds : angle 4.37011 ( 867) SS BOND : bond 0.00247 ( 4) SS BOND : angle 0.92808 ( 8) covalent geometry : bond 0.00426 ( 5803) covalent geometry : angle 0.53965 ( 7890) *********************** 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 : 0.650 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: 0.2076 time to fit residues: 24.5524 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 : 0.641 ------------------------------------------------------------------------------- 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: 0.3980 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: 0.1838 ------------------------------------------------------------------------------- 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 = 0.3245 r_free = 0.3245 target = 0.121647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.100550 restraints weight = 6550.557| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.44 r_work: 0.2822 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5807 Z= 0.082 Angle : 0.439 7.067 7898 Z= 0.224 Chirality : 0.045 0.131 962 Planarity : 0.005 0.043 995 Dihedral : 4.671 58.914 840 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.15 % Allowed : 13.70 % 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 (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: 1.03 (0.30), residues: 805 helix: 1.13 (0.26), residues: 433 sheet: 0.85 (0.38), residues: 172 loop : -0.25 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 167 HIS 0.002 0.000 HIS B 10 PHE 0.027 0.001 PHE A 119 TYR 0.004 0.001 TYR A 127 ARG 0.003 0.000 ARG A 97 Details of bonding type rmsd hydrogen bonds : bond 0.02100 ( 289) hydrogen bonds : angle 4.05724 ( 867) SS BOND : bond 0.00176 ( 4) SS BOND : angle 0.62384 ( 8) covalent geometry : bond 0.00189 ( 5803) covalent geometry : angle 0.43889 ( 7890) *********************** 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 105 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: D 24 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7186 (tm-30) REVERT: D 25 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7637 (mm-30) REVERT: C 7 PHE cc_start: 0.9060 (m-80) cc_final: 0.8671 (m-80) REVERT: C 194 ARG cc_start: 0.8050 (mmm160) cc_final: 0.7640 (mtp-110) REVERT: A 63 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: A 81 MET cc_start: 0.8186 (mtt) cc_final: 0.7780 (mtp) REVERT: A 121 LYS cc_start: 0.8333 (ttpt) cc_final: 0.7845 (ttpp) REVERT: A 128 MET cc_start: 0.9140 (ttp) cc_final: 0.8893 (ttp) REVERT: B 188 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7902 (mt-10) outliers start: 11 outliers final: 4 residues processed: 100 average time/residue: 0.2104 time to fit residues: 26.8670 Evaluate side-chains 95 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 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: 0.7980 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3181 r_free = 0.3181 target = 0.116789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.096851 restraints weight = 6545.486| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.38 r_work: 0.2795 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5807 Z= 0.189 Angle : 0.555 9.205 7898 Z= 0.283 Chirality : 0.049 0.176 962 Planarity : 0.005 0.049 995 Dihedral : 3.905 26.014 830 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % 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 (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: 0.64 (0.30), residues: 805 helix: 0.82 (0.25), residues: 439 sheet: 0.58 (0.37), residues: 178 loop : -0.37 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 167 HIS 0.003 0.001 HIS C 125 PHE 0.022 0.002 PHE B 99 TYR 0.005 0.001 TYR D 127 ARG 0.003 0.000 ARG D 37 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 289) hydrogen bonds : angle 4.38440 ( 867) SS BOND : bond 0.00343 ( 4) SS BOND : angle 1.84639 ( 8) covalent geometry : bond 0.00493 ( 5803) covalent geometry : angle 0.55237 ( 7890) *********************** 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 105 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: D 24 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7158 (tm-30) REVERT: C 7 PHE cc_start: 0.9140 (m-80) cc_final: 0.8749 (m-10) REVERT: C 57 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.6539 (pp-130) REVERT: C 194 ARG cc_start: 0.8182 (mmm160) cc_final: 0.7848 (mtp-110) REVERT: A 63 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.7443 (m-80) REVERT: A 81 MET cc_start: 0.8168 (mtt) cc_final: 0.7733 (mtp) REVERT: A 128 MET cc_start: 0.9177 (ttp) cc_final: 0.8964 (ttp) REVERT: B 39 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8757 (mp) REVERT: B 188 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7974 (mt-10) outliers start: 16 outliers final: 10 residues processed: 98 average time/residue: 0.1858 time to fit residues: 23.6460 Evaluate side-chains 102 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 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 39 ILE 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: 2.9990 chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 15 optimal weight: 0.0000 chunk 24 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.4582 ------------------------------------------------------------------------------- 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 = 0.3215 r_free = 0.3215 target = 0.119318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.098253 