Starting phenix.real_space_refine on Sat Feb 17 14:31:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6i_23726/02_2024/7n6i_23726_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6i_23726/02_2024/7n6i_23726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6i_23726/02_2024/7n6i_23726.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6i_23726/02_2024/7n6i_23726.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6i_23726/02_2024/7n6i_23726_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6i_23726/02_2024/7n6i_23726_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 55 5.49 5 Mg 7 5.21 5 S 64 5.16 5 C 11744 2.51 5 N 3472 2.21 5 O 3597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 264": "OD1" <-> "OD2" Residue "C GLU 270": "OE1" <-> "OE2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 264": "OD1" <-> "OD2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "E TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 264": "OD1" <-> "OD2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "F TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 264": "OD1" <-> "OD2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 145": "OE1" <-> "OE2" Residue "G PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 264": "OD1" <-> "OD2" Residue "G GLU 270": "OE1" <-> "OE2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "H PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 264": "OD1" <-> "OD2" Residue "H GLU 270": "OE1" <-> "OE2" Residue "I ASP 44": "OD1" <-> "OD2" Residue "I TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 139": "OE1" <-> "OE2" Residue "I ASP 147": "OD1" <-> "OD2" Residue "I PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 264": "OD1" <-> "OD2" Residue "I GLU 270": "OE1" <-> "OE2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 145": "OE1" <-> "OE2" Residue "J PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 264": "OD1" <-> "OD2" Residue "J GLU 270": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18939 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 745 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 11, 'TRANS': 139} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 499 Unresolved non-hydrogen angles: 637 Unresolved non-hydrogen dihedrals: 444 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 5, 'HIS:plan': 7, 'PHE:plan': 7, 'GLU:plan': 11, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 297 Chain: "B" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 745 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 11, 'TRANS': 139} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 499 Unresolved non-hydrogen angles: 637 Unresolved non-hydrogen dihedrals: 444 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 5, 'HIS:plan': 7, 'PHE:plan': 7, 'GLU:plan': 11, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 297 Chain: "C" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "D" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "E" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "F" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "G" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "H" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "I" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "J" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "K" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 340 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "L" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 357 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.22, per 1000 atoms: 0.54 Number of scatterers: 18939 At special positions: 0 Unit cell: (126.35, 143.64, 136.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 64 16.00 P 55 15.00 Mg 7 11.99 O 3597 8.00 N 3472 7.00 C 11744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.78 Conformation dependent library (CDL) restraints added in 3.4 seconds 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4420 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 16 sheets defined 51.7% alpha, 4.5% beta 14 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 7.36 Creating SS restraints... Processing helix chain 'A' and resid 22 through 32 Processing helix chain 'A' and resid 37 through 48 Processing helix chain 'A' and resid 62 through 73 Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 112 through 115 Processing helix chain 'A' and resid 142 through 145 No H-bonds generated for 'chain 'A' and resid 142 through 145' Processing helix chain 'B' and resid 22 through 32 Processing helix chain 'B' and resid 37 through 48 Processing helix chain 'B' and resid 62 through 73 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 112 through 115 Processing helix chain 'B' and resid 142 through 145 No H-bonds generated for 'chain 'B' and resid 142 through 145' Processing helix chain 'C' and resid 20 through 28 Processing helix chain 'C' and resid 37 through 52 Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 102 through 113 removed outlier: 3.858A pdb=" N PHE C 106 " --> pdb=" O PRO C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 133 removed outlier: 4.659A pdb=" N ASP C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 163 removed outlier: 3.585A pdb=" N ALA C 155 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG C 158 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP C 159 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP C 163 " --> pdb=" O ILE C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 182 removed outlier: 4.120A pdb=" N ALA C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG C 182 " --> pdb=" O ALA C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 189 removed outlier: 3.610A pdb=" N ARG C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 214 removed outlier: 3.679A pdb=" N ASN C 206 " --> pdb=" O ASP C 203 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 212 " --> pdb=" O GLU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 removed