Starting phenix.real_space_refine on Sun May 3 22:18:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ssl_55189/05_2026/9ssl_55189.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ssl_55189/05_2026/9ssl_55189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ssl_55189/05_2026/9ssl_55189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ssl_55189/05_2026/9ssl_55189.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ssl_55189/05_2026/9ssl_55189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ssl_55189/05_2026/9ssl_55189.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.089 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: 7 Type Number sf(0) Gaussians K 5 8.98 5 P 41 5.49 5 Mg 5 5.21 5 S 84 5.16 5 C 9795 2.51 5 N 2820 2.21 5 O 3098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15848 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "B" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2409 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 302} Chain breaks: 1 Chain: "C" Number of atoms: 2414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2414 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 303} Chain breaks: 1 Chain: "D" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2413 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 303} Chain breaks: 1 Chain: "E" Number of atoms: 2410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2410 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 303} Chain breaks: 1 Chain: "F" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2403 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 302} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 71 Unusual residues: {'ACE': 1} Classifications: {'peptide': 9, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 1, 'TRANS': 7} Chain: "H" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 133 Unusual residues: {'ACE': 1} Classifications: {'peptide': 17, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 3, 'TRANS': 13} Chain breaks: 1 Chain: "I" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 145 Unusual residues: {'ACE': 1} Classifications: {'peptide': 19, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 4, 'TRANS': 14} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 149 Unusual residues: {'ACE': 1} Classifications: {'peptide': 19, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 4, 'TRANS': 14} Chain breaks: 1 Chain: "K" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 143 Unusual residues: {'ACE': 1} Classifications: {'peptide': 19, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 4, 'TRANS': 14} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 131 Unusual residues: {'ACE': 1} Classifications: {'peptide': 18, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'ACE_C-N': 1, 'PTRANS': 4, 'TRANS': 13} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Z" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 407 Classifications: {'DNA': 20} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' K': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.81, per 1000 atoms: 0.24 Number of scatterers: 15848 At special positions: 0 Unit cell: (122.64, 121.8, 163.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 5 19.00 S 84 16.00 P 41 15.00 Mg 5 11.99 O 3098 8.00 N 2820 7.00 C 9795 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 788.6 milliseconds 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3634 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 18 sheets defined 50.4% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 removed outlier: 3.843A pdb=" N GLU A 29 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY A 32 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 45 Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 56 through 62 removed outlier: 3.695A pdb=" N LEU A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 80 removed outlier: 3.730A pdb=" N LYS A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 133 through 145 removed outlier: 4.100A pdb=" N GLN A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 179 removed outlier: 3.871A pdb=" N LEU A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 188 Processing helix chain 'A' and resid 196 through 213 removed outlier: 3.510A pdb=" N GLN A 200 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 209 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.595A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 237 through 260 Processing helix chain 'A' and resid 288 through 295 removed outlier: 3.559A pdb=" N ILE A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 32 removed outlier: 4.298A pdb=" N GLU B 29 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 32 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 44 removed outlier: 3.600A pdb=" N ALA B 44 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 55 Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 67 through 80 removed outlier: 3.608A pdb=" N LYS B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 97 Processing helix chain 'B' and resid 106 through 114 Processing helix chain 'B' and resid 132 through 144 removed outlier: 3.583A pdb=" N VAL B 142 " --> pdb=" O HIS B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.664A pdb=" N LEU B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 188 Processing helix chain 'B' and resid 196 through 211 removed outlier: 3.892A pdb=" N LEU B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 206 " --> pdb=" O GLN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 removed outlier: 3.827A pdb=" N ARG B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 260 Processing helix chain 'B' and resid 288 through 296 removed outlier: 3.767A pdb=" N ILE B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 removed outlier: 3.889A pdb=" N GLU C 29 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 25 through 30' Processing helix chain 'C' and resid 34 through 44 Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 56 through 62 Processing helix chain 'C' and resid 67 through 82 removed outlier: 3.685A pdb=" N LEU C 81 " --> pdb=" O GLU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 97 Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 132 through 144 removed outlier: 3.532A pdb=" N VAL C 142 " --> pdb=" O HIS C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 146 No H-bonds generated for 'chain 'C' and resid 145 through 146' Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.539A pdb=" N GLY C 151 " --> pdb=" O ILE C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 178 removed outlier: 3.864A pdb=" N LEU C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 188 Processing helix chain 'C' and resid 196 through 212 removed outlier: 3.896A pdb=" N LEU C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN C 206 " --> pdb=" O GLN C 202 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 removed outlier: 4.050A pdb=" N THR C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 260 Processing helix chain 'C' and resid 288 through 296 removed outlier: 4.047A pdb=" N ILE C 292 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 32 removed outlier: 3.507A pdb=" N GLN D 30 " --> pdb=" O ARG D 27 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY D 32 " --> pdb=" O GLU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 45 removed outlier: 3.710A pdb=" N ALA D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY D 45 " --> pdb=" O LEU D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 54 Processing helix chain 'D' and resid 56 through 62 removed outlier: 3.835A pdb=" N LEU D 60 " --> pdb=" O PRO D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 79 removed outlier: 3.522A pdb=" N LYS D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 82 No H-bonds generated for 'chain 'D' and resid 80 through 82' Processing helix chain 'D' and resid 89 through 97 Processing helix chain 'D' and resid 106 through 113 Processing helix chain 'D' and resid 132 through 145 removed outlier: 3.631A pdb=" N VAL D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN D 145 " --> pdb=" O ALA