Starting phenix.real_space_refine on Fri Jan 17 00:55:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uwl_26835/01_2025/7uwl_26835.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uwl_26835/01_2025/7uwl_26835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uwl_26835/01_2025/7uwl_26835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uwl_26835/01_2025/7uwl_26835.map" model { file = "/net/cci-nas-00/data/ceres_data/7uwl_26835/01_2025/7uwl_26835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uwl_26835/01_2025/7uwl_26835.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 6326 2.51 5 N 1792 2.21 5 O 1902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 10100 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 88} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 88} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 232} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1947 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 234} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2180 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 252} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2186 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 252} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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 Chain: "B" 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 Chain: "C" 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: "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: "E" 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: "F" 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 Time building chain proxies: 6.94, per 1000 atoms: 0.69 Number of scatterers: 10100 At special positions: 0 Unit cell: (201.948, 95.4352, 100.548, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 1902 8.00 N 1792 7.00 C 6326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 112 " distance=2.03 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 112 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 99 " distance=2.05 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 187 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 257 " - pdb=" SG CYS C 261 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 102 " distance=2.04 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 99 " distance=2.05 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 187 " - pdb=" SG CYS D 271 " distance=2.03 Simple disulfide: pdb=" SG CYS D 257 " - pdb=" SG CYS D 261 " distance=2.06 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 50 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 185 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 245 " - pdb=" SG CYS E 276 " distance=2.03 Simple disulfide: pdb=" SG CYS E 290 " - pdb=" SG CYS E 294 " distance=2.04 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 50 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 185 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 245 " - pdb=" SG CYS F 276 " distance=2.03 Simple disulfide: pdb=" SG CYS F 290 " - pdb=" SG CYS F 294 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 301 " - " ASN A 136 " " NAG B 301 " - " ASN B 136 " " NAG C 401 " - " ASN C 156 " " NAG C 402 " - " ASN C 67 " " NAG C 403 " - " ASN C 103 " " NAG D 401 " - " ASN D 103 " " NAG D 402 " - " ASN D 156 " " NAG D 403 " - " ASN D 67 " " NAG E 401 " - " ASN E 225 " " NAG E 402 " - " ASN E 265 " " NAG E 403 " - " ASN E 67 " " NAG F 401 " - " ASN F 67 " " NAG F 402 " - " ASN F 225 " " NAG F 403 " - " ASN F 265 " " NAG G 1 " - " ASN C 197 " " NAG H 1 " - " ASN C 183 " " NAG I 1 " - " ASN D 197 " " NAG J 1 " - " ASN D 183 " Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 1.2 seconds 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2360 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 25 sheets defined 7.5% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.510A pdb=" N SER A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'C' and resid 31 through 36 removed outlier: 4.327A pdb=" N MET C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU C 36 " --> pdb=" O PRO C 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 31 through 36' Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 254 through 258 removed outlier: 3.543A pdb=" N CYS C 257 " --> pdb=" O PHE C 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 36 removed outlier: 4.305A pdb=" N MET D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU D 36 " --> pdb=" O PRO D 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 31 through 36' Processing helix chain 'D' and resid 164 through 168 removed outlier: 3.822A pdb=" N LYS D 168 " --> pdb=" O HIS D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 176 removed outlier: 3.748A pdb=" N LYS D 175 " --> pdb=" O LYS D 171 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 109 removed outlier: 3.525A pdb=" N LEU E 109 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 192 removed outlier: 3.725A pdb=" N VAL