outlier: 4.483A pdb=" N ILE C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 258 removed outlier: 3.559A pdb=" N ARG C 258 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 274 removed outlier: 3.926A pdb=" N GLU C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 28 Processing helix chain 'D' and resid 37 through 52 Processing helix chain 'D' and resid 66 through 76 Processing helix chain 'D' and resid 102 through 112 removed outlier: 3.858A pdb=" N PHE D 106 " --> pdb=" O PRO D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 133 removed outlier: 4.007A pdb=" N ASP D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG D 128 " --> pdb=" O ASP D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 163 removed outlier: 3.585A pdb=" N ALA D 155 " --> pdb=" O GLU D 152 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG D 158 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP D 159 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP D 163 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 removed outlier: 4.257A pdb=" N ALA D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 187 No H-bonds generated for 'chain 'D' and resid 184 through 187' Processing helix chain 'D' and resid 201 through 215 removed outlier: 3.679A pdb=" N ASN D 206 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU D 212 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN D 213 " --> pdb=" O MET D 210 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET D 214 " --> pdb=" O TRP D 211 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL D 215 " --> pdb=" O GLU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 237 removed outlier: 4.483A pdb=" N ILE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 258 removed outlier: 3.561A pdb=" N ARG D 258 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 274 removed outlier: 3.927A pdb=" N GLU D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 28 Processing helix chain 'E' and resid 37 through 52 Processing helix chain 'E' and resid 66 through 76 Processing helix chain 'E' and resid 102 through 113 removed outlier: 3.857A pdb=" N PHE E 106 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 133 removed outlier: 3.598A pdb=" N ASP E 127 " --> pdb=" O SER E 123 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG E 128 " --> pdb=" O ASP E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 163 removed outlier: 3.585A pdb=" N ALA E 155 " --> pdb=" O GLU E 152 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG E 158 " --> pdb=" O ALA E 155 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP E 159 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP E 163 " --> pdb=" O ILE E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 182 removed outlier: 4.041A pdb=" N LYS E 181 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 removed outlier: 3.511A pdb=" N ARG E 189 " --> pdb=" O GLN E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 214 removed outlier: 3.678A pdb=" N ASN E 206 " --> pdb=" O ASP E 203 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET E 214 " --> pdb=" O TRP E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 237 removed outlier: 4.345A pdb=" N ILE E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 258 removed outlier: 3.560A pdb=" N ARG E 258 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 274 removed outlier: 3.927A pdb=" N GLU E 274 " --> pdb=" O GLU E 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 28 Processing helix chain 'F' and resid 37 through 52 Processing helix chain 'F' and resid 66 through 76 Processing helix chain 'F' and resid 102 through 112 removed outlier: 3.856A pdb=" N PHE F 106 " --> pdb=" O PRO F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 133 Processing helix chain 'F' and resid 151 through 163 removed outlier: 3.585A pdb=" N ALA F 155 " --> pdb=" O GLU F 152 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG F 158 " --> pdb=" O ALA F 155 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP F 159 " --> pdb=" O ASP F 156 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP F 163 " --> pdb=" O ILE F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 182 removed outlier: 4.040A pdb=" N LYS F 181 " --> pdb=" O ALA F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 removed outlier: 3.510A pdb=" N ARG F 189 " --> pdb=" O GLN F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 214 removed outlier: 3.679A pdb=" N ASN F 206 " --> pdb=" O ASP F 203 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU F 212 " --> pdb=" O GLU F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 237 removed outlier: 4.483A pdb=" N ILE F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 258 removed outlier: 3.560A pdb=" N ARG F 258 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 274 removed outlier: 3.928A pdb=" N GLU F 274 " --> pdb=" O GLU F 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 28 Processing helix chain 'G' and resid 37 through 52 Processing helix chain 'G' and resid 66 through 76 Processing helix chain 'G' and resid 102 through 112 removed outlier: 3.857A pdb=" N PHE G 106 " --> pdb=" O PRO G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 133 removed outlier: 4.658A pdb=" N ASP G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG G 128 " --> pdb=" O ASP G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 163 removed outlier: 3.584A pdb=" N ALA G 155 " --> pdb=" O GLU G 152 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG G 158 " --> pdb=" O ALA G 155 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP G 159 " --> pdb=" O ASP G 156 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP G 163 " --> pdb=" O ILE G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 182 removed outlier: 4.041A pdb=" N LYS G 181 " --> pdb=" O ALA G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 189 Processing helix chain 'G' and resid 201 through 214 removed outlier: 3.678A pdb=" N ASN G 206 " --> pdb=" O