D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 151 removed outlier: 6.000A pdb=" N ASP D 149 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 179 Processing helix chain 'D' and resid 181 through 188 Processing helix chain 'D' and resid 196 through 211 removed outlier: 3.838A pdb=" N LEU D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN D 206 " --> pdb=" O GLN D 202 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA D 209 " --> pdb=" O TYR D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 232 removed outlier: 3.669A pdb=" N ARG D 229 " --> pdb=" O THR D 225 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 260 Processing helix chain 'D' and resid 288 through 296 removed outlier: 3.715A pdb=" N ILE D 292 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER D 296 " --> pdb=" O ILE D 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 32 Processing helix chain 'E' and resid 34 through 45 removed outlier: 3.649A pdb=" N VAL E 38 " --> pdb=" O ASN E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 54 removed outlier: 3.554A pdb=" N VAL E 52 " --> pdb=" O THR E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 62 Processing helix chain 'E' and resid 67 through 82 Processing helix chain 'E' and resid 89 through 97 Processing helix chain 'E' and resid 106 through 114 Processing helix chain 'E' and resid 132 through 144 Processing helix chain 'E' and resid 167 through 179 removed outlier: 3.896A pdb=" N LEU E 171 " --> pdb=" O ARG E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'E' and resid 196 through 211 removed outlier: 3.812A pdb=" N LEU E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 232 removed outlier: 3.887A pdb=" N ARG E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 260 Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'F' and resid 27 through 32 removed outlier: 3.530A pdb=" N GLY F 32 " --> pdb=" O GLU F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 43 removed outlier: 3.892A pdb=" N GLU F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 55 Processing helix chain 'F' and resid 56 through 63 removed outlier: 3.654A pdb=" N LEU F 60 " --> pdb=" O PRO F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 82 removed outlier: 3.539A pdb=" N LYS F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU F 77 " --> pdb=" O LYS F 73 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS F 80 " --> pdb=" O ALA F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 98 removed outlier: 3.516A pdb=" N PHE F 92 " --> pdb=" O THR F 88 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU F 98 " --> pdb=" O GLN F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 114 Processing helix chain 'F' and resid 132 through 144 removed outlier: 3.578A pdb=" N VAL F 142 " --> pdb=" O HIS F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 146 No H-bonds generated for 'chain 'F' and resid 145 through 146' Processing helix chain 'F' and resid 147 through 151 Processing helix chain 'F' and resid 167 through 178 removed outlier: 3.709A pdb=" N LEU F 171 " --> pdb=" O ARG F 167 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL F 174 " --> pdb=" O ARG F 170 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 188 Processing helix chain 'F' and resid 196 through 214 removed outlier: 3.531A pdb=" N THR F 201 " --> pdb=" O THR F 197 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU F 204 " --> pdb=" O GLN F 200 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN F 206 " --> pdb=" O GLN F 202 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER F 208 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA F 209 " --> pdb=" O TYR F 205 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU F 213 " --> pdb=" O ALA F 209 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER F 214 " --> pdb=" O MET F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 232 removed outlier: 4.214A pdb=" N THR F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 236 No H-bonds generated for 'chain 'F' and resid 234 through 236' Processing helix chain 'F' and resid 237 through 260 Processing helix chain 'F' and resid 288 through 296 removed outlier: 3.804A pdb=" N ILE F 292 " --> pdb=" O GLY F 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 6 removed outlier: 3.609A pdb=" N ALA H 6 " --> pdb=" O ARG H 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 6 removed outlier: 3.584A pdb=" N ALA I 6 " --> pdb=" O ARG I 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 10 removed outlier: 3.658A pdb=" N LEU J 10 " --> pdb=" O PRO J 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 6 removed outlier: 3.613A pdb=" N ALA K 6 " --> pdb=" O ARG K 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 6 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 5.575A pdb=" N LYS B 156 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 218 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG B 299 " --> pdb=" O TYR B 315 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N CYS B 312 " --> pdb=" O ALA B 325 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 193 removed outlier: 5.571A pdb=" N LYS A 156 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 218 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 220 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 262 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY A 127 " --> pdb=" O ASN A 267 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE A 122 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N LEU A 300 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLU A 124 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU A 302 " --> pdb=" O GLU A 124 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE A 126 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N LYS A 304 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG A 299 " --> pdb=" O TYR A 315 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA5, first strand: chain 'B' and resid 87 through 88 removed outlier: 5.360A pdb=" N LYS C 156 " --> pdb=" O TYR C 216 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA C 217 " --> pdb=" O ALA C 262 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL C 264 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU C 219 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N THR C 266 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL C 221 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY C 127 " --> pdb=" O ASN C 267 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TYR C 301 " --> pdb=" O ILE C 314 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE C 314 " --> pdb=" O TYR C 301 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ARG C 303 " --> pdb=" O CYS C 312 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N CYS C 312 " --> pdb=" O ARG C 303 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'B' and resid 269 through 271 Processing sheet with id=AA8, first strand: chain 'C' and resid 87 through 88 removed outlier: 5.203A pdb=" N LYS D 156 " --> pdb=" O TYR D 216 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA D 217 " --> pdb=" O ALA D 262 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL D 264 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU D 219 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N THR D 266 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL D 221 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY D 127 " --> pdb=" O ASN D 267 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR D 298 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ARG D 299 " --> pdb=" O TYR D 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AB1, first strand: chain 'C' and resid 269 through 271 Processing sheet with id=AB2, first strand: chain 'D' and resid 87 through 88 removed outlier: 6.907A pdb=" N LYS E 156 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU E 219 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N MET E 158 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL E 221 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE E 160 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR E 123 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ASN E 267 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N MET E 125 " --> pdb=" O ASN E 267 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR E 301 " --> pdb=" O ILE E 314 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ILE E 314 " --> pdb=" O TYR E 301 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ARG E 303 " --> pdb=" O CYS E 312 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N CYS E 312 " --> pdb=" O ARG E 303 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS E 312 " --> pdb=" O ALA E 325 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY E 333 " --> pdb=" O ASN E 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AB4, first strand: chain 'D' and resid 269 through 271 Processing sheet with id=AB5, first strand: chain 'E' and resid 87 through 88 removed outlier: 5.275A pdb=" N LYS F 156 " --> pdb=" O TYR F 216 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA F 217 " --> pdb=" O ALA F 262 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N VAL F 264 " --> pdb=" O ALA F 217 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU F 219 " --> pdb=" O VAL F 264 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N THR F 266 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL F 221 " --> pdb=" O THR F 266 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY F 127 " --> pdb=" O ASN F 267 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARG F 299 " --> pdb=" O TYR F 315 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 101 through 102 Processing sheet with id=AB7, first strand: chain 'E' and resid 269 through 271 Processing sheet with id=AB8, first strand: chain 'F' and resid 101 through 102 Processing sheet with id=AB9, first strand: chain 'F' and resid 269 through 271 749 hydrogen bonds defined for protein. 2088 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3945 1.33 - 1.45: 2963 1.45 - 1.57: 9008 1.57 - 1.69: 74 1.69 - 1.81: 138 Bond restraints: 16128 Sorted by residual: bond pdb=" C ACE H 0 " pdb=" N MET H 1 " ideal model delta sigma weight residual 1.329 1.420 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C ACE J 0 " pdb=" N MET J 1 " ideal model delta sigma weight residual 1.329 1.418 -0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" C ACE G 0 " pdb=" N MET G 1 " ideal model delta sigma weight residual 1.329 1.418 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C ACE K 0 " pdb=" N MET K 1 " ideal model delta sigma weight residual 1.329 1.418 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C ACE L 0 " pdb=" N MET L 1 " ideal model delta sigma weight residual 1.329 1.417 -0.088 2.00e-02 2.50e+03 1.93e+01 ... (remaining 16123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 21629 2.68 - 5.36: 207 5.36 - 8.05: 21 8.05 - 10.73: 9 10.73 - 13.41: 2 Bond angle restraints: 21868 Sorted by residual: angle pdb=" N ARG J 3 " pdb=" CA ARG J 3 " pdb=" CB ARG J 3 " ideal model delta sigma weight residual 110.22 97.68 12.54 1.54e+00 4.22e-01 6.63e+01 angle pdb=" C ARG J 3 " pdb=" CA ARG J 3 " pdb=" CB ARG J 3 " ideal model delta sigma weight residual 110.63 124.04 -13.41 1.85e+00 2.92e-01 5.26e+01 angle pdb=" O ARG J 2 " pdb=" C ARG J 2 " pdb=" N ARG J 3 " ideal model delta sigma weight residual 123.23 117.18 6.05 1.30e+00 5.92e-01 2.17e+01 angle pdb=" N ALA J 5 " pdb=" CA ALA J 5 " pdb=" C ALA J 5 " ideal model delta sigma weight residual 112.38 107.28 5.10 1.22e+00 6.72e-01 1.75e+01 angle pdb=" C ARG J 2 " pdb=" N ARG J 3 " pdb=" CA ARG J 3 " ideal model delta sigma weight residual 120.28 114.48 5.80 1.44e+00 4.82e-01 1.62e+01 ... (remaining 21863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 8242 17.80 - 35.60: 1166 35.60 - 53.40: 418 53.40 - 71.20: 86 71.20 - 89.00: 22 Dihedral angle restraints: 9934 sinusoidal: 4277 harmonic: 5657 Sorted by residual: dihedral pdb=" N ARG J 3 " pdb=" C ARG J 3 " pdb=" CA ARG J 3 " pdb=" CB ARG J 3 " ideal model delta harmonic sigma weight residual 122.80 113.38 9.42 0 2.50e+00 1.60e-01 1.42e+01 dihedral pdb=" CG ARG L 2 " pdb=" CD ARG L 2 " pdb=" NE ARG L 2 " pdb=" CZ ARG L 2 " ideal model delta sinusoidal sigma weight residual -90.00 -39.50 -50.50 2 1.50e+01 4.44e-03 1.27e+01 dihedral pdb=" CG ARG D 95 " pdb=" CD ARG D 95 " pdb=" NE ARG D 95 " pdb=" CZ ARG D 95 " ideal model delta sinusoidal sigma weight residual -90.00 -39.50 -50.50 2 1.50e+01 4.44e-03 1.27e+01 ... (remaining 9931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1950 0.047 - 0.093: 385 0.093 - 0.140: 123 0.140 - 0.186: 6 0.186 - 0.233: 4 Chirality restraints: 2468 Sorted by residual: chirality pdb=" CA SER J 8 " pdb=" N SER J 8 " pdb=" C SER J 8 " pdb=" CB SER J 8 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PRO J 7 " pdb=" N PRO J 7 " pdb=" C PRO J 7 " pdb=" CB PRO J 7 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CG LEU B 300 " pdb=" CB LEU B 300 " pdb=" CD1 LEU B 300 " pdb=" CD2 LEU B 300 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2465 not shown) Planarity restraints: 2745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN K 9 " -0.034 2.00e-02 2.50e+03 6.86e-02 4.70e+01 pdb=" C GLN K 9 " 0.119 2.00e-02 2.50e+03 pdb=" O GLN K 9 " -0.045 2.00e-02 2.50e+03 pdb=" N LEU K 10 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 3 " -0.522 9.50e-02 1.11e+02 2.34e-01 3.36e+01 pdb=" NE ARG J 3 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG J 3 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG J 3 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG J 3 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG J 2 " -0.025 2.00e-02 2.50e+03 4.86e-02 2.36e+01 pdb=" C ARG J 2 " 0.084 2.00e-02 2.50e+03 pdb=" O ARG J 2 " -0.031 2.00e-02 2.50e+03 pdb=" N ARG J 3 " -0.028 2.00e-02 2.50e+03 ... (remaining 2742 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.56: 11 2.56 - 3.21: 13768 3.21 - 3.85: 29403 3.85 - 4.50: 42267 4.50 - 5.14: 68268 Nonbonded interactions: 153717 Sorted by model distance: nonbonded pdb="MG MG E 401 " pdb=" O1G ATP E 403 " model vdw 1.917 2.170 nonbonded pdb=" N LEU K 10 " pdb=" O LEU K 10 " model vdw 2.422 2.496 nonbonded pdb=" CB ARG J 3 " pdb=" NE ARG J 3 " model vdw 2.449 2.816 nonbonded pdb=" O LEU C 253 " pdb=" OD1 ASP C 257 " model vdw 2.465 3.040 nonbonded pdb=" N GLU A 91 " pdb=" OE1 GLU A 91 " model vdw 2.471 3.120 ... (remaining 153712 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 71 or (resid 72 and (name N or name CA or name \ C or name O or name CB )) or resid 73 through 339)) selection = (chain 'B' and (resid 19 through 71 or (resid 72 and (name N or name CA or name \ C or name O or name CB )) or resid 73 through 273 or resid 283 through 339)) selection = (chain 'C' and (resid 19 through 71 or (resid 72 and (name N or name CA or name \ C or name O or name CB )) or resid 73 through 273 or resid 283 through 339)) selection = (chain 'D' and (resid 19 through 71 or (resid 72 and (name N or name CA or name \ C or name O or name CB )) or resid 73 through 273 or resid 283 through 339)) selection = (chain 'E' and (resid 19 through 71 or (resid 72 and (name N or name CA or name \ C or name O or name CB )) or resid 73 through 273 or resid 283 through 339)) selection = (chain 'F' and (resid 19 through 273 or resid 283 through 339)) } ncs_group { reference = (chain 'H' and (resid 0 through 9 or resid 20 through 24 or (resid 25 and (name \ N or name CA or name C or name O or name CB )) or resid 26)) selection = (chain 'I' and (resid 0 through 9 or resid 20 through 24 or (resid 25 and (name \ N or name CA or name C or name O or name CB )) or resid 26)) selection = (chain 'J' and (resid 0 through 9 or resid 20 through 24 or (resid 25 and (name \ N or name CA or name C or name O or name CB )) or resid 26)) selection = (chain 'K' and (resid 0 through 9 or resid 20 through 26)) selection = (chain 'L' and (resid 0 through 9 or resid 20 through 26)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.770 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 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 : 0.004 0.091 16128 Z= 0.195 Angle : 0.644 