Starting phenix.real_space_refine on Fri Jul 3 21:03:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ssl_55189/07_2026/9ssl_55189.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ssl_55189/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ssl_55189/07_2026/9ssl_55189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ssl_55189/07_2026/9ssl_55189.map" model { file = "/net/cci-nas-00/data/ceres_data/9ssl_55189/07_2026/9ssl_55189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ssl_55189/07_2026/9ssl_55189.cif" } 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-dev-6108/lib/python3.11/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, 31 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Chain breaks: 1 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Chain breaks: 1 Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Chain breaks: 1 Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Chain breaks: 1 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: 3.40, per 1000 atoms: 0.21 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: 1.20 Conformation dependent library (CDL) restraints added in 595.5 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: 0.28 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: 2.19 Time building geometry restraints manager: 1.44 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: 1928 0.047 - 0.093: 404 0.093 - 0.140: 126 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: 4.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.240 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 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= 0.224 Angle : 0.652 13.412 21868 Z= 0.362 Chirality : 0.042 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/Z covalent geometry : bond 0.00396 / 0.22 (16128) covalent geometry : angle 0.65155 / 0.36 (21868) hydrogen bonds : bond 0.20717 / 13.52 ( 749) hydrogen bonds : angle 7.12229 / 5.04 ( 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 : 0.585 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: 0.7690 (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: 0.7665 (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: 0.6575 (mt-10) REVERT: F 68 GLU cc_start: 0.7480 (tp30) cc_final: 0.7150 (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: 0.6980 time to fit residues: 213.2076 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 : 0.589 ------------------------------------------------------------------------------- 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: 0.2980 chunk 91 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 HIS A 267 ASN ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 HIS D 272 GLN E 330 ASN F 202 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.187703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.156426 restraints weight = 19390.947| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.12 r_work: 0.3836 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1214 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= 0.152 Angle : 0.548 7.854 21868 Z= 0.296 Chirality : 0.041 0.150 2468 Planarity : 0.004 0.045 2745 Dihedral : 11.936 88.881 2679 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.91 % Allowed : 30.81 % Favored : 64.27 % 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: 0.16 (0.18), residues: 1940 helix: 0.48 (0.18), residues: 834 sheet: 1.28 (0.31), residues: 276 loop : -0.59 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 95 TYR 0.012 0.001 TYR F 159 PHE 0.010 0.001 PHE D 259 HIS 0.004 0.001 HIS F 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (16128) covalent geometry : angle 0.54798 / 0.30 (21868) hydrogen bonds : bond 0.05201 / 3.41 ( 749) hydrogen bonds : angle 5.30423 / 3.79 ( 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 274 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 196 time to evaluate : 0.604 Fit side-chains REVERT: A 96 ARG cc_start: 0.8020 (tpt-90) cc_final: 0.7809 (mtp85) REVERT: A 247 ARG cc_start: 0.7804 (ttm-80) cc_final: 0.7310 (mmt-90) REVERT: A 329 ILE cc_start: 0.5403 (mt) cc_final: 0.5176 (mt) REVERT: B 108 GLU cc_start: 0.7792 (mt-10) cc_final: 0.6924 (tm-30) REVERT: B 136 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7485 (mp) REVERT: B 202 GLN cc_start: 0.7251 (mt0) cc_final: 0.6814 (tm-30) REVERT: B 243 MET cc_start: 0.7266 (mtp) cc_final: 0.6450 (mpt) REVERT: B 251 MET cc_start: 0.7716 (mtt) cc_final: 0.6591 (tpt) REVERT: B 306 ARG cc_start: 0.6767 (ptm-80) cc_final: 0.5992 (mmp-170) REVERT: C 27 ARG cc_start: 0.8571 (tpp-160) cc_final: 0.8023 (mmm160) REVERT: C 39 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7164 (mmtm) REVERT: C 103 THR cc_start: 0.8223 (OUTLIER) cc_final: 0.7797 (p) REVERT: C 133 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7623 (pttm) REVERT: C 193 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7030 (ttp-170) REVERT: D 37 ASP cc_start: 0.7255 (OUTLIER) cc_final: 0.6502 (t0) REVERT: D 39 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7886 (mmtt) REVERT: D 95 ARG cc_start: 0.8275 (ttm-80) cc_final: 0.7729 (tmt170) REVERT: D 243 MET cc_start: 0.8526 (mtp) cc_final: 0.8185 (mtt) REVERT: D 247 ARG cc_start: 0.8057 (mmm-85) cc_final: 0.7710 (mtm180) REVERT: E 39 LYS cc_start: 0.7856 (ttpt) cc_final: 0.7274 (tmmt) REVERT: E 98 GLU cc_start: 0.6515 (mp0) cc_final: 0.6030 (tp30) REVERT: E 107 LYS cc_start: 0.7055 (ttmm) cc_final: 0.6655 (tppp) REVERT: E 150 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7259 (mtm180) REVERT: E 163 GLU cc_start: 0.7373 (mm-30) cc_final: 0.6822 (pt0) REVERT: F 107 LYS cc_start: 0.7280 (mmpt) cc_final: 0.6375 (mttm) REVERT: F 250 ARG cc_start: 0.6714 (mtt180) cc_final: 0.5431 (tpt-90) REVERT: F 270 VAL cc_start: 0.7429 (OUTLIER) cc_final: 0.7114 (p) REVERT: F 326 MET cc_start: 0.8638 (ttm) cc_final: 0.8321 (ttp) REVERT: H 2 ARG cc_start: 0.7563 (tpp80) cc_final: 0.7204 (mtp180) REVERT: L 1 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7341 (mpp) outliers start: 78 outliers final: 27 residues processed: 257 average time/residue: 0.7302 time to fit residues: 203.7276 Evaluate side-chains 215 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 136 ILE 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 49 VAL 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 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 125 MET Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 88 THR 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 F residue 37 ASP Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 270 VAL 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: 0.7980 chunk 74 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 148 optimal weight: 0.5980 chunk 65 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 HIS ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.188705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.157345 restraints weight = 19452.660| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.12 r_work: 0.3840 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16128 Z= 0.115 Angle : 0.492 7.766 21868 Z= 0.263 Chirality : 0.040 0.146 2468 Planarity : 0.004 0.041 2745 Dihedral : 11.804 89.022 2669 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 4.47 % Allowed : 30.37 % 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: 0.27 (0.19), residues: 1940 helix: 0.59 (0.18), residues: 845 sheet: 1.07 (0.31), residues: 279 loop : -0.47 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 95 TYR 0.011 0.001 TYR D 216 PHE 0.011 0.001 PHE D 259 HIS 0.003 0.001 HIS D 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (16128) covalent geometry : angle 0.49191 / 0.26 (21868) hydrogen bonds : bond 0.04061 / 2.67 ( 749) hydrogen bonds : angle 4.85293 / 3.46 ( 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 270 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 199 time to evaluate : 0.412 Fit side-chains REVERT: A 96 ARG cc_start: 0.8004 (tpt-90) cc_final: 0.7685 (mtp85) REVERT: A 247 ARG cc_start: 0.7747 (ttm-80) cc_final: 0.7260 (mmt-90) REVERT: A 329 ILE cc_start: 0.5350 (mt) cc_final: 0.5150 (mt) REVERT: B 108 GLU cc_start: 0.7794 (mt-10) cc_final: 0.6919 (tm-30) REVERT: B 136 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7477 (mp) REVERT: B 202 GLN cc_start: 0.7292 (mt0) cc_final: 0.6791 (tm-30) REVERT: B 243 MET cc_start: 0.7180 (mtp) cc_final: 0.6384 (mpt) REVERT: B 251 MET cc_start: 0.7420 (mtt) cc_final: 0.6698 (tpt) REVERT: B 306 ARG cc_start: 0.6741 (ptm-80) cc_final: 0.5951 (mmp-170) REVERT: C 27 ARG cc_start: 0.8542 (tpp-160) cc_final: 0.7957 (mmm160) REVERT: C 39 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7154 (mmtm) REVERT: C 103 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7774 (p) REVERT: C 133 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7610 (pttm) REVERT: C 193 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7088 (ttp-170) REVERT: D 95 ARG cc_start: 0.8286 (ttm-80) cc_final: 0.7693 (ttp-170) REVERT: D 107 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7727 (mmtt) REVERT: D 148 ILE cc_start: 0.6569 (tp) cc_final: 0.6302 (mt) REVERT: D 243 MET cc_start: 0.8496 (mtp) cc_final: 0.8139 (mtt) REVERT: D 247 ARG cc_start: 0.8042 (mmm-85) cc_final: 0.7674 (ttm170) REVERT: E 39 LYS cc_start: 0.7919 (ttpt) cc_final: 0.7290 (tmmt) REVERT: E 98 GLU cc_start: 0.6441 (mp0) cc_final: 0.5950 (tp30) REVERT: E 107 LYS cc_start: 0.6986 (ttmm) cc_final: 0.6592 (tppp) REVERT: E 150 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7207 (mtm180) REVERT: E 163 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6726 (pt0) REVERT: F 75 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6765 (mt) REVERT: F 107 LYS cc_start: 0.7330 (mmpt) cc_final: 0.6359 (mttm) REVERT: F 250 ARG cc_start: 0.6706 (mtt180) cc_final: 0.5332 (tpt-90) REVERT: F 326 MET cc_start: 0.8645 (ttm) cc_final: 0.8331 (ttp) REVERT: G 1 MET cc_start: 0.6601 (OUTLIER) cc_final: 0.6294 (mmm) REVERT: H 2 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7208 (mtp180) REVERT: L 1 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7420 (mpp) outliers start: 71 outliers final: 24 residues processed: 255 average time/residue: 0.6844 time to fit residues: 189.8649 Evaluate side-chains 219 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 61 ILE Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 43 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 311 ILE 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 G residue 1 MET Chi-restraints excluded: chain H residue 2 ARG Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain L residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 183 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 HIS A 267 ASN ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN E 242 GLN F 206 GLN F 242 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.186754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.155489 restraints weight = 19278.171| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.10 r_work: 0.3822 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1765 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= 0.128 Angle : 0.489 8.951 21868 Z= 0.262 Chirality : 0.040 0.146 2468 Planarity : 0.004 0.041 2745 Dihedral : 11.862 87.968 2667 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 4.66 % Allowed : 30.56 % 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: 0.26 (0.19), residues: 1940 helix: 0.60 (0.18), residues: 850 sheet: 0.91 (0.32), residues: 280 loop : -0.43 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 3 TYR 0.010 0.001 TYR F 159 PHE 0.010 0.001 PHE B 327 HIS 0.004 0.001 HIS F 