Starting phenix.real_space_refine on Sun Aug 24 03:54:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8so3_40646/08_2025/8so3_40646_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8so3_40646/08_2025/8so3_40646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8so3_40646/08_2025/8so3_40646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8so3_40646/08_2025/8so3_40646.map" model { file = "/net/cci-nas-00/data/ceres_data/8so3_40646/08_2025/8so3_40646_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8so3_40646/08_2025/8so3_40646_trim.cif" } resolution = 3.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 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: 5 Type Number sf(0) Gaussians S 34 5.16 5 C 5517 2.51 5 N 1509 2.21 5 O 1711 1.98 5 H 7947 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16718 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 2308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2308 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 19, 'TRANS': 153} Chain breaks: 3 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASP:plan': 5, 'ARG:plan': 10, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 90 Chain: "H" Number of atoms: 3005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3005 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "L" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3010 Classifications: {'peptide': 216} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 202} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 43 Chain: "X" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 2279 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 19, 'TRANS': 155} Chain breaks: 3 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'ARG:plan': 11, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 127 Chain: "Y" Number of atoms: 3035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3035 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "Z" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3025 Classifications: {'peptide': 216} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 202} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.79, per 1000 atoms: 0.17 Number of scatterers: 16718 At special positions: 0 Unit cell: (96.32, 100.8, 128.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 O 1711 8.00 N 1509 7.00 C 5517 6.00 H 7947 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS D 44 " - pdb=" SG CYS D 160 " distance=2.03 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 241 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS X 44 " - pdb=" SG CYS X 160 " distance=2.03 Simple disulfide: pdb=" SG CYS X 189 " - pdb=" SG CYS X 241 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 144 " - pdb=" SG CYS Y 200 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 138 " - pdb=" SG CYS Z 198 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 474.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 31 sheets defined 5.9% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'D' and resid 206 through 210 Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.205A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 189 through 193 removed outlier: 3.588A pdb=" N LEU H 193 " --> pdb=" O SER H 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 67 removed outlier: 3.513A pdb=" N PHE L 66 " --> pdb=" O PRO L 63 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER L 67 " --> pdb=" O ALA L 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 63 through 67' Processing helix chain 'L' and resid 125 through 132 removed outlier: 3.554A pdb=" N LEU L 129 " --> pdb=" O SER L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 193 removed outlier: 3.987A pdb=" N HIS L 193 " --> pdb=" O ASP L 189 " (cutoff:3.500A) Processing helix chain 'X' and resid 232 through 236 Processing helix chain 'Y' and resid 28 through 32 removed outlier: 3.553A pdb=" N ASP Y 31 " --> pdb=" O THR Y 28 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR Y 32 " --> pdb=" O PHE Y 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 28 through 32' Processing helix chain 'Y' and resid 160 through 162 No H-bonds generated for 'chain 'Y' and resid 160 through 162' Processing helix chain 'Y' and resid 189 through 195 removed outlier: 3.631A pdb=" N LEU Y 193 " --> pdb=" O SER Y 190 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY Y 194 " --> pdb=" O SER Y 191 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 131 removed outlier: 3.650A pdb=" N SER Z 131 " --> pdb=" O GLU Z 127 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 192 Processing sheet with id=AA1, first strand: chain 'D' and resid 41 through 42 Processing sheet with id=AA2, first strand: chain 'D' and resid 99 through 103 removed outlier: 3.686A pdb=" N TYR D 99 " --> pdb=" O HIS D 65 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N TRP D 63 " --> pdb=" O VAL D 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 185 through 187 removed outlier: 3.548A pdb=" N LEU D 226 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 199 through 203 removed outlier: 3.882A pdb=" N GLY D 240 " --> pdb=" O PHE D 203 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP D 239 " --> pdb=" O TYR D 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.851A pdb=" N THR H 116 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL H 34 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ASP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.851A pdb=" N THR H 116 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR H 100 " --> pdb=" O MET H 106 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N MET H 106 " --> pdb=" O TYR H 100 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 124 through 128 removed outlier: 3.646A pdb=" N SER H 124 " --> pdb=" O LYS H 147 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS H 147 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE H 126 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU H 145 " --> pdb=" O PHE H 126 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY H 143 " --> pdb=" O LEU H 128 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 124 through 128 removed outlier: 3.646A pdb=" N