Starting phenix.real_space_refine on Wed Mar 4 22:55:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ley_23294/03_2026/7ley_23294.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ley_23294/03_2026/7ley_23294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ley_23294/03_2026/7ley_23294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ley_23294/03_2026/7ley_23294.map" model { file = "/net/cci-nas-00/data/ceres_data/7ley_23294/03_2026/7ley_23294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ley_23294/03_2026/7ley_23294.cif" } resolution = 3.05 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= 0.009 sd= 0.071 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 Mn 6 7.51 5 S 63 5.16 5 C 10746 2.51 5 N 2931 2.21 5 O 3363 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17109 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "D" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1660 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1632 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 202} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1632 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 202} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1632 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 202} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "C" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "G" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1660 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1660 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.45, per 1000 atoms: 0.20 Number of scatterers: 17109 At special positions: 0 Unit cell: (136.24, 139.36, 123.76, 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) Mn 6 24.99 S 63 16.00 O 3363 8.00 N 2931 7.00 C 10746 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.02 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.02 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 150 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 205 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 770.6 milliseconds 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4098 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 30 sheets defined 19.9% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 23 through 25 No H-bonds generated for 'chain 'A' and resid 23 through 25' Processing helix chain 'A' and resid 26 through 34 removed outlier: 3.880A pdb=" N VAL A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 69 through 90 removed outlier: 3.627A pdb=" N VAL A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.620A pdb=" N HIS A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 183 through 193 Processing helix chain 'A' and resid 199 through 220 removed outlier: 6.871A pdb=" N ILE A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N GLY A 209 " --> pdb=" O ARG A 205 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 267 removed outlier: 3.548A pdb=" N THR A 267 " --> pdb=" O GLU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 304 removed outlier: 3.606A pdb=" N PHE A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 182 through 189 removed outlier: 3.640A pdb=" N ARG E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N HIS E 189 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 123 through 127 Processing helix chain 'F' and resid 182 through 189 removed outlier: 3.639A pdb=" N ARG F 188 " --> pdb=" O ASP F 184 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N HIS F 189 " --> pdb=" O GLU F 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'I' and resid 123 through 127 Processing helix chain 'I' and resid 182 through 189 removed outlier: 3.639A pdb=" N ARG I 188 " --> pdb=" O ASP I 184 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N HIS I 189 " --> pdb=" O GLU I 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 25 No H-bonds generated for 'chain 'B' and resid 23 through 25' Processing helix chain 'B' and resid 26 through 34 removed outlier: 3.880A pdb=" N VAL B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 69 through 90 removed outlier: 3.627A pdb=" N VAL B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.620A pdb=" N HIS B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 183 through 193 Processing helix chain 'B' and resid 199 through 220 removed outlier: 6.871A pdb=" N ILE B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N GLY B 209 " --> pdb=" O ARG B 205 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 267 removed outlier: 3.548A pdb=" N THR B 267 " --> pdb=" O GLU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 304 removed outlier: 3.606A pdb=" N PHE B 304 " --> pdb=" O THR B 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 25 No H-bonds generated for 'chain 'C' and resid 23 through 25' Processing helix chain 'C' and resid 26 through 34 removed outlier: 3.880A pdb=" N VAL C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 41 Processing helix chain 'C' and resid 69 through 90 removed outlier: 3.627A pdb=" N VAL C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.621A pdb=" N HIS C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL C 114 " --> pdb=" O GLY C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 183 through 193 Processing helix chain 'C' and resid 199 through 220 removed outlier: 6.871A pdb=" N ILE C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N GLY C 209 " --> pdb=" O ARG C 205 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS C 210 " --> pdb=" O LEU C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 267 removed outlier: 3.549A pdb=" N THR C 267 " --> pdb=" O GLU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 304 removed outlier: 3.605A pdb=" N PHE C 304 " --> pdb=" O THR C 300 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 52 removed outlier: 6.671A pdb=" N ILE A 8 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N TYR A 50 