Starting phenix.real_space_refine on Tue Apr 7 02:24:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m2x_63593/04_2026/9m2x_63593.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m2x_63593/04_2026/9m2x_63593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m2x_63593/04_2026/9m2x_63593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m2x_63593/04_2026/9m2x_63593.map" model { file = "/net/cci-nas-00/data/ceres_data/9m2x_63593/04_2026/9m2x_63593.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m2x_63593/04_2026/9m2x_63593.cif" } resolution = 3.27 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= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 10 5.21 5 S 120 5.16 5 C 15122 2.51 5 N 4058 2.21 5 O 4597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23937 Number of models: 1 Model: "" Number of chains: 21 Chain: "J" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2317 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Chain: "I" Number of atoms: 2344 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 295, 2333 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 295, 2333 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 1 bond proxies already assigned to first conformer: 2358 Chain: "H" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2360 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 13, 'TRANS': 285} Chain breaks: 1 Chain: "G" Number of atoms: 2379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2379 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 14, 'TRANS': 287} Chain breaks: 1 Chain: "F" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2350 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 1 Chain: "E" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2360 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 13, 'TRANS': 285} Chain breaks: 1 Chain: "D" Number of atoms: 2363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2363 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 14, 'TRANS': 285} Chain breaks: 1 Chain: "C" Number of atoms: 2359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2359 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 13, 'TRANS': 285} Chain breaks: 1 Chain: "B" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2350 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 1 Chain: "A" Number of atoms: 2325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2325 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 13, 'TRANS': 280} Chain breaks: 1 Chain: "K" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG I 74 " occ=0.59 ... (20 atoms not shown) pdb=" NH2BARG I 74 " occ=0.41 Time building chain proxies: 5.11, per 1000 atoms: 0.21 Number of scatterers: 23937 At special positions: 0 Unit cell: (125.46, 136.94, 135.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 120 16.00 P 30 15.00 Mg 10 11.99 O 4597 8.00 N 4058 7.00 C 15122 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: 1.82 Conformation dependent library (CDL) restraints added in 1.2 seconds 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5702 Finding SS restraints... Secondary structure from input PDB file: 178 helices and 10 sheets defined 62.1% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'J' and resid 43 through 61 Processing helix chain 'J' and resid 62 through 66 removed outlier: 3.695A pdb=" N GLU J 66 " --> pdb=" O ALA J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 78 Processing helix chain 'J' and resid 89 through 93 Processing helix chain 'J' and resid 96 through 107 Processing helix chain 'J' and resid 107 through 113 Processing helix chain 'J' and resid 113 through 118 removed outlier: 3.963A pdb=" N TYR J 117 " --> pdb=" O MET J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 120 through 124 Processing helix chain 'J' and resid 138 through 151 removed outlier: 3.659A pdb=" N SER J 150 " --> pdb=" O LEU J 146 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY J 151 " --> pdb=" O ALA J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 163 removed outlier: 4.035A pdb=" N ILE J 162 " --> pdb=" O ARG J 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 184 Processing helix chain 'J' and resid 193 through 198 removed outlier: 4.314A pdb=" N PHE J 197 " --> pdb=" O GLN J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 226 removed outlier: 3.596A pdb=" N ASP J 221 " --> pdb=" O MET J 217 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY J 222 " --> pdb=" O THR J 218 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU J 223 " --> pdb=" O LEU J 219 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU J 224 " --> pdb=" O TRP J 220 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASN J 225 " --> pdb=" O ASP J 221 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN J 226 " --> pdb=" O GLY J 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 242 through 247 Processing helix chain 'J' and resid 259 through 271 Processing helix chain 'J' and resid 282 through 290 removed outlier: 3.792A pdb=" N ILE J 286 " --> pdb=" O ASP J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 294 through 319 removed outlier: 4.942A pdb=" N GLU J 312 " --> pdb=" O ASP J 308 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TYR J 313 " --> pdb=" O ALA J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 340 through 348 removed outlier: 3.762A pdb=" N PHE J 344 " --> pdb=" O LYS J 340 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS J 347 " --> pdb=" O ASP J 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 61 Processing helix chain 'I' and resid 62 through 66 removed outlier: 3.653A pdb=" N ALA I 65 " --> pdb=" O PRO I 62 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU I 66 " --> pdb=" O ALA I 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 66' Processing helix chain 'I' and resid 70 through 78 removed outlier: 3.587A pdb=" N SER I 78 " --> pdb=" O AARG I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 86 Processing helix chain 'I' and resid 89 through 93 Processing helix chain 'I' and resid 96 through 107 Processing helix chain 'I' and resid 107 through 113 Processing helix chain 'I' and resid 116 through 120 removed outlier: 4.139A pdb=" N ASN I 119 " --> pdb=" O VAL I 116 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER I 120 " --> pdb=" O TYR I 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 116 through 120' Processing helix chain 'I' and resid 138 through 149 Processing helix chain 'I' and resid 158 through 163 Processing helix chain 'I' and resid 168 through 184 Processing helix chain 'I' and resid 193 through 198 removed outlier: 4.188A pdb=" N PHE I 197 " --> pdb=" O GLN I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 221 Processing helix chain 'I' and resid 237 through 241 Processing helix chain 'I' and resid 242 through 248 Processing helix chain 'I' and resid 259 through 271 Processing helix chain 'I' and resid 282 through 290 removed outlier: 3.550A pdb=" N ILE I 286 " --> pdb=" O ASP I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 310 Processing helix chain 'I' and resid 310 through 320 Processing helix chain 'I' and resid 340 through 348 removed outlier: 3.947A pdb=" N PHE I 344 " --> pdb=" O LYS I 340 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 61 Processing helix chain 'H' and resid 62 through 66 removed outlier: 3.724A pdb=" N GLU H 66 " --> pdb=" O ALA H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 77 Processing helix chain 'H' and resid 89 through 93 Processing helix chain 'H' and resid 96 through 107 Processing helix chain 'H' and resid 107 through 113 Processing helix chain 'H' and resid 113 through 118 removed outlier: 3.816A