SER H 124 " --> pdb=" O LYS H 147 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS H 147 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE H 126 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU H 145 " --> pdb=" O PHE H 126 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY H 143 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER H 181 " --> pdb=" O VAL H 173 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 154 through 158 removed outlier: 3.541A pdb=" N THR H 155 " --> pdb=" O ASN H 203 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS H 213 " --> pdb=" O CYS H 200 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.703A pdb=" N CYS L 23 " --> pdb=" O PHE L 75 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE L 75 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 19 through 20 Processing sheet with id=AB4, first strand: chain 'L' and resid 57 through 58 removed outlier: 6.223A pdb=" N LEU L 50 " --> pdb=" O GLN L 41 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLN L 41 " --> pdb=" O LEU L 50 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE L 52 " --> pdb=" O TRP L 39 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 118 through 122 removed outlier: 3.947A pdb=" N VAL L 137 " --> pdb=" O PHE L 122 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR L 177 " --> pdb=" O ASN L 142 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER L 180 " --> pdb=" O SER L 166 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER L 166 " --> pdb=" O SER L 180 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 149 through 154 removed outlier: 3.515A pdb=" N LYS L 149 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU L 199 " --> pdb=" O GLN L 151 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL L 200 " --> pdb=" O VAL L 209 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL L 209 " --> pdb=" O VAL L 200 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'X' and resid 40 through 43 Processing sheet with id=AB8, first strand: chain 'X' and resid 99 through 100 Processing sheet with id=AB9, first strand: chain 'X' and resid 172 through 173 removed outlier: 3.748A pdb=" N ASN X 188 " --> pdb=" O THR X 172 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU X 187 " --> pdb=" O LEU X 226 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU X 226 " --> pdb=" O LEU X 187 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS X 220 " --> pdb=" O PHE X 227 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'X' and resid 199 through 203 Processing sheet with id=AC2, first strand: chain 'Y' and resid 3 through 4 removed outlier: 3.794A pdb=" N LEU Y 3 " --> pdb=" O SER Y 25 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER Y 25 " --> pdb=" O LEU Y 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'Y' and resid 10 through 12 removed outlier: 3.915A pdb=" N GLU Y 10 " --> pdb=" O SER Y 114 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR Y 116 " --> pdb=" O GLU Y 10 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL Y 12 " --> pdb=" O THR Y 116 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL Y 34 " --> pdb=" O ASP Y 50 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ASP Y 50 " --> pdb=" O VAL Y 34 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP Y 36 " --> pdb=" O ILE Y 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Y' and resid 10 through 12 removed outlier: 3.915A pdb=" N GLU Y 10 " --> pdb=" O SER Y 114 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR Y 116 " --> pdb=" O GLU Y 10 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL Y 12 " --> pdb=" O THR Y 116 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Y' and resid 19 through 21 Processing sheet with id=AC6, first strand: chain 'Y' and resid 124 through 128 removed outlier: 3.559A pdb=" N GLY Y 143 " --> pdb=" O LEU Y 128 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ALA Y 141 " --> pdb=" O VAL Y 188 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL Y 188 " --> pdb=" O ALA Y 141 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLY Y 143 " --> pdb=" O VAL Y 186 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL Y 186 " --> pdb=" O GLY Y 143 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU Y 145 " --> pdb=" O SER Y 184 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER Y 184 " --> pdb=" O LEU Y 145 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS Y 147 " --> pdb=" O LEU Y 182 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU Y 182 " --> pdb=" O LYS Y 147 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL Y 185 " --> pdb=" O HIS Y 168 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Y' and resid 124 through 128 removed outlier: 3.559A pdb=" N GLY Y 143 " --> pdb=" O LEU Y 128 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ALA Y 141 " --> pdb=" O VAL Y 188 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL Y 188 " --> pdb=" O ALA Y 141 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLY Y 143 " --> pdb=" O VAL Y 186 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL Y 186 " --> pdb=" O GLY Y 143 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU Y 145 " --> pdb=" O SER Y 184 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER Y 184 " --> pdb=" O LEU Y 145 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS Y 147 " --> pdb=" O LEU Y 182 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU Y 182 " --> pdb=" O LYS Y 147 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL Y 173 " --> pdb=" O SER Y 181 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Y' and resid 155 through 158 removed outlier: 4.606A pdb=" N TYR Y 198 " --> pdb=" O VAL Y 215 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS Y 213 " --> pdb=" O CYS Y 200 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL Y 211 " --> pdb=" O VAL Y 202 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Z' and resid 4 through 5 Processing sheet with id=AD1, first strand: chain 'Z' and resid 10 through 12 removed outlier: 6.788A pdb=" N LEU Z 11 " --> pdb=" O GLU Z 109 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N MET Z 37 " --> pdb=" O SER Z 53 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SER Z 53 " --> pdb=" O MET Z 37 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TRP Z 39 " --> pdb=" O LEU Z 51 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU Z 51 " --> pdb=" O TRP Z 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Z' and resid 19 through 20 Processing sheet with id=AD3, first strand: chain 'Z' and resid 118 through 122 removed outlier: 3.662A pdb=" N VAL Z 137 " --> pdb=" O PHE Z 122 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TYR Z 177 " --> pdb=" O ASN Z 142 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Z' and resid 148 through 154 removed outlier: 3.974A pdb=" N TYR Z 196 " --> pdb=" O PHE Z 213 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE Z 213 " --> pdb=" O TYR Z 196 " (cutoff:3.500A) 265 hydrogen bonds defined for protein. 