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE A 10 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASP A 52 " --> pdb=" O ILE A 10 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLY A 12 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER A 94 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE A 227 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LEU A 273 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 229 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE A 275 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N PHE A 231 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLY A 119 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N SER A 230 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE A 121 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASP A 232 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 123 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A 120 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ILE A 177 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP A 122 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE A 174 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N PHE A 198 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TYR A 176 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA3, first strand: chain 'D' and resid 59 through 60 removed outlier: 6.766A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 130 through 131 removed outlier: 3.629A pdb=" N LEU D 148 " --> pdb=" O THR D 192 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER D 190 " --> pdb=" O CYS D 150 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY D 154 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N THR D 186 " --> pdb=" O GLY D 154 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER D 189 " --> pdb=" O PRO D 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 161 through 164 Processing sheet with id=AA6, first strand: chain 'E' and resid 5 through 6 removed outlier: 4.185A pdb=" N PHE E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER E 65 " --> pdb=" O THR E 72 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'E' and resid 35 through 37 removed outlier: 6.441A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 114 through 118 removed outlier: 3.748A pdb=" N ASN E 137 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER E 174 " --> pdb=" O THR E 164 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 153 through 154 removed outlier: 3.821A pdb=" N THR E 193 " --> pdb=" O LYS E 149 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 5 through 6 removed outlier: 4.186A pdb=" N PHE F 71 " --> pdb=" O CYS F 23 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER F 65 " --> pdb=" O THR F 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AB4, first strand: chain 'F' and resid 35 through 37 removed outlier: 6.441A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 114 through 118 removed outlier: 3.748A pdb=" N ASN F 137 " --> pdb=" O THR F 114 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR F 173 " --> pdb=" O ASN F 138 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER F 174 " --> pdb=" O THR F 164 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 153 through 154 removed outlier: 3.820A pdb=" N THR F 193 " --> pdb=" O LYS F 149 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 5 through 6 removed outlier: 4.185A pdb=" N PHE I 71 " --> pdb=" O CYS I 23 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER I 65 " --> pdb=" O THR I 72 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 10 through 12 Processing sheet with id=AB9, first strand: chain 'I' and resid 35 through 37 removed outlier: 6.440A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 114 through 118 removed outlier: 3.748A pdb=" N ASN I 137 " --> pdb=" O THR I 114 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N TYR I 173 " --> pdb=" O ASN I 138 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER I 174 " --> pdb=" O THR I 164 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 153 through 154 removed outlier: 3.820A pdb=" N THR I 193 " --> pdb=" O LYS I 149 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 52 removed outlier: 6.671A pdb=" N ILE B 8 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N TYR B 50 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE B 10 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASP B 52 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLY B 12 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER B 94 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE B 227 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LEU B 273 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU B 229 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE B 275 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N PHE B 231 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY B 119 " --> pdb=" O HIS B 228 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N SER B 230 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE B 121 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASP B 232 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL B 123 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B 120 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ILE B 177 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP B 122 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE B 174 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N PHE B 198 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TYR B 176 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 48 through 52 removed outlier: 6.670A pdb=" N ILE C 8 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N TYR C 50 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE C 10 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASP C 52 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLY C 12 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER C 94 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE C 227 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LEU C 273 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU C 229 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE C 275 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N PHE C 231 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLY C 119 " --> pdb=" O HIS C 228 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N SER C 230 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE C 121 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASP C 232 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL C 123 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL C 120 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE C 177 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP C 122 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE C 174 " --> pdb=" O LYS C 196 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE C 198 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR C 176 " --> pdb=" O PHE C 198 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'G' and resid 59 through 60 removed outlier: 6.766A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 130 through 131 removed outlier: 3.629A pdb=" N LEU G 148 " --> pdb=" O THR G 192 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER G 190 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY G 154 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N THR G 186 " --> pdb=" O GLY G 154 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER G 189 " --> pdb=" O PRO G 177 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 161 through 164 Processing sheet with id=AC9, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'H' and resid 59 through 60 removed outlier: 6.767A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 130 through 131 removed outlier: 3.630A pdb=" N LEU H 148 " --> pdb=" O THR H 192 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER H 190 " --> pdb=" O CYS H 150 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY H 154 " --> pdb=" O THR H 186 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR H 186 " --> pdb=" O GLY H 154 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N SER H 189 " --> pdb=" O PRO H 177 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 161 through 164 507 hydrogen bonds defined for protein. 1323 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: 2.10 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5442 1.33 - 1.45: 2597 1.45 - 1.57: 9343 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 17472 Sorted by residual: bond pdb=" C VAL B 165 " pdb=" N THR B 166 " ideal model delta sigma weight residual 1.333 1.289 0.044 1.61e-02 3.86e+03 7.58e+00 bond pdb=" C VAL A 165 " pdb=" N THR A 166 " ideal model delta sigma weight residual 1.333 1.289 0.044 1.61e-02 3.86e+03 7.45e+00 bond pdb=" C VAL C 165 " pdb=" N THR C 166 " ideal model delta sigma weight residual 1.333 1.289 0.044 1.61e-02 3.86e+03 7.44e+00 bond pdb=" CB ASN G 52 " pdb=" CG ASN G 52 " ideal model delta sigma weight residual 1.516 1.453 0.063 2.50e-02 1.60e+03 6.38e+00 bond pdb=" CB ASN H 52 " pdb=" CG ASN H 52 " ideal model delta sigma weight residual 1.516 1.453 0.063 2.50e-02 1.60e+03 6.26e+00 ... (remaining 17467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 23478 3.51 - 7.01: 255 7.01 - 10.52: 12 10.52 - 14.03: 3 14.03 - 17.53: 3 Bond angle restraints: 23751 Sorted by residual: angle pdb=" CB MET C 200 " pdb=" CG MET C 200 " pdb=" SD MET C 200 " ideal model delta sigma weight residual 112.70 130.23 -17.53 3.00e+00 1.11e-01 3.42e+01 angle pdb=" CB MET B 200 " pdb=" CG MET B 200 " pdb=" SD MET B 200 " ideal model delta sigma weight residual 112.70 130.20 -17.50 3.00e+00 1.11e-01 3.40e+01 angle pdb=" CB MET A 200 " pdb=" CG MET A 200 " pdb=" SD MET A 200 " ideal model delta sigma weight residual 112.70 130.16 -17.46 3.00e+00 1.11e-01 3.39e+01 angle pdb=" N PRO G 128 " pdb=" CD PRO G 128 " pdb=" CG PRO G 128 " ideal model delta sigma weight residual 103.20 97.48 5.72 1.50e+00 4.44e-01 1.46e+01 angle pdb=" N PRO D 128 " pdb=" CD PRO D 128 " pdb=" CG PRO D 128 " ideal model delta sigma weight residual 103.20 97.52 5.68 1.50e+00 4.44e-01 1.44e+01 ... (remaining 23746 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.51: 9562 15.51 - 31.01: 695 31.01 - 46.52: 189 46.52 - 62.03: 42 62.03 - 77.53: 12 Dihedral angle restraints: 10500 sinusoidal: 4071 harmonic: 6429 Sorted by residual: dihedral pdb=" CB CYS G 150 " pdb=" SG CYS G 150 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual 93.00 170.53 -77.53 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS D 150 " pdb=" SG CYS D 150 " pdb=" SG CYS D 205 " pdb=" CB CYS D 205 " ideal model delta sinusoidal sigma weight residual 93.00 170.52 -77.52 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS H 150 " pdb=" SG CYS H 150 " pdb=" SG CYS H 205 " pdb=" CB CYS H 205 " ideal model delta sinusoidal sigma weight residual 93.00 170.50 -77.50 1 1.00e+01 1.00e-02 7.52e+01 ... (remaining 10497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1460 0.038 - 0.077: 809 0.077 - 0.115: 336 0.115 - 0.153: 89 0.153 - 0.191: 9 Chirality restraints: 2703 Sorted by residual: chirality pdb=" CB THR G 28 " pdb=" CA THR G 28 " pdb=" OG1 THR G 28 " pdb=" CG2 THR G 28 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.14e-01 chirality pdb=" CB THR H 28 " pdb=" CA THR H 28 " pdb=" OG1 THR H 28 " pdb=" CG2 THR H 28 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.14e-01 chirality pdb=" CB THR D 28 " pdb=" CA THR D 28 " pdb=" OG1 THR D 28 " pdb=" CG2 THR D 28 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.93e-01 ... (remaining 2700 not shown) Planarity restraints: 3069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 139 " -0.032 2.00e-02 