pdb=" N TYR H 117 " --> pdb=" O MET H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 124 removed outlier: 3.765A pdb=" N GLN H 124 " --> pdb=" O PRO H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 149 Processing helix chain 'H' and resid 158 through 163 Processing helix chain 'H' and resid 168 through 184 Processing helix chain 'H' and resid 193 through 198 removed outlier: 4.103A pdb=" N PHE H 197 " --> pdb=" O GLN H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 221 Processing helix chain 'H' and resid 242 through 248 Processing helix chain 'H' and resid 259 through 271 Processing helix chain 'H' and resid 282 through 290 Processing helix chain 'H' and resid 294 through 310 Processing helix chain 'H' and resid 310 through 320 Processing helix chain 'H' and resid 340 through 346 removed outlier: 3.752A pdb=" N PHE H 344 " --> pdb=" O LYS H 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 61 Processing helix chain 'G' and resid 62 through 66 removed outlier: 3.807A pdb=" N GLU G 66 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 78 removed outlier: 3.878A pdb=" N SER G 78 " --> pdb=" O ARG G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 93 Processing helix chain 'G' and resid 96 through 108 Processing helix chain 'G' and resid 108 through 113 Processing helix chain 'G' and resid 138 through 149 Processing helix chain 'G' and resid 169 through 184 Processing helix chain 'G' and resid 193 through 198 removed outlier: 4.228A pdb=" N PHE G 197 " --> pdb=" O GLN G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 221 Processing helix chain 'G' and resid 237 through 241 Processing helix chain 'G' and resid 242 through 249 removed outlier: 3.529A pdb=" N ARG G 248 " --> pdb=" O ALA G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 271 Processing helix chain 'G' and resid 282 through 290 removed outlier: 3.514A pdb=" N ILE G 286 " --> pdb=" O ASP G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 310 Processing helix chain 'G' and resid 310 through 321 removed outlier: 3.666A pdb=" N LYS G 315 " --> pdb=" O LYS G 311 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN G 316 " --> pdb=" O GLU G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 348 removed outlier: 3.683A pdb=" N LYS G 347 " --> pdb=" O ASP G 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 61 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 70 through 78 Processing helix chain 'F' and resid 89 through 93 Processing helix chain 'F' and resid 96 through 107 Processing helix chain 'F' and resid 107 through 113 Processing helix chain 'F' and resid 138 through 150 removed outlier: 3.673A pdb=" N SER F 150 " --> pdb=" O LEU F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 184 Processing helix chain 'F' and resid 193 through 198 removed outlier: 4.119A pdb=" N PHE F 197 " --> pdb=" O GLN F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 221 Processing helix chain 'F' and resid 237 through 241 Processing helix chain 'F' and resid 242 through 248 Processing helix chain 'F' and resid 259 through 271 Processing helix chain 'F' and resid 282 through 290 Processing helix chain 'F' and resid 294 through 320 removed outlier: 5.347A pdb=" N GLU F 312 " --> pdb=" O ASP F 308 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N TYR F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 348 Processing helix chain 'E' and resid 43 through 61 Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 70 through 78 Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'E' and resid 96 through 107 Processing helix chain 'E' and resid 107 through 113 Processing helix chain 'E' and resid 138 through 149 Processing helix chain 'E' and resid 158 through 163 Processing helix chain 'E' and resid 168 through 184 removed outlier: 3.513A pdb=" N LYS E 172 " --> pdb=" O GLY E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 198 removed outlier: 3.989A pdb=" N PHE E 197 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 221 Processing helix chain 'E' and resid 242 through 248 Processing helix chain 'E' and resid 259 through 271 Processing helix chain 'E' and resid 282 through 290 removed outlier: 3.748A pdb=" N ILE E 286 " --> pdb=" O ASP E 282 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR E 290 " --> pdb=" O ILE E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 310 Processing helix chain 'E' and resid 310 through 320 Processing helix chain 'E' and resid 340 through 348 removed outlier: 3.540A pdb=" N PHE E 344 " --> pdb=" O LYS E 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 61 Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 70 through 78 Processing helix chain 'D' and resid 96 through 107 Processing helix chain 'D' and resid 107 through 113 Processing helix chain 'D' and resid 120 through 124 removed outlier: 4.039A pdb=" N GLN D 124 " --> pdb=" O PRO D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 150 removed outlier: 3.518A pdb=" N SER D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 168 through 184 Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.050A pdb=" N PHE D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 221 removed outlier: 3.743A pdb=" N ASP D 221 " --> pdb=" O MET D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 241 Processing helix chain 'D' and resid 242 through 248 removed outlier: 3.568A pdb=" N ARG D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 271 Processing helix chain 'D' and resid 282 through 290 removed outlier: 4.086A pdb=" N ILE D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 320 removed outlier: 5.042A pdb=" N GLU D 312 " --> pdb=" O ASP D 308 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N TYR D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 346 removed outlier: 3.709A pdb=" N PHE D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 61 Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.532A pdb=" N ALA C 65 " --> pdb=" O PRO C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 70 through 77 Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 96 through 107 Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 116 through 120 removed outlier: 4.298A pdb=" N ASN C 119 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER C 120 " --> pdb=" O TYR C 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 116 through 120' Processing helix chain 'C' and resid 138 through 150 Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 168 through 184 Processing helix chain 'C' and resid 193 through 198 removed outlier: 4.150A pdb=" N PHE C 197 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 221 Processing helix chain 'C' and resid 237 through 241 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 259 through 271 Processing helix chain 'C' and resid 282 through 290 removed outlier: 3.908A pdb=" N ILE C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 310 Processing helix chain 'C' and resid 310 through 320 Processing helix chain 'C' and resid 340 through 348 removed outlier: 3.562A pdb=" N PHE C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 61 Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 70 through 77 Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 96 through 107 Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 113 through 118 removed outlier: 3.706A pdb=" N TYR B 117 " --> pdb=" O MET B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 158 through 163 removed outlier: 3.658A pdb=" N ILE B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 184 removed outlier: 4.060A pdb=" N LYS B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 198 removed outlier: 4.216A pdb=" N PHE B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 