609 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: 3.92 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: 0.84 - 1.04: 7947 1.04 - 1.23: 389 1.23 - 1.43: 3482 1.43 - 1.63: 5080 1.63 - 1.82: 44 Bond restraints: 16942 Sorted by residual: bond pdb=" N THR Y 120 " pdb=" CA THR Y 120 " ideal model delta sigma weight residual 1.463 1.516 -0.053 1.24e-02 6.50e+03 1.80e+01 bond pdb=" NZ LYS Z 24 " pdb=" HZ1 LYS Z 24 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS H 63 " pdb=" HZ1 LYS H 63 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS Y 38 " pdb=" HZ2 LYS Y 38 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS Z 211 " pdb=" HZ1 LYS Z 211 " ideal model delta sigma weight residual 0.890 0.970 -0.080 2.00e-02 2.50e+03 1.62e+01 ... (remaining 16937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.69: 30372 9.69 - 19.39: 10 19.39 - 29.08: 3 29.08 - 38.78: 0 38.78 - 48.47: 2 Bond angle restraints: 30387 Sorted by residual: angle pdb=" CA GLY D 130 " pdb=" N GLY D 130 " pdb=" H GLY D 130 " ideal model delta sigma weight residual 114.00 162.47 -48.47 3.00e+00 1.11e-01 2.61e+02 angle pdb=" CA ASP X 131 " pdb=" N ASP X 131 " pdb=" H ASP X 131 " ideal model delta sigma weight residual 114.00 159.67 -45.67 3.00e+00 1.11e-01 2.32e+02 angle pdb=" C ARG D 165 " pdb=" N LEU D 166 " pdb=" CA LEU D 166 " ideal model delta sigma weight residual 120.90 136.32 -15.42 1.41e+00 5.03e-01 1.20e+02 angle pdb=" CA GLY D 60 " pdb=" N GLY D 60 " pdb=" H GLY D 60 " ideal model delta sigma weight residual 114.00 141.42 -27.42 3.00e+00 1.11e-01 8.35e+01 angle pdb=" CA GLY D 93 " pdb=" N GLY D 93 " pdb=" H GLY D 93 " ideal model delta sigma weight residual 114.00 86.74 27.26 3.00e+00 1.11e-01 8.26e+01 ... (remaining 30382 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7605 17.97 - 35.94: 524 35.94 - 53.91: 173 53.91 - 71.88: 39 71.88 - 89.85: 13 Dihedral angle restraints: 8354 sinusoidal: 4305 harmonic: 4049 Sorted by residual: dihedral pdb=" CB CYS Z 23 " pdb=" SG CYS Z 23 " pdb=" SG CYS Z 92 " pdb=" CB CYS Z 92 " ideal model delta sinusoidal sigma weight residual 93.00 165.95 -72.95 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CB CYS Y 144 " pdb=" SG CYS Y 144 " pdb=" SG CYS Y 200 " pdb=" CB CYS Y 200 " ideal model delta sinusoidal sigma weight residual 93.00 142.20 -49.20 1 1.00e+01 1.00e-02 3.33e+01 dihedral pdb=" CA ARG D 165 " pdb=" C ARG D 165 " pdb=" N LEU D 166 " pdb=" CA LEU D 166 " ideal model delta harmonic sigma weight residual -180.00 -152.49 -27.51 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 8351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1204 0.068 - 0.136: 186 0.136 - 0.204: 13 0.204 - 0.272: 3 0.272 - 0.340: 1 Chirality restraints: 1407 Sorted by residual: chirality pdb=" CA ARG D 165 " pdb=" N ARG D 165 " pdb=" C ARG D 165 " pdb=" CB ARG D 165 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA MET X 171 " pdb=" N MET X 171 " pdb=" C MET X 171 " pdb=" CB MET X 171 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA LYS H 38 " pdb=" N LYS H 38 " pdb=" C LYS H 38 " pdb=" CB LYS H 38 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1404 not shown) Planarity restraints: 2697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER X 69 " -0.023 2.00e-02 2.50e+03 4.63e-02 2.15e+01 pdb=" C SER X 69 " 0.080 2.00e-02 2.50e+03 pdb=" O SER X 69 " -0.030 2.00e-02 2.50e+03 pdb=" N GLY X 70 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 163 " 0.020 2.00e-02 2.50e+03 4.21e-02 1.78e+01 pdb=" C ARG D 163 " -0.073 2.00e-02 2.50e+03 pdb=" O ARG D 163 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU D 164 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 165 " -0.018 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C ARG D 165 " 0.067 2.00e-02 2.50e+03 pdb=" O ARG D 165 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU D 166 " -0.023 2.00e-02 2.50e+03 ... (remaining 2694 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.87: 75 1.87 - 2.55: 14518 2.55 - 3.24: 46249 3.24 - 3.92: 58238 3.92 - 4.60: 90498 Nonbonded interactions: 209578 Sorted by model distance: nonbonded pdb=" H TYR X 147 " pdb=" HA ARG X 163 " model vdw 1.188 2.270 nonbonded pdb=" HE3 MET X 171 " pdb=" HB2 CYS X 241 " model vdw 1.276 2.440 nonbonded pdb=" HG3 GLU X 146 " pdb=" CB ARG X 163 " model vdw 1.315 2.920 nonbonded pdb=" HA GLU X 146 " pdb=" O ARG X 163 " model vdw 1.327 2.620 nonbonded pdb=" HE2 TYR X 255 " pdb="HD21 LEU X 257 " model vdw 1.330 2.270 ... (remaining 209573 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 'D' and (resid 27 or (resid 28 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 29 through 71 or (resid 72 and (nam \ e N or name CA or name C or name O or name CB or name HA )) or resid 93 through \ 104 or (resid 131 through 132 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 133 through 134 or (resid 135 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 136 th \ rough 157 or (resid 158 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 159 through 167 or (resid 168 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 169 through \ 203 or (resid 204 through 206 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 207 through 214 or (resid 215 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 216 th \ rough 222 or (resid 223 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 224 