2.50e+03 3.04e-02 1.62e+01 pdb=" CG PHE E 139 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE E 139 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE E 139 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE E 139 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE E 139 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE E 139 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 139 " 0.032 2.00e-02 2.50e+03 3.02e-02 1.60e+01 pdb=" CG PHE I 139 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE I 139 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE I 139 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE I 139 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE I 139 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE I 139 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 139 " -0.032 2.00e-02 2.50e+03 3.02e-02 1.59e+01 pdb=" CG PHE F 139 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE F 139 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE F 139 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE F 139 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE F 139 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE F 139 " -0.007 2.00e-02 2.50e+03 ... (remaining 3066 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 86 2.33 - 2.97: 9458 2.97 - 3.61: 25602 3.61 - 4.26: 42107 4.26 - 4.90: 69778 Nonbonded interactions: 147031 Sorted by model distance: nonbonded pdb=" OD2 ASP A 124 " pdb="MN MN A1001 " model vdw 1.683 2.320 nonbonded pdb=" OD2 ASP C 124 " pdb="MN MN C1001 " model vdw 1.684 2.320 nonbonded pdb=" OD2 ASP B 124 " pdb="MN MN B1001 " model vdw 1.684 2.320 nonbonded pdb=" OD1 ASP A 124 " pdb="MN MN A1002 " model vdw 1.766 2.320 nonbonded pdb=" OD1 ASP B 124 " pdb="MN MN B1002 " model vdw 1.766 2.320 ... (remaining 147026 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 14.290 Find NCS groups from input model: 0.090 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.077 17484 Z= 0.427 Angle : 0.975 17.533 23775 Z= 0.521 Chirality : 0.053 0.191 2703 Planarity : 0.007 0.092 3069 Dihedral : 12.242 75.264 6366 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.14 % Favored : 87.59 % Rotamer: Outliers : 1.74 % Allowed : 1.37 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.28 % Twisted Proline : 2.17 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.17), residues: 2241 helix: -0.10 (0.26), residues: 378 sheet: -2.48 (0.19), residues: 660 loop : -2.43 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG I 24 TYR 0.028 0.002 TYR D 32 PHE 0.070 0.003 PHE E 139 TRP 0.024 0.003 TRP D 113 HIS 0.019 0.002 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00997 (17472) covalent geometry : angle 0.97419 (23751) SS BOND : bond 0.00618 ( 12) SS BOND : angle 1.42419 ( 24) hydrogen bonds : bond 0.22356 ( 507) hydrogen bonds : angle 9.54074 ( 1323) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 132 TYR cc_start: 0.5415 (m-80) cc_final: 0.5053 (m-80) REVERT: C 21 ARG cc_start: 0.8202 (ptt180) cc_final: 0.7777 (ptt180) REVERT: G 80 TYR cc_start: 0.8152 (m-80) cc_final: 0.7666 (m-10) REVERT: G 187 LEU cc_start: 0.8477 (mt) cc_final: 0.7973 (tt) REVERT: H 187 LEU cc_start: 0.8395 (mt) cc_final: 0.7963 (tt) outliers start: 33 outliers final: 5 residues processed: 160 average time/residue: 0.1543 time to fit residues: 35.6489 Evaluate side-chains 124 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain E residue 139 PHE Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain H residue 76 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 0.0050 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN D 3 GLN D 165 ASN E 89 GLN B 90 ASN C 90 ASN C 141 HIS G 3 GLN G 39 GLN H 3 GLN H 165 ASN H 206 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.125601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.075762 restraints weight = 30412.587| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.24 r_work: 0.2991 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17484 Z= 0.156 Angle : 0.730 11.128 23775 Z= 0.371 Chirality : 0.048 0.179 2703 Planarity : 0.007 0.087 3069 Dihedral : 6.899 56.571 2442 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.22 % Favored : 89.51 % Rotamer: Outliers : 1.05 % Allowed : 3.84 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.28 % Twisted Proline : 1.45 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.17), residues: 2241 helix: 0.28 (0.27), residues: 384 sheet: -2.10 (0.20), residues: 618 loop : -2.24 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 24 TYR 0.014 0.002 TYR D 32 PHE 0.020 0.002 PHE E 98 TRP 0.019 0.002 TRP D 113 HIS 0.005 0.001 HIS D 209 Details of bonding type rmsd covalent geometry : bond 0.00360 (17472) covalent geometry : angle 0.72959 (23751) SS BOND : bond 0.00579 ( 12) SS BOND : angle 0.97130 ( 24) hydrogen bonds : bond 0.04233 ( 507) hydrogen bonds : angle 6.39081 ( 1323) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8564 (ptt180) cc_final: 0.8097 (ptt180) REVERT: A 212 MET cc_start: 0.8748 (mmm) cc_final: 0.8303 (mmm) REVERT: D 30 ASP cc_start: 0.8864 (p0) cc_final: 0.8365 (p0) REVERT: D 185 TYR cc_start: 0.7791 (m-10) cc_final: 0.7453 (m-10) REVERT: D 220 ILE cc_start: -0.0214 (OUTLIER) cc_final: -0.0810 (tt) REVERT: I 175 MET cc_start: 0.6802 (ttt) cc_final: 0.6567 (tpt) REVERT: I 192 TYR cc_start: 0.6418 (m-80) cc_final: 0.6141 (m-10) REVERT: C 21 ARG cc_start: 0.8719 (ptt180) cc_final: 0.8391 (ptt180) REVERT: G 3 GLN cc_start: 0.8750 (mm110) cc_final: 0.8497 (mp10) REVERT: G 5 VAL cc_start: 0.8618 (t) cc_final: 0.8408 (m) REVERT: H 73 ASP cc_start: 0.8562 (m-30) cc_final: 0.8173 (m-30) REVERT: H 76 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8287 (ptpp) REVERT: H 164 TRP cc_start: 0.5233 (m100) cc_final: 0.4887 (m-10) REVERT: H 215 LYS cc_start: 0.6612 (tttp) cc_final: 0.6388 (tptp) outliers start: 20 outliers final: 11 