restraints weight = 6527.691| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.43 r_work: 0.2786 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3060 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= 0.117 Angle : 0.474 8.294 7898 Z= 0.243 Chirality : 0.047 0.152 962 Planarity : 0.005 0.046 995 Dihedral : 3.694 25.000 830 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.94 % Allowed : 14.87 % 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: 0.83 (0.30), residues: 805 helix: 1.05 (0.25), residues: 433 sheet: 0.63 (0.38), residues: 173 loop : -0.43 (0.45), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 167 HIS 0.002 0.001 HIS A 30 PHE 0.025 0.002 PHE B 99 TYR 0.004 0.001 TYR D 127 ARG 0.003 0.000 ARG A 97 Details of bonding type rmsd hydrogen bonds : bond 0.02626 ( 289) hydrogen bonds : angle 4.23286 ( 867) SS BOND : bond 0.00185 ( 4) SS BOND : angle 1.24058 ( 8) covalent geometry : bond 0.00295 ( 5803) covalent geometry : angle 0.47221 ( 7890) *********************** 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 105 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: D 24 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7092 (tm-30) REVERT: C 7 PHE cc_start: 0.9104 (m-80) cc_final: 0.8730 (m-10) REVERT: C 57 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.6228 (pp-130) REVERT: C 194 ARG cc_start: 0.8139 (mmm160) cc_final: 0.7802 (mtp-110) REVERT: A 63 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.7457 (m-80) REVERT: A 81 MET cc_start: 0.8253 (mtt) cc_final: 0.7829 (mtp) REVERT: A 128 MET cc_start: 0.9157 (ttp) cc_final: 0.8933 (ttp) REVERT: B 39 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8761 (mp) REVERT: B 188 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7970 (mt-10) outliers start: 15 outliers final: 11 residues processed: 99 average time/residue: 0.1970 time to fit residues: 24.9624 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 : 0.632 ------------------------------------------------------------------------------- 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 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 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 39 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 29 optimal weight: 0.0270 chunk 73 optimal weight: 0.8980 chunk 25 optimal weight: 0.0770 chunk 40 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.3222 r_free = 0.3222 target = 0.119717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.098226 restraints weight = 6451.320| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.48 r_work: 0.2830 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5807 Z= 0.111 Angle : 0.471 8.315 7898 Z= 0.241 Chirality : 0.047 0.146 962 Planarity : 0.005 0.046 995 Dihedral : 3.666 24.051 830 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 : 14.87 % 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: 0.92 (0.30), residues: 805 helix: 1.17 (0.25), residues: 433 sheet: 0.65 (0.38), residues: 173 loop : -0.48 (0.45), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 167 HIS 0.002 0.001 HIS A 30 PHE 0.026 0.002 PHE A 119 TYR 0.004 0.001 TYR D 127 ARG 0.004 0.000 ARG A 97 Details of bonding type rmsd hydrogen bonds : bond 0.02542 ( 289) hydrogen bonds : angle 4.17932 ( 867) SS BOND : bond 0.00168 ( 4) SS BOND : angle 1.04822 ( 8) covalent geometry : bond 0.00275 ( 5803) covalent geometry : angle 0.47047 ( 7890) *********************** 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 105 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: D 24 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7056 (tm-30) REVERT: C 7 PHE cc_start: 0.9084 (m-80) cc_final: 0.8724 (m-10) REVERT: C 57 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.6365 (pp-130) REVERT: C 194 ARG cc_start: 0.8135 (mmm160) cc_final: 0.7792 (mtp-110) REVERT: A 63 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.7462 (m-80) REVERT: A 81 MET cc_start: 0.8174 (mtt) cc_final: 0.7733 (mtp) REVERT: A 128 MET cc_start: 0.9143 (ttp) cc_final: 0.8919 (ttp) REVERT: B 39 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8733 (mp) REVERT: B 188 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7968 (mt-10) outliers start: 16 outliers final: 10 residues processed: 98 average time/residue: 0.2093 time to fit residues: 26.1015 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 : 0.663 ------------------------------------------------------------------------------- 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 39 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 52 optimal weight: 0.1980 chunk 48 optimal weight: 0.6980 chunk 77 optimal weight: 0.2980 chunk 34 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 0.0010 chunk 22 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.3586 ------------------------------------------------------------------------------- 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 = 0.3235 r_free = 0.3235 target = 0.120579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.098240 restraints weight = 6488.610| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.56 r_work: 0.2827 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5807 Z= 0.100 Angle : 0.456 8.153 7898 Z= 0.233 Chirality : 0.046 0.148 962 Planarity : 0.005 0.045 995 Dihedral : 3.534 22.912 830 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.13 % Allowed : 14.29 % Favored : 82.58 % 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: 1.05 (0.30), residues: 805 helix: 1.27 (0.25), residues: 434 sheet: 0.69 (0.39), residues: 161 loop : -0.35 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 167 HIS 0.002 0.001 HIS A 30 PHE 0.026 0.002 PHE B 99 TYR 0.003 0.001 TYR D 127 ARG 0.004 0.000 ARG A 97 Details of bonding type rmsd hydrogen bonds : bond 0.02364 ( 289) hydrogen bonds : angle 4.11290 ( 867) SS BOND : bond 0.00157 ( 4) SS BOND : angle 0.93353 ( 8) covalent geometry : bond 0.00246 ( 5803) covalent geometry : angle 0.45565 ( 7890) *********************** 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: 16 poor density : 95 time to evaluate : 0.797 Fit side-chains REVERT: D 24 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7030 (tm-30) REVERT: D 25 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7510 (mm-30) REVERT: C 7 PHE cc_start: 0.9028 (m-80) cc_final: 0.8723 (m-10) REVERT: C 57 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.6331 (pp-130) REVERT: C 194 ARG cc_start: 0.8119 (mmm160) cc_final: 0.7287 (ttp-110) REVERT: A 63 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.7453 (m-80) REVERT: A 81 MET cc_start: 0.8181 (mtt) cc_final: 0.7747 (mtp) REVERT: A 121 LYS cc_start: 0.8406 (ttpt) cc_final: 0.7926 (ttpp) REVERT: A 128 MET cc_start: 0.9151 (ttp) cc_final: 0.8922 (ttp) REVERT: B 39 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8744 (mp) REVERT: B 188 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7942 (mt-10) outliers start: 16 outliers final: 10 residues processed: 105 average time/residue: 0.2329 time to fit residues: 31.2389 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 : 1.018 ------------------------------------------------------------------------------- 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 119 LYS Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain B residue 39 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 chunk 2 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 30 optimal weight: 0.0170 chunk 7 optimal weight: 0.1980 chunk 77 optimal weight: 0.0050 overall best weight: 0.1432 ------------------------------------------------------------------------------- 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 = 0.3271 r_free = 0.3271 target = 0.123270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.101175 restraints weight = 6526.848| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.54 r_work: 0.2867 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5807 Z= 0.078 Angle : 0.433 7.862 7898 Z= 0.221 Chirality : 0.045 0.138 962 Planarity : 0.004 0.043 995 Dihedral : 3.296 20.274 830 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.54 % Allowed : 15.66 % 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: 1.34 (0.30), residues: 805 helix: 1.57 (0.25), residues: 429 sheet: 0.77 (0.39), residues: 168 loop : -0.32 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 167 HIS 0.001 0.000 HIS B 10 PHE 0.028 0.001 PHE D 119 TYR 0.004 0.001 TYR A 127 ARG 0.002 0.000 ARG B 195 Details of bonding type rmsd hydrogen bonds : bond 0.01910 ( 289) hydrogen bonds : angle 3.96893 ( 867) SS BOND : bond 0.00341 ( 4) SS BOND : angle 0.72831 ( 8) covalent geometry : bond 0.00173 ( 5803) covalent geometry : angle 0.43223 ( 7890) ********************** 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 107 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: D 24 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7144 (tm-30) REVERT: D 25 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7645 (mm-30) REVERT: C 7 PHE cc_start: 0.8987 (m-80) cc_final: 0.8780 (m-10) REVERT: A 63 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.7479 (m-80) REVERT: A 81 MET cc_start: 0.8105 (mtt) cc_final: 0.7662 (mtp) REVERT: A 121 LYS cc_start: 0.8345 (ttpt) cc_final: 0.7829 (ttpp) REVERT: A 128 MET cc_start: 0.9151 (ttp) cc_final: 0.8928 (ttp) REVERT: B 78 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6502 (mt-10) outliers start: 13 outliers final: 10 residues processed: 101 average time/residue: 0.2998 time to fit residues: 39.2257 Evaluate side-chains 102 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3207 r_free = 0.3207 target = 0.118439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.097856 restraints weight = 6627.072| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.45 r_work: 0.2790 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5807 Z= 0.192 Angle : 0.550 9.116 7898 Z= 0.281 Chirality : 0.049 0.167 962 Planarity : 0.005 0.049 995 Dihedral : 3.825 24.069 830 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.96 % Allowed : 16.24 % 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: 0.96 (0.30), residues: 805 helix: 1.20 (0.25), residues: 433 sheet: 0.66 (0.37), residues: 179 loop : -0.49 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 167 HIS 0.004 0.001 HIS C 125 PHE 0.028 0.002 PHE A 119 TYR 0.005 0.001 TYR D 138 ARG 0.003 0.000 ARG D 37 Details of bonding type rmsd hydrogen bonds : bond 0.03357 ( 289) hydrogen bonds : angle 4.30981 ( 867) SS BOND : bond 0.00226 ( 4) SS BOND : angle 1.32304 ( 8) covalent geometry : bond 0.00504 ( 5803) covalent geometry : angle 0.54892 ( 7890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5468.49 seconds wall clock time: 97 minutes 32.13 seconds (5852.13 seconds total)