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (16128) covalent geometry : angle 0.48917 / 0.26 (21868) hydrogen bonds : bond 0.03899 / 2.58 ( 749) hydrogen bonds : angle 4.68039 / 3.33 ( 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 268 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 194 time to evaluate : 0.582 Fit side-chains REVERT: A 96 ARG cc_start: 0.8020 (tpt-90) cc_final: 0.7688 (mtp85) REVERT: A 247 ARG cc_start: 0.7791 (ttm-80) cc_final: 0.7308 (mmt-90) REVERT: A 329 ILE cc_start: 0.5433 (mt) cc_final: 0.5216 (mt) REVERT: B 108 GLU cc_start: 0.7790 (mt-10) cc_final: 0.6883 (tm-30) REVERT: B 136 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7465 (mp) REVERT: B 202 GLN cc_start: 0.7249 (mt0) cc_final: 0.6842 (tm-30) REVERT: B 210 MET cc_start: 0.7631 (ttp) cc_final: 0.7426 (ttp) REVERT: B 243 MET cc_start: 0.7169 (mtp) cc_final: 0.6383 (mpt) REVERT: B 251 MET cc_start: 0.7421 (mtt) cc_final: 0.6749 (tpt) REVERT: B 306 ARG cc_start: 0.6762 (ptm-80) cc_final: 0.5971 (mmp-170) REVERT: C 27 ARG cc_start: 0.8565 (tpp-160) cc_final: 0.7884 (mmm160) REVERT: C 30 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6734 (mt0) REVERT: C 39 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7208 (mmtm) REVERT: C 133 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7710 (ptpp) REVERT: C 193 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.7105 (ttp-170) REVERT: D 37 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.6625 (t0) REVERT: D 39 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7868 (mmtt) REVERT: D 95 ARG cc_start: 0.8306 (ttm-80) cc_final: 0.7742 (ttp-170) REVERT: D 107 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7735 (mmtt) REVERT: D 148 ILE cc_start: 0.6499 (tp) cc_final: 0.6233 (mt) REVERT: D 243 MET cc_start: 0.8470 (mtp) cc_final: 0.8141 (mtt) REVERT: D 247 ARG cc_start: 0.8027 (mmm-85) cc_final: 0.7703 (ttm170) REVERT: E 39 LYS cc_start: 0.8010 (ttpt) cc_final: 0.7315 (tmmt) REVERT: E 91 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: E 95 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7604 (ttt180) REVERT: E 98 GLU cc_start: 0.6458 (mp0) cc_final: 0.5990 (tp30) REVERT: E 107 LYS cc_start: 0.7060 (ttmm) cc_final: 0.6625 (tppp) REVERT: E 150 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7188 (mtm180) REVERT: E 163 GLU cc_start: 0.7359 (mm-30) cc_final: 0.6684 (mt-10) REVERT: F 75 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6832 (mt) REVERT: F 107 LYS cc_start: 0.7413 (mmpt) cc_final: 0.6374 (mttm) REVERT: F 250 ARG cc_start: 0.6713 (mtt180) cc_final: 0.5310 (tpt-90) REVERT: F 251 MET cc_start: 0.8518 (tpt) cc_final: 0.7334 (ttp) REVERT: F 270 VAL cc_start: 0.7449 (OUTLIER) cc_final: 0.7135 (p) REVERT: F 326 MET cc_start: 0.8663 (ttm) cc_final: 0.8346 (ttp) REVERT: G 1 MET cc_start: 0.6634 (mmt) cc_final: 0.6279 (mmm) REVERT: H 2 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7212 (mtp180) REVERT: L 1 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7378 (mpp) outliers start: 74 outliers final: 31 residues processed: 254 average time/residue: 0.6882 time to fit residues: 189.9966 Evaluate side-chains 229 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 196 ASN Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 30 GLN 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 90 THR Chi-restraints excluded: chain C residue 99 ILE 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 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 230 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 95 ARG 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 E residue 311 ILE 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 F residue 270 VAL 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 L residue 1 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 44 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 180 optimal weight: 0.0980 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 HIS ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.181755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.150563 restraints weight = 19479.427| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.07 r_work: 0.3766 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16128 Z= 0.207 Angle : 0.572 11.956 21868 Z= 0.303 Chirality : 0.043 0.153 2468 Planarity : 0.005 0.056 2745 Dihedral : 12.122 88.837 2667 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 6.11 % Allowed : 29.30 % Favored : 64.59 % 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: 0.05 (0.19), residues: 1940 helix: 0.35 (0.18), residues: 846 sheet: 0.79 (0.32), residues: 280 loop : -0.45 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 95 TYR 0.015 0.002 TYR F 159 PHE 0.015 0.002 PHE F 195 HIS 0.006 0.001 HIS F 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (16128) covalent geometry : angle 0.57176 / 0.30 (21868) hydrogen bonds : bond 0.04722 / 3.14 ( 749) hydrogen bonds : angle 4.82345 / 3.43 ( 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 292 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 195 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.8124 (tpt-90) cc_final: 0.7693 (mtp85) REVERT: A 247 ARG cc_start: 0.7838 (ttm-80) cc_final: 0.7351 (mmt-90) REVERT: A 329 ILE cc_start: 0.5451 (mt) cc_final: 0.5176 (mt) REVERT: B 95 ARG cc_start: 0.8275 (ttp80) cc_final: 0.7917 (tmm160) REVERT: B 108 GLU cc_start: 0.7789 (mt-10) cc_final: 0.6971 (tm-30) REVERT: B 130 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7631 (ttp-170) REVERT: B 136 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7549 (mp) REVERT: B 202 GLN cc_start: 0.7335 (mt0) cc_final: 0.6517 (tm-30) REVERT: B 243 MET cc_start: 0.7312 (mtp) cc_final: 0.6457 (mpt) REVERT: B 251 MET cc_start: 0.7555 (mtt) cc_final: 0.6867 (tpt) REVERT: B 306 ARG cc_start: 0.6750 (ptm-80) cc_final: 0.5958 (mmp-170) REVERT: C 39 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7267 (mmtm) REVERT: C 94 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7964 (tp40) REVERT: C 133 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7459 (mttt) REVERT: C 193 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.7152 (ttp-170) REVERT: C 306 ARG cc_start: 0.6525 (OUTLIER) cc_final: 0.6077 (mmt-90) REVERT: D 39 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7935 (mmtt) REVERT: D 95 ARG cc_start: 0.8393 (ttm-80) cc_final: 0.7846 (ttp-170) REVERT: D 107 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7745 (mmtt) REVERT: D 148 ILE cc_start: 0.6591 (tp) cc_final: 0.6305 (mt) REVERT: D 218 LEU cc_start: 0.7893 (tp) cc_final: 0.7639 (tp) REVERT: D 243 MET cc_start: 0.8524 (mtp) cc_final: 0.8206 (mtt) REVERT: D 247 ARG cc_start: 0.8071 (mmm-85) cc_final: 0.7736 (ttm170) REVERT: E 39 LYS cc_start: 0.8039 (ttpt) cc_final: 0.7408 (tmmt) REVERT: E 95 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7573 (ttt180) REVERT: E 98 GLU cc_start: 0.6646 (mp0) cc_final: 0.6018 (tp30) REVERT: E 107 LYS cc_start: 0.7142 (ttmm) cc_final: 0.6701 (tppp) REVERT: E 150 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7193 (mtt180) REVERT: E 163 GLU cc_start: 0.7648 (mm-30) cc_final: 0.6821 (mt-10) REVERT: F 75 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6901 (mt) REVERT: F 103 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.8127 (t) REVERT: F 107 LYS cc_start: 0.7510 (mmpt) cc_final: 0.6463 (mttm) REVERT: F 111 LYS cc_start: 0.7830 (mtpp) cc_final: 0.7263 (ttpp) REVERT: F 250 ARG cc_start: 0.6735 (mtt180) cc_final: 0.5328 (tpt-90) REVERT: F 251 MET cc_start: 0.8565 (tpt) cc_final: 0.7415 (ttp) REVERT: F 308 GLU cc_start: 0.6375 (mm-30) cc_final: 0.5846 (tp30) REVERT: F 326 MET cc_start: 0.8690 (ttm) cc_final: 0.8249 (ttm) REVERT: G 1 MET cc_start: 0.6755 (mmt) cc_final: 0.6321 (mmm) REVERT: H 2 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7309 (mtp180) REVERT: L 1 MET cc_start: 0.7939 (mtp) cc_final: 0.7305 (mpp) outliers start: 97 outliers final: 44 residues processed: 275 average time/residue: 0.7040 time to fit residues: 210.6715 Evaluate side-chains 236 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 178 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 48 THR 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 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 130 ARG 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 39 LYS Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 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 121 SER 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 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 162 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 95 ARG 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 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 90 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain H residue 2 ARG Chi-restraints excluded: chain I residue 21 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 154 optimal weight: 0.3980 chunk 125 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 HIS A 267 ASN A 272 GLN D 272 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.185535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.154402 restraints weight = 19402.499| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.08 r_work: 0.3812 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16128 Z= 0.111 Angle : 0.478 10.515 21868 Z= 0.256 Chirality : 0.040 0.147 2468 Planarity : 0.004 0.048 2745 Dihedral : 11.935 87.830 2667 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 3.91 % Allowed : 31.25 % 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: 0.21 (0.19), residues: 1940 helix: 0.48 (0.18), residues: 855 sheet: 0.92 (0.32), residues: 276 loop : -0.39 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 95 TYR 0.007 0.001 TYR F 159 PHE 0.010 0.001 PHE D 126 HIS 0.002 0.000 HIS C 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (16128) covalent geometry : angle 0.47795 / 0.26 (21868) hydrogen bonds : bond 0.03610 / 2.40 ( 749) hydrogen bonds : angle 4.55906 / 3.24 ( 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 260 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 198 time to evaluate : 0.589 Fit side-chains REVERT: A 96 ARG cc_start: 0.8094 (tpt-90) cc_final: 0.7706 (mtp85) REVERT: A 247 ARG cc_start: 0.7843 (ttm-80) cc_final: 0.7356 (mmt-90) REVERT: A 329 ILE cc_start: 0.5391 (mt) cc_final: 0.5141 (mt) REVERT: B 58 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7832 (ptpp) REVERT: B 95 ARG cc_start: 0.8250 (ttp80) cc_final: 0.7953 (tmm160) REVERT: B 108 GLU cc_start: 0.7779 (mt-10) cc_final: 0.6906 (tm-30) REVERT: B 130 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7396 (ttp-170) REVERT: B 136 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7525 (mp) REVERT: B 202 GLN cc_start: 0.7283 (mt0) cc_final: 0.6846 (tm-30) REVERT: B 243 MET cc_start: 0.7257 (mtp) cc_final: 0.6462 (mpt) REVERT: B 251 MET cc_start: 0.7477 (mtt) cc_final: 0.6850 (tpt) REVERT: B 306 ARG cc_start: 0.6777 (ptm-80) cc_final: 0.5966 (mmp-170) REVERT: C 133 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7715 (pttm) REVERT: C 193 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.7087 (ttp-170) REVERT: C 306 ARG cc_start: 0.6465 (OUTLIER) cc_final: 0.6102 (mmt-90) REVERT: D 39 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7864 (mmtt) REVERT: D 95 ARG cc_start: 0.8405 (ttm-80) cc_final: 0.7798 (ttp-170) REVERT: D 107 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7716 (mmtt) REVERT: D 148 ILE cc_start: 0.6646 (tp) cc_final: 0.6387 (mt) REVERT: D 218 LEU cc_start: 0.7805 (tp) cc_final: 0.7465 (tp) REVERT: D 243 MET cc_start: 0.8485 (mtp) cc_final: 0.8167 (mtt) REVERT: D 247 ARG cc_start: 0.8015 (mmm-85) cc_final: 