residues processed: 157 average time/residue: 0.1461 time to fit residues: 34.0051 Evaluate side-chains 145 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 ASN Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 164 TRP Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 99 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 31 optimal weight: 0.9980 chunk 218 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 111 optimal weight: 9.9990 chunk 8 optimal weight: 0.7980 chunk 206 optimal weight: 2.9990 chunk 217 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 179 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS B 141 HIS ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 ASN H 3 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.125350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.076165 restraints weight = 30682.256| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.52 r_work: 0.2975 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17484 Z= 0.167 Angle : 0.680 9.206 23775 Z= 0.344 Chirality : 0.047 0.178 2703 Planarity : 0.006 0.083 3069 Dihedral : 5.996 50.850 2431 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.44 % Favored : 89.29 % Rotamer: Outliers : 1.37 % Allowed : 6.62 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.18), residues: 2241 helix: 0.65 (0.27), residues: 360 sheet: -2.01 (0.20), residues: 642 loop : -2.06 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 21 TYR 0.018 0.002 TYR G 80 PHE 0.013 0.002 PHE I 98 TRP 0.020 0.002 TRP D 164 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00401 (17472) covalent geometry : angle 0.67947 (23751) SS BOND : bond 0.00477 ( 12) SS BOND : angle 1.22836 ( 24) hydrogen bonds : bond 0.03438 ( 507) hydrogen bonds : angle 5.56992 ( 1323) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8658 (ptt180) cc_final: 0.8302 (ptt180) REVERT: A 101 HIS cc_start: 0.8743 (OUTLIER) cc_final: 0.8228 (m170) REVERT: D 30 ASP cc_start: 0.8955 (p0) cc_final: 0.8608 (p0) REVERT: D 146 VAL cc_start: 0.5449 (t) cc_final: 0.5175 (m) REVERT: D 185 TYR cc_start: 0.7833 (m-10) cc_final: 0.7383 (m-10) REVERT: E 81 GLU cc_start: 0.8254 (pp20) cc_final: 0.8051 (pp20) REVERT: E 82 ASP cc_start: 0.7670 (m-30) cc_final: 0.7347 (m-30) REVERT: F 70 ASP cc_start: 0.8910 (p0) cc_final: 0.8705 (p0) REVERT: F 173 TYR cc_start: 0.6687 (m-10) cc_final: 0.6333 (m-10) REVERT: F 175 MET cc_start: 0.5627 (OUTLIER) cc_final: 0.5420 (tpp) REVERT: I 163 TRP cc_start: 0.8167 (m100) cc_final: 0.7704 (m100) REVERT: B 101 HIS cc_start: 0.8755 (OUTLIER) cc_final: 0.8245 (m170) REVERT: B 183 ASP cc_start: 0.8371 (m-30) cc_final: 0.8083 (m-30) REVERT: C 101 HIS cc_start: 0.8789 (OUTLIER) cc_final: 0.8230 (m170) REVERT: G 5 VAL cc_start: 0.8593 (t) cc_final: 0.8379 (m) REVERT: G 34 MET cc_start: 0.9131 (mmm) cc_final: 0.8704 (mmm) REVERT: G 73 ASP cc_start: 0.7952 (t0) cc_final: 0.7659 (t0) REVERT: G 215 LYS cc_start: 0.6398 (tttp) cc_final: 0.5781 (tptt) REVERT: H 73 ASP cc_start: 0.8704 (m-30) cc_final: 0.8408 (m-30) REVERT: H 215 LYS cc_start: 0.6701 (tttp) cc_final: 0.6099 (tptt) outliers start: 26 outliers final: 17 residues processed: 160 average time/residue: 0.1446 time to fit residues: 34.1432 Evaluate side-chains 155 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain H residue 112 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 188 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 218 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 142 optimal weight: 0.9980 chunk 52 optimal weight: 20.0000 chunk 88 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.126182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.078588 restraints weight = 30691.626| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.43 r_work: 0.3004 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17484 Z= 0.145 Angle : 0.639 7.831 23775 Z= 0.323 Chirality : 0.046 0.177 2703 Planarity : 0.006 0.079 3069 Dihedral : 5.627 27.926 2427 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.64 % Favored : 90.09 % Rotamer: Outliers : 1.63 % Allowed : 8.57 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.18), residues: 2241 helix: 0.60 (0.27), residues: 381 sheet: -1.85 (0.20), residues: 642 loop : -2.05 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 24 TYR 0.011 0.001 TYR E 32 PHE 0.011 0.001 PHE F 71 TRP 0.025 0.002 TRP H 164 HIS 0.004 0.001 HIS G 209 Details of bonding type rmsd covalent geometry : bond 0.00349 (17472) covalent geometry : angle 0.63842 (23751) SS BOND : bond 0.00648 ( 12) SS BOND : angle 1.32973 ( 24) hydrogen bonds : bond 0.03105 ( 507) hydrogen bonds : angle 5.20998 ( 1323) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 HIS cc_start: 0.8733 (OUTLIER) cc_final: 0.8257 (m170) REVERT: A 212 MET cc_start: 0.8739 (mmm) cc_final: 0.8314 (mmm) REVERT: D 185 TYR cc_start: 0.7849 (m-10) cc_final: 0.7361 (m-10) REVERT: E 81 GLU cc_start: 0.8236 (pp20) cc_final: 0.8009 (pp20) REVERT: E 139 PHE cc_start: 0.6178 (p90) cc_final: 0.5412 (p90) REVERT: F 70 ASP cc_start: 0.8915 (p0) cc_final: 0.8681 (p0) REVERT: I 163 TRP cc_start: 0.8038 (m100) cc_final: 0.7489 (m100) REVERT: B 246 THR cc_start: 0.9171 (p) cc_final: 0.8885 (p) REVERT: C 101 HIS cc_start: 0.8783 (OUTLIER) cc_final: 0.8238 (m170) REVERT: G 34 MET cc_start: 0.9118 (mmm) cc_final: 0.8706 (mmm) REVERT: G 215 LYS cc_start: 0.6440 (tttp) cc_final: 0.6030 (tptp) REVERT: H 73 ASP cc_start: 0.8683 (m-30) cc_final: 0.8458 (m-30) REVERT: H 187 LEU cc_start: 0.8396 (tt) cc_final: 0.7913 (mt) REVERT: H 215 LYS cc_start: 0.6816 (tttp) cc_final: 0.6498 (tptp) outliers start: 31 outliers final: 18 residues processed: 163 average time/residue: 0.1368 time to fit residues: 33.4727 Evaluate side-chains 151 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain D residue 52 ASN Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 112 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 215 optimal weight: 0.8980 chunk 208 optimal weight: 6.9990 chunk 201 optimal weight: 0.0670 chunk 199 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 chunk 138 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 64 optimal weight: 7.