through 601)) selection = (chain 'X' and (resid 27 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 37 through 72 or resid 9 \ 3 through 137 or (resid 138 and (name N or name CA or name C or name O or name C \ B or name HA )) or resid 139 through 178 or (resid 179 through 180 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 181 th \ rough 229 or (resid 230 through 232 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 233 through 252 or (resid 253 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 254 through 601)) } ncs_group { reference = (chain 'H' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 4 or (resid 5 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 6 through 9 or ( \ resid 10 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 11 through 24 or (resid 25 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 26 through 85 or (resid 86 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 87 through 217 or (resid 218 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 219)) selection = (chain 'Y' and (resid 2 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 14 through 17 or (resid 1 \ 8 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 19 through 29 or (resid 30 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 31 through 40 or (resid 41 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 42 \ through 61 or (resid 62 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 63 through 64 or (resid 65 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 66 through 68 o \ r (resid 69 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 70 through 88 or (resid 89 through 90 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 91 through 219)) \ } ncs_group { reference = (chain 'L' and (resid 1 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 35 through 84 or (resid 8 \ 5 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 86 through 216)) selection = (chain 'Z' and (resid 1 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 28 through 45 or (resid 4 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 47 through 96 or (resid 97 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 98 through 216)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 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: 0.080 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.070 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 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 : 0.006 0.373 9008 Z= 0.482 Angle : 0.854 16.221 12340 Z= 0.497 Chirality : 0.051 0.340 1407 Planarity : 0.007 0.065 1598 Dihedral : 13.957 89.848 3097 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.46 % Favored : 93.37 % Rotamer: Outliers : 0.68 % Allowed : 0.90 % Favored : 98.42 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 12.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.24), residues: 1177 helix: -0.48 (0.83), residues: 34 sheet: -0.53 (0.24), residues: 479 loop : -1.37 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 165 TYR 0.014 0.001 TYR D 245 PHE 0.016 0.002 PHE L 75 TRP 0.025 0.002 TRP H 109 HIS 0.013 0.001 HIS X 65 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 8995) covalent geometry : angle 0.85228 (12316) SS BOND : bond 0.00380 ( 12) SS BOND : angle 1.61812 ( 24) hydrogen bonds : bond 0.26872 ( 243) hydrogen bonds : angle 10.42994 ( 609) Misc. bond : bond 0.37327 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 61 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.446 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR L 76 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR Z 76 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: D 166 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8364 (tt) REVERT: X 32 VAL cc_start: 0.8175 (p) cc_final: 0.7837 (m) REVERT: X 161 ARG cc_start: 0.7799 (ttm110) cc_final: 0.7503 (ttm110) outliers start: 6 outliers final: 3 residues processed: 135 average time/residue: 0.1785 time to fit residues: 33.6093 Evaluate side-chains 108 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain X residue 162 LEU Chi-restraints excluded: chain X residue 172 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.0980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 152 HIS X 250 ASN Y 6 GLN Y 168 HIS Y 204 HIS Z 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.172250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.151139 restraints weight = 41130.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.155902 restraints weight = 21718.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.158932 restraints weight = 13600.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.160828 restraints weight = 9543.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.161866 restraints weight = 7318.775| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4027 r_free = 0.4027 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4027 r_free = 0.4027 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9008 Z= 0.155 Angle : 0.662 6.878 12340 Z= 0.348 Chirality : 0.046 0.173 1407 Planarity : 0.006 0.062 1598 Dihedral : 6.360 57.565 1364 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.20 % Favored : 93.63 % Rotamer: Outliers : 1.01 % Allowed : 7.32 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.25), residues: 1177 helix: -0.80 (0.75), residues: 36 sheet: -0.55 (0.24), residues: 490 loop : -1.26 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 84 TYR 0.011 0.001 TYR X 147 PHE 0.015 0.001 PHE L 75 TRP 0.011 0.001 TRP D 239 HIS 0.012 0.001 HIS X 65 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 8995) covalent geometry : angle 0.65945 (12316) SS BOND : bond 0.00519 ( 12) SS BOND : angle 1.43688 ( 24) hydrogen bonds : bond 0.05645 ( 243) hydrogen bonds : angle 7.76159 ( 609) Misc. bond : bond 0.00090 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 61 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.489 Fit side-chains TARDY: cannot create tardy model for: "THR L 76 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR Z 76 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: X 32 VAL cc_start: 0.7985 (p) cc_final: 0.7619 (m) outliers start: 9 outliers final: 9 residues processed: 117 average time/residue: 0.1742 time to fit residues: 29.8275 Evaluate side-chains 110 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain X residue 162 LEU Chi-restraints excluded: chain Y residue 6 GLN Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 179 LEU Chi-restraints excluded: chain Y residue 201 ASN Chi-restraints excluded: chain Z residue 125 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 74 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.170441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.149148 restraints weight = 41177.