221 Processing helix chain 'B' and resid 242 through 249 Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 283 through 290 Processing helix chain 'B' and resid 294 through 310 Processing helix chain 'B' and resid 310 through 320 Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'A' and resid 43 through 61 Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 70 through 77 Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.632A pdb=" N ILE A 93 " --> pdb=" O PHE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 107 Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.696A pdb=" N SER A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 removed outlier: 3.761A pdb=" N ILE A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.503A pdb=" N LYS A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 206 through 221 Processing helix chain 'A' and resid 242 through 249 Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 294 through 310 Processing helix chain 'A' and resid 310 through 320 Processing helix chain 'A' and resid 340 through 346 Processing sheet with id=AA1, first strand: chain 'J' and resid 80 through 81 removed outlier: 3.894A pdb=" N PHE J 154 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN J 153 " --> pdb=" O ILE J 188 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE J 190 " --> pdb=" O ASN J 153 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE J 155 " --> pdb=" O PHE J 190 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ASP J 192 " --> pdb=" O ILE J 155 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N CYS J 187 " --> pdb=" O MET J 230 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE J 232 " --> pdb=" O CYS J 187 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ILE J 189 " --> pdb=" O ILE J 232 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ALA J 234 " --> pdb=" O ILE J 189 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE J 191 " --> pdb=" O ALA J 234 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL J 129 " --> pdb=" O GLY J 233 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N THR J 235 " --> pdb=" O VAL J 129 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU J 131 " --> pdb=" O THR J 235 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY J 128 " --> pdb=" O LYS J 251 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N PHE J 253 " --> pdb=" O GLY J 128 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU J 130 " --> pdb=" O PHE J 253 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 80 through 81 removed outlier: 3.915A pdb=" N PHE I 154 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASN I 153 " --> pdb=" O ILE I 188 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N PHE I 190 " --> pdb=" O ASN I 153 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE I 155 " --> pdb=" O PHE I 190 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ASP I 192 " --> pdb=" O ILE I 155 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ILE I 157 " --> pdb=" O ASP I 192 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA I 234 " --> pdb=" O ILE I 191 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL I 129 " --> pdb=" O GLY I 233 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY I 128 " --> pdb=" O LYS I 251 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N PHE I 253 " --> pdb=" O GLY I 128 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU I 130 " --> pdb=" O PHE I 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 80 through 81 removed outlier: 3.778A pdb=" N PHE H 154 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASN H 153 " --> pdb=" O ILE H 188 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N PHE H 190 " --> pdb=" O ASN H 153 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE H 155 " --> pdb=" O PHE H 190 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASP H 192 " --> pdb=" O ILE H 155 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N CYS H 187 " --> pdb=" O MET H 230 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE H 232 " --> pdb=" O CYS H 187 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE H 189 " --> pdb=" O ILE H 232 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ALA H 234 " --> pdb=" O ILE H 189 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE H 191 " --> pdb=" O ALA H 234 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY H 128 " --> pdb=" O LYS H 251 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N PHE H 253 " --> pdb=" O GLY H 128 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU H 130 " --> pdb=" O PHE H 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 80 through 81 removed outlier: 3.784A pdb=" N PHE G 154 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA G 234 " --> pdb=" O ILE G 191 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL G 129 " --> pdb=" O GLY G 233 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N THR G 235 " --> pdb=" O VAL G 129 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU G 131 " --> pdb=" O THR G 235 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY G 128 " --> pdb=" O LYS G 251 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N PHE G 253 " --> pdb=" O GLY G 128 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU G 130 " --> pdb=" O PHE G 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 153 through 155 removed outlier: 6.778A pdb=" N CYS F 187 " --> pdb=" O MET F 230 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE F 232 " --> pdb=" O CYS F 187 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE F 189 " --> pdb=" O ILE F 232 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ALA F 234 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE F 191 " --> pdb=" O ALA F 234 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY F 128 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N PHE F 253 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU F 130 " --> pdb=" O PHE F 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 80 through 81 removed outlier: 3.712A pdb=" N PHE E 154 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP E 192 " --> pdb=" O ILE E 157 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL E 129 " --> pdb=" O GLY E 233 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N THR E 235 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU E 131 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLY E 128 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N PHE E 253 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU E 130 " --> pdb=" O PHE E 253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 80 through 81 removed outlier: 3.921A pdb=" N PHE D 154 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN D 153 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N PHE D 190 " --> pdb=" O ASN D 153 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE D 155 " --> pdb=" O PHE D 190 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ASP D 192 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE D 157 " --> pdb=" O ASP D 192 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N CYS D 187 " --> pdb=" O MET D 230 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE D 232 " --> pdb=" O CYS D 187 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE D 189 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALA D 234 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE D 191 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY D 128 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N PHE D 253 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU D 130 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 