13.412 21868 Z= 0.347 Chirality : 0.041 0.233 2468 Planarity : 0.007 0.234 2745 Dihedral : 18.849 88.995 6300 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.82 % Allowed : 36.11 % Favored : 63.07 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.18), residues: 1940 helix: 0.03 (0.17), residues: 836 sheet: 1.25 (0.31), residues: 280 loop : -0.68 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 306 TYR 0.009 0.001 TYR D 216 PHE 0.011 0.001 PHE C 259 HIS 0.003 0.001 HIS F 138 Details of bonding type rmsd covalent geometry : bond 0.00383 (16128) covalent geometry : angle 0.64428 (21868) hydrogen bonds : bond 0.20717 ( 749) hydrogen bonds : angle 7.12229 ( 2088) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 277 time to evaluate : 0.607 Fit side-chains REVERT: A 96 ARG cc_start: 0.7996 (tpt-90) cc_final: 0.7552 (mtp85) REVERT: A 247 ARG cc_start: 0.8040 (ttm-80) cc_final: 0.7691 (mmt-90) REVERT: A 329 ILE cc_start: 0.6099 (mt) cc_final: 0.5855 (mt) REVERT: B 108 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7759 (tm-30) REVERT: B 202 GLN cc_start: 0.7415 (mt0) cc_final: 0.6875 (tm-30) REVERT: B 243 MET cc_start: 0.7663 (mtp) cc_final: 0.6985 (mpt) REVERT: B 251 MET cc_start: 0.7652 (mtt) cc_final: 0.6689 (tpt) REVERT: B 306 ARG cc_start: 0.7049 (ptm-80) cc_final: 0.6315 (mmp-170) REVERT: C 27 ARG cc_start: 0.8379 (tpp-160) cc_final: 0.8019 (mmm160) REVERT: D 95 ARG cc_start: 0.8168 (ttm-80) cc_final: 0.7676 (ttt-90) REVERT: D 243 MET cc_start: 0.8136 (mtp) cc_final: 0.7777 (mtt) REVERT: D 247 ARG cc_start: 0.7881 (mmm-85) cc_final: 0.7664 (ttm110) REVERT: D 254 ARG cc_start: 0.7530 (ttp-170) cc_final: 0.7266 (ttt180) REVERT: E 39 LYS cc_start: 0.8133 (ttpt) cc_final: 0.7803 (tmmt) REVERT: E 98 GLU cc_start: 0.6561 (mp0) cc_final: 0.6227 (tp30) REVERT: E 107 LYS cc_start: 0.7241 (ttmm) cc_final: 0.6958 (tppp) REVERT: E 163 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6576 (mt-10) REVERT: F 68 GLU cc_start: 0.7480 (tp30) cc_final: 0.7151 (mm-30) REVERT: F 107 LYS cc_start: 0.7650 (mmpt) cc_final: 0.7039 (mttm) REVERT: F 250 ARG cc_start: 0.7068 (mtt180) cc_final: 0.5777 (tpt-90) REVERT: F 326 MET cc_start: 0.8456 (ttm) cc_final: 0.8246 (ttt) REVERT: F 330 ASN cc_start: 0.7649 (m-40) cc_final: 0.7428 (m-40) REVERT: H 2 ARG cc_start: 0.7778 (tpp80) cc_final: 0.7556 (mtp180) REVERT: J 3 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6731 (mmm-85) outliers start: 13 outliers final: 7 residues processed: 282 average time/residue: 0.8350 time to fit residues: 253.5412 Evaluate side-chains 205 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 197 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain J residue 3 ARG Chi-restraints excluded: chain K residue 1 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS A 267 ASN ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 HIS D 272 GLN E 242 GLN E 330 ASN F 202 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.186716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.155372 restraints weight = 19417.268| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.12 r_work: 0.3819 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16128 Z= 0.149 Angle : 0.528 8.921 21868 Z= 0.281 Chirality : 0.041 0.148 2468 Planarity : 0.004 0.041 2745 Dihedral : 12.012 89.459 2679 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 5.67 % Allowed : 29.36 % Favored : 64.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.18), residues: 1940 helix: 0.45 (0.18), residues: 842 sheet: 1.08 (0.31), residues: 278 loop : -0.53 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 95 TYR 0.010 0.001 TYR F 159 PHE 0.013 0.001 PHE F 195 HIS 0.005 0.001 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00336 (16128) covalent geometry : angle 0.52845 (21868) hydrogen bonds : bond 0.04451 ( 749) hydrogen bonds : angle 5.02724 ( 2088) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 194 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.8026 (tpt-90) cc_final: 0.7728 (mtp85) REVERT: A 247 ARG cc_start: 0.7807 (ttm-80) cc_final: 0.7311 (mmt-90) REVERT: B 108 GLU cc_start: 0.7745 (mt-10) cc_final: 0.6892 (tm-30) REVERT: B 202 GLN cc_start: 0.7284 (mt0) cc_final: 0.6839 (tm-30) REVERT: B 243 MET cc_start: 0.7254 (mtp) cc_final: 0.6466 (mpt) REVERT: B 251 MET cc_start: 0.7602 (mtt) cc_final: 0.6826 (tpt) REVERT: B 306 ARG cc_start: 0.6744 (ptm-80) cc_final: 0.5974 (mmp-170) REVERT: C 27 ARG cc_start: 0.8571 (tpp-160) cc_final: 0.7938 (mmm160) REVERT: C 39 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7198 (mmtm) REVERT: C 133 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7814 (pttm) REVERT: C 193 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.7058 (ttp-170) REVERT: D 37 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.6603 (t0) REVERT: D 57 LYS cc_start: 0.7956 (ttpp) cc_final: 0.7622 (tttm) REVERT: D 95 ARG cc_start: 0.8288 (ttm-80) cc_final: 0.7750 (ttp-170) REVERT: D 107 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7726 (mmtt) REVERT: D 148 ILE cc_start: 0.6851 (tp) cc_final: 0.6411 (mt) REVERT: D 243 MET cc_start: 0.8499 (mtp) cc_final: 0.8183 (mtt) REVERT: D 247 ARG cc_start: 0.8006 (mmm-85) cc_final: 0.7663 (ttm110) REVERT: E 39 LYS cc_start: 0.7916 (ttpt) cc_final: 0.7288 (tmmt) REVERT: E 98 GLU cc_start: 0.6470 (mp0) cc_final: 0.6021 (tp30) REVERT: E 107 LYS cc_start: 0.7060 (ttmm) cc_final: 0.6624 (tppp) REVERT: E 150 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7211 (mtm180) REVERT: E 163 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6862 (pt0) REVERT: E 326 MET cc_start: 0.7799 (tpt) cc_final: 0.7386 (tpt) REVERT: F 75 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6888 (mt) REVERT: F 107 LYS cc_start: 0.7363 (mmpt) cc_final: 0.6379 (mttm) REVERT: F 250 ARG cc_start: 0.6634 (mtt180) cc_final: 0.5312 (tpt-90) REVERT: F 326 MET cc_start: 0.8670 (ttm) cc_final: 0.8349 (ttp) REVERT: H 1 MET cc_start: 0.7822 (mtp) cc_final: 0.7399 (mtt) REVERT: H 2 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7185 (mtp180) REVERT: L 1 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7391 (mpp) outliers start: 90 outliers final: 29 residues processed: 265 average time/residue: 0.7595 time to fit residues: 218.0673 Evaluate side-chains 213 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 306 ARG Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain H residue 2 ARG Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain L residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 52 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 123 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN D 272 GLN F 206 GLN F 242 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.186533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.155824 restraints weight = 19402.176| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.06 r_work: 0.3825 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16128 Z= 0.120 Angle : 0.478 8.539 21868 Z= 0.254 Chirality : 0.040 0.146 2468 Planarity : 0.004 0.037 2745 Dihedral : 11.936 86.039 2670 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 5.17 % Allowed : 29.68 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.19), residues: 1940 helix: 0.63 (0.18), residues: 847 sheet: 0.98 (0.32), residues: 280 loop : -0.43 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 95 TYR 0.009 0.001 TYR F 159 PHE 0.010 0.001 PHE D 126 HIS 0.004 0.001 HIS F 138 Details of bonding type rmsd covalent geometry : bond 0.00272 (16128) covalent geometry : angle 0.47831 (21868) hydrogen bonds : bond 0.03718 ( 749) hydrogen bonds : angle 4.61067 ( 2088) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 204 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.8024 (pt0) REVERT: A 96 ARG cc_start: 0.8061 (tpt-90) cc_final: 0.7672 (mtp85) REVERT: A 247 ARG cc_start: 0.7770 (ttm-80) cc_final: 0.7280 (mmt-90) REVERT: A 329 ILE cc_start: 0.5372 (mt) cc_final: 0.5152 (mt) REVERT: B 95 ARG cc_start: 0.8282 (ttp80) cc_final: 0.7959 (tmm160) REVERT: B 108 GLU cc_start: 0.7769 (mt-10) cc_final: 0.6877 (tm-30) REVERT: B 136 