ASP G 203 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU G 212 " --> pdb=" O GLU G 209 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET G 214 " --> pdb=" O TRP G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 237 removed outlier: 4.488A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 258 removed outlier: 3.560A pdb=" N ARG G 258 " --> pdb=" O ARG G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 274 removed outlier: 3.928A pdb=" N GLU G 274 " --> pdb=" O GLU G 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 28 Processing helix chain 'H' and resid 37 through 52 Processing helix chain 'H' and resid 66 through 76 Processing helix chain 'H' and resid 102 through 112 removed outlier: 3.856A pdb=" N PHE H 106 " --> pdb=" O PRO H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 133 removed outlier: 3.599A pdb=" N ASP H 127 " --> pdb=" O SER H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 163 removed outlier: 3.584A pdb=" N ALA H 155 " --> pdb=" O GLU H 152 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG H 158 " --> pdb=" O ALA H 155 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP H 159 " --> pdb=" O ASP H 156 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP H 163 " --> pdb=" O ILE H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 182 removed outlier: 4.040A pdb=" N LYS H 181 " --> pdb=" O ALA H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 189 removed outlier: 3.602A pdb=" N ARG H 189 " --> pdb=" O GLN H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 214 removed outlier: 3.678A pdb=" N ASN H 206 " --> pdb=" O ASP H 203 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET H 214 " --> pdb=" O TRP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 237 removed outlier: 4.487A pdb=" N ILE H 232 " --> pdb=" O GLU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 258 removed outlier: 3.560A pdb=" N ARG H 258 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 274 removed outlier: 3.928A pdb=" N GLU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 28 Processing helix chain 'I' and resid 37 through 52 removed outlier: 3.817A pdb=" N GLY I 48 " --> pdb=" O ASP I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 76 Processing helix chain 'I' and resid 102 through 112 removed outlier: 3.858A pdb=" N PHE I 106 " --> pdb=" O PRO I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 133 removed outlier: 4.657A pdb=" N ASP I 127 " --> pdb=" O SER I 123 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG I 128 " --> pdb=" O ASP I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 163 removed outlier: 3.586A pdb=" N ALA I 155 " --> pdb=" O GLU I 152 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG I 158 " --> pdb=" O ALA I 155 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP I 159 " --> pdb=" O ASP I 156 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP I 163 " --> pdb=" O ILE I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 182 removed outlier: 4.041A pdb=" N LYS I 181 " --> pdb=" O ALA I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 189 removed outlier: 3.533A pdb=" N ARG I 189 " --> pdb=" O GLN I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 214 removed outlier: 3.679A pdb=" N ASN I 206 " --> pdb=" O ASP I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 237 removed outlier: 4.490A pdb=" N ILE I 232 " --> pdb=" O GLU I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 258 removed outlier: 3.560A pdb=" N ARG I 258 " --> pdb=" O ARG I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 274 removed outlier: 3.928A pdb=" N GLU I 274 " --> pdb=" O GLU I 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 28 Processing helix chain 'J' and resid 37 through 52 Processing helix chain 'J' and resid 66 through 76 Processing helix chain 'J' and resid 102 through 112 removed outlier: 3.857A pdb=" N PHE J 106 " --> pdb=" O PRO J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 133 removed outlier: 4.657A pdb=" N ASP J 127 " --> pdb=" O SER J 123 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG J 128 " --> pdb=" O ASP J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 163 removed outlier: 3.585A pdb=" N ALA J 155 " --> pdb=" O GLU J 152 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG J 158 " --> pdb=" O ALA J 155 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP J 159 " --> pdb=" O ASP J 156 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP J 163 " --> pdb=" O ILE J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 182 removed outlier: 4.041A pdb=" N LYS J 181 " --> pdb=" O ALA J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 189 removed outlier: 3.527A pdb=" N ARG J 189 " --> pdb=" O GLN J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 201 through 214 removed outlier: 3.679A pdb=" N ASN J 206 " --> pdb=" O ASP J 203 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET J 214 " --> pdb=" O TRP J 211 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 237 removed outlier: 4.481A pdb=" N ILE J 232 " --> pdb=" O GLU J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 258 removed outlier: 3.561A pdb=" N ARG J 258 " --> pdb=" O ARG J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 274 removed outlier: 3.909A pdb=" N GLU J 274 " --> pdb=" O GLU J 270 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 193 through 195 removed outlier: 7.045A pdb=" N ARG C 57 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 60 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 91 through 95 removed outlier: 6.527A pdb=" N MET C 140 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE C 94 " --> pdb=" O MET C 140 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE C 142 " --> pdb=" O ILE C 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'D' and resid 57 through 59 Processing sheet with id= D, first strand: chain 'D' and resid 91 through 95 removed outlier: 6.555A pdb=" N MET D 140 " --> pdb=" O