E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 197 Processing helix chain 'E' and resid 256 through 260 Processing helix chain 'F' and resid 103 through 109 removed outlier: 3.590A pdb=" N ILE F 106 " --> pdb=" O ASP F 103 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU F 109 " --> pdb=" O ILE F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 192 removed outlier: 4.206A pdb=" N VAL F 192 " --> pdb=" O ALA F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 198 Processing helix chain 'F' and resid 256 through 260 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96 Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 116 removed outlier: 3.790A pdb=" N CYS A 115 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 131 Processing sheet with id=AA5, first strand: chain 'A' and resid 134 through 143 removed outlier: 3.615A pdb=" N VAL A 164 " --> pdb=" O HIS A 135 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 175 through 176 removed outlier: 7.462A pdb=" N MET A 176 " --> pdb=" O LYS D 265 " (cutoff:3.500A) removed outlier: 9.757A pdb=" N THR D 267 " --> pdb=" O MET A 176 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS D 264 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ILE D 211 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE D 217 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 175 through 176 removed outlier: 7.462A pdb=" N MET A 176 " --> pdb=" O LYS D 265 " (cutoff:3.500A) removed outlier: 9.757A pdb=" N THR D 267 " --> pdb=" O MET A 176 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ILE D 184 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N VAL D 269 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA D 186 " --> pdb=" O VAL D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.631A pdb=" N ARG B 91 " --> pdb=" O ARG B 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 95 through 96 Processing sheet with id=AB1, first strand: chain 'B' and resid 129 through 141 removed outlier: 4.151A pdb=" N ALA B 167 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N HIS B 135 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N SER B 165 " --> pdb=" O HIS B 135 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLN B 137 " --> pdb=" O ARG B 163 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ARG B 163 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL B 139 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LEU B 161 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N TYR B 141 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG B 159 " --> pdb=" O TYR B 141 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 175 through 176 removed outlier: 3.690A pdb=" N LYS C 265 " --> pdb=" O MET B 176 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR C 207 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA C 209 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER C 220 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE C 211 " --> pdb=" O GLY C 218 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY C 218 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 175 through 176 removed outlier: 3.690A pdb=" N LYS C 265 " --> pdb=" O MET B 176 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ILE C 184 " --> pdb=" O LYS C 265 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N THR C 267 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA C 186 " --> pdb=" O THR C 267 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 22 through 24 removed outlier: 3.520A pdb=" N GLN C 23 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER C 98 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL C 88 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C 100 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 86 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA C 83 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C 138 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET C 153 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.951A pdb=" N THR C 55 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER C 63 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C 68 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR C 123 " --> pdb=" O VAL C 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 22 through 24 removed outlier: 3.864A pdb=" N SER D 98 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL D 88 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS D 102 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL D 133 " --> pdb=" O LYS D 91 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA D 138 " --> pdb=" O MET D 153 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N MET D 153 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 47 through 54 removed outlier: 3.677A pdb=" N GLY D 125 " --> pdb=" O MET D 66 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL D 68 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR D 123 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP D 70 " --> pdb=" O PHE D 121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 206 through 207 removed outlier: 3.641A pdb=" N TYR D 207 " --> pdb=" O VAL D 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 74 through 83 removed outlier: 5.245A pdb=" N ASP E 75 " --> pdb=" O THR E 99 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 125 through 128 removed outlier: 3.821A pdb=" N VAL E 159 " --> pdb=" O LYS E 178 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS E 178 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN E 176 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 208 through 210 removed outlier: 3.694A pdb=" N ARG E 218 " --> pdb=" O GLU E 210 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 246 through 252 removed outlier: 3.768A pdb=" N PHE E 246 " --> pdb=" O SER E 236 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 74 through 83 removed outlier: 5.117A pdb=" N ASP F 75 " --> pdb=" O THR F 99 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 124 through 128 removed outlier: 3.684A pdb=" N GLY F 111 " --> pdb=" O LEU F 164 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL F 159 " --> pdb=" O LYS F 178 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN F 176 " --> pdb=" O VAL F 161 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 208 through 210 Processing sheet with id=AC7, first strand: chain 'F' and resid 246 through 252 removed outlier: 3.734A pdb=" N PHE F 246 " --> pdb=" O SER F 236 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN F 231 " --> pdb=" O GLN F 284 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN F 284 " --> pdb=" O GLN F 231 " (cutoff:3.500A) 256 hydrogen bonds defined for protein. 627 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: 2.63 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1601 1.32 - 1.44: 2926 1.44 - 1.57: 5727 1.57 - 1.70: 0 1.70 - 1.83: 104 Bond restraints: 10358 Sorted by residual: bond pdb=" CD GLN E 231 " pdb=" NE2 GLN E 231 " ideal model delta sigma weight residual 1.328 1.230 0.098 2.10e-02 2.27e+03 2.16e+01 bond pdb=" C1 NAG F 402 " pdb=" O5 NAG F 402 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C1 NAG E 401 " pdb=" O5 NAG E 401 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" N THR F 69 " pdb=" CA THR F 69 " ideal model delta sigma weight residual 1.455 1.500 -0.045 1.60e-02 3.91e+03 7.79e+00 bond pdb=" N CYS D 102 " pdb=" CA CYS D 102 " ideal model delta sigma weight residual 1.455 1.489 -0.033 1.23e-02 6.61e+03 7.39e+00 ... (remaining 10353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 13597 1.96 - 3.92: 434 3.92 - 5.87: 47 5.87 - 7.83: 10 7.83 - 9.79: 5 Bond angle restraints: 14093 Sorted by residual: angle pdb=" C SER C 98 " pdb=" N CYS C 99 " pdb=" CA CYS C 99 " ideal model delta sigma weight residual 121.87 115.24 6.63 1.64e+00 3.72e-01 1.64e+01 angle pdb=" C LEU F 212 " pdb=" CA LEU F 212 " pdb=" CB LEU F 212 " ideal model delta sigma weight residual 116.34 110.90 5.44 1.40e+00 5.10e-01 1.51e+01 angle pdb=" C CYS D 102 " pdb=" CA CYS D 102 " pdb=" CB CYS D 102 " ideal model delta sigma weight residual 109.37 102.55 6.82 1.91e+00 2.74e-01 1.27e+01 angle pdb=" CA CYS C 102 " pdb=" C CYS C 102 " pdb=" O CYS C 102 " ideal model delta sigma weight residual 121.11 117.38 3.73 1.13e+00 7.83e-01 1.09e+01 angle pdb=" N CYS C 99 " pdb=" CA CYS C 99 " pdb=" C CYS C 99 " ideal model delta sigma weight residual 108.96 113.67 -4.71 1.49e+00 4.50e-01 9.99e+00 ... (remaining 14088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.62: 5959 23.62 - 47.24: 528 47.24 - 70.87: 81 70.87 - 94.49: 9 94.49 - 118.11: 6 Dihedral angle restraints: 6583 sinusoidal: 2965 harmonic: 3618 Sorted by residual: dihedral pdb=" CB CYS C 162 " pdb=" SG CYS C 162 " pdb=" SG CYS C 173 " pdb=" CB CYS C 173 " ideal model delta sinusoidal sigma weight residual -86.00 -176.12 90.12 1 1.00e+01 1.00e-02 9.62e+01 dihedral pdb=" CB CYS D 87 " pdb=" SG CYS D 87 " pdb=" SG CYS D 99 " pdb=" CB CYS D 99 " ideal model delta sinusoidal sigma weight residual 93.00 14.71 78.29 1 1.00e+01 1.00e-02 7.65e+01 dihedral pdb=" CB CYS C 87 " pdb=" SG CYS C 87 " pdb=" SG CYS C 99 " pdb=" CB CYS C 99 " ideal model delta sinusoidal sigma weight residual 93.00 38.21 54.79 1 1.00e+01 1.00e-02 4.06e+01 ... (remaining 6580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1223 0.048 - 0.097: 291 0.097 - 0.145: 99 0.145 - 0.193: 10 0.193 - 0.241: 8 Chirality restraints: 1631 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 6.24e+00 chirality pdb=" CA CYS D 102 " pdb=" N CYS D 102 " pdb=" C CYS D 102 " pdb=" CB CYS D 102 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA CYS D 87 " pdb=" N CYS D 87 " pdb=" C CYS D 87 " pdb=" CB CYS D 87 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1628 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN E 231 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" CD GLN E 231 " -0.063 2.00e-02 2.50e+03 pdb=" OE1 GLN E 231 " 0.024 2.00e-02 2.50e+03 