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7531 (mp) REVERT: B 202 GLN cc_start: 0.7354 (mt0) cc_final: 0.6805 (tm-30) REVERT: B 243 MET cc_start: 0.7191 (mtp) cc_final: 0.6409 (mpt) REVERT: B 251 MET cc_start: 0.7571 (mtt) cc_final: 0.6876 (tpt) REVERT: B 306 ARG cc_start: 0.6779 (ptm-80) cc_final: 0.5968 (mmp-170) REVERT: B 324 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7694 (mt-10) REVERT: C 39 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7275 (mmtm) REVERT: C 193 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.7063 (ttp-170) REVERT: D 39 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7873 (mmtt) REVERT: D 75 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7363 (mm) REVERT: D 95 ARG cc_start: 0.8302 (ttm-80) cc_final: 0.7769 (ttp-170) REVERT: D 107 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7720 (mmtt) REVERT: D 148 ILE cc_start: 0.6684 (tp) cc_final: 0.6440 (mt) REVERT: D 214 SER cc_start: 0.8370 (OUTLIER) cc_final: 0.8060 (t) REVERT: D 243 MET cc_start: 0.8480 (mtp) cc_final: 0.8186 (mtt) REVERT: D 247 ARG cc_start: 0.8004 (mmm-85) cc_final: 0.7649 (ttm170) REVERT: E 39 LYS cc_start: 0.8003 (ttpt) cc_final: 0.7398 (tmmt) REVERT: E 98 GLU cc_start: 0.6580 (mp0) cc_final: 0.5989 (tp30) REVERT: E 107 LYS cc_start: 0.7057 (ttmm) cc_final: 0.6638 (tppp) REVERT: E 150 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7130 (mtm180) REVERT: E 163 GLU cc_start: 0.7464 (mm-30) cc_final: 0.6904 (pt0) REVERT: F 75 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6875 (mt) REVERT: F 107 LYS cc_start: 0.7503 (mmpt) cc_final: 0.6418 (mttm) REVERT: F 230 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7816 (p) REVERT: F 250 ARG cc_start: 0.6723 (mtt180) cc_final: 0.5318 (tpt-90) REVERT: F 251 MET cc_start: 0.8518 (tpt) cc_final: 0.7333 (ttp) REVERT: F 270 VAL cc_start: 0.7574 (OUTLIER) cc_final: 0.7243 (p) REVERT: F 326 MET cc_start: 0.8669 (ttm) cc_final: 0.8332 (ttp) REVERT: H 1 MET cc_start: 0.7846 (mtp) cc_final: 0.7499 (mtt) REVERT: H 2 ARG cc_start: 0.7490 (tpp80) cc_final: 0.7142 (mtp180) REVERT: I 20 PHE cc_start: 0.6620 (t80) cc_final: 0.6388 (t80) REVERT: L 1 MET cc_start: 0.7884 (mtp) cc_final: 0.7415 (mpp) outliers start: 82 outliers final: 26 residues processed: 268 average time/residue: 0.7567 time to fit residues: 220.1571 Evaluate side-chains 225 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 186 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain I residue 21 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 183 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS A 244 HIS A 267 ASN ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 HIS D 272 GLN F 206 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.181210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.150323 restraints weight = 19302.342| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.05 r_work: 0.3759 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16128 Z= 0.197 Angle : 0.563 13.562 21868 Z= 0.296 Chirality : 0.043 0.151 2468 Planarity : 0.004 0.042 2745 Dihedral : 12.342 89.865 2667 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 6.30 % Allowed : 28.29 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.19), residues: 1940 helix: 0.40 (0.18), residues: 846 sheet: 0.81 (0.32), residues: 280 loop : -0.40 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 3 TYR 0.014 0.002 TYR F 159 PHE 0.010 0.002 PHE B 327 HIS 0.005 0.001 HIS F 138 Details of bonding type rmsd covalent geometry : bond 0.00468 (16128) covalent geometry : angle 0.56329 (21868) hydrogen bonds : bond 0.04725 ( 749) hydrogen bonds : angle 4.83005 ( 2088) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 209 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8065 (pt0) REVERT: A 96 ARG cc_start: 0.8132 (tpt-90) cc_final: 0.7872 (mtp85) REVERT: A 247 ARG cc_start: 0.7858 (ttm-80) cc_final: 0.7369 (mmt-90) REVERT: A 292 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7368 (tp) REVERT: A 329 ILE cc_start: 0.5411 (mt) cc_final: 0.5131 (mt) REVERT: B 58 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7853 (ptpp) REVERT: B 91 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6499 (mp0) REVERT: B 95 ARG cc_start: 0.8270 (ttp80) cc_final: 0.7964 (tmm160) REVERT: B 136 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7531 (mp) REVERT: B 202 GLN cc_start: 0.7379 (mt0) cc_final: 0.6647 (tm-30) REVERT: B 243 MET cc_start: 0.7265 (mtp) cc_final: 0.6416 (mpt) REVERT: B 251 MET cc_start: 0.7644 (mtt) cc_final: 0.6880 (tpt) REVERT: B 306 ARG cc_start: 0.6756 (ptm-80) cc_final: 0.5967 (mmp-170) REVERT: C 39 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7215 (mmtm) REVERT: C 94 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7991 (tp40) REVERT: C 193 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7135 (ttp-170) REVERT: C 306 ARG cc_start: 0.6500 (OUTLIER) cc_final: 0.6256 (mmt-90) REVERT: D 39 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7885 (mmtt) REVERT: D 95 ARG cc_start: 0.8350 (ttm-80) cc_final: 0.7891 (ttp-170) REVERT: D 107 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7692 (mmtt) REVERT: D 218 LEU cc_start: 0.7882 (tp) cc_final: 0.7660 (tp) REVERT: D 243 MET cc_start: 0.8508 (mtp) cc_final: 0.8191 (mtt) REVERT: D 247 ARG cc_start: 0.8045 (mmm-85) cc_final: 0.7682 (ttm170) REVERT: E 39 LYS cc_start: 0.8006 (ttpt) cc_final: 0.7361 (tmmt) REVERT: E 98 GLU cc_start: 0.6738 (mp0) cc_final: 0.5936 (tp30) REVERT: E 107 LYS cc_start: 0.7104 (ttmm) cc_final: 0.6682 (tppp) REVERT: E 150 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7189 (mtt180) REVERT: E 163 GLU cc_start: 0.7650 (mm-30) cc_final: 0.6842 (mt-10) REVERT: E 251 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.6811 (tpt) REVERT: F 75 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.7030 (mp) REVERT: F 103 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8163 (t) REVERT: F 107 LYS cc_start: 0.7483 (mmpt) cc_final: 0.6433 (mttm) REVERT: F 111 LYS cc_start: 0.7770 (mtpp) cc_final: 0.7247 (ttpp) REVERT: F 230 THR cc_start: 0.8019 (OUTLIER) cc_final: 0.7729 (p) REVERT: F 250 ARG cc_start: 0.6819 (mtt180) cc_final: 0.5329 (tpt-90) REVERT: F 326 MET cc_start: 0.8697 (ttm) cc_final: 0.8209 (ttm) REVERT: H 2 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7265 (mtp180) REVERT: L 1 MET cc_start: 0.7958 (mtp) cc_final: 0.7261 (mpp) outliers start: 100 outliers final: 40 residues processed: 288 average time/residue: 0.7396 time to fit residues: 231.2321 Evaluate side-chains 244 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 187 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 306 ARG Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain H residue 2 ARG Chi-restraints excluded: chain I residue 21 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 44 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 199 HIS ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN D 272 GLN F 206 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.181249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.150407 restraints weight = 19463.383| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.05 r_work: 0.3762 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16128 Z= 0.176 Angle : 0.541 13.480 21868 Z= 0.283 Chirality : 0.042 0.152 2468 Planarity : 0.004 0.044 2745 Dihedral : 12.353 89.857 2667 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 6.11 % Allowed : 29.11 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.19), residues: 1940 helix: 0.30 (0.18), residues: 856 sheet: 0.71 (0.32), residues: 275 loop : -0.42 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 3 TYR 0.013 0.001 TYR F 159 PHE 0.011 0.001 PHE B 327 HIS 0.004 0.001 HIS F 138 Details of bonding type rmsd covalent geometry : bond 0.00416 (16128) covalent geometry : angle 0.54088 (21868) hydrogen bonds : bond 0.04333 ( 749) hydrogen bonds : angle 4.74663 ( 2088) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 198 time to evaluate : 0.593 Fit side-chains REVERT: A 23 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7936 (pt0) REVERT: A 124 GLU cc_start: 