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.153898 restraints weight = 21869.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.156855 restraints weight = 13740.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.158754 restraints weight = 9705.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.159930 restraints weight = 7473.116| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4005 r_free = 0.4005 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4005 r_free = 0.4005 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9008 Z= 0.144 Angle : 0.606 6.298 12340 Z= 0.317 Chirality : 0.045 0.165 1407 Planarity : 0.005 0.058 1598 Dihedral : 5.646 56.470 1361 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.29 % Favored : 93.54 % Rotamer: Outliers : 1.80 % Allowed : 8.56 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.25), residues: 1177 helix: -0.07 (0.85), residues: 36 sheet: -0.77 (0.23), residues: 517 loop : -1.24 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 193 TYR 0.010 0.001 TYR H 100 PHE 0.016 0.001 PHE L 75 TRP 0.009 0.001 TRP D 239 HIS 0.010 0.001 HIS X 65 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8995) covalent geometry : angle 0.60436 (12316) SS BOND : bond 0.00562 ( 12) SS BOND : angle 1.16523 ( 24) hydrogen bonds : bond 0.04600 ( 243) hydrogen bonds : angle 6.97611 ( 609) Misc. bond : bond 0.00051 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 61 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.553 Fit side-chains TARDY: cannot create tardy model for: "THR L 76 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR Z 76 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: L 144 TYR cc_start: 0.8088 (t80) cc_final: 0.7845 (t80) REVERT: X 32 VAL cc_start: 0.7878 (p) cc_final: 0.7500 (m) outliers start: 16 outliers final: 14 residues processed: 121 average time/residue: 0.1857 time to fit residues: 32.0318 Evaluate side-chains 114 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 135 TRP Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain X residue 162 LEU Chi-restraints excluded: chain X residue 244 THR Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 179 LEU Chi-restraints excluded: chain Y residue 201 ASN Chi-restraints excluded: chain Z residue 125 SER Chi-restraints excluded: chain Z residue 201 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 58 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 GLN Z 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.166194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.144678 restraints weight = 40962.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.149205 restraints weight = 22269.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.152076 restraints weight = 14248.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.153905 restraints weight = 10225.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.155003 restraints weight = 8008.484| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3949 r_free = 0.3949 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3949 r_free = 0.3949 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9008 Z= 0.178 Angle : 0.627 5.971 12340 Z= 0.330 Chirality : 0.045 0.168 1407 Planarity : 0.006 0.057 1598 Dihedral : 5.737 53.895 1361 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.48 % Favored : 92.35 % Rotamer: Outliers : 2.14 % Allowed : 9.91 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.25), residues: 1177 helix: 0.17 (0.89), residues: 36 sheet: -0.88 (0.24), residues: 502 loop : -1.43 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 40 TYR 0.013 0.001 TYR H 100 PHE 0.016 0.002 PHE L 75 TRP 0.011 0.001 TRP X 202 HIS 0.012 0.001 HIS X 65 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 8995) covalent geometry : angle 0.62516 (12316) SS BOND : bond 0.00487 ( 12) SS BOND : angle 1.29806 ( 24) hydrogen bonds : bond 0.04402 ( 243) hydrogen bonds : angle 6.57562 ( 609) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 61 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.439 Fit side-chains TARDY: cannot create tardy model for: "THR L 76 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR Z 76 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: L 38 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8447 (m-40) REVERT: L 144 TYR cc_start: 0.8197 (t80) cc_final: 0.7985 (t80) outliers start: 19 outliers final: 17 residues processed: 112 average time/residue: 0.1669 time to fit residues: 27.5896 Evaluate side-chains 109 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 135 TRP Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 200 CYS Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain X residue 162 LEU Chi-restraints excluded: chain X residue 244 THR Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 93 VAL Chi-restraints excluded: chain Y residue 179 LEU Chi-restraints excluded: chain Y residue 182 LEU Chi-restraints excluded: chain Y residue 201 ASN Chi-restraints excluded: chain Z residue 38 ASN Chi-restraints excluded: chain Z residue 125 SER Chi-restraints excluded: chain Z residue 201 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 105 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 0.0050 chunk 26 optimal weight: 0.6980 chunk 69 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.168819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.147749 restraints weight = 40846.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.152376 restraints weight = 21729.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.155256 restraints weight = 13734.