0.7678 (ttm170) REVERT: E 39 LYS cc_start: 0.8021 (ttpt) cc_final: 0.7421 (tmmt) REVERT: E 98 GLU cc_start: 0.6558 (mp0) cc_final: 0.5909 (tp30) REVERT: E 107 LYS cc_start: 0.7099 (ttmm) cc_final: 0.6666 (tppp) REVERT: E 150 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7095 (mtm180) REVERT: E 163 GLU cc_start: 0.7578 (mm-30) cc_final: 0.6807 (mt-10) REVERT: E 316 ASP cc_start: 0.7820 (t70) cc_final: 0.7617 (t70) REVERT: F 75 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6926 (mt) REVERT: F 103 THR cc_start: 0.8252 (OUTLIER) cc_final: 0.8010 (t) REVERT: F 107 LYS cc_start: 0.7491 (mmpt) cc_final: 0.6471 (mttm) REVERT: F 111 LYS cc_start: 0.7789 (mtpp) cc_final: 0.7279 (ttpp) REVERT: F 250 ARG cc_start: 0.6712 (mtt180) cc_final: 0.5355 (tpt-90) REVERT: F 251 MET cc_start: 0.8507 (tpt) cc_final: 0.7335 (ttp) REVERT: F 326 MET cc_start: 0.8694 (ttm) cc_final: 0.8273 (ttm) REVERT: G 1 MET cc_start: 0.6576 (mmt) cc_final: 0.6271 (mmm) REVERT: H 2 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7207 (mtp180) REVERT: L 1 MET cc_start: 0.7928 (mtp) cc_final: 0.7361 (mpp) outliers start: 62 outliers final: 27 residues processed: 249 average time/residue: 0.7151 time to fit residues: 193.6031 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 : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 136 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 130 ARG Chi-restraints excluded: chain B residue 136 ILE 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 82 VAL Chi-restraints excluded: chain C residue 90 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 133 LYS 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 39 LYS Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 125 MET 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 233 SER 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 103 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 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: 9.9990 chunk 182 optimal weight: 4.9990 chunk 188 optimal weight: 0.9980 chunk 99 optimal weight: 0.0070 chunk 26 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 HIS A 267 ASN D 272 GLN E 145 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.185948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.154919 restraints weight = 19396.169| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.08 r_work: 0.3816 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16128 Z= 0.110 Angle : 0.468 10.426 21868 Z= 0.250 Chirality : 0.039 0.145 2468 Planarity : 0.004 0.040 2745 Dihedral : 11.863 88.622 2667 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 4.03 % Allowed : 31.19 % 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: 0.31 (0.19), residues: 1940 helix: 0.59 (0.18), residues: 862 sheet: 0.87 (0.32), residues: 276 loop : -0.34 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 95 TYR 0.009 0.001 TYR E 205 PHE 0.013 0.001 PHE A 248 HIS 0.002 0.001 HIS C 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (16128) covalent geometry : angle 0.46780 / 0.25 (21868) hydrogen bonds : bond 0.03459 / 2.30 ( 749) hydrogen bonds : angle 4.46456 / 3.17 ( 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 260 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 196 time to evaluate : 0.621 Fit side-chains REVERT: A 96 ARG cc_start: 0.8088 (tpt-90) cc_final: 0.7671 (mtp85) REVERT: A 247 ARG cc_start: 0.7826 (ttm-80) cc_final: 0.7331 (mmt-90) REVERT: A 329 ILE cc_start: 0.5373 (mt) cc_final: 0.5125 (mt) REVERT: B 58 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7823 (ptpp) REVERT: B 95 ARG cc_start: 0.8239 (ttp80) cc_final: 0.7908 (tmm160) REVERT: B 108 GLU cc_start: 0.7759 (mt-10) cc_final: 0.6886 (tm-30) REVERT: B 136 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7493 (mp) REVERT: B 202 GLN cc_start: 0.7289 (mt0) cc_final: 0.6738 (tm-30) REVERT: B 210 MET cc_start: 0.7720 (ttp) cc_final: 0.7466 (ttp) REVERT: B 243 MET cc_start: 0.7222 (mtp) cc_final: 0.6418 (mpt) REVERT: B 251 MET cc_start: 0.7432 (mtt) cc_final: 0.6829 (tpt) REVERT: B 306 ARG cc_start: 0.6767 (ptm-80) cc_final: 0.5897 (mmp-170) REVERT: C 39 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7184 (mmtm) REVERT: C 133 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7742 (pttm) REVERT: C 193 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.7086 (ttp-170) REVERT: C 306 ARG cc_start: 0.6467 (OUTLIER) cc_final: 0.6156 (mmt-90) REVERT: D 95 ARG cc_start: 0.8390 (ttm-80) cc_final: 0.7803 (ttp-170) REVERT: D 107 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7720 (mmtt) REVERT: D 148 ILE cc_start: 0.6652 (tp) cc_final: 0.6379 (mt) REVERT: D 218 LEU cc_start: 0.7789 (tp) cc_final: 0.7443 (tp) REVERT: D 243 MET cc_start: 0.8475 (mtp) cc_final: 0.8159 (mtt) REVERT: D 247 ARG cc_start: 0.7995 (mmm-85) cc_final: 0.7672 (ttm170) REVERT: E 39 LYS cc_start: 0.8004 (ttpt) cc_final: 0.7376 (tmmt) REVERT: E 98 GLU cc_start: 0.6501 (mp0) cc_final: 0.5915 (tp30) REVERT: E 107 LYS cc_start: 0.7106 (ttmm) cc_final: 0.6680 (tppp) REVERT: E 150 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7092 (mtm180) REVERT: E 163 GLU cc_start: 0.7515 (mm-30) cc_final: 0.6768 (mt-10) REVERT: F 75 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6897 (mt) REVERT: F 103 THR cc_start: 0.8211 (OUTLIER) cc_final: 0.7980 (t) REVERT: F 107 LYS cc_start: 0.7471 (mmpt) cc_final: 0.6429 (mttm) REVERT: F 111 LYS cc_start: 0.7768 (mtpp) cc_final: 0.7277 (ttpp) REVERT: F 250 ARG cc_start: 0.6747 (mtt180) cc_final: 0.5341 (tpt-90) REVERT: F 251 MET cc_start: 0.8495 (tpt) cc_final: 0.7328 (ttp) REVERT: F 308 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.5890 (tp30) REVERT: F 326 MET cc_start: 0.8694 (ttm) cc_final: 0.8273 (ttm) REVERT: G 1 MET cc_start: 0.6591 (mmt) cc_final: 0.6305 (mmm) REVERT: H 2 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.7210 (mtp180) REVERT: L 1 MET cc_start: 0.7920 (mtp) cc_final: 0.7360 (mpp) outliers start: 64 outliers final: 27 residues processed: 248 average time/residue: 0.6949 time to fit residues: 188.2011 Evaluate side-chains 221 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 82 VAL Chi-restraints excluded: chain C residue 90 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 133 LYS 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 61 ILE Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 107 LYS 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 150 ARG 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 103 THR Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain H residue 2 ARG Chi-restraints excluded: chain I residue 21 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 196 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 195 optimal weight: 10.0000 chunk 193 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 HIS A 244 HIS A 267 ASN D 272 GLN E 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.184474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.153360 restraints weight = 19541.460| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.08 r_work: 0.3801 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16128 Z= 0.137 Angle : 0.497 11.344 21868 Z= 0.265 Chirality : 0.041 0.147 2468 Planarity : 0.004 0.041 2745 Dihedral : 11.935 88.984 2667 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 4.41 % Allowed : 30.75 % 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: 0.25 (0.19), residues: 1940 helix: 0.58 (0.18), residues: 856 sheet: 0.83 (0.32), residues: 275 loop : -0.39 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 95 TYR 0.011 0.001 TYR F 159 PHE 0.010 0.001 PHE A 46 HIS 0.003 0.001 HIS F 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (16128) covalent geometry : angle 0.49738 / 0.26 (21868) hydrogen bonds : bond 0.03755 / 2.50 ( 749) hydrogen bonds : angle 4.51170 / 3.20 ( 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 257 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 187 time to evaluate : 0.463 Fit side-chains REVERT: A 96 ARG cc_start: 0.8081 (tpt-90) cc_final: 0.7652 (mtp85) REVERT: A 247 ARG cc_start: 0.7851 (ttm-80) cc_final: 0.7336 (mmt-90) REVERT: A 329 ILE cc_start: 0.5405 (mt) cc_final: 0.5082 (mt) REVERT: B 95 ARG cc_start: 0.8233 (ttp80) cc_final: 0.7901 (tmm160) REVERT: B 108 GLU cc_start: 0.7766 (mt-10) cc_final: 0.6933 (tm-30) REVERT: B 202 GLN cc_start: 0.7297 (mt0) cc_final: 0.6750 (tm-30) REVERT: B 243 MET cc_start: 0.7249 (mtp) cc_final: 0.6445 (mpt) REVERT: B 251 MET cc_start: 0.7436 (mtt) cc_final: 0.6815 (tpt) REVERT: B 306 ARG cc_start: 0.6779 (ptm-80) cc_final: 0.5904 (mmp-170) REVERT: C 39 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7232 (mmtm) REVERT: C 61 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7646 (mp) REVERT: C 133 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7567 (mttp) REVERT: C 193 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.7144 (ttp-170) REVERT: C 306 ARG cc_start: 0.6469 (OUTLIER) cc_final: 0.6203 (mmt-90) REVERT: D 75 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7286 (mm) REVERT: D 77 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7825 (tm-30) REVERT: D 95 ARG cc_start: 0.8410 (ttm-80) cc_final: 0.7777 (ttp-170) REVERT: D 107 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7714 (mmtt) REVERT: D 148 ILE cc_start: 0.6635 (tp) cc_final: 0.6366 (mt) REVERT: D 218 LEU cc_start: 0.7852 (tp) cc_final: 0.7526 (tp) REVERT: D 243 MET cc_start: 0.8462 (mtp) cc_final: 0.8151 (mtt) REVERT: D 247 ARG cc_start: 0.8002 (mmm-85) cc_final: 0.7590 (ttm170) REVERT: E 39 LYS cc_start: 0.8017 (ttpt) cc_final: 0.7385 (tmmt) REVERT: E 98 GLU cc_start: 0.6562 (mp0) cc_final: 0.5867 (tp30) REVERT: E 107 LYS cc_start: 0.7085 (ttmm) cc_final: 0.6650 (tppp) REVERT: E 150 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7089 (mtm180) REVERT: E 163 GLU cc_start: 0.7579 (mm-30) cc_final: 0.6774 (mt-10) REVERT: F 75 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6909 (mt) REVERT: F 103 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.8018 (t) REVERT: F 107 LYS cc_start: 0.7453 (mmpt) cc_final: 0.6437 (mttm) REVERT: F 111 LYS cc_start: 0.7756 (mtpp) cc_final: 0.7268 (ttpp) REVERT: F 250 ARG cc_start: 0.6830 (mtt180) cc_final: 0.5358 (tpt-90) REVERT: F 251 MET cc_start: 0.8489 (tpt) cc_final: 0.7327 (ttp) REVERT: F 308 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.5890 (tp30) REVERT: G 1 MET cc_start: 0.6615 (OUTLIER) cc_final: 0.6296 (mmm) REVERT: H 2 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7214 (mtp180) REVERT: L 1 MET cc_start: 0.7925 (mtp) cc_final: 0.7336 (mpp) outliers start: 70 outliers final: 33 residues processed: 245 average time/residue: 0.6282 time to fit residues: 167.7638 Evaluate side-chains 228 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 181 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 121 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 161 ASP 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 39 LYS Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 90 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 133 LYS 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 61 ILE Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 107 LYS 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 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 F residue 37 ASP Chi-restraints excluded: chain F residue 75 LEU 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 208 SER Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain H residue 2 ARG Chi-restraints excluded: chain I residue 21 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 164 optimal weight: 2.9990 chunk 7 optimal weight: 0.0870 chunk 131 optimal weight: 