VAL D 92 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE D 94 " --> pdb=" O MET D 140 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE D 142 " --> pdb=" O ILE D 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'E' and resid 193 through 195 removed outlier: 6.404A pdb=" N ARG E 57 " --> pdb=" O LEU E 194 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 91 through 95 removed outlier: 6.545A pdb=" N MET E 140 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE E 94 " --> pdb=" O MET E 140 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE E 142 " --> pdb=" O ILE E 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'F' and resid 57 through 59 Processing sheet with id= H, first strand: chain 'F' and resid 91 through 95 removed outlier: 6.579A pdb=" N MET F 140 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE F 94 " --> pdb=" O MET F 140 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE F 142 " --> pdb=" O ILE F 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'G' and resid 57 through 60 Processing sheet with id= J, first strand: chain 'G' and resid 91 through 95 removed outlier: 6.514A pdb=" N MET G 140 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE G 94 " --> pdb=" O MET G 140 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE G 142 " --> pdb=" O ILE G 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'H' and resid 57 through 59 Processing sheet with id= L, first strand: chain 'H' and resid 91 through 95 removed outlier: 6.584A pdb=" N MET H 140 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE H 94 " --> pdb=" O MET H 140 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE H 142 " --> pdb=" O ILE H 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'I' and resid 57 through 60 Processing sheet with id= N, first strand: chain 'I' and resid 91 through 95 removed outlier: 6.564A pdb=" N MET I 140 " --> pdb=" O VAL I 92 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ILE I 94 " --> pdb=" O MET I 140 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE I 142 " --> pdb=" O ILE I 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'J' and resid 57 through 59 Processing sheet with id= P, first strand: chain 'J' and resid 91 through 95 removed outlier: 6.657A pdb=" N MET J 140 " --> pdb=" O VAL J 92 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE J 94 " --> pdb=" O MET J 140 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE J 142 " --> pdb=" O ILE J 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= P 714 hydrogen bonds defined for protein. 1692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 5.14 Time building geometry restraints manager: 8.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3118 1.31 - 1.44: 4801 1.44 - 1.56: 11152 1.56 - 1.69: 108 1.69 - 1.81: 96 Bond restraints: 19275 Sorted by residual: bond pdb=" C4 ATP J 300 " pdb=" C5 ATP J 300 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.79e+01 bond pdb=" C4 ATP E 300 " pdb=" C5 ATP E 300 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.78e+01 bond pdb=" C4 ATP I 300 " pdb=" C5 ATP I 300 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.75e+01 bond pdb=" C4 ATP H 300 " pdb=" C5 ATP H 300 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.66e+01 bond pdb=" C4 ATP F 300 " pdb=" C5 ATP F 300 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.64e+01 ... (remaining 19270 not shown) Histogram of bond angle deviations from ideal: 95.41 - 103.56: 233 103.56 - 111.71: 9187 111.71 - 119.87: 8936 119.87 - 128.02: 7654 128.02 - 136.18: 157 Bond angle restraints: 26167 Sorted by residual: angle pdb=" PB ATP E 300 " pdb=" O3B ATP E 300 " pdb=" PG ATP E 300 " ideal model delta sigma weight residual 139.87 119.21 20.66 1.00e+00 1.00e+00 4.27e+02 angle pdb=" PB ATP D 300 " pdb=" O3B ATP D 300 " pdb=" PG ATP D 300 " ideal model delta sigma weight residual 139.87 119.28 20.59 1.00e+00 1.00e+00 4.24e+02 angle pdb=" PB ATP H 300 " pdb=" O3B ATP H 300 " pdb=" PG ATP H 300 " ideal model delta sigma weight residual 139.87 119.34 20.53 1.00e+00 1.00e+00 4.22e+02 angle pdb=" PB ATP I 300 " pdb=" O3B ATP I 300 " pdb=" PG ATP I 300 " ideal model delta sigma weight residual 139.87 119.54 20.33 1.00e+00 1.00e+00 4.13e+02 angle pdb=" PB ATP G 300 " pdb=" O3B ATP G 300 " pdb=" PG ATP G 300 " ideal model delta sigma weight residual 139.87 119.88 19.99 1.00e+00 1.00e+00 4.00e+02 ... (remaining 26162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.41: 11463 31.41 - 62.81: 439 62.81 - 94.22: 70 94.22 - 125.63: 1 125.63 - 157.04: 3 Dihedral angle restraints: 11976 sinusoidal: 5152 harmonic: 6824 Sorted by residual: dihedral pdb=" N ARG B 30 " pdb=" C ARG B 30 " pdb=" CA ARG B 30 " pdb=" CB ARG B 30 " ideal model delta harmonic sigma weight residual 122.80 162.49 -39.69 0 2.50e+00 1.60e-01 2.52e+02 dihedral pdb=" N ARG A 30 " pdb=" C ARG A 30 " pdb=" CA ARG A 30 " pdb=" CB ARG A 30 " ideal model delta harmonic sigma weight residual 122.80 162.46 -39.66 0 2.50e+00 1.60e-01 2.52e+02 dihedral pdb=" C ARG B 30 " pdb=" N ARG B 30 " pdb=" CA ARG B 30 " pdb=" CB ARG B 30 " ideal model delta harmonic sigma weight residual -122.60 -160.03 37.43 0 2.50e+00 1.60e-01 2.24e+02 ... (remaining 11973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.347: 2950 0.347 - 0.693: 34 0.693 - 1.040: 4 1.040 - 1.387: 0 1.387 - 1.733: 2 Chirality restraints: 2990 Sorted by residual: chirality pdb=" CA ARG B 30 " pdb=" N ARG B 30 " pdb=" C ARG B 30 " pdb=" CB ARG B 30 " both_signs ideal model delta sigma weight residual False 2.51 0.78 1.73 2.00e-01 2.50e+01 7.51e+01 chirality pdb=" CA ARG A 30 " pdb=" N ARG A 30 " pdb=" C ARG A 30 " pdb=" CB ARG A 30 " both_signs ideal model delta sigma weight residual False 2.51 0.78 1.73 2.00e-01 2.50e+01 7.50e+01 chirality pdb=" CA TYR A 116 " pdb=" N TYR A 116 " pdb=" C TYR A 116 " pdb=" CB TYR A 116 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.32e+01 ... (remaining 2987 not shown) Planarity restraints: 