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.157142 restraints weight = 9739.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.158243 restraints weight = 7507.972| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3986 r_free = 0.3986 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3986 r_free = 0.3986 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9008 Z= 0.108 Angle : 0.553 4.806 12340 Z= 0.287 Chirality : 0.044 0.164 1407 Planarity : 0.005 0.053 1598 Dihedral : 5.317 52.845 1361 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.18 % Favored : 94.65 % Rotamer: Outliers : 1.80 % Allowed : 11.26 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.25), residues: 1177 helix: 1.97 (1.01), residues: 28 sheet: -0.73 (0.24), residues: 512 loop : -1.30 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 193 TYR 0.010 0.001 TYR X 147 PHE 0.014 0.001 PHE L 75 TRP 0.009 0.001 TRP X 202 HIS 0.007 0.001 HIS X 218 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8995) covalent geometry : angle 0.55274 (12316) SS BOND : bond 0.00383 ( 12) SS BOND : angle 0.83380 ( 24) hydrogen bonds : bond 0.03643 ( 243) hydrogen bonds : angle 6.15657 ( 609) Misc. bond : bond 0.00210 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 61 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.415 Fit side-chains TARDY: cannot create tardy model for: "THR L 76 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR Z 76 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 16 outliers final: 15 residues processed: 112 average time/residue: 0.1586 time to fit residues: 26.6831 Evaluate side-chains 108 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 135 TRP Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain X residue 162 LEU Chi-restraints excluded: chain X residue 244 THR Chi-restraints excluded: chain Y residue 93 VAL Chi-restraints excluded: chain Y residue 179 LEU Chi-restraints excluded: chain Y residue 201 ASN Chi-restraints excluded: chain Z residue 125 SER Chi-restraints excluded: chain Z residue 176 THR Chi-restraints excluded: chain Z residue 201 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 86 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 55 ASN Y 203 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.166364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.145115 restraints weight = 40914.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.149678 restraints weight = 22008.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.152589 restraints weight = 13958.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.154415 restraints weight = 9915.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.155631 restraints weight = 7731.519| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3956 r_free = 0.3956 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3956 r_free = 0.3956 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9008 Z= 0.148 Angle : 0.571 4.564 12340 Z= 0.298 Chirality : 0.044 0.164 1407 Planarity : 0.005 0.051 1598 Dihedral : 5.111 49.523 1358 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.65 % Favored : 92.18 % Rotamer: Outliers : 2.25 % Allowed : 11.26 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.25), residues: 1177 helix: 1.08 (0.97), residues: 34 sheet: -0.61 (0.24), residues: 501 loop : -1.43 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 193 TYR 0.011 0.001 TYR H 100 PHE 0.015 0.002 PHE L 75 TRP 0.008 0.001 TRP D 239 HIS 0.007 0.001 HIS X 65 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 8995) covalent geometry : angle 0.56782 (12316) SS BOND : bond 0.00471 ( 12) SS BOND : angle 1.38982 ( 24) hydrogen bonds : bond 0.03816 ( 243) hydrogen bonds : angle 6.10521 ( 609) Misc. bond : bond 0.00092 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 61 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.459 Fit side-chains TARDY: cannot create tardy model for: "THR L 76 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR Z 76 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: D 166 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7862 (tt) outliers start: 20 outliers final: 18 residues processed: 106 average time/residue: 0.1672 time to fit residues: 25.9963 Evaluate side-chains 107 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 135 TRP Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain X residue 68 ASP Chi-restraints excluded: chain X residue 162 LEU Chi-restraints excluded: chain X residue 244 THR Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 148 ASP Chi-restraints excluded: chain Y residue 179 LEU Chi-restraints excluded: chain Y residue 201 ASN Chi-restraints excluded: chain Z residue 125 SER Chi-restraints excluded: chain Z residue 176 THR Chi-restraints excluded: chain Z residue 201 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.166221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.145065 restraints weight = 40907.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.149628 restraints weight = 21909.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.152486 restraints weight = 13901.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.154348 restraints weight = 9903.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.155512 restraints weight = 7674.514| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3957 r_free = 0.3957 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3957 r_free = 0.3957 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9008 Z= 0.138 Angle : 0.567 5.516 12340 Z= 0.295 Chirality : 0.044 0.166 1407 Planarity : 0.005 0.051 1598 Dihedral : 5.082 47.899 1358 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.29 % Favored : 93.46 % Rotamer: Outliers : 2.36 % Allowed : 11.94 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.25), residues: 1177 helix: 1.17 (0.98), residues: 34 sheet: -0.53 (0.24), residues: 504 loop : -1.47 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 204 TYR 0.011 0.001 TYR X 147 PHE 0.017 0.001 PHE L 75 TRP 0.008 0.001 TRP D 239 HIS 0.007 0.001 HIS X 218 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8995) covalent geometry : angle 0.56238 (12316) SS BOND : bond 0.00433 ( 