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 3 GLN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.126061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.078706 restraints weight = 30499.875| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.40 r_work: 0.3001 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17484 Z= 0.144 Angle : 0.638 8.475 23775 Z= 0.321 Chirality : 0.046 0.215 2703 Planarity : 0.006 0.075 3069 Dihedral : 5.461 28.199 2427 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.77 % Favored : 90.05 % Rotamer: Outliers : 1.42 % Allowed : 9.83 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.18), residues: 2241 helix: 0.70 (0.27), residues: 381 sheet: -1.85 (0.20), residues: 660 loop : -1.98 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 24 TYR 0.012 0.001 TYR I 32 PHE 0.010 0.001 PHE F 71 TRP 0.023 0.001 TRP F 163 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00345 (17472) covalent geometry : angle 0.63675 (23751) SS BOND : bond 0.00281 ( 12) SS BOND : angle 1.20140 ( 24) hydrogen bonds : bond 0.03002 ( 507) hydrogen bonds : angle 4.95189 ( 1323) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 HIS cc_start: 0.8778 (OUTLIER) cc_final: 0.8327 (m170) REVERT: A 212 MET cc_start: 0.8779 (mmm) cc_final: 0.8268 (mmm) REVERT: D 185 TYR cc_start: 0.7887 (m-10) cc_final: 0.7405 (m-10) REVERT: E 24 ARG cc_start: 0.8562 (ttm110) cc_final: 0.8123 (ttm-80) REVERT: E 81 GLU cc_start: 0.8227 (pp20) cc_final: 0.8008 (pp20) REVERT: E 139 PHE cc_start: 0.6313 (p90) cc_final: 0.5379 (p90) REVERT: F 70 ASP cc_start: 0.8939 (p0) cc_final: 0.8704 (p0) REVERT: F 175 MET cc_start: 0.5339 (tpp) cc_final: 0.4934 (tpt) REVERT: I 163 TRP cc_start: 0.7951 (m100) cc_final: 0.7144 (m100) REVERT: B 246 THR cc_start: 0.9175 (p) cc_final: 0.8885 (p) REVERT: C 101 HIS cc_start: 0.8808 (OUTLIER) cc_final: 0.8277 (m170) REVERT: G 34 MET cc_start: 0.9141 (mmm) cc_final: 0.8707 (mmm) REVERT: G 187 LEU cc_start: 0.8431 (tt) cc_final: 0.7999 (mt) REVERT: G 215 LYS cc_start: 0.6473 (tttp) cc_final: 0.6040 (tptp) REVERT: H 30 ASP cc_start: 0.9009 (p0) cc_final: 0.8776 (p0) REVERT: H 187 LEU cc_start: 0.8408 (tt) cc_final: 0.7920 (mt) REVERT: H 215 LYS cc_start: 0.6871 (tttp) cc_final: 0.6535 (tptp) outliers start: 27 outliers final: 17 residues processed: 152 average time/residue: 0.1333 time to fit residues: 30.8823 Evaluate side-chains 148 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain D residue 52 ASN Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 112 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 95 optimal weight: 4.9990 chunk 195 optimal weight: 0.0980 chunk 43 optimal weight: 0.2980 chunk 73 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 171 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 3 GLN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.126359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.079337 restraints weight = 30484.533| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.40 r_work: 0.3011 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17484 Z= 0.136 Angle : 0.621 7.473 23775 Z= 0.313 Chirality : 0.045 0.190 2703 Planarity : 0.006 0.073 3069 Dihedral : 5.326 27.467 2427 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.42 % Favored : 90.45 % Rotamer: Outliers : 1.21 % Allowed : 10.46 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.18), residues: 2241 helix: 0.77 (0.27), residues: 384 sheet: -1.69 (0.20), residues: 642 loop : -1.93 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 24 TYR 0.020 0.001 TYR G 80 PHE 0.010 0.001 PHE I 71 TRP 0.034 0.002 TRP F 163 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00327 (17472) covalent geometry : angle 0.62049 (23751) SS BOND : bond 0.00395 ( 12) SS BOND : angle 1.17250 ( 24) hydrogen bonds : bond 0.02896 ( 507) hydrogen bonds : angle 4.74913 ( 1323) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 HIS cc_start: 0.8778 (OUTLIER) cc_final: 0.8321 (m170) REVERT: A 212 MET cc_start: 0.8750 (mmm) cc_final: 0.8213 (mmm) REVERT: D 185 TYR cc_start: 0.7891 (m-10) cc_final: 0.7502 (m-80) REVERT: E 24 ARG cc_start: 0.8551 (ttm110) cc_final: 0.8139 (ttm-80) REVERT: E 43 VAL cc_start: 0.8528 (OUTLIER) cc_final: 0.8295 (p) REVERT: E 81 GLU cc_start: 0.8153 (pp20) cc_final: 0.7910 (pp20) REVERT: E 139 PHE cc_start: 0.6263 (p90) cc_final: 0.5159 (p90) REVERT: F 70 ASP cc_start: 0.8890 (p0) cc_final: 0.8666 (p0) REVERT: F 175 MET cc_start: 0.5101 (tpp) cc_final: 0.4430 (tpp) REVERT: I 163 TRP cc_start: 0.7950 (m100) cc_final: 0.7029 (m100) REVERT: B 246 THR cc_start: 0.9160 (p) cc_final: 0.8870 (p) REVERT: C 21 ARG cc_start: 0.8752 (ptt180) cc_final: 0.8505 (ptt180) REVERT: C 101 HIS cc_start: 0.8795 (OUTLIER) cc_final: 0.8260 (m170) REVERT: G 34 MET cc_start: 0.9107 (mmm) cc_final: 0.8696 (mmm) REVERT: G 215 LYS cc_start: 0.6580 (tttp) cc_final: 0.6145 (tptp) REVERT: H 73 ASP cc_start: 0.8514 (m-30) cc_final: 0.8039 (m-30) REVERT: H 187 LEU cc_start: 0.8324 (tt) cc_final: 0.7821 (mt) REVERT: H 215 LYS cc_start: 0.7018 (tttp) cc_final: 0.6659 (tptp) outliers start: 23 outliers final: 18 residues processed: 149 average time/residue: 0.1351 time to fit residues: 30.6074 Evaluate side-chains 151 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain D residue 52 ASN Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 99 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 137 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 32 optimal weight: 0.0870 chunk 58 optimal weight: 0.0570 chunk 211 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 217 optimal weight: 0.0670 chunk 71 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 0.0020 overall best weight: 0.