4.9990 chunk 171 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 HIS C 62 ASN D 272 GLN E 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.184467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.153964 restraints weight = 19454.722| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 2.06 r_work: 0.3811 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16128 Z= 0.113 Angle : 0.478 10.858 21868 Z= 0.255 Chirality : 0.040 0.145 2468 Planarity : 0.003 0.040 2745 Dihedral : 11.870 88.822 2667 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.72 % Allowed : 31.38 % Favored : 64.90 % 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: 0.35 (0.19), residues: 1940 helix: 0.64 (0.18), residues: 869 sheet: 0.91 (0.32), residues: 273 loop : -0.34 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 3 TYR 0.008 0.001 TYR F 159 PHE 0.009 0.001 PHE B 327 HIS 0.002 0.000 HIS F 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (16128) covalent geometry : angle 0.47789 / 0.25 (21868) hydrogen bonds : bond 0.03433 / 2.28 ( 749) hydrogen bonds : angle 4.44263 / 3.15 ( 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 251 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 192 time to evaluate : 0.577 Fit side-chains REVERT: A 96 ARG cc_start: 0.8118 (tpt-90) cc_final: 0.7640 (mtp85) REVERT: A 247 ARG cc_start: 0.7812 (ttm-80) cc_final: 0.7310 (mmt-90) REVERT: A 252 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7448 (mp) REVERT: A 329 ILE cc_start: 0.5320 (mt) cc_final: 0.5103 (mt) REVERT: B 58 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7814 (ptpp) REVERT: B 95 ARG cc_start: 0.8220 (ttp80) cc_final: 0.7904 (tmm160) REVERT: B 108 GLU cc_start: 0.7743 (mt-10) cc_final: 0.6882 (tm-30) REVERT: B 202 GLN cc_start: 0.7250 (mt0) cc_final: 0.6758 (tm-30) REVERT: B 243 MET cc_start: 0.7226 (mtp) cc_final: 0.6421 (mpt) REVERT: B 251 MET cc_start: 0.7332 (mtt) cc_final: 0.6826 (tpt) REVERT: B 306 ARG cc_start: 0.6774 (ptm-80) cc_final: 0.5726 (mmp-170) REVERT: C 39 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7221 (mmtm) REVERT: C 61 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7628 (mp) REVERT: C 193 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.7124 (ttp-170) REVERT: C 306 ARG cc_start: 0.6442 (OUTLIER) cc_final: 0.6191 (mmt-90) REVERT: D 75 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7318 (mm) REVERT: D 77 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7873 (tm-30) REVERT: D 95 ARG cc_start: 0.8380 (ttm-80) cc_final: 0.7775 (ttp-170) REVERT: D 107 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7701 (mmtt) REVERT: D 148 ILE cc_start: 0.6679 (tp) cc_final: 0.6408 (mt) REVERT: D 218 LEU cc_start: 0.7815 (tp) cc_final: 0.7463 (tp) REVERT: D 243 MET cc_start: 0.8448 (mtp) cc_final: 0.8137 (mtt) REVERT: D 247 ARG cc_start: 0.8002 (mmm-85) cc_final: 0.7599 (ttm170) REVERT: E 39 LYS cc_start: 0.8027 (ttpt) cc_final: 0.7382 (tmmt) REVERT: E 98 GLU cc_start: 0.6406 (mp0) cc_final: 0.5796 (tp30) REVERT: E 107 LYS cc_start: 0.7056 (ttmm) cc_final: 0.6624 (tppp) REVERT: E 150 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7064 (mtm180) REVERT: E 163 GLU cc_start: 0.7570 (mm-30) cc_final: 0.6803 (mt-10) REVERT: F 75 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6878 (mt) REVERT: F 103 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7973 (t) REVERT: F 107 LYS cc_start: 0.7443 (mmpt) cc_final: 0.6382 (mttm) REVERT: F 111 LYS cc_start: 0.7735 (mtpp) cc_final: 0.7254 (ttpp) REVERT: F 250 ARG cc_start: 0.6779 (mtt180) cc_final: 0.5352 (tpt-90) REVERT: F 251 MET cc_start: 0.8466 (tpt) cc_final: 0.7305 (ttp) REVERT: F 270 VAL cc_start: 0.7538 (OUTLIER) cc_final: 0.7221 (p) REVERT: F 308 GLU cc_start: 0.6413 (OUTLIER) cc_final: 0.5924 (tp30) REVERT: F 326 MET cc_start: 0.8678 (ttp) cc_final: 0.8277 (ttm) REVERT: G 1 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.6297 (mmm) REVERT: H 2 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7230 (mtp180) REVERT: L 1 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7337 (mpp) outliers start: 59 outliers final: 29 residues processed: 239 average time/residue: 0.6858 time to fit residues: 178.8731 Evaluate side-chains 228 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 182 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 136 ILE Chi-restraints excluded: chain A residue 252 LEU 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 161 ASP Chi-restraints excluded: chain B residue 165 THR 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 61 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 90 THR 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 306 ARG Chi-restraints excluded: chain D residue 28 LEU 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 77 GLU Chi-restraints excluded: chain D residue 107 LYS 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 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 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 208 SER Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain G residue 1 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 171 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 100 optimal weight: 0.3980 chunk 190 optimal weight: 0.0470 chunk 40 optimal weight: 0.3980 chunk 136 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 187 optimal weight: 6.9990 chunk 57 optimal weight: 0.3980 chunk 126 optimal weight: 1.