12) SS BOND : angle 1.72178 ( 24) hydrogen bonds : bond 0.03675 ( 243) hydrogen bonds : angle 6.01916 ( 609) Misc. bond : bond 0.00145 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 61 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.459 Fit side-chains TARDY: cannot create tardy model for: "THR L 76 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR Z 76 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: D 166 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7847 (tt) outliers start: 21 outliers final: 20 residues processed: 111 average time/residue: 0.1614 time to fit residues: 26.9346 Evaluate side-chains 110 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 135 TRP Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 184 TRP Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 200 CYS Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain X residue 162 LEU Chi-restraints excluded: chain X residue 244 THR Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 93 VAL Chi-restraints excluded: chain Y residue 179 LEU Chi-restraints excluded: chain Y residue 201 ASN Chi-restraints excluded: chain Z residue 38 ASN Chi-restraints excluded: chain Z residue 125 SER Chi-restraints excluded: chain Z residue 176 THR Chi-restraints excluded: chain Z residue 201 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 36 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.164780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.143555 restraints weight = 41100.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.148036 restraints weight = 22239.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.150936 restraints weight = 14212.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.152754 restraints weight = 10142.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.153952 restraints weight = 7930.442| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3941 r_free = 0.3941 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3941 r_free = 0.3941 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9008 Z= 0.158 Angle : 0.583 5.112 12340 Z= 0.304 Chirality : 0.044 0.169 1407 Planarity : 0.005 0.050 1598 Dihedral : 5.134 48.070 1358 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.99 % Favored : 91.76 % Rotamer: Outliers : 2.48 % Allowed : 12.73 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.25), residues: 1177 helix: 1.06 (0.96), residues: 34 sheet: -0.57 (0.24), residues: 509 loop : -1.48 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 204 TYR 0.013 0.001 TYR X 147 PHE 0.019 0.002 PHE L 213 TRP 0.014 0.001 TRP D 239 HIS 0.006 0.001 HIS X 218 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8995) covalent geometry : angle 0.57881 (12316) SS BOND : bond 0.00411 ( 12) SS BOND : angle 1.70292 ( 24) hydrogen bonds : bond 0.03804 ( 243) hydrogen bonds : angle 6.02397 ( 609) Misc. bond : bond 0.00100 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 61 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.502 Fit side-chains TARDY: cannot create tardy model for: "THR L 76 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR Z 76 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: D 166 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7860 (tt) REVERT: X 230 GLN cc_start: 0.7765 (pm20) cc_final: 0.7498 (pm20) outliers start: 22 outliers final: 21 residues processed: 106 average time/residue: 0.1665 time to fit residues: 26.1465 Evaluate side-chains 110 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 135 TRP Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 184 TRP Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 200 CYS Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain X residue 162 LEU Chi-restraints excluded: chain X residue 244 THR Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 93 VAL Chi-restraints excluded: chain Y residue 148 ASP Chi-restraints excluded: chain Y residue 179 LEU Chi-restraints excluded: chain Y residue 201 ASN Chi-restraints excluded: chain Z residue 38 ASN Chi-restraints excluded: chain Z residue 125 SER Chi-restraints excluded: chain Z residue 176 THR Chi-restraints excluded: chain Z residue 201 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 43 optimal weight: 0.0020 chunk 12 optimal weight: 0.0770 chunk 66 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 overall best weight: 0.4346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.166702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.145837 restraints weight = 40879.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.150416 restraints weight = 21745.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.153309 restraints weight = 13698.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.155133 restraints weight = 9716.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.156285 restraints weight = 7517.079| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3967 r_free = 0.3967 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3967 r_free = 0.3967 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9008 Z= 0.108 Angle : 0.549 5.099 12340 Z= 0.284 Chirality : 0.044 0.168 1407 Planarity : 0.005 0.050 1598 Dihedral : 4.939 46.451 1358 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.86 % Favored : 93.88 % Rotamer: Outliers : 2.25 % Allowed : 13.29 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.25), residues: 1177 helix: 1.18 (0.98), residues: 34 sheet: -0.52 (0.24), residues: 511 loop : -1.36 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 193 TYR 0.010 0.001 TYR X 147 PHE 0.016 0.001 PHE L 75 TRP 0.010 0.001 TRP D 239 HIS 0.006 0.001 HIS X 218 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 8995) covalent geometry : angle 0.54635 (12316) SS BOND : bond 0.00367 ( 12) SS BOND : angle 1.30606 ( 24) hydrogen bonds : bond 0.03380 ( 243) hydrogen bonds : angle 5.79067 ( 609) Misc. bond : bond 0.00207 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 61 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.483 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR L 76 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR Z 76 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: D 166 