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 166 GLN G 3 GLN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.129386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.080632 restraints weight = 30315.711| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.33 r_work: 0.3078 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17484 Z= 0.101 Angle : 0.596 7.222 23775 Z= 0.300 Chirality : 0.044 0.183 2703 Planarity : 0.005 0.066 3069 Dihedral : 5.072 26.311 2427 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.88 % Favored : 90.99 % Rotamer: Outliers : 1.16 % Allowed : 10.67 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.18), residues: 2241 helix: 1.22 (0.28), residues: 369 sheet: -1.56 (0.21), residues: 639 loop : -1.81 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 24 TYR 0.012 0.001 TYR C 254 PHE 0.010 0.001 PHE F 71 TRP 0.035 0.002 TRP F 163 HIS 0.005 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00233 (17472) covalent geometry : angle 0.59541 (23751) SS BOND : bond 0.00366 ( 12) SS BOND : angle 1.12529 ( 24) hydrogen bonds : bond 0.02718 ( 507) hydrogen bonds : angle 4.45520 ( 1323) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 HIS cc_start: 0.8699 (OUTLIER) cc_final: 0.8050 (m170) REVERT: A 212 MET cc_start: 0.8728 (mmm) cc_final: 0.8203 (mmm) REVERT: D 73 ASP cc_start: 0.8667 (m-30) cc_final: 0.8193 (m-30) REVERT: D 80 TYR cc_start: 0.8781 (m-80) cc_final: 0.8380 (m-80) REVERT: E 24 ARG cc_start: 0.8486 (ttm110) cc_final: 0.8062 (ttm-80) REVERT: E 81 GLU cc_start: 0.8150 (pp20) cc_final: 0.7905 (pp20) REVERT: E 194 CYS cc_start: 0.4582 (p) cc_final: 0.4101 (p) REVERT: F 70 ASP cc_start: 0.8926 (p0) cc_final: 0.8709 (p0) REVERT: F 175 MET cc_start: 0.5148 (tpp) cc_final: 0.4251 (tpp) REVERT: C 101 HIS cc_start: 0.8768 (OUTLIER) cc_final: 0.8187 (m170) REVERT: G 34 MET cc_start: 0.9076 (mmm) cc_final: 0.8612 (mmm) REVERT: G 209 HIS cc_start: 0.5108 (t-90) cc_final: 0.4809 (t-90) REVERT: G 215 LYS cc_start: 0.6610 (tttp) cc_final: 0.6192 (tptp) REVERT: H 187 LEU cc_start: 0.8320 (tt) cc_final: 0.7829 (mt) REVERT: H 215 LYS cc_start: 0.7002 (tttp) cc_final: 0.6376 (tptt) outliers start: 22 outliers final: 17 residues processed: 163 average time/residue: 0.1508 time to fit residues: 36.2305 Evaluate side-chains 152 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain D residue 52 ASN Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain H residue 99 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 85 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 160 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 chunk 92 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN F 166 GLN G 3 GLN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.125224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.076994 restraints weight = 30500.256| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.24 r_work: 0.2983 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17484 Z= 0.205 Angle : 0.664 7.976 23775 Z= 0.337 Chirality : 0.047 0.172 2703 Planarity : 0.006 0.074 3069 Dihedral : 5.266 27.463 2427 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.86 % Favored : 89.87 % Rotamer: Outliers : 1.47 % Allowed : 10.73 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.18), residues: 2241 helix: 0.96 (0.27), residues: 375 sheet: -1.44 (0.21), residues: 624 loop : -1.81 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 24 TYR 0.022 0.002 TYR H 80 PHE 0.011 0.001 PHE I 98 TRP 0.048 0.002 TRP F 163 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00500 (17472) covalent geometry : angle 0.66278 (23751) SS BOND : bond 0.00337 ( 12) SS BOND : angle 1.23654 ( 24) hydrogen bonds : bond 0.03073 ( 507) hydrogen bonds : angle 4.57128 ( 1323) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.8840 (mmm) cc_final: 0.8287 (mmm) REVERT: D 62 ASP cc_start: 0.8527 (m-30) cc_final: 0.8316 (m-30) REVERT: E 24 ARG cc_start: 0.8649 (ttm110) cc_final: 0.8296 (ttm-80) REVERT: E 43 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8386 (p) REVERT: E 81 GLU cc_start: 0.8196 (pp20) cc_final: 0.7963 (pp20) REVERT: E 139 PHE cc_start: 0.6474 (p90) cc_final: 0.5586 (p90) REVERT: F 70 ASP cc_start: 0.8936 (p0) cc_final: 0.8694 (p0) REVERT: F 173 TYR cc_start: 0.6102 (m-10) cc_final: 0.5855 (m-10) REVERT: I 163 TRP cc_start: 0.7921 (m100) cc_final: 0.7127 (m100) REVERT: B 246 THR cc_start: 0.9161 (p) cc_final: 0.8861 (p) REVERT: C 101 HIS cc_start: 0.8869 (OUTLIER) cc_final: 0.8442 (m170) REVERT: G 34 MET cc_start: 0.9100 (mmm) cc_final: 0.8653 (mmm) REVERT: G 209 HIS cc_start: 0.5073 (t-90) cc_final: 0.4804 (t70) REVERT: G 215 LYS cc_start: 0.6638 (tttp) cc_final: 0.6222 (tptp) REVERT: H 187 LEU cc_start: 0.8324 (tt) cc_final: 0.7810 (mt) REVERT: H 215 LYS cc_start: 0.6934 (tttp) cc_final: 0.6223 (tptt) outliers start: 28 outliers final: 22 residues processed: 147 average time/residue: 0.1467 time to fit residues: 32.2142 Evaluate side-chains 154 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain D residue 52 ASN Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 112 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 131 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 53 optimal weight: 0.0070 chunk 145 optimal weight: 0.7980 chunk 44 optimal weight: 20.0000 chunk 75 optimal weight: 0.0770 chunk 171 optimal weight: 0.2980 chunk 62 optimal weight: 0.5980 chunk 69 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 138 ASN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 ASN H 206 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.128870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.080966 restraints weight = 30549.479| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.39 r_work: 0.3049 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17484 Z= 0.109 Angle : 0.613 7.829 