0.7966 (tp30) cc_final: 0.7674 (mm-30) REVERT: A 247 ARG cc_start: 0.7876 (ttm-80) cc_final: 0.7373 (mmt-90) REVERT: A 252 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7407 (mp) REVERT: A 292 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7348 (tp) REVERT: B 58 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.7929 (ptpp) REVERT: B 95 ARG cc_start: 0.8276 (ttp80) cc_final: 0.7972 (tmm160) REVERT: B 136 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7535 (mp) REVERT: B 202 GLN cc_start: 0.7383 (mt0) cc_final: 0.6691 (tm-30) REVERT: B 243 MET cc_start: 0.7256 (mtp) cc_final: 0.6418 (mpt) REVERT: B 251 MET cc_start: 0.7586 (mtt) cc_final: 0.6841 (tpt) REVERT: B 306 ARG cc_start: 0.6729 (ptm-80) cc_final: 0.5942 (mmp-170) REVERT: C 193 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7121 (ttp-170) REVERT: C 306 ARG cc_start: 0.6525 (OUTLIER) cc_final: 0.6190 (mmt-90) REVERT: D 39 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7867 (mmtt) REVERT: D 72 ASP cc_start: 0.8380 (t0) cc_final: 0.7626 (p0) REVERT: D 95 ARG cc_start: 0.8311 (ttm-80) cc_final: 0.7820 (ttp-170) REVERT: D 107 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7709 (mmtt) REVERT: D 148 ILE cc_start: 0.6729 (tp) cc_final: 0.6327 (mm) REVERT: D 218 LEU cc_start: 0.7915 (tp) cc_final: 0.7687 (tp) REVERT: D 243 MET cc_start: 0.8526 (mtp) cc_final: 0.8206 (mtt) REVERT: D 247 ARG cc_start: 0.8028 (mmm-85) cc_final: 0.7663 (ttm170) REVERT: D 308 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7309 (pm20) REVERT: E 39 LYS cc_start: 0.7977 (ttpt) cc_final: 0.7334 (tmmt) REVERT: E 98 GLU cc_start: 0.6806 (mp0) cc_final: 0.5905 (tp30) REVERT: E 107 LYS cc_start: 0.7099 (ttmm) cc_final: 0.6700 (tppp) REVERT: E 150 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7145 (mtt180) REVERT: E 163 GLU cc_start: 0.7647 (mm-30) cc_final: 0.6856 (mt-10) REVERT: F 75 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.7037 (mp) REVERT: F 103 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.8115 (t) REVERT: F 107 LYS cc_start: 0.7526 (mmpt) cc_final: 0.6387 (mttm) REVERT: F 111 LYS cc_start: 0.7757 (mtpp) cc_final: 0.7250 (ttpp) REVERT: F 230 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7677 (p) REVERT: F 250 ARG cc_start: 0.6840 (mtt180) cc_final: 0.5385 (tpt-90) REVERT: F 306 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6780 (mmt180) REVERT: F 326 MET cc_start: 0.8716 (ttm) cc_final: 0.8262 (ttm) REVERT: H 2 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7251 (mtp180) outliers start: 97 outliers final: 44 residues processed: 274 average time/residue: 0.7502 time to fit residues: 222.8924 Evaluate side-chains 245 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 185 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 306 ARG Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 306 ARG Chi-restraints excluded: chain H residue 2 ARG Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 3 ARG Chi-restraints excluded: chain J residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 154 optimal weight: 0.1980 chunk 125 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 137 optimal weight: 0.0980 chunk 123 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 168 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 HIS A 267 ASN A 272 GLN C 62 ASN D 272 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.186340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.155833 restraints weight = 19297.121| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.04 r_work: 0.3825 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16128 Z= 0.096 Angle : 0.454 10.346 21868 Z= 0.240 Chirality : 0.039 0.154 2468 Planarity : 0.003 0.039 2745 Dihedral : 11.949 83.473 2667 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.40 % Allowed : 31.57 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.19), residues: 1940 helix: 0.63 (0.18), residues: 858 sheet: 0.73 (0.32), residues: 267 loop : -0.39 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 3 TYR 0.010 0.001 TYR E 205 PHE 0.010 0.001 PHE B 126 HIS 0.002 0.000 HIS C 93 Details of bonding type rmsd covalent geometry : bond 0.00206 (16128) covalent geometry : angle 0.45393 (21868) hydrogen bonds : bond 0.03061 ( 749) hydrogen bonds : angle 4.38322 ( 2088) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 204 time to evaluate : 0.586 Fit side-chains REVERT: A 23 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7957 (pt0) REVERT: A 125 MET cc_start: 0.6890 (mmt) cc_final: 0.6627 (mmt) REVERT: A 247 ARG cc_start: 0.7887 (ttm-80) cc_final: 0.7350 (mmt-90) REVERT: A 292 ILE cc_start: 0.7562 (OUTLIER) cc_final: 0.7342 (tp) REVERT: B 95 ARG cc_start: 0.8228 (ttp80) cc_final: 0.7886 (tmm160) REVERT: B 108 GLU cc_start: 0.7581 (mt-10) cc_final: 0.6722 (tm-30) REVERT: B 136 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7477 (mp) REVERT: B 202 GLN cc_start: 0.7340 (mt0) cc_final: 0.6680 (tm-30) REVERT: B 243 MET cc_start: 0.7169 (mtp) cc_final: 0.6384 (mpt) REVERT: B 251 MET cc_start: 0.7455 (mtt) cc_final: 0.6937 (tpt) REVERT: B 306 ARG cc_start: 0.6805 (ptm-80) cc_final: 0.5859 (mmp-170) REVERT: C 39 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7290 (mmtm) REVERT: D 57 LYS cc_start: 0.7895 (ttpp) cc_final: 0.7542 (tttm) REVERT: D 95 ARG cc_start: 0.8350 (ttm-80) cc_final: 0.7770 (ttt-90) REVERT: D 107 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7717 (mmtt) REVERT: D 148 ILE cc_start: 0.6749 (tp) cc_final: 0.6374 (mm) REVERT: D 218 LEU cc_start: 0.7736 (tp) cc_final: 0.7395 (tp) REVERT: D 243 MET cc_start: 0.8438 (mtp) cc_final: 0.8146 (mtt) REVERT: D 247 ARG cc_start: 0.7999 (mmm-85) cc_final: 0.7615 (ttm170) REVERT: D 254 ARG cc_start: 0.7240 (ttp-170) cc_final: 0.6132 (tpp-160) REVERT: E 39 LYS cc_start: 0.7946 (ttpt) cc_final: 0.7304 (tmmt) REVERT: E 98 GLU cc_start: 0.6568 (mp0) cc_final: 0.5851 (tp30) REVERT: E 107 LYS cc_start: 0.7079 (ttmm) cc_final: 0.6639 (tppp) REVERT: E 163 GLU cc_start: 0.7502 (mm-30) cc_final: 0.6905 (pt0) REVERT: F 57 LYS cc_start: 0.7965 (tttt) cc_final: 0.7759 (ttpp) REVERT: F 75 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6908 (mp) REVERT: F 103 THR cc_start: 0.8208 (OUTLIER) cc_final: 0.7992 (t) REVERT: F 107 LYS cc_start: 0.7398 (mmpt) cc_final: 0.6293 (mttm) REVERT: F 111 LYS cc_start: 0.7728 (mtpp) cc_final: 0.7301 (ttpp) REVERT: F 230 THR cc_start: 0.7951 (OUTLIER) cc_final: 0.7666 (p) REVERT: F 250 ARG cc_start: 0.6785 (mtt180) cc_final: 0.5314 (tpt-90) REVERT: F 251 MET cc_start: 0.8477 (tpt) cc_final: 0.7325 (ttp) REVERT: F 270 VAL cc_start: 0.7546 (OUTLIER) cc_final: 0.7280 (p) REVERT: F 308 GLU cc_start: 0.6478 (mm-30) cc_final: 0.5853 (tp30) REVERT: H 1 MET cc_start: 0.7904 (mtm) cc_final: 0.7615 (mtt) REVERT: H 2 ARG cc_start: 0.7525 (tpp80) cc_final: 0.7156 (mtp180) REVERT: L 1 MET cc_start: 0.7870 (mtp) cc_final: 0.7319 (mpp) outliers start: 54 outliers final: 21 residues processed: 245 average time/residue: 0.7895 time to fit residues: 209.4401 Evaluate side-chains 217 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 306 ARG Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain J residue 1 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 192 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 188 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 HIS C 62 ASN D 272 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.183506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.152880 restraints weight = 19325.078| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.04 r_work: 0.3784 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16128 Z= 0.131 Angle : 0.493 11.823 21868 Z= 0.258 Chirality : 0.040 0.165 2468 Planarity : 0.004 0.046 2745 Dihedral : 12.086 84.617 2667 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.97 % Allowed : 31.19 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.19), residues: 1940 helix: 0.63 (0.18), residues: 859 sheet: 0.75 (0.32), residues: 277 loop : -0.30 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 3 TYR 0.010 0.001 TYR F 159 PHE 0.009 0.001 PHE B 327 HIS 0.002 