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7884 (tt) REVERT: H 156 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8673 (m) REVERT: L 18 ARG cc_start: 0.5973 (tmm-80) cc_final: 0.5732 (ttm170) REVERT: X 230 GLN cc_start: 0.7762 (pm20) cc_final: 0.7498 (pm20) REVERT: X 254 MET cc_start: 0.7474 (tpp) cc_final: 0.7203 (tpp) outliers start: 20 outliers final: 18 residues processed: 109 average time/residue: 0.1506 time to fit residues: 24.5263 Evaluate side-chains 112 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 135 TRP Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 184 TRP Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 200 CYS Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain X residue 68 ASP Chi-restraints excluded: chain X residue 162 LEU Chi-restraints excluded: chain X residue 244 THR Chi-restraints excluded: chain Y residue 93 VAL Chi-restraints excluded: chain Y residue 179 LEU Chi-restraints excluded: chain Y residue 201 ASN Chi-restraints excluded: chain Z residue 38 ASN Chi-restraints excluded: chain Z residue 125 SER Chi-restraints excluded: chain Z residue 176 THR Chi-restraints excluded: chain Z residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 95 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.164996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.144877 restraints weight = 40807.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.148996 restraints weight = 22902.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.151626 restraints weight = 14962.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.153340 restraints weight = 10898.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.154325 restraints weight = 8564.975| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3942 r_free = 0.3942 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3942 r_free = 0.3942 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 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 : 0.003 0.037 9008 Z= 0.144 Angle : 0.570 4.779 12340 Z= 0.296 Chirality : 0.044 0.170 1407 Planarity : 0.005 0.049 1598 Dihedral : 4.977 46.670 1358 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.73 % Favored : 92.01 % Rotamer: Outliers : 2.48 % Allowed : 12.95 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.25), residues: 1177 helix: 1.15 (0.97), residues: 34 sheet: -0.47 (0.25), residues: 506 loop : -1.40 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 193 TYR 0.015 0.001 TYR Y 149 PHE 0.018 0.002 PHE L 75 TRP 0.010 0.001 TRP D 239 HIS 0.006 0.001 HIS X 218 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8995) covalent geometry : angle 0.56643 (12316) SS BOND : bond 0.00422 ( 12) SS BOND : angle 1.51468 ( 24) hydrogen bonds : bond 0.03607 ( 243) hydrogen bonds : angle 5.83425 ( 609) Misc. bond : bond 0.00126 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 61 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue ILE 186 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.437 Fit side-chains TARDY: cannot create tardy model for: "THR L 76 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR Z 76 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: D 166 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7875 (tt) REVERT: H 156 VAL cc_start: 0.8894 (OUTLIER) cc_final: 0.8682 (m) REVERT: L 18 ARG cc_start: 0.5944 (tmm-80) cc_final: 0.5710 (ttm170) REVERT: X 230 GLN cc_start: 0.7745 (pm20) cc_final: 0.7516 (pm20) outliers start: 22 outliers final: 19 residues processed: 108 average time/residue: 0.1563 time to fit residues: 25.2008 Evaluate side-chains 110 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 135 TRP Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 184 TRP Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 200 CYS Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain X residue 68 ASP Chi-restraints excluded: chain X residue 162 LEU Chi-restraints excluded: chain X residue 244 THR Chi-restraints excluded: chain Y residue 93 VAL Chi-restraints excluded: chain Y residue 148 ASP Chi-restraints excluded: chain Y residue 179 LEU Chi-restraints excluded: chain Y residue 201 ASN Chi-restraints excluded: chain Z residue 38 ASN Chi-restraints excluded: chain Z residue 125 SER Chi-restraints excluded: chain Z residue 176 THR Chi-restraints excluded: chain Z residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 0.0770 chunk 18 optimal weight: 0.0170 chunk 55 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 35 optimal weight: 0.0030 overall best weight: 0.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.167465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.146960 restraints weight = 40837.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.151440 restraints weight = 21961.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.154288 restraints weight = 13912.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.156126 restraints weight = 9854.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.157297 restraints weight = 7607.176| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3978 r_free = 0.3978 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3978 r_free = 0.3978 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9008 Z= 0.098 Angle : 0.536 5.848 12340 Z= 0.275 Chirality : 0.044 0.167 1407 Planarity : 0.005 0.049 1598 Dihedral : 4.779 45.140 1358 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.44 % Favored : 94.31 % Rotamer: Outliers : 2.14 % Allowed : 13.06 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.25), residues: 1177 helix: 1.23 (0.99), residues: 34 sheet: -0.43 (0.24), residues: 507 loop : -1.28 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 193 TYR 0.009 0.001 TYR Y 149 PHE 0.015 0.001 PHE L 75 TRP 0.010 0.001 TRP D 239 HIS 0.006 0.001 HIS X 218 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8995) covalent geometry : angle 0.53393 (12316) SS BOND : bond 0.00336 ( 12) SS BOND : angle 1.12408 ( 24) hydrogen bonds : bond 0.03196 ( 243) hydrogen bonds : angle 5.53145 ( 609) Misc. bond : bond 0.00262 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2988.11 seconds wall clock time: 51 minutes 49.77 seconds (3109.77 seconds total)