80 through 81 removed outlier: 3.931A pdb=" N PHE C 154 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ASN C 153 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE C 190 " --> pdb=" O ASN C 153 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE C 155 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ASP C 192 " --> pdb=" O ILE C 155 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ILE C 157 " --> pdb=" O ASP C 192 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY C 128 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE C 253 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU C 130 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 80 through 81 removed outlier: 3.795A pdb=" N PHE B 154 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASN B 153 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N PHE B 190 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE B 155 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ASP B 192 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N CYS B 187 " --> pdb=" O MET B 230 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE B 232 " --> pdb=" O CYS B 187 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE B 189 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ALA B 234 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE B 191 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL B 129 " --> pdb=" O GLY B 233 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N THR B 235 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU B 131 " --> pdb=" O THR B 235 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.832A pdb=" N PHE A 154 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASN A 153 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE A 190 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ILE A 155 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASP A 192 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILE A 157 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N CYS A 187 " --> pdb=" O MET A 230 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ILE A 232 " --> pdb=" O CYS A 187 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE A 189 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ALA A 234 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE A 191 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLY A 128 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N PHE A 253 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU A 130 " --> pdb=" O PHE A 253 " (cutoff:3.500A) 1156 hydrogen bonds defined for protein. 3343 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: 4.09 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7597 1.34 - 1.46: 4179 1.46 - 1.58: 12285 1.58 - 1.70: 51 1.70 - 1.82: 210 Bond restraints: 24322 Sorted by residual: bond pdb=" C4 ATP B 401 " pdb=" C5 ATP B 401 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.78e+01 bond pdb=" C4 ATP J 401 " pdb=" C5 ATP J 401 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.75e+01 bond pdb=" C4 ATP H 401 " pdb=" C5 ATP H 401 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.70e+01 bond pdb=" C4 ATP E 401 " pdb=" C5 ATP E 401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.57e+01 bond pdb=" C4 ATP G 401 " pdb=" C5 ATP G 401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.49e+01 ... (remaining 24317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.19: 32553 4.19 - 8.38: 236 8.38 - 12.56: 34 12.56 - 16.75: 7 16.75 - 20.94: 12 Bond angle restraints: 32842 Sorted by residual: angle pdb=" PB ATP E 401 " pdb=" O3B ATP E 401 " pdb=" PG ATP E 401 " ideal model delta sigma weight residual 139.87 118.93 20.94 1.00e+00 1.00e+00 4.39e+02 angle pdb=" PB ATP F 401 " pdb=" O3B ATP F 401 " pdb=" PG ATP F 401 " ideal model delta sigma weight residual 139.87 120.46 19.41 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB ATP J 401 " pdb=" O3B ATP J 401 " pdb=" PG ATP J 401 " ideal model delta sigma weight residual 139.87 120.51 19.36 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PA ATP E 401 " pdb=" O3A ATP E 401 " pdb=" PB ATP E 401 " ideal model delta sigma weight residual 136.83 118.46 18.37 1.00e+00 1.00e+00 3.38e+02 angle pdb=" PB ATP I 401 " pdb=" O3B ATP I 401 " pdb=" PG ATP I 401 " ideal model delta sigma weight residual 139.87 121.67 18.20 1.00e+00 1.00e+00 3.31e+02 ... (remaining 32837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 12834 18.04 - 36.08: 1877 36.08 - 54.11: 485 54.11 - 72.15: 76 72.15 - 90.19: 29 Dihedral angle restraints: 15301 sinusoidal: 6549 harmonic: 8752 Sorted by residual: dihedral pdb=" CA LEU C 184 " pdb=" C LEU C 184 " pdb=" N GLN C 185 " pdb=" CA GLN C 185 " ideal model delta harmonic sigma weight residual -180.00 -156.37 -23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA LEU B 184 " pdb=" C LEU B 184 " pdb=" N GLN B 185 " pdb=" CA GLN B 185 " ideal model delta harmonic sigma weight residual 180.00 -157.62 -22.38 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LEU A 184 " pdb=" C LEU A 184 " pdb=" N GLN A 185 " pdb=" CA GLN A 185 " ideal model delta harmonic sigma weight residual -180.00 -157.87 -22.13 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 15298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2936 0.052 - 0.105: 646 0.105 - 0.157: 161 0.157 - 0.209: 15 0.209 - 0.262: 4 Chirality restraints: 3762 Sorted by residual: chirality pdb=" CA LEU D 246 " pdb=" N LEU D 246 " pdb=" C LEU D 246 " pdb=" CB LEU D 246 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C1' ATP I 401 " pdb=" C2' ATP I 401 " pdb=" N9 ATP I 401 " pdb=" O4' ATP I 401 " both_signs ideal model delta sigma weight residual False 2.41 2.63 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA GLU B 149 " pdb=" N GLU B 149 " pdb=" C GLU B 149 " pdb=" CB GLU B 149 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 3759 not shown) Planarity restraints: 4113 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 134 " -0.081 5.00e-02 4.00e+02 1.22e-01 2.40e+01 pdb=" N PRO A 135 " 0.212 5.00e-02 4.00e+02 pdb=" CA PRO A 135 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 135 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 82 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO E 83 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 83 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 83 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY J 133 " 0.033 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO J 134 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO J 134 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO J 134 " 0.028 5.00e-02 4.00e+02 ... (remaining 4110 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 40 2.35 - 2.99: 11697 2.99 - 3.62: 38123 3.62 - 4.26: 58206 4.26 - 4.90: 97516 Nonbonded interactions: 205582 Sorted by model distance: nonbonded pdb=" O1G ATP J 401 " pdb="MG MG J 402 " model vdw 1.712 2.170 nonbonded pdb=" O3G ATP G 401 " pdb="MG MG G 402 " model vdw 1.764 2.170 nonbonded pdb=" OG1 THR J 140 " pdb="MG MG J 402 " model vdw 1.764 2.170 nonbonded pdb=" CG2 THR B 140 " pdb="MG MG B 402 " model vdw 1.772 2.590 nonbonded pdb=" OG1 THR E 140 " pdb="MG MG E 402 " model vdw 1.786 2.170 ... (remaining 205577 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 43 through 73 or resid 75 through 319 or resid 336 through \ 402)) selection = (chain 'B' and (resid 43 through 73 or resid 75 through 319 or resid 336 through \ 402)) selection = (chain 'C' and (resid 43 through 73 or resid 75 through 319 or resid 336 through \ 402)) selection = (chain 'D' and (resid 43 through 73 or resid 75 through 319 or resid 336 through \ 402)) selection = (chain 'E' and (resid 43 through 73 or resid 75 through 319 or resid 336 through \ 402)) selection = (chain 'F' and (resid 43 through 73 or resid 75 through 319 or resid 336 through \ 402)) selection = (chain 'G' and (resid 43 through 73 or resid 75 through 319 or resid 321 or resi \ d 337 through 402)) selection = (chain 'H' and (resid 43 through 73 or resid 75 through 319 or resid 336 through \ 402)) selection = (chain 'I' and (resid 43 through 73 or resid 75 through 319 or resid 336 through \ 402)) selection = (chain 'J' and (resid 43 through 73 or resid 75 through 319 or resid 336 through \ 402)) } 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=0.00 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: 12.