3205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 92 " -0.016 2.00e-02 2.50e+03 3.12e-02 9.71e+00 pdb=" C MET A 92 " 0.054 2.00e-02 2.50e+03 pdb=" O MET A 92 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN A 93 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 92 " -0.016 2.00e-02 2.50e+03 3.11e-02 9.66e+00 pdb=" C MET B 92 " 0.054 2.00e-02 2.50e+03 pdb=" O MET B 92 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN B 93 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 138 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C VAL H 138 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL H 138 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU H 139 " -0.014 2.00e-02 2.50e+03 ... (remaining 3202 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 13 2.05 - 2.76: 1907 2.76 - 3.47: 26421 3.47 - 4.19: 42041 4.19 - 4.90: 73155 Nonbonded interactions: 143537 Sorted by model distance: nonbonded pdb=" CB ARG B 155 " pdb=" NH2 ARG I 128 " model vdw 1.336 3.520 nonbonded pdb=" CB ARG B 155 " pdb=" CZ ARG I 128 " model vdw 1.350 3.670 nonbonded pdb=" OD2 ASP I 245 " pdb=" O2' ATP I 300 " model vdw 1.484 2.440 nonbonded pdb=" OD2 ASP E 245 " pdb=" O2' ATP E 300 " model vdw 1.584 2.440 nonbonded pdb=" CB HIS B 34 " pdb=" OE2 GLU H 131 " model vdw 1.701 3.440 ... (remaining 143532 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 19 through 275) selection = (chain 'E' and resid 19 through 275) selection = (chain 'F' and resid 19 through 275) selection = (chain 'G' and resid 19 through 275) selection = (chain 'H' and resid 19 through 275) selection = (chain 'I' and resid 19 through 275) selection = (chain 'J' and resid 19 through 275) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 0.020 Extract box with map and model: 4.500 Check model and map are aligned: 0.260 Set scattering table: 0.180 Process input model: 53.400 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6175 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 : 0.014 0.082 19275 Z= 0.910 Angle : 1.720 20.658 26167 Z= 1.347 Chirality : 0.126 1.733 2990 Planarity : 0.006 0.057 3205 Dihedral : 16.033 157.036 7556 Min Nonbonded Distance : 1.336 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 0.45 % Allowed : 3.07 % Favored : 96.48 % Cbeta Deviations : 1.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.16), residues: 2338 helix: -0.21 (0.13), residues: 1262 sheet: -0.04 (0.51), residues: 96 loop : -0.28 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 45 HIS 0.001 0.000 HIS G 43 PHE 0.007 0.001 PHE H 125 TYR 0.007 0.000 TYR E 75 ARG 0.003 0.000 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 834 time to evaluate : 2.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 LEU cc_start: 0.7134 (mt) cc_final: 0.6871 (mp) REVERT: C 39 VAL cc_start: 0.8217 (t) cc_final: 0.7998 (t) REVERT: C 42 LEU cc_start: 0.9103 (tp) cc_final: 0.8583 (tp) REVERT: C 194 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8253 (tt) REVERT: C 199 LEU cc_start: 0.7136 (mt) cc_final: 0.6832 (mt) REVERT: D 244 LEU cc_start: 0.8751 (tp) cc_final: 0.8527 (tt) REVERT: E 49 LYS cc_start: 0.8872 (mmtt) cc_final: 0.8667 (mptt) REVERT: E 133 LEU cc_start: 0.8473 (mt) cc_final: 0.8252 (mt) REVERT: E 240 TYR cc_start: 0.8769 (m-80) cc_final: 0.8505 (m-80) REVERT: F 38 GLN cc_start: 0.7982 (tp40) cc_final: 0.7622 (tp40) REVERT: F 45 TRP cc_start: 0.8591 (t60) cc_final: 0.8387 (t60) REVERT: F 70 CYS cc_start: 0.7889 (m) cc_final: 0.7463 (m) REVERT: F 164 LEU cc_start: 0.8028 (mt) cc_final: 0.7790 (mt) REVERT: F 183 ASP cc_start: 0.6544 (t70) cc_final: 0.6316 (t70) REVERT: H 41 THR cc_start: 0.8869 (m) cc_final: 0.8527 (m) REVERT: H 163 ASP cc_start: 0.6463 (m-30) cc_final: 0.5819 (m-30) REVERT: I 77 HIS cc_start: 0.5999 (m-70) cc_final: 0.5791 (m-70) REVERT: I 204 PHE cc_start: 0.8420 (t80) cc_final: 0.7889 (t80) REVERT: J 100 CYS cc_start: 0.1713 (t) cc_final: 0.1485 (t) REVERT: J 211 TRP cc_start: 0.6531 (t-100) cc_final: 0.5891 (t-100) outliers start: 8 outliers final: 1 residues processed: 838 average time/residue: 0.3479 time to fit residues: 414.8518 Evaluate side-chains 401 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 399 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 196 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 181 optimal weight: 20.0000 chunk 70 optimal weight: 0.4980 chunk 110 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 GLN C 185 GLN D 22 GLN F 77 HIS F 185 GLN ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN J 37 GLN J 98 GLN J 193 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19275 Z= 0.220 Angle : 0.684 13.501 26167 Z= 0.352 Chirality : 0.043 0.223 2990 Planarity : 0.005 0.049 3205 Dihedral : 16.398 155.117 3240 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.19 % Allowed : 17.63 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.16), residues: 2338 helix: 0.65 (0.14), residues: 1208 sheet: 0.37 (0.55), residues: 96 loop : 0.01 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 45 HIS 0.006 0.001 HIS J 193 PHE 0.024 0.002 PHE D 125 TYR 0.023 0.002 TYR D 73 ARG 0.007 0.001 ARG G 258 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 411 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 115 TYR cc_start: 0.8162 (m-10) cc_final: 0.7820 (m-10) REVERT: C 187 LEU cc_start: 0.8589 (pp) cc_final: 0.8064 (tt) REVERT: C 229 MET cc_start: 0.4086 (ptp) cc_final: 0.3571 (ptp) REVERT: D 187 LEU cc_start: 0.8220 (tp) cc_final: 0.7987 (tp) REVERT: E 233 LEU cc_start: 0.8801 (mt) cc_final: 0.8499 (mt) REVERT: F 62 SER cc_start: 0.7721 (m) cc_final: 0.7468 (t) REVERT: F 70 CYS cc_start: 0.8079 (m) cc_final: 0.7740 (m) REVERT: G 42 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8819 (tp) REVERT: G 142 ILE cc_start: 0.9346 (mp) cc_final: 0.9090 (mt) REVERT: H 54 LYS cc_start: 0.8308 (tttp) cc_final: 0.7457 (tptp) REVERT: H 140 MET cc_start: 0.6436 (ttp) cc_final: 0.6170 (ttm) REVERT: H 156 