pdb=" NE2 GLN E 231 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 156 " -0.023 2.00e-02 2.50e+03 2.82e-02 9.95e+00 pdb=" CG ASN C 156 " 0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN C 156 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN C 156 " -0.004 2.00e-02 2.50e+03 pdb=" C1 NAG C 401 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 156 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.03e+00 pdb=" CG ASN C 156 " 0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN C 156 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN C 156 " -0.017 2.00e-02 2.50e+03 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 296 2.69 - 3.24: 9298 3.24 - 3.79: 14646 3.79 - 4.35: 18403 4.35 - 4.90: 30313 Nonbonded interactions: 72956 Sorted by model distance: nonbonded pdb=" OG1 THR F 85 " pdb=" O ASP F 89 " model vdw 2.137 3.040 nonbonded pdb=" OD1 ASP F 89 " pdb=" OG1 THR F 194 " model vdw 2.164 3.040 nonbonded pdb=" OD1 ASP A 97 " pdb=" N LEU A 98 " model vdw 2.166 3.120 nonbonded pdb=" NE2 GLN E 231 " pdb=" OE1 GLN E 284 " model vdw 2.169 3.120 nonbonded pdb=" O SER B 88 " pdb=" OG SER B 88 " model vdw 2.217 3.040 ... (remaining 72951 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 19 through 272 or resid 401 through 403)) } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 33 through 123 or (resid 124 and (name N or name CA or nam \ e C or name O or name CB )) or resid 125 through 303 or resid 401 through 403)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.780 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 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 : 0.005 0.098 10358 Z= 0.314 Angle : 0.780 9.792 14093 Z= 0.396 Chirality : 0.049 0.241 1631 Planarity : 0.005 0.042 1800 Dihedral : 16.739 118.111 4145 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.63 % Allowed : 23.99 % Favored : 75.38 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.23), residues: 1216 helix: -1.68 (0.99), residues: 26 sheet: -0.13 (0.24), residues: 487 loop : -1.52 (0.21), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 70 HIS 0.021 0.001 HIS E 139 PHE 0.010 0.001 PHE F 180 TYR 0.027 0.003 TYR C 253 ARG 0.019 0.001 ARG F 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 276 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.7193 (p-80) cc_final: 0.6918 (p-80) REVERT: D 265 LYS cc_start: 0.8081 (mtmt) cc_final: 0.7853 (mtmt) REVERT: F 142 TRP cc_start: 0.7501 (m100) cc_final: 0.6586 (m100) REVERT: F 154 ASP cc_start: 0.7543 (t0) cc_final: 0.7318 (m-30) outliers start: 7 outliers final: 4 residues processed: 279 average time/residue: 0.2848 time to fit residues: 104.4486 Evaluate side-chains 271 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 267 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 212 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 0.0770 chunk 49 optimal weight: 1.9990 chunk 95 optimal weight: 0.0060 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 0.2980 chunk 71 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 overall best weight: 0.3154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN C 143 ASN D 93 ASN D 131 ASN E 45 GLN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 HIS ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN ** F 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN F 231 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.201019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.157242 restraints weight = 17897.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.162209 restraints weight = 9419.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.165546 restraints weight = 5854.449| |-----------------------------------------------------------------------------| r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10358 Z= 0.202 Angle : 0.718 9.860 14093 Z= 0.350 Chirality : 0.046 0.263 1631 Planarity : 0.005 0.042 1800 Dihedral : 10.691 97.254 1807 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.97 % Allowed : 21.37 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.23), residues: 1216 helix: -1.76 (0.99), residues: 26 sheet: -0.03 (0.23), residues: 533 loop : -1.63 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 70 HIS 0.008 0.001 HIS E 148 PHE 0.009 0.001 PHE E 149 TYR 0.022 0.002 TYR F 157 ARG 0.012 0.000 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 273 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.6736 (OUTLIER) cc_final: 0.6429 (p-80) REVERT: A 163 ARG cc_start: 0.7394 (tpp80) cc_final: 0.6992 (ttt90) REVERT: C 155 VAL cc_start: 0.7122 (OUTLIER) cc_final: 0.6776 (m) REVERT: C 230 GLN cc_start: 0.5880 (OUTLIER) cc_final: 0.5513 (tm-30) REVERT: D 193 THR cc_start: 0.8378 (m) cc_final: 0.7864 (p) REVERT: D 265 LYS cc_start: 0.7895 (mtmt) cc_final: 0.7674 (mtmt) REVERT: F 79 GLN cc_start: 0.6675 (mm-40) cc_final: 0.6269 (tm-30) REVERT: F 80 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7452 (mt) REVERT: F 142 TRP cc_start: 0.7468 (m100) cc_final: 0.6580 (m100) REVERT: F 147 SER cc_start: 0.7898 (t) cc_final: 0.7688 (t) REVERT: F 212 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5746 (tt) outliers start: 44 outliers final: 24 residues processed: 295 average time/residue: 0.2673 time to fit residues: 103.6950 Evaluate side-chains 297 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 268 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 212 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 52 optimal weight: 0.0770 chunk 119 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 10 optimal weight: 0.0070 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN D 93 ASN D 131 ASN E 45 GLN E 79 GLN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 HIS F 175 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.199467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.155078 restraints weight = 18124.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.160157 restraints weight = 9561.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.163455 restraints weight = 5918.740| |-----------------------------------------------------------------------------| r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10358 Z= 0.221 Angle : 0.704 10.354 14093 Z= 0.343 Chirality : 0.046 0.266 1631 Planarity : 0.005 0.044 1800 Dihedral : 10.366 94.052 1806 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.60 % Allowed : 22.72 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.23), residues: 1216 helix: -1.60 (0.98), residues: 26 sheet: -0.15 (0.23), residues: 525 loop : -1.57 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 70 HIS 0.009 0.001 HIS E 148 PHE 0.012 0.001 PHE E 149 TYR 0.015 0.002 TYR D 253 ARG 0.007 0.000 ARG F 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 268 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.6639 (OUTLIER) cc_final: 0.6269 (p-80) REVERT: A 163 ARG cc_start: 0.7427 (tpp80) cc_final: 0.6978 (ttt90) REVERT: A 166 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6431 (mp) REVERT: B 124 MET cc_start: 0.5430 (ppp) cc_final: 0.5174 (ppp) REVERT: C 155 VAL cc_start: 0.7024 (OUTLIER) cc_final: 0.6683 (m) REVERT: C 230 GLN cc_start: 0.5808 (OUTLIER) cc_final: 0.5464 (tm-30) REVERT: C 265 LYS cc_start: 0.8011 (tmtt) cc_final: 0.7797 (tmtt) REVERT: D 193 THR cc_start: 0.8346 (m) cc_final: 0.7851 (p) REVERT: F 142 TRP cc_start: 0.7458 (m100) cc_final: 0.6634 (m100) REVERT: F 197 MET cc_start: 0.5195 (tpp) cc_final: 0.4992 (tpp) REVERT: F 212 LEU cc_start: 0.6074 (OUTLIER) cc_final: 0.5802 (tt) outliers start: 51 outliers final: 31 residues processed: 291 average time/residue: 0.2715 time to fit residues: 103.9231 Evaluate side-chains 298 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 262 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 281 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.5727 > 50: distance: 62 - 128: 26.054 distance: 65 - 125: 33.129 distance: 71 - 108: 21.080 distance: 74 - 105: 17.388 distance: 100 - 105: 18.551 distance: 105 - 106: 42.091 distance: 106 - 107: 15.367 distance: 106 - 109: 22.616 distance: 107 - 108: 10.810 distance: 107 - 115: 19.004 distance: 109 - 110: 23.293 distance: 110 - 111: 23.692 distance: 110 - 112: 16.564 distance: 113 - 114: 40.125 distance: 115 - 116: 30.628 distance: 116 - 117: 36.336 distance: 116 - 119: 15.726 distance: 117 - 118: 16.833 distance: 117 - 125: 32.000 distance: 119 - 120: 17.160 distance: 120 - 122: 12.977 distance: 121 - 123: 14.662 distance: 122 - 124: 10.511 distance: 123 - 124: 11.721 distance: 125 - 126: 9.955 distance: 126 - 127: 9.225 distance: 126 - 129: 8.529 distance: 127 - 128: 13.163 distance: 127 - 133: 22.474 distance: 129 - 130: 11.578 distance: 130 - 131: 3.284 distance: 130 - 132: 20.985 distance: 133 - 134: 4.701 distance: 133 - 139: 13.920 distance: 134 - 135: 29.212 distance: 134 - 137: 46.958 distance: 135 - 136: 24.959 distance: 135 - 140: 30.972 distance: 137 - 138: 39.728 distance: 138 - 139: 40.831 distance: 140 - 141: 33.683 distance: 141 - 142: 8.912 distance: 141 - 144: 21.063 distance: 142 - 143: 19.465 distance: 142 - 149: 44.881 distance: 144 - 145: 15.931 distance: 145 - 146: 25.973 distance: 146 - 147: 26.286 distance: 149 - 150: 32.852 distance: 149 - 155: 18.562 distance: 150 - 151: 24.070 distance: 150 - 153: 16.929 distance: 151 - 152: 14.695 distance: 151 - 156: 13.231 distance: 153 - 154: 23.449 distance: 154 - 155: 33.974 distance: 156 - 157: 39.824 distance: 157 - 158: 41.232 distance: 157 - 160: 9.391 distance: 158 - 159: 32.663 distance: 160 - 161: 13.654 distance: 160 - 162: 22.512 distance: 161 - 163: 26.885 distance: 164 - 170: 40.204 distance: 166 - 171: 34.552 distance: 168 - 169: 13.376 distance: 169 - 170: 25.888 distance: 171 - 172: 8.070 distance: 172 - 173: 49.527 distance: 172 - 175: 11.233 distance: 173 - 174: 6.465 distance: 173 - 179: 47.448 distance: 179 - 180: 38.970 distance: 180 - 181: 27.798 distance: 181 - 182: 28.614 distance: 181 - 183: 17.074