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.980 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 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 : 0.006 0.112 24322 Z= 0.372 Angle : 0.964 20.941 32842 Z= 0.649 Chirality : 0.047 0.262 3762 Planarity : 0.005 0.122 4113 Dihedral : 17.793 90.188 9599 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.30 % Allowed : 25.98 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.74 (0.15), residues: 2940 helix: 0.84 (0.13), residues: 1559 sheet: -0.53 (0.34), residues: 247 loop : 0.49 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 248 TYR 0.030 0.002 TYR J 313 PHE 0.028 0.002 PHE A 190 TRP 0.012 0.001 TRP I 166 HIS 0.003 0.001 HIS J 206 Details of bonding type rmsd covalent geometry : bond 0.00611 (24322) covalent geometry : angle 0.96447 (32842) hydrogen bonds : bond 0.15309 ( 1156) hydrogen bonds : angle 5.76362 ( 3343) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 429 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 112 MET cc_start: 0.7571 (mmp) cc_final: 0.7327 (mmt) REVERT: I 59 LYS cc_start: 0.8853 (mtpp) cc_final: 0.8275 (mttm) outliers start: 8 outliers final: 4 residues processed: 432 average time/residue: 0.1644 time to fit residues: 111.0721 Evaluate side-chains 397 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 393 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain A residue 157 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.3980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 236 ASN H 53 GLN H 236 ASN H 289 ASN F 236 ASN E 50 GLN D 226 ASN D 236 ASN D 262 GLN C 316 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.148291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.114122 restraints weight = 36449.123| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.46 r_work: 0.3266 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24322 Z= 0.120 Angle : 0.553 8.837 32842 Z= 0.273 Chirality : 0.040 0.184 3762 Planarity : 0.004 0.078 4113 Dihedral : 10.645 88.488 3560 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.09 % Allowed : 25.68 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.16), residues: 2940 helix: 1.40 (0.13), residues: 1592 sheet: -0.58 (0.35), residues: 231 loop : 0.84 (0.20), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 248 TYR 0.015 0.001 TYR G 313 PHE 0.010 0.001 PHE C 190 TRP 0.005 0.001 TRP I 166 HIS 0.001 0.000 HIS G 104 Details of bonding type rmsd covalent geometry : bond 0.00279 (24322) covalent geometry : angle 0.55273 (32842) hydrogen bonds : bond 0.03755 ( 1156) hydrogen bonds : angle 4.62251 ( 3343) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 424 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 141 MET cc_start: 0.8562 (mmm) cc_final: 0.8310 (mtp) REVERT: J 171 ASN cc_start: 0.8639 (m110) cc_final: 0.8308 (m110) REVERT: I 224 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8258 (mm) REVERT: H 221 ASP cc_start: 0.8157 (t0) cc_final: 0.7887 (t0) REVERT: G 313 TYR cc_start: 0.8582 (t80) cc_final: 0.7910 (t80) REVERT: F 347 LYS cc_start: 0.7919 (mmtm) cc_final: 0.7498 (mmmt) REVERT: C 284 GLN cc_start: 0.8723 (tp-100) cc_final: 0.7864 (tp-100) REVERT: B 340 LYS cc_start: 0.7803 (mmmt) cc_final: 0.7459 (mmmt) outliers start: 55 outliers final: 23 residues processed: 458 average time/residue: 0.1551 time to fit residues: 112.4736 Evaluate side-chains 425 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 401 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain I residue 350 MET Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 236 ASN Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 177 MET Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 209 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 8 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 256 optimal weight: 10.0000 chunk 274 optimal weight: 7.9990 chunk 182 optimal weight: 0.0060 chunk 147 optimal weight: 7.9990 chunk 288 optimal weight: 0.6980 chunk 168 optimal weight: 0.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 53 GLN H 236 ASN F 236 ASN E 50 GLN E 236 ASN D 236 ASN D 262 GLN C 316 GLN A 153 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.148113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.112635 restraints weight = 60747.836| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.36 r_work: 0.3191 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24322 Z= 0.123 Angle : 0.515 6.822 32842 Z= 0.253 Chirality : 0.039 0.144 3762 Planarity : 0.004 0.062 4113 Dihedral : 10.401 87.831 3553 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.74 % Allowed : 24.72 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.16), residues: 2940 helix: 1.75 (0.13), residues: 1591 sheet: -0.75 (0.34), residues: 249 loop : 0.98 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 60 TYR 0.023 0.001 TYR J 313 PHE 0.012 0.001 PHE J 245 TRP 0.005 0.001 TRP C 166 HIS 0.004 0.001 HIS G 104 Details of bonding type rmsd covalent geometry : bond 0.00293 (24322) covalent geometry : angle 0.51480 (32842) hydrogen bonds : bond 0.03256 ( 1156) hydrogen bonds : angle 4.39414 ( 3343) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 423 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: J 112 MET cc_start: 0.7293 (mmt) cc_final: 0.7067 (mmp) REVERT: I 224 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8273 (mm) REVERT: H 221 ASP cc_start: 0.8247 (t0) cc_final: 0.7974 (t0) REVERT: G 77 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9087 (tt) REVERT: G 141 MET cc_start: 0.8439 (mtp) cc_final: 0.8104 (mmt) REVERT: G 158 ARG cc_start: 0.8310 (ttp-110) cc_final: 0.8101 (ttp-110) REVERT: G 308 ASP cc_start: 0.8363 (t70) cc_final: 0.7981 (t70) REVERT: G 313 TYR cc_start: 0.8593 (t80) cc_final: 0.7773 (t80) REVERT: F 289 ASN cc_start: 0.8550 (m-40) cc_final: 0.8156 (m-40) REVERT: F 347 LYS cc_start: 0.7875 (mmtm) cc_final: 0.7446 (mmmt) REVERT: F 350 MET cc_start: 0.6138 (tpp) cc_final: 0.5912 (tpp) REVERT: E 346 LYS cc_start: 0.8597 (ptmm) cc_final: 0.8320 (ptpp) REVERT: E 348 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7960 (mp) REVERT: C 240 ASP cc_start: 0.8527 (m-30) cc_final: 0.7762 (t0) REVERT: C 284 GLN cc_start: 0.8739 (tp-100) cc_final: 0.7928 (tp-100) REVERT: B 308 ASP cc_start: 0.6728 (t0) cc_final: 0.6494 (t0) REVERT: B 313 TYR cc_start: 0.7875 (t80) cc_final: 0.7584 (t80) REVERT: A 298 LEU cc_start: 0.5989 (OUTLIER) cc_final: 0.5762 (mp) outliers start: 72 outliers final: 31 residues processed: 463 average time/residue: 0.1525 time to fit residues: 112.9016 Evaluate side-chains 434 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 399 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 236 ASN Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 200 GLU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 177 MET Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 335 LYS Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 298 