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7087 (t70) REVERT: H 237 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8786 (p) REVERT: I 106 PHE cc_start: 0.6557 (m-10) cc_final: 0.6111 (m-10) REVERT: J 98 GLN cc_start: 0.7063 (tp-100) cc_final: 0.6540 (tp-100) REVERT: J 240 TYR cc_start: 0.7020 (m-80) cc_final: 0.6808 (m-10) outliers start: 75 outliers final: 36 residues processed: 464 average time/residue: 0.2947 time to fit residues: 207.2014 Evaluate side-chains 361 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 322 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 147 ASP Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain H residue 253 ILE Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 115 TYR Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 226 SER Chi-restraints excluded: chain J residue 269 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 175 optimal weight: 9.9990 chunk 143 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 187 optimal weight: 0.5980 chunk 209 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN E 22 GLN E 38 GLN ** G 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN I 38 GLN I 77 HIS J 37 GLN ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19275 Z= 0.193 Angle : 0.625 13.778 26167 Z= 0.314 Chirality : 0.041 0.188 2990 Planarity : 0.004 0.042 3205 Dihedral : 16.071 154.138 3238 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.35 % Allowed : 19.92 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.17), residues: 2338 helix: 0.58 (0.14), residues: 1272 sheet: 0.15 (0.53), residues: 96 loop : 0.20 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 20 HIS 0.004 0.001 HIS I 97 PHE 0.030 0.002 PHE I 125 TYR 0.023 0.001 TYR H 73 ARG 0.007 0.000 ARG H 258 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 359 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.3350 (mmtm) cc_final: 0.2982 (mmtm) REVERT: C 115 TYR cc_start: 0.8242 (m-80) cc_final: 0.8027 (m-10) REVERT: C 194 LEU cc_start: 0.8823 (tp) cc_final: 0.8485 (tt) REVERT: E 233 LEU cc_start: 0.8839 (mt) cc_final: 0.8557 (mt) REVERT: F 70 CYS cc_start: 0.7929 (m) cc_final: 0.7645 (m) REVERT: G 142 ILE cc_start: 0.9382 (mp) cc_final: 0.9131 (mt) REVERT: H 73 TYR cc_start: 0.7300 (t80) cc_final: 0.7084 (t80) REVERT: H 159 ASP cc_start: 0.6565 (t0) cc_final: 0.5641 (t0) REVERT: J 166 ILE cc_start: 0.5470 (OUTLIER) cc_final: 0.5098 (tt) outliers start: 60 outliers final: 42 residues processed: 397 average time/residue: 0.2760 time to fit residues: 169.0613 Evaluate side-chains 349 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 306 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain H residue 38 GLN Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 147 ASP Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 253 ILE Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 115 TYR Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 229 MET Chi-restraints excluded: chain J residue 269 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 23 optimal weight: 50.0000 chunk 100 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 211 optimal weight: 0.0060 chunk 224 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 200 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 HIS H 38 GLN I 38 GLN I 77 HIS J 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19275 Z= 0.191 Angle : 0.599 12.630 26167 Z= 0.304 Chirality : 0.041 0.260 2990 Planarity : 0.004 0.039 3205 Dihedral : 15.849 153.737 3238 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.02 % Allowed : 19.92 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.17), residues: 2338 helix: 0.57 (0.14), residues: 1284 sheet: 0.14 (0.54), residues: 96 loop : 0.23 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 20 HIS 0.006 0.001 HIS J 97 PHE 0.030 0.002 PHE I 196 TYR 0.017 0.001 TYR F 112 ARG 0.009 0.000 ARG I 231 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 332 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.3254 (mmtm) cc_final: 0.2686 (mmtm) REVERT: E 268 LEU cc_start: 0.8558 (pp) cc_final: 0.8327 (pp) REVERT: F 145 GLU cc_start: 0.7732 (tt0) cc_final: 0.7148 (tm-30) REVERT: G 142 ILE cc_start: 0.9405 (mp) cc_final: 0.9183 (mt) REVERT: G 162 GLU cc_start: 0.6165 (pt0) cc_final: 0.5931 (mt-10) REVERT: I 38 GLN cc_start: 0.7160 (OUTLIER) cc_final: 0.6882 (tt0) REVERT: I 140 MET cc_start: 0.6271 (tpp) cc_final: 0.5866 (tpp) outliers start: 72 outliers final: 46 residues processed: 380 average time/residue: 0.3057 time to fit residues: 180.7698 Evaluate side-chains 343 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 296 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain H residue 147 ASP Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 115 TYR Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 229 MET Chi-restraints excluded: chain J residue 269 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 114 optimal weight: 0.6980 chunk 201 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN D 185 GLN E 223 ASN F 77 HIS ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN J 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.6264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19275 Z= 0.265 Angle : 0.603 10.789 26167 Z= 0.313 Chirality : 0.041 0.175 2990 Planarity : 0.004 0.036 3205 Dihedral : 15.692 154.142 3238 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.08 % Allowed : 20.20 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2338 helix: 0.55 (0.15), residues: 1290 sheet: -0.00 (0.39), residues: 192 loop : 0.25 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 20 HIS 0.005 0.001 HIS H 77 PHE 0.027 0.002 PHE I 125 TYR 0.022 0.001 TYR F 112 ARG 0.007 0.001 ARG F 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 297 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.3610 (mmtm) cc_final: 0.2878 (mmtm) REVERT: E 49 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8383 (mppt) REVERT: F 145 GLU cc_start: 0.7933 (tt0) cc_final: 0.7403 (tm-30) REVERT: F 214 MET cc_start: 0.7519 (mmm) cc_final: 0.7281 (mmm) REVERT: G 142 ILE cc_start: 0.9339 (mp) cc_final: 0.9128 (mt) REVERT: H 54 LYS cc_start: 0.8523 (mmmt) cc_final: 0.8157 (tttp) REVERT: H 244 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9086 (tt) REVERT: I 140 MET cc_start: 0.6483 (tpp) cc_final: 0.5821 (tpp) outliers start: 91 outliers final: 61 residues processed: 362 average time/residue: 0.2911 time to fit residues: 161.7811 Evaluate side-chains 335 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 272 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain H residue 147 ASP Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 115 TYR Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain J residue 176 LEU Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 225 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 7.9990 chunk 201 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 224 optimal weight: 8.9990 chunk 186 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 18 optimal weight: 40.0000 chunk 74 optimal weight: 6.9990 chunk 117 optimal weight: 0.0570 overall best weight: 3.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 HIS F 81 GLN ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 213 GLN J 38 GLN J 223 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.7194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 19275 Z= 0.376 Angle : 0.714 10.816 26167 Z= 0.372 Chirality : 0.043 0.238 2990 Planarity : 0.005 0.079 3205 Dihedral : 15.723 155.829 3236 Min Nonbonded Distance : 1.600 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.47 % Allowed : 21.99 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.17), residues: 2338 helix: 0.17 (0.14), residues: 1308 sheet: -0.24 (0.38), residues: 192 loop : 0.06 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 211 HIS 0.005 0.001 HIS I 97 PHE 0.025 0.002 PHE I 125 TYR 0.027 0.002 TYR F 112 ARG 0.007 0.001 ARG F 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 267 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.3992 (mmtm) cc_final: 0.2492 (tptm) REVERT: C 115 TYR cc_start: 0.8478 (m-10) cc_final: 0.8096 (m-10) REVERT: E 49 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8578 (mppt) REVERT: F 145 GLU cc_start: 0.8246 (tt0) cc_final: 0.7742 (tm-30) REVERT: H 54 LYS cc_start: 0.8637 (mmmt) cc_final: 0.8268 (tttp) outliers start: 98 outliers final: 75 residues processed: 336 average time/residue: 0.2877 time to fit residues: 149.2196 Evaluate side-chains 315 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 239 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain H residue 147 ASP Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 115 TYR Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 225 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 10.0000 chunk 25 optimal weight: 30.0000 chunk 127 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 188 optimal weight: 4.9990 chunk 125 optimal weight: 0.0570 chunk 223 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 136 optimal weight: 0.0770 chunk 103 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 43 HIS F 81 GLN ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.7335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19275 Z= 0.166 Angle : 0.642 12.009 26167 Z= 0.321 Chirality : 0.042 0.263 2990 Planarity : 0.004 0.035 3205 Dihedral : 15.496 155.632 3236 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.34 % Allowed : 25.28 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.18), residues: 2338 helix: 0.48 (0.15), residues: 1250 sheet: -0.27 (0.38), residues: 192 loop : 0.04 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 20 HIS 0.008 0.001 HIS J 193 PHE 0.027 0.001 PHE I 125 TYR 0.013 0.001 TYR J 93 ARG 0.010 0.000 ARG D 231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 297 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.3375 (mmtm) cc_final: 0.2844 (tptm) REVERT: C 115 TYR cc_start: 0.8250 (m-10) cc_final: 0.7854 (m-10) REVERT: C 138 VAL cc_start: 0.8962 (m) cc_final: 0.8689 (p) REVERT: C 229 MET cc_start: 0.4781 (pmm) cc_final: 0.4477 (pmm) REVERT: D 42 LEU cc_start: 0.8618 (tt) cc_final: 0.8292 (tp) REVERT: D 129 THR cc_start: 0.8894 (p) cc_final: 0.8683 (t) REVERT: E 49 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8293 (ttmm) REVERT: E 56 CYS cc_start: 0.7678 (m) cc_final: 0.7424 (m) REVERT: F 145 GLU cc_start: 0.8107 (tt0) cc_final: 0.7775 (tm-30) REVERT: H 54 LYS cc_start: 0.8523 (mmmt) cc_final: 0.8274 (tttp) outliers start: 42 outliers final: 31 residues processed: 331 average time/residue: 0.2897 time to fit residues: 146.6876 Evaluate side-chains 285 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 253 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 115 TYR Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 225 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 chunk 67 optimal weight: 0.5980 chunk 43 optimal weight: 0.4980 chunk 142 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 110 optimal weight: 0.0010 chunk 20 optimal weight: 50.0000 chunk 175 optimal weight: 0.4980 chunk 203 optimal weight: 5.9990 chunk 214 optimal weight: 4.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.7480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19275 Z= 0.161 Angle : 0.636 16.272 26167 Z= 0.318 Chirality : 0.042 0.320 2990 Planarity : 0.004 0.068 3205 Dihedral : 15.334 155.417 3236 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.18 % Allowed : 25.33 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 2338 helix: 0.44 (0.15), residues: 1290 sheet: -0.22 (0.39), residues: 192 loop : 0.09 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 20 HIS 0.004 0.001 HIS F 77 PHE 0.026 0.001 PHE I 125 TYR 0.019 0.001 TYR J 75 ARG 0.008 0.000 ARG D 231 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 269 time to evaluate : 2.