23775 Z= 0.309 Chirality : 0.045 0.182 2703 Planarity : 0.006 0.065 3069 Dihedral : 5.112 25.869 2427 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.79 % Favored : 91.08 % Rotamer: Outliers : 0.95 % Allowed : 11.36 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.18), residues: 2241 helix: 0.81 (0.27), residues: 393 sheet: -1.37 (0.21), residues: 633 loop : -1.86 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 24 TYR 0.018 0.001 TYR H 80 PHE 0.010 0.001 PHE F 71 TRP 0.049 0.002 TRP F 163 HIS 0.005 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00261 (17472) covalent geometry : angle 0.61245 (23751) SS BOND : bond 0.00256 ( 12) SS BOND : angle 1.15839 ( 24) hydrogen bonds : bond 0.02751 ( 507) hydrogen bonds : angle 4.36085 ( 1323) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.8791 (mmm) cc_final: 0.8183 (mmm) REVERT: E 24 ARG cc_start: 0.8561 (ttm110) cc_final: 0.8169 (ttm-80) REVERT: E 81 GLU cc_start: 0.8187 (pp20) cc_final: 0.7939 (pp20) REVERT: E 139 PHE cc_start: 0.6392 (p90) cc_final: 0.5399 (p90) REVERT: F 70 ASP cc_start: 0.8946 (p0) cc_final: 0.8722 (p0) REVERT: F 173 TYR cc_start: 0.6044 (m-10) cc_final: 0.5791 (m-10) REVERT: I 163 TRP cc_start: 0.7872 (m100) cc_final: 0.7006 (m100) REVERT: B 246 THR cc_start: 0.9126 (p) cc_final: 0.8822 (p) REVERT: C 101 HIS cc_start: 0.8811 (OUTLIER) cc_final: 0.8248 (m170) REVERT: G 34 MET cc_start: 0.9083 (mmm) cc_final: 0.8630 (mmm) REVERT: G 209 HIS cc_start: 0.4995 (t-90) cc_final: 0.4773 (t-90) REVERT: G 215 LYS cc_start: 0.6675 (tttp) cc_final: 0.6256 (tptp) REVERT: H 187 LEU cc_start: 0.8260 (tt) cc_final: 0.7799 (mt) REVERT: H 215 LYS cc_start: 0.7042 (tttp) cc_final: 0.6528 (tptp) outliers start: 18 outliers final: 16 residues processed: 147 average time/residue: 0.1474 time to fit residues: 32.0947 Evaluate side-chains 145 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain D residue 52 ASN Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 99 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 chunk 191 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 214 optimal weight: 40.0000 chunk 152 optimal weight: 0.6980 chunk 204 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 197 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN G 3 GLN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.126279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.077280 restraints weight = 30414.643| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.22 r_work: 0.2995 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17484 Z= 0.192 Angle : 0.659 9.934 23775 Z= 0.332 Chirality : 0.046 0.209 2703 Planarity : 0.006 0.071 3069 Dihedral : 5.206 27.601 2427 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.73 % Favored : 90.09 % Rotamer: Outliers : 1.00 % Allowed : 11.72 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.18), residues: 2241 helix: 0.89 (0.27), residues: 381 sheet: -1.36 (0.21), residues: 636 loop : -1.83 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 24 TYR 0.029 0.002 TYR G 80 PHE 0.010 0.001 PHE I 98 TRP 0.068 0.002 TRP F 163 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00473 (17472) covalent geometry : angle 0.65821 (23751) SS BOND : bond 0.00422 ( 12) SS BOND : angle 1.17449 ( 24) hydrogen bonds : bond 0.03008 ( 507) hydrogen bonds : angle 4.44348 ( 1323) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.8833 (mmm) cc_final: 0.8279 (mmm) REVERT: E 24 ARG cc_start: 0.8634 (ttm110) cc_final: 0.8259 (ttm-80) REVERT: E 81 GLU cc_start: 0.8166 (pp20) cc_final: 0.7921 (pp20) REVERT: E 139 PHE cc_start: 0.6336 (p90) cc_final: 0.5098 (p90) REVERT: F 70 ASP cc_start: 0.8960 (p0) cc_final: 0.8730 (p0) REVERT: F 173 TYR cc_start: 0.6022 (m-10) cc_final: 0.5795 (m-10) REVERT: I 81 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7992 (tm-30) REVERT: B 246 THR cc_start: 0.9150 (p) cc_final: 0.8852 (p) REVERT: C 101 HIS cc_start: 0.8852 (OUTLIER) cc_final: 0.8427 (m170) REVERT: G 34 MET cc_start: 0.9059 (mmm) cc_final: 0.8632 (mmm) REVERT: G 209 HIS cc_start: 0.5005 (t-90) cc_final: 0.4710 (t-90) REVERT: G 215 LYS cc_start: 0.6818 (tttp) cc_final: 0.6401 (tptp) REVERT: H 215 LYS cc_start: 0.6978 (tttp) cc_final: 0.6449 (tptp) outliers start: 19 outliers final: 17 residues processed: 143 average time/residue: 0.1479 time to fit residues: 31.2771 Evaluate side-chains 147 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain D residue 52 ASN Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 99 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 214 optimal weight: 20.0000 chunk 180 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 185 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN G 3 GLN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.127382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.079556 restraints weight = 30568.001| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.43 r_work: 0.3023 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17484 Z= 0.135 Angle : 0.626 7.922 23775 Z= 0.316 Chirality : 0.045 0.211 2703 Planarity : 0.006 0.067 3069 Dihedral : 5.145 26.395 2427 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.84 % Favored : 91.03 % Rotamer: Outliers : 1.31 % Allowed : 11.62 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.18), residues: 2241 helix: 0.86 (0.27), residues: 387 sheet: -1.34 (0.21), residues: 636 loop : -1.69 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 24 TYR 0.018 0.001 TYR H 80 PHE 0.009 0.001 PHE F 71 TRP 0.055 0.002 TRP F 163 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00333 (17472) covalent geometry : angle 0.62561 (23751) SS BOND : bond 0.00294 ( 12) SS BOND : angle 1.13937 ( 24) hydrogen bonds : bond 0.02822 ( 507) hydrogen bonds : angle 4.34400 ( 1323) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4979.85 seconds wall clock time: 86 minutes 9.49 seconds (5169.49 seconds total)