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 204 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 291 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 chunk 267 optimal weight: 5.9990 chunk 264 optimal weight: 0.7980 chunk 270 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 236 ASN I 193 GLN H 236 ASN F 236 ASN E 50 GLN D 236 ASN D 262 GLN C 153 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.143363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.107248 restraints weight = 45582.504| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.89 r_work: 0.3126 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 24322 Z= 0.244 Angle : 0.585 9.239 32842 Z= 0.287 Chirality : 0.042 0.148 3762 Planarity : 0.004 0.054 4113 Dihedral : 10.365 88.597 3553 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.08 % Allowed : 24.61 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.16), residues: 2940 helix: 1.73 (0.13), residues: 1600 sheet: -0.44 (0.35), residues: 251 loop : 0.91 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 201 TYR 0.019 0.001 TYR J 313 PHE 0.015 0.002 PHE J 245 TRP 0.011 0.001 TRP E 220 HIS 0.003 0.001 HIS I 104 Details of bonding type rmsd covalent geometry : bond 0.00584 (24322) covalent geometry : angle 0.58486 (32842) hydrogen bonds : bond 0.03456 ( 1156) hydrogen bonds : angle 4.42785 ( 3343) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 397 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: J 112 MET cc_start: 0.7384 (mmt) cc_final: 0.7177 (mmp) REVERT: H 221 ASP cc_start: 0.8369 (t0) cc_final: 0.8086 (t0) REVERT: G 308 ASP cc_start: 0.8371 (t70) cc_final: 0.7973 (t70) REVERT: G 313 TYR cc_start: 0.8455 (t80) cc_final: 0.7829 (t80) REVERT: F 289 ASN cc_start: 0.8589 (m-40) cc_final: 0.8205 (m-40) REVERT: F 347 LYS cc_start: 0.7922 (mmtm) cc_final: 0.7504 (mmmt) REVERT: F 350 MET cc_start: 0.6150 (tpp) cc_final: 0.5844 (tpp) REVERT: E 346 LYS cc_start: 0.8655 (ptmm) cc_final: 0.8350 (ptpp) REVERT: E 348 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8022 (mp) REVERT: C 57 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.8959 (mp) REVERT: C 149 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8139 (mt-10) REVERT: C 284 GLN cc_start: 0.8758 (tp-100) cc_final: 0.8053 (tp-100) REVERT: B 308 ASP cc_start: 0.6864 (t0) cc_final: 0.6657 (t0) REVERT: B 313 TYR cc_start: 0.7910 (t80) cc_final: 0.7519 (t80) REVERT: A 60 ARG cc_start: 0.8101 (ttp80) cc_final: 0.7536 (ttp80) REVERT: A 298 LEU cc_start: 0.6090 (OUTLIER) cc_final: 0.5862 (mp) outliers start: 81 outliers final: 48 residues processed: 444 average time/residue: 0.1589 time to fit residues: 112.1745 Evaluate side-chains 424 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 372 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 139 LYS Chi-restraints excluded: chain J residue 245 PHE Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain I residue 350 MET Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 236 ASN Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 200 GLU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 177 MET Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain E residue 335 LYS Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 298 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 292 optimal weight: 20.0000 chunk 102 optimal weight: 0.9990 chunk 272 optimal weight: 6.9990 chunk 271 optimal weight: 7.9990 chunk 240 optimal weight: 1.9990 chunk 256 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 227 optimal weight: 7.9990 chunk 222 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 236 ASN E 50 GLN E 53 GLN D 236 ASN C 182 ASN C 316 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.145393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.109127 restraints weight = 60509.980| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.50 r_work: 0.3117 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24322 Z= 0.147 Angle : 0.532 7.506 32842 Z= 0.260 Chirality : 0.040 0.183 3762 Planarity : 0.004 0.050 4113 Dihedral : 10.332 89.715 3551 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.61 % Allowed : 24.46 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.16), residues: 2940 helix: 1.84 (0.13), residues: 1601 sheet: -0.52 (0.35), residues: 247 loop : 0.93 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 60 TYR 0.017 0.001 TYR J 313 PHE 0.016 0.001 PHE H 197 TRP 0.007 0.001 TRP C 166 HIS 0.002 0.000 HIS G 104 Details of bonding type rmsd covalent geometry : bond 0.00355 (24322) covalent geometry : angle 0.53193 (32842) hydrogen bonds : bond 0.03156 ( 1156) hydrogen bonds : angle 4.36615 ( 3343) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 396 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: J 112 MET cc_start: 0.7392 (mmt) cc_final: 0.7153 (mmp) REVERT: H 221 ASP cc_start: 0.8378 (t0) cc_final: 0.8076 (t0) REVERT: G 308 ASP cc_start: 0.8412 (t70) cc_final: 0.8035 (t70) REVERT: G 313 TYR cc_start: 0.8453 (t80) cc_final: 0.7886 (t80) REVERT: F 289 ASN cc_start: 0.8603 (m-40) cc_final: 0.8305 (m-40) REVERT: F 347 LYS cc_start: 0.7848 (mmtm) cc_final: 0.7437 (mmmt) REVERT: F 350 MET cc_start: 0.6225 (tpp) cc_final: 0.6006 (tpp) REVERT: E 346 LYS cc_start: 0.8655 (ptmm) cc_final: 0.8341 (ptpp) REVERT: E 348 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8033 (mp) REVERT: C 284 GLN cc_start: 0.8742 (tp-100) cc_final: 0.8058 (tp-100) REVERT: C 346 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8214 (mttp) REVERT: B 308 ASP cc_start: 0.6915 (t0) cc_final: 0.6557 (t0) REVERT: A 60 ARG cc_start: 0.8097 (ttp80) cc_final: 0.7609 (ttp80) outliers start: 95 outliers final: 49 residues processed: 455 average time/residue: 0.1580 time to fit residues: 114.3811 Evaluate side-chains 429 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 378 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 245 PHE Chi-restraints excluded: chain J residue 301 LEU Chi-restraints excluded: chain J residue 316 GLN Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain I residue 350 MET Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 236 ASN Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 200 GLU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 335 LYS Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 346 LYS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 163 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 143 optimal weight: 5.9990 chunk 245 optimal weight: 4.9990 chunk 288 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 223 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 236 ASN I 104 HIS H 236 ASN E 50 GLN D 236 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.143611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.108172 restraints weight = 44398.055| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.90 r_work: 0.3129 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24322 Z= 0.227 Angle : 0.582 9.343 32842 Z= 0.283 Chirality : 0.042 0.231 3762 Planarity : 0.004 0.047 4113 Dihedral : 10.318 87.864 3551 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.61 % Allowed : 24.65 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.16), residues: 2940 helix: 1.77 (0.13), residues: 1616 sheet: -0.44 (0.36), residues: 236 loop : 0.85 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 201 TYR 0.023 0.001 TYR J 313 PHE 0.018 0.002 PHE J 245 TRP 0.009 0.001 TRP E 220 HIS 0.002 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00548 (24322) covalent geometry : angle 0.58213 (32842) hydrogen bonds : bond 0.03326 ( 1156) hydrogen bonds : angle 4.41653 ( 3343) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 380 