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.3401 (mmtm) cc_final: 0.2716 (tptm) REVERT: C 115 TYR cc_start: 0.8249 (m-10) cc_final: 0.7838 (m-10) REVERT: C 229 MET cc_start: 0.4821 (pmm) cc_final: 0.4155 (pmm) REVERT: E 49 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8347 (ttmm) REVERT: F 145 GLU cc_start: 0.8132 (tt0) cc_final: 0.7807 (tm-30) outliers start: 57 outliers final: 38 residues processed: 309 average time/residue: 0.2871 time to fit residues: 136.7871 Evaluate side-chains 288 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 249 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 115 TYR Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain J residue 176 LEU Chi-restraints excluded: chain J residue 225 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 2.9990 chunk 208 optimal weight: 0.0870 chunk 214 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 163 optimal weight: 0.3980 chunk 63 optimal weight: 0.7980 chunk 188 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 136 optimal weight: 0.0870 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 223 ASN ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.7627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 19275 Z= 0.163 Angle : 0.653 13.441 26167 Z= 0.326 Chirality : 0.042 0.260 2990 Planarity : 0.004 0.034 3205 Dihedral : 15.214 155.354 3236 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.51 % Allowed : 26.34 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.18), residues: 2338 helix: 0.43 (0.15), residues: 1296 sheet: 0.05 (0.55), residues: 96 loop : -0.01 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 45 HIS 0.003 0.000 HIS G 77 PHE 0.026 0.001 PHE I 125 TYR 0.019 0.001 TYR J 75 ARG 0.007 0.000 ARG D 231 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 259 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.3623 (mmtm) cc_final: 0.3053 (tptm) REVERT: C 115 TYR cc_start: 0.8256 (m-10) cc_final: 0.7871 (m-10) REVERT: C 138 VAL cc_start: 0.8775 (m) cc_final: 0.8498 (p) REVERT: C 229 MET cc_start: 0.4832 (pmm) cc_final: 0.4166 (pmm) REVERT: E 196 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7793 (m-80) REVERT: F 77 HIS cc_start: 0.6838 (m-70) cc_final: 0.6582 (m170) REVERT: F 145 GLU cc_start: 0.8085 (tt0) cc_final: 0.7791 (tm-30) REVERT: H 100 CYS cc_start: 0.7346 (t) cc_final: 0.6624 (t) outliers start: 45 outliers final: 32 residues processed: 291 average time/residue: 0.2845 time to fit residues: 129.5574 Evaluate side-chains 270 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 237 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 115 TYR Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain J residue 176 LEU Chi-restraints excluded: chain J residue 225 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 chunk 231 optimal weight: 10.0000 chunk 212 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 chunk 19 optimal weight: 30.0000 chunk 142 optimal weight: 0.2980 chunk 112 optimal weight: 0.5980 chunk 146 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.7786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19275 Z= 0.210 Angle : 0.673 11.630 26167 Z= 0.338 Chirality : 0.043 0.329 2990 Planarity : 0.004 0.036 3205 Dihedral : 15.177 155.598 3236 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.51 % Allowed : 25.84 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.18), residues: 2338 helix: 0.42 (0.15), residues: 1294 sheet: 0.06 (0.55), residues: 96 loop : -0.05 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 45 HIS 0.003 0.001 HIS H 77 PHE 0.025 0.001 PHE I 125 TYR 0.019 0.001 TYR J 75 ARG 0.007 0.000 ARG D 231 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 239 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.3339 (mmtm) cc_final: 0.1968 (tptp) REVERT: C 115 TYR cc_start: 0.8349 (m-10) cc_final: 0.7963 (m-10) REVERT: C 229 MET cc_start: 0.4978 (pmm) cc_final: 0.4183 (pmm) REVERT: F 145 GLU cc_start: 0.8204 (tt0) cc_final: 0.7825 (tm-30) REVERT: F 229 MET cc_start: 0.7692 (pmm) cc_final: 0.7232 (pmm) outliers start: 45 outliers final: 39 residues processed: 274 average time/residue: 0.2804 time to fit residues: 120.2615 Evaluate side-chains 271 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 232 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 115 TYR Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain J residue 176 LEU Chi-restraints excluded: chain J residue 225 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 0.0870 chunk 56 optimal weight: 6.9990 chunk 169 optimal weight: 0.3980 chunk 27 optimal weight: 30.0000 chunk 51 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 189 optimal weight: 5.9990 chunk 23 optimal weight: 40.0000 chunk 33 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 overall best weight: 2.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN F 81 GLN ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 GLN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.099002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.068146 restraints weight = 64473.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.070100 restraints weight = 36586.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.071435 restraints weight = 25634.428| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.8202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19275 Z= 0.279 Angle : 0.707 11.848 26167 Z= 0.358 Chirality : 0.044 0.312 2990 Planarity : 0.004 0.042 3205 Dihedral : 15.183 156.670 3236 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.73 % Allowed : 25.39 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.18), residues: 2338 helix: 0.47 (0.15), residues: 1268 sheet: -0.49 (0.35), residues: 232 loop : -0.08 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 211 HIS 0.005 0.001 HIS F 77 PHE 0.024 0.002 PHE I 125 TYR 0.026 0.002 TYR F 112 ARG 0.007 0.001 ARG D 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4061.57 seconds wall clock time: 74 minutes 29.68 seconds (4469.68 seconds total)