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 HIS C 62 ASN D 272 GLN E 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.186968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.156574 restraints weight = 19397.871| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.05 r_work: 0.3834 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3709 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16128 Z= 0.097 Angle : 0.460 10.005 21868 Z= 0.246 Chirality : 0.039 0.143 2468 Planarity : 0.003 0.038 2745 Dihedral : 11.775 88.581 2667 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.77 % Allowed : 32.58 % 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: 0.44 (0.19), residues: 1940 helix: 0.71 (0.18), residues: 874 sheet: 0.98 (0.32), residues: 272 loop : -0.32 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 3 TYR 0.011 0.001 TYR E 205 PHE 0.009 0.001 PHE A 46 HIS 0.002 0.000 HIS C 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (16128) covalent geometry : angle 0.45952 / 0.25 (21868) hydrogen bonds : bond 0.03103 / 2.06 ( 749) hydrogen bonds : angle 4.35391 / 3.09 ( 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 239 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 0.493 Fit side-chains REVERT: A 96 ARG cc_start: 0.8103 (tpt-90) cc_final: 0.7650 (mtp85) REVERT: A 125 MET cc_start: 0.6791 (mmt) cc_final: 0.6520 (mmt) REVERT: A 247 ARG cc_start: 0.7809 (ttm-80) cc_final: 0.7305 (mmt-90) REVERT: A 252 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7446 (mp) REVERT: B 95 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7888 (tmm160) REVERT: B 108 GLU cc_start: 0.7780 (mt-10) cc_final: 0.6857 (tm-30) REVERT: B 136 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7535 (mp) REVERT: B 202 GLN cc_start: 0.7241 (mt0) cc_final: 0.6704 (tm-30) REVERT: B 243 MET cc_start: 0.7189 (mtp) cc_final: 0.6407 (mpt) REVERT: B 251 MET cc_start: 0.7282 (mtt) cc_final: 0.6845 (tpt) REVERT: B 306 ARG cc_start: 0.6802 (ptm-80) cc_final: 0.5710 (mmp-170) REVERT: C 39 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7220 (mmtm) REVERT: C 61 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7629 (mp) REVERT: C 306 ARG cc_start: 0.6448 (OUTLIER) cc_final: 0.6193 (mmt-90) REVERT: D 77 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7889 (tm-30) REVERT: D 95 ARG cc_start: 0.8380 (ttm-80) cc_final: 0.7767 (ttp-170) REVERT: D 107 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7722 (mmtt) REVERT: D 148 ILE cc_start: 0.6698 (tp) cc_final: 0.6420 (mt) REVERT: D 218 LEU cc_start: 0.7738 (tp) cc_final: 0.7339 (tp) REVERT: D 243 MET cc_start: 0.8424 (mtp) cc_final: 0.8128 (mtt) REVERT: D 247 ARG cc_start: 0.7978 (mmm-85) cc_final: 0.7610 (ttm170) REVERT: D 254 ARG cc_start: 0.7288 (ttp-170) cc_final: 0.6115 (tpp-160) REVERT: E 39 LYS cc_start: 0.8015 (ttpt) cc_final: 0.7389 (tmmt) REVERT: E 98 GLU cc_start: 0.6358 (mp0) cc_final: 0.5839 (tp30) REVERT: E 107 LYS cc_start: 0.7062 (ttmm) cc_final: 0.6646 (tppp) REVERT: E 150 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.6993 (mtm180) REVERT: E 163 GLU cc_start: 0.7472 (mm-30) cc_final: 0.6740 (mt-10) REVERT: F 75 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6825 (mp) REVERT: F 103 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7928 (t) REVERT: F 107 LYS cc_start: 0.7367 (mmpt) cc_final: 0.6313 (mttm) REVERT: F 111 LYS cc_start: 0.7710 (mtpp) cc_final: 0.7275 (ttpp) REVERT: F 250 ARG cc_start: 0.6769 (mtt180) cc_final: 0.5359 (tpt-90) REVERT: F 251 MET cc_start: 0.8438 (tpt) cc_final: 0.7321 (ttp) REVERT: F 308 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.5952 (tp30) REVERT: G 1 MET cc_start: 0.6514 (OUTLIER) cc_final: 0.6262 (mmm) REVERT: H 2 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7168 (mtp180) REVERT: L 1 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7379 (mpp) outliers start: 44 outliers final: 22 residues processed: 230 average time/residue: 0.7143 time to fit residues: 178.5456 Evaluate side-chains 221 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 136 ILE Chi-restraints excluded: chain A residue 252 LEU 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 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 61 ILE Chi-restraints excluded: chain C residue 90 THR 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 C residue 306 ARG Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 107 LYS 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 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 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 208 SER Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain H residue 2 ARG Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain L residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 113 optimal weight: 0.6980 chunk 139 optimal weight: 0.4980 chunk 138 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 192 optimal weight: 8.9990 chunk 119 optimal weight: 0.9990 chunk 37 optimal weight: 0.0030 chunk 195 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 GLN A 199 HIS C 62 ASN D 272 GLN E 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.185955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.155451 restraints weight = 19351.835| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.06 r_work: 0.3826 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2455 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= 0.111 Angle : 0.474 10.429 21868 Z= 0.252 Chirality : 0.039 0.165 2468 Planarity : 0.003 0.039 2745 Dihedral : 11.795 88.390 2666 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.09 % Allowed : 32.33 % Favored : 64.59 % 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: 0.44 (0.19), residues: 1940 helix: 0.76 (0.18), residues: 868 sheet: 0.86 (0.32), residues: 266 loop : -0.31 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 3 TYR 0.008 0.001 TYR F 159 PHE 0.009 0.001 PHE A 129 HIS 0.002 0.000 HIS F 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (16128) covalent geometry : angle 0.47352 / 0.25 (21868) hydrogen bonds : bond 0.03255 / 2.16 ( 749) hydrogen bonds : angle 4.35137 / 3.08 ( 2088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6316.92 seconds wall clock time: 108 minutes 5.13 seconds (6485.13 seconds total)