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: H 221 ASP cc_start: 0.8359 (t0) cc_final: 0.8053 (t0) REVERT: G 77 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9086 (tt) REVERT: G 308 ASP cc_start: 0.8387 (t70) cc_final: 0.7988 (t70) REVERT: G 313 TYR cc_start: 0.8448 (t80) cc_final: 0.8207 (t80) REVERT: F 289 ASN cc_start: 0.8604 (m-40) cc_final: 0.8251 (m-40) REVERT: F 347 LYS cc_start: 0.7895 (mmtm) cc_final: 0.7479 (mmmt) REVERT: F 350 MET cc_start: 0.6251 (tpp) cc_final: 0.5956 (tpp) REVERT: E 346 LYS cc_start: 0.8693 (ptmm) cc_final: 0.8375 (ptpp) REVERT: E 348 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8032 (mp) REVERT: C 284 GLN cc_start: 0.8744 (tp-100) cc_final: 0.8123 (tp-100) REVERT: A 60 ARG cc_start: 0.8086 (ttp80) cc_final: 0.7590 (ttp80) outliers start: 95 outliers final: 62 residues processed: 435 average time/residue: 0.1531 time to fit residues: 106.2450 Evaluate side-chains 438 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 374 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 139 LYS Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 245 PHE Chi-restraints excluded: chain J residue 316 GLN Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain I residue 350 MET Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 236 ASN Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 161 SER Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 200 GLU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain E residue 335 LYS Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 163 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 271 optimal weight: 8.9990 chunk 266 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 217 optimal weight: 0.6980 chunk 264 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 166 optimal weight: 0.3980 chunk 192 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 236 ASN H 236 ASN E 50 GLN D 236 ASN C 182 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.148592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.112405 restraints weight = 54496.093| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.36 r_work: 0.3181 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24322 Z= 0.114 Angle : 0.536 10.308 32842 Z= 0.259 Chirality : 0.040 0.227 3762 Planarity : 0.004 0.046 4113 Dihedral : 10.217 87.164 3551 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.89 % Allowed : 25.64 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.16), residues: 2940 helix: 1.91 (0.13), residues: 1606 sheet: -0.61 (0.34), residues: 245 loop : 0.95 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 60 TYR 0.021 0.001 TYR J 313 PHE 0.017 0.001 PHE J 245 TRP 0.006 0.001 TRP C 166 HIS 0.002 0.000 HIS G 104 Details of bonding type rmsd covalent geometry : bond 0.00271 (24322) covalent geometry : angle 0.53599 (32842) hydrogen bonds : bond 0.02991 ( 1156) hydrogen bonds : angle 4.33846 ( 3343) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 413 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: H 221 ASP cc_start: 0.8305 (t0) cc_final: 0.7988 (t0) REVERT: G 77 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9088 (tt) REVERT: G 308 ASP cc_start: 0.8366 (t70) cc_final: 0.7962 (t70) REVERT: G 313 TYR cc_start: 0.8338 (t80) cc_final: 0.7852 (t80) REVERT: F 289 ASN cc_start: 0.8605 (m-40) cc_final: 0.8271 (m-40) REVERT: F 337 ARG cc_start: 0.7582 (tmt170) cc_final: 0.7356 (ttt90) REVERT: F 347 LYS cc_start: 0.7845 (mmtm) cc_final: 0.7409 (mmmt) REVERT: F 350 MET cc_start: 0.6283 (tpp) cc_final: 0.6078 (tpp) REVERT: E 346 LYS cc_start: 0.8671 (ptmm) cc_final: 0.8348 (ptpp) REVERT: E 348 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7985 (mp) REVERT: D 313 TYR cc_start: 0.7567 (t80) cc_final: 0.7257 (t80) REVERT: C 284 GLN cc_start: 0.8724 (tp-100) cc_final: 0.8107 (tp-100) REVERT: C 350 MET cc_start: 0.7352 (mmm) cc_final: 0.6388 (mmt) REVERT: B 340 LYS cc_start: 0.7473 (mmmt) cc_final: 0.7271 (mmmt) REVERT: A 60 ARG cc_start: 0.8071 (ttp80) cc_final: 0.7639 (ttp80) outliers start: 76 outliers final: 49 residues processed: 460 average time/residue: 0.1558 time to fit residues: 113.7399 Evaluate side-chains 443 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 392 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 139 LYS Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 301 LEU Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 236 ASN Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 161 SER Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 335 LYS Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 157 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 138 optimal weight: 3.9990 chunk 249 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 203 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 276 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 236 ASN G 53 GLN E 50 GLN D 236 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.144635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.109787 restraints weight = 59046.347| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.28 r_work: 0.3142 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24322 Z= 0.163 Angle : 0.560 9.084 32842 Z= 0.270 Chirality : 0.041 0.231 3762 Planarity : 0.004 0.044 4113 Dihedral : 10.189 85.585 3551 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.55 % Allowed : 26.36 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.16), residues: 2940 helix: 1.91 (0.13), residues: 1611 sheet: -0.50 (0.35), residues: 242 loop : 0.97 (0.20), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 60 TYR 0.024 0.001 TYR J 313 PHE 0.015 0.001 PHE J 245 TRP 0.008 0.001 TRP D 220 HIS 0.002 0.000 HIS G 104 Details of bonding type rmsd covalent geometry : bond 0.00397 (24322) covalent geometry : angle 0.56012 (32842) hydrogen bonds : bond 0.03067 ( 1156) hydrogen bonds : angle 4.31907 ( 3343) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 392 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: J 52 LEU cc_start: 0.8752 (tp) cc_final: 0.8390 (mm) REVERT: I 60 ARG cc_start: 0.8033 (mtp85) cc_final: 0.7774 (mtp85) REVERT: H 221 ASP cc_start: 0.8350 (t0) cc_final: 0.8033 (t0) REVERT: G 77 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9098 (tt) REVERT: G 308 ASP cc_start: 0.8411 (t70) cc_final: 0.8003 (t70) REVERT: F 289 ASN cc_start: 0.8607 (m-40) cc_final: 0.8288 (m-40) REVERT: F 347 LYS cc_start: 0.7894 (mmtm) cc_final: 0.7470 (mmmt) REVERT: F 350 MET cc_start: 0.6309 (tpp) cc_final: 0.6072 (tpp) REVERT: E 346 LYS cc_start: 0.8718 (ptmm) cc_final: 0.8385 (ptpp) REVERT: E 348 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8058 (mp) REVERT: D 313 TYR cc_start: 0.7559 (t80) cc_final: 0.7268 (t80) REVERT: C 284 GLN cc_start: 0.8737 (tp-100) cc_final: 0.8152 (tp-100) REVERT: C 350 MET cc_start: 0.7356 (mmm) cc_final: 0.6482 (mmt) REVERT: B 340 LYS cc_start: 0.7533 (mmmt) cc_final: 0.7325 (mmmt) REVERT: A 60 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7681 (ttp80) outliers start: 67 outliers final: 50 residues processed: 431 average time/residue: 0.1575 time to fit residues: 108.0130 Evaluate side-chains 436 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 384 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 139 LYS Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 301 LEU Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 236 ASN Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 161 SER Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain E residue 335 LYS Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 157 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 213 optimal weight: 0.0030 chunk 182 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 