0.001 HIS F 138 Details of bonding type rmsd covalent geometry : bond 0.00302 (16128) covalent geometry : angle 0.49267 (21868) hydrogen bonds : bond 0.03649 ( 749) hydrogen bonds : angle 4.45391 ( 2088) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 189 time to evaluate : 0.653 Fit side-chains REVERT: A 23 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7989 (pt0) REVERT: A 247 ARG cc_start: 0.7871 (ttm-80) cc_final: 0.7330 (mmt-90) REVERT: B 95 ARG cc_start: 0.8229 (ttp80) cc_final: 0.7896 (tmm160) REVERT: B 108 GLU cc_start: 0.7551 (mt-10) cc_final: 0.6759 (tm-30) REVERT: B 136 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7502 (mp) REVERT: B 202 GLN cc_start: 0.7353 (mt0) cc_final: 0.6679 (tm-30) REVERT: B 243 MET cc_start: 0.7213 (mtp) cc_final: 0.6400 (mpt) REVERT: B 251 MET cc_start: 0.7474 (mtt) cc_final: 0.6874 (tpt) REVERT: B 306 ARG cc_start: 0.6809 (ptm-80) cc_final: 0.5861 (mmp-170) REVERT: C 61 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7615 (mp) REVERT: D 37 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.6738 (t0) REVERT: D 39 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7791 (mmtt) REVERT: D 57 LYS cc_start: 0.7868 (ttpp) cc_final: 0.7481 (tttm) REVERT: D 75 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7344 (mm) REVERT: D 95 ARG cc_start: 0.8307 (ttm-80) cc_final: 0.7783 (ttp-170) REVERT: D 107 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7693 (mmtt) REVERT: D 148 ILE cc_start: 0.6696 (tp) cc_final: 0.6442 (mt) REVERT: D 218 LEU cc_start: 0.7852 (tp) cc_final: 0.7565 (tp) REVERT: D 243 MET cc_start: 0.8482 (mtp) cc_final: 0.8178 (mtt) REVERT: D 247 ARG cc_start: 0.8039 (mmm-85) cc_final: 0.7598 (ttm170) REVERT: D 254 ARG cc_start: 0.7341 (ttp-170) cc_final: 0.6138 (tpp-160) REVERT: D 308 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7349 (pm20) REVERT: E 39 LYS cc_start: 0.7996 (ttpt) cc_final: 0.7323 (tmmt) REVERT: E 59 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: E 98 GLU cc_start: 0.6604 (mp0) cc_final: 0.5814 (tp30) REVERT: E 107 LYS cc_start: 0.7065 (ttmm) cc_final: 0.6610 (tppp) REVERT: E 163 GLU cc_start: 0.7544 (mm-30) cc_final: 0.6814 (mt-10) REVERT: F 75 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6957 (mp) REVERT: F 103 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.8011 (t) REVERT: F 107 LYS cc_start: 0.7437 (mmpt) cc_final: 0.6316 (mttm) REVERT: F 111 LYS cc_start: 0.7711 (mtpp) cc_final: 0.7277 (ttpp) REVERT: F 230 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7690 (p) REVERT: F 250 ARG cc_start: 0.6834 (mtt180) cc_final: 0.5330 (tpt-90) REVERT: F 251 MET cc_start: 0.8472 (tpt) cc_final: 0.7320 (ttp) REVERT: F 306 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6671 (mmt180) REVERT: F 308 GLU cc_start: 0.6482 (mm-30) cc_final: 0.5818 (tp30) REVERT: F 326 MET cc_start: 0.8720 (ttp) cc_final: 0.8316 (ttm) REVERT: H 2 ARG cc_start: 0.7575 (tpp80) cc_final: 0.7265 (mtp180) REVERT: L 1 MET cc_start: 0.7935 (mtp) cc_final: 0.7303 (mpp) outliers start: 63 outliers final: 33 residues processed: 242 average time/residue: 0.7545 time to fit residues: 198.3330 Evaluate side-chains 227 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 306 ARG Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 306 ARG Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 3 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 196 optimal weight: 6.9990 chunk 182 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS C 62 ASN ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.180595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.152129 restraints weight = 19776.246| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 1.79 r_work: 0.3794 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 16128 Z= 0.265 Angle : 0.645 16.265 21868 Z= 0.334 Chirality : 0.046 0.191 2468 Planarity : 0.005 0.052 2745 Dihedral : 12.757 89.034 2667 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.17 % Allowed : 30.37 % Favored : 64.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.19), residues: 1940 helix: 0.18 (0.18), residues: 856 sheet: 0.60 (0.32), residues: 275 loop : -0.46 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 3 TYR 0.018 0.002 TYR E 228 PHE 0.012 0.002 PHE A 46 HIS 0.005 0.001 HIS F 138 Details of bonding type rmsd covalent geometry : bond 0.00637 (16128) covalent geometry : angle 0.64543 (21868) hydrogen bonds : bond 0.05286 ( 749) hydrogen bonds : angle 4.91539 ( 2088) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 184 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: A 205 TYR cc_start: 0.7934 (m-80) cc_final: 0.7617 (m-10) REVERT: A 247 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7639 (mmt-90) REVERT: B 91 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6755 (mp0) REVERT: B 95 ARG cc_start: 0.8441 (ttp80) cc_final: 0.8132 (tmm160) REVERT: B 202 GLN cc_start: 0.7542 (mt0) cc_final: 0.6944 (tm-30) REVERT: B 251 MET cc_start: 0.7731 (mtt) cc_final: 0.7113 (tpt) REVERT: C 61 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7928 (mp) REVERT: C 306 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6715 (mmt-90) REVERT: D 39 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7956 (mmtt) REVERT: D 57 LYS cc_start: 0.7873 (ttpp) cc_final: 0.7526 (tttm) REVERT: D 72 ASP cc_start: 0.8383 (t0) cc_final: 0.7813 (p0) REVERT: D 75 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7552 (mm) REVERT: D 95 ARG cc_start: 0.8223 (ttm-80) cc_final: 0.7929 (ttp-170) REVERT: D 107 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7800 (mmtt) REVERT: D 148 ILE cc_start: 0.6904 (tp) cc_final: 0.6649 (mt) REVERT: D 243 MET cc_start: 0.8590 (mtp) cc_final: 0.8295 (mtt) REVERT: D 247 ARG cc_start: 0.7959 (mmm-85) cc_final: 0.7745 (ttm170) REVERT: D 272 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7964 (mt0) REVERT: D 308 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7508 (pm20) REVERT: E 39 LYS cc_start: 0.8151 (ttpt) cc_final: 0.7700 (tmmt) REVERT: E 42 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: E 59 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: E 98 GLU cc_start: 0.6899 (mp0) cc_final: 0.6133 (tp30) REVERT: E 107 LYS cc_start: 0.7429 (ttmm) cc_final: 0.7132 (tppp) REVERT: E 163 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7142 (mt-10) REVERT: F 75 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7273 (mp) REVERT: F 111 LYS cc_start: 0.7980 (mtpp) cc_final: 0.7435 (ttpp) REVERT: F 230 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.7967 (p) REVERT: F 250 ARG cc_start: 0.7059 (mtt180) cc_final: 0.5762 (tpt-90) REVERT: F 306 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6985 (mmt180) REVERT: F 308 GLU cc_start: 0.6717 (mm-30) cc_final: 0.6012 (tp30) REVERT: F 326 MET cc_start: 0.8659 (ttp) cc_final: 0.8260 (ttm) REVERT: H 2 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7251 (mtp180) outliers start: 82 outliers final: 44 residues processed: 247 average time/residue: 0.7353 time to fit residues: 197.0151 Evaluate side-chains 232 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 174 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 306 ARG Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 306 ARG Chi-restraints excluded: chain H residue 2 ARG Chi-restraints excluded: chain J residue 3 ARG Chi-restraints excluded: chain J residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 164 optimal weight: 0.8980 chunk 7 optimal weight: 0.0970 chunk 131 optimal weight: 6.9990 chunk 171 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 180 optimal weight: 0.9980 chunk 139 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 167 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS C 62 ASN C 199 HIS D 272 GLN E 290 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.187282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.159762 restraints weight = 19613.317| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 1.74 r_work: 0.3883 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16128 Z= 0.103 Angle : 0.478 11.634 21868 Z= 0.252 Chirality : 0.040 0.166 2468 