180 optimal weight: 0.0670 chunk 34 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 chunk 290 optimal weight: 0.0970 chunk 136 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.5928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 53 GLN H 236 ASN E 50 GLN D 236 ASN C 316 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.148957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.112775 restraints weight = 51213.495| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.20 r_work: 0.3207 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24322 Z= 0.111 Angle : 0.549 10.638 32842 Z= 0.264 Chirality : 0.040 0.227 3762 Planarity : 0.004 0.043 4113 Dihedral : 10.024 86.932 3551 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.40 % Allowed : 26.51 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.16), residues: 2940 helix: 1.98 (0.13), residues: 1611 sheet: -0.58 (0.34), residues: 250 loop : 1.02 (0.20), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 337 TYR 0.024 0.001 TYR J 313 PHE 0.012 0.001 PHE J 245 TRP 0.007 0.001 TRP C 166 HIS 0.001 0.000 HIS I 206 Details of bonding type rmsd covalent geometry : bond 0.00265 (24322) covalent geometry : angle 0.54936 (32842) hydrogen bonds : bond 0.02879 ( 1156) hydrogen bonds : angle 4.27548 ( 3343) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 417 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: J 52 LEU cc_start: 0.8737 (tp) cc_final: 0.8373 (mm) REVERT: I 60 ARG cc_start: 0.7997 (mtp85) cc_final: 0.7769 (mtp85) REVERT: G 77 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9111 (tt) REVERT: G 346 LYS cc_start: 0.8342 (ptmt) cc_final: 0.7993 (mmtm) REVERT: F 289 ASN cc_start: 0.8595 (m-40) cc_final: 0.8236 (m-40) REVERT: F 347 LYS cc_start: 0.7876 (mmtm) cc_final: 0.7367 (mmmt) REVERT: F 350 MET cc_start: 0.6302 (tpp) cc_final: 0.6090 (tpp) REVERT: E 346 LYS cc_start: 0.8692 (ptmm) cc_final: 0.8344 (ptpp) REVERT: E 348 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8034 (mp) REVERT: D 313 TYR cc_start: 0.7509 (t80) cc_final: 0.7245 (t80) REVERT: C 284 GLN cc_start: 0.8720 (tp-100) cc_final: 0.8136 (tp-100) REVERT: C 346 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8208 (mttp) REVERT: C 350 MET cc_start: 0.7293 (mmm) cc_final: 0.6484 (mmt) REVERT: B 340 LYS cc_start: 0.7516 (mmmt) cc_final: 0.7314 (mmmt) REVERT: A 60 ARG cc_start: 0.8066 (ttp80) cc_final: 0.7669 (ttp80) outliers start: 63 outliers final: 47 residues processed: 457 average time/residue: 0.1526 time to fit residues: 110.8824 Evaluate side-chains 446 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 396 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 139 LYS Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 301 LEU Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 236 ASN Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 161 SER Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain E residue 335 LYS Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 346 LYS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 195 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 162 optimal weight: 8.9990 chunk 278 optimal weight: 0.0270 chunk 164 optimal weight: 2.9990 chunk 276 optimal weight: 0.7980 chunk 237 optimal weight: 0.8980 chunk 209 optimal weight: 0.0770 chunk 240 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 236 ASN E 50 GLN D 236 ASN C 316 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.150109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.114548 restraints weight = 49622.773| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.17 r_work: 0.3225 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24322 Z= 0.110 Angle : 0.554 12.786 32842 Z= 0.266 Chirality : 0.040 0.229 3762 Planarity : 0.004 0.071 4113 Dihedral : 9.880 86.841 3551 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.86 % Allowed : 26.97 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.16), residues: 2940 helix: 1.97 (0.13), residues: 1623 sheet: -0.37 (0.34), residues: 258 loop : 1.10 (0.20), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG F 248 TYR 0.023 0.001 TYR J 313 PHE 0.012 0.001 PHE J 245 TRP 0.007 0.001 TRP C 166 HIS 0.001 0.000 HIS G 104 Details of bonding type rmsd covalent geometry : bond 0.00262 (24322) covalent geometry : angle 0.55442 (32842) hydrogen bonds : bond 0.02803 ( 1156) hydrogen bonds : angle 4.23358 ( 3343) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 414 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: J 52 LEU cc_start: 0.8712 (tp) cc_final: 0.8344 (mm) REVERT: J 159 MET cc_start: 0.8432 (mmm) cc_final: 0.8209 (tpt) REVERT: I 60 ARG cc_start: 0.7978 (mtp85) cc_final: 0.7660 (mtp85) REVERT: I 224 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8361 (mm) REVERT: G 77 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9119 (tt) REVERT: G 308 ASP cc_start: 0.8335 (t70) cc_final: 0.7900 (t70) REVERT: G 346 LYS cc_start: 0.8327 (ptmt) cc_final: 0.7983 (mmtm) REVERT: F 289 ASN cc_start: 0.8611 (m-40) cc_final: 0.8243 (m-40) REVERT: F 347 LYS cc_start: 0.7869 (mmtm) cc_final: 0.7349 (mmmt) REVERT: E 346 LYS cc_start: 0.8702 (ptmm) cc_final: 0.8343 (ptpp) REVERT: E 348 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8045 (mp) REVERT: D 313 TYR cc_start: 0.7476 (t80) cc_final: 0.7197 (t80) REVERT: C 284 GLN cc_start: 0.8715 (tp-100) cc_final: 0.8142 (tp-100) REVERT: C 346 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8209 (mttp) REVERT: C 350 MET cc_start: 0.7227 (mmm) cc_final: 0.6537 (mmt) REVERT: A 60 ARG cc_start: 0.8065 (ttp80) cc_final: 0.7681 (ttp80) outliers start: 49 outliers final: 43 residues processed: 444 average time/residue: 0.1537 time to fit residues: 108.9681 Evaluate side-chains 451 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 404 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 139 LYS Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 301 LEU Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 236 ASN Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 161 SER Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 335 LYS Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 346 LYS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 195 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 91 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 231 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 267 optimal weight: 7.9990 chunk 291 optimal weight: 10.0000 chunk 134 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 236 ASN E 50 GLN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.146647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.110764 restraints weight = 49827.621| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.03 r_work: 0.3164 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24322 Z= 0.182 Angle : 0.589 12.150 32842 Z= 0.283 Chirality : 0.041 0.250 3762 Planarity : 0.004 0.043 4113 Dihedral : 9.900 88.166 3551 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.05 % Allowed : 26.78 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.16), residues: 2940 helix: 1.93 (0.13), residues: 1630 sheet: -0.51 (0.35), residues: 248 loop : 1.05 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 248 TYR 0.023 0.001 TYR J 313 PHE 0.013 0.001 PHE J 245 TRP 0.011 0.001 TRP G 166 HIS 0.002 0.000 HIS G 104 Details of bonding type rmsd covalent geometry : bond 0.00443 (24322) covalent geometry : angle 0.58922 (32842) hydrogen bonds : bond 0.03042 ( 1156) hydrogen bonds : angle 4.27648 ( 3343) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8261.62 seconds wall clock time: 141 minutes 42.74 seconds (8502.74 seconds total)