Planarity : 0.004 0.049 2745 Dihedral : 12.113 83.488 2667 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.96 % Allowed : 32.39 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.19), residues: 1940 helix: 0.52 (0.18), residues: 860 sheet: 0.66 (0.32), residues: 277 loop : -0.38 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 3 TYR 0.007 0.001 TYR F 159 PHE 0.009 0.001 PHE B 126 HIS 0.002 0.000 HIS F 138 Details of bonding type rmsd covalent geometry : bond 0.00226 (16128) covalent geometry : angle 0.47837 (21868) hydrogen bonds : bond 0.03190 ( 749) hydrogen bonds : angle 4.45914 ( 2088) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 0.653 Fit side-chains REVERT: A 125 MET cc_start: 0.6840 (mmt) cc_final: 0.6630 (mmt) REVERT: A 205 TYR cc_start: 0.7897 (m-80) cc_final: 0.7605 (m-10) REVERT: A 247 ARG cc_start: 0.8053 (ttm-80) cc_final: 0.7541 (mmt-90) REVERT: B 95 ARG cc_start: 0.8357 (ttp80) cc_final: 0.8070 (tmm160) REVERT: B 202 GLN cc_start: 0.7460 (mt0) cc_final: 0.6883 (tm-30) REVERT: B 243 MET cc_start: 0.7385 (mtp) cc_final: 0.6653 (mpt) REVERT: B 251 MET cc_start: 0.7566 (mtt) cc_final: 0.7213 (tpt) REVERT: B 306 ARG cc_start: 0.6829 (ptm-80) cc_final: 0.5822 (mmp-170) REVERT: C 39 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7498 (mmtm) REVERT: D 72 ASP cc_start: 0.8328 (t0) cc_final: 0.7760 (p0) REVERT: D 77 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7478 (tm-30) REVERT: D 95 ARG cc_start: 0.8218 (ttm-80) cc_final: 0.7812 (ttp-170) REVERT: D 148 ILE cc_start: 0.6837 (tp) cc_final: 0.6520 (mm) REVERT: D 243 MET cc_start: 0.8424 (mtp) cc_final: 0.8156 (mtt) REVERT: D 254 ARG cc_start: 0.7194 (ttp-170) cc_final: 0.6251 (tpp-160) REVERT: E 42 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: E 98 GLU cc_start: 0.6688 (mp0) cc_final: 0.5983 (tp30) REVERT: E 107 LYS cc_start: 0.7310 (ttmm) cc_final: 0.6990 (tppp) REVERT: E 163 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7105 (mt-10) REVERT: F 75 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7186 (mp) REVERT: F 107 LYS cc_start: 0.7580 (mmpt) cc_final: 0.6659 (mttm) REVERT: F 111 LYS cc_start: 0.7961 (mtpp) cc_final: 0.7412 (ttpp) REVERT: F 193 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.7829 (ttp-170) REVERT: F 230 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7956 (p) REVERT: F 250 ARG cc_start: 0.6987 (mtt180) cc_final: 0.5699 (tpt-90) REVERT: F 251 MET cc_start: 0.8522 (tpt) cc_final: 0.7515 (ttp) REVERT: F 308 GLU cc_start: 0.6553 (mm-30) cc_final: 0.5936 (tp30) REVERT: F 326 MET cc_start: 0.8653 (ttp) cc_final: 0.8298 (ttm) REVERT: H 2 ARG cc_start: 0.7550 (tpp80) cc_final: 0.7235 (mtp180) REVERT: L 1 MET cc_start: 0.7807 (mtp) cc_final: 0.7307 (mpp) outliers start: 47 outliers final: 26 residues processed: 231 average time/residue: 0.7553 time to fit residues: 189.2268 Evaluate side-chains 217 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 306 ARG Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 171 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 192 optimal weight: 0.2980 chunk 100 optimal weight: 4.9990 chunk 190 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 136 optimal weight: 0.4980 chunk 21 optimal weight: 8.9990 chunk 187 optimal weight: 0.0370 chunk 57 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS B 196 ASN C 62 ASN D 272 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.188849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.161338 restraints weight = 19575.882| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 1.76 r_work: 0.3893 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16128 Z= 0.099 Angle : 0.473 9.702 21868 Z= 0.248 Chirality : 0.039 0.159 2468 Planarity : 0.004 0.054 2745 Dihedral : 11.917 84.708 2667 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.46 % Allowed : 32.45 % Favored : 65.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.19), residues: 1940 helix: 0.72 (0.18), residues: 870 sheet: 0.88 (0.33), residues: 262 loop : -0.33 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 3 TYR 0.010 0.001 TYR E 205 PHE 0.011 0.001 PHE A 129 HIS 0.002 0.000 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00216 (16128) covalent geometry : angle 0.47261 (21868) hydrogen bonds : bond 0.03020 ( 749) hydrogen bonds : angle 4.32329 ( 2088) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 0.620 Fit side-chains REVERT: A 46 PHE cc_start: 0.6295 (m-80) cc_final: 0.6052 (m-80) REVERT: A 205 TYR cc_start: 0.7936 (m-80) cc_final: 0.7645 (m-10) REVERT: A 247 ARG cc_start: 0.8053 (ttm-80) cc_final: 0.7524 (mmt-90) REVERT: B 95 ARG cc_start: 0.8344 (ttp80) cc_final: 0.8038 (tmm160) REVERT: B 108 GLU cc_start: 0.7695 (mt-10) cc_final: 0.6954 (tm-30) REVERT: B 202 GLN cc_start: 0.7355 (mt0) cc_final: 0.7013 (tm-30) REVERT: B 243 MET cc_start: 0.7402 (mtp) cc_final: 0.6658 (mpt) REVERT: B 251 MET cc_start: 0.7483 (mtt) cc_final: 0.7231 (tpt) REVERT: B 306 ARG cc_start: 0.6938 (ptm-80) cc_final: 0.5915 (mmp-170) REVERT: C 61 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7832 (mp) REVERT: D 72 ASP cc_start: 0.8306 (t0) cc_final: 0.7736 (p0) REVERT: D 77 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7772 (tm-30) REVERT: D 95 ARG cc_start: 0.8103 (ttm-80) cc_final: 0.7740 (ttt-90) REVERT: D 148 ILE cc_start: 0.6873 (tp) cc_final: 0.6570 (mt) REVERT: D 243 MET cc_start: 0.8419 (mtp) cc_final: 0.8169 (mtt) REVERT: D 254 ARG cc_start: 0.7129 (ttp-170) cc_final: 0.6271 (tpp-160) REVERT: E 23 GLN cc_start: 0.8128 (mp10) cc_final: 0.7774 (mt0) REVERT: E 42 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: E 98 GLU cc_start: 0.6557 (mp0) cc_final: 0.5939 (tp30) REVERT: E 107 LYS cc_start: 0.7295 (ttmm) cc_final: 0.6963 (tppp) REVERT: E 163 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7093 (pt0) REVERT: F 75 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7141 (mp) REVERT: F 107 LYS cc_start: 0.7456 (mmpt) cc_final: 0.6539 (mttm) REVERT: F 109 LEU cc_start: 0.8222 (mm) cc_final: 0.7941 (mm) REVERT: F 111 LYS cc_start: 0.7993 (mtpp) cc_final: 0.7397 (ttpp) REVERT: F 230 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7934 (p) REVERT: F 250 ARG cc_start: 0.6877 (mtt180) cc_final: 0.5589 (tpt-90) REVERT: F 251 MET cc_start: 0.8412 (tpt) cc_final: 0.7448 (ttp) REVERT: F 308 GLU cc_start: 0.6458 (mm-30) cc_final: 0.5855 (tp30) REVERT: F 326 MET cc_start: 0.8689 (ttp) cc_final: 0.8341 (ttm) REVERT: H 2 ARG cc_start: 0.7538 (tpp80) cc_final: 0.7182 (mtp180) REVERT: L 1 MET cc_start: 0.7789 (mtp) cc_final: 0.7273 (mpp) outliers start: 39 outliers final: 26 residues processed: 230 average time/residue: 0.7358 time to fit residues: 183.8744 Evaluate side-chains 215 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 306 ARG Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 113 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 192 optimal weight: 7.9990 chunk 119 optimal weight: 0.0270 chunk 37 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS B 196 ASN C 62 ASN D 272 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.188179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.160819 restraints weight = 19467.319| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 1.73 r_work: 0.3872 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16128 Z= 0.107 Angle : 0.485 9.849 21868 Z= 0.253 Chirality : 0.040 0.159 2468 Planarity : 0.004 0.056 2745 Dihedral : 11.928 85.579 2667 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.08 % Allowed : 33.21 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.19), residues: 1940 helix: 0.73 (0.18), residues: 870 sheet: 0.82 (0.33), residues: 265 loop : -0.29 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 3 TYR 0.010 0.001 TYR B 216 PHE 0.009 0.001 PHE B 126 HIS 0.002 0.000 HIS F 138 Details of bonding type rmsd covalent geometry : bond 0.00240 (16128) covalent geometry : angle 0.48527 (21868) hydrogen bonds : bond 0.03139 ( 749) hydrogen bonds : angle 4.32516 ( 2088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6854.68 seconds wall clock time: 117 minutes 7.15 seconds (7027.15 seconds total)