Starting phenix.real_space_refine on Sat Aug 23 23:47:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o7s_70207/08_2025/9o7s_70207.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o7s_70207/08_2025/9o7s_70207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o7s_70207/08_2025/9o7s_70207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o7s_70207/08_2025/9o7s_70207.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o7s_70207/08_2025/9o7s_70207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o7s_70207/08_2025/9o7s_70207.map" } resolution = 2.71 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 8 9.91 5 K 3 8.98 5 S 120 5.16 5 Cl 8 4.86 5 C 9987 2.51 5 N 2661 2.21 5 O 2752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15539 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2884 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 6, 'TRANS': 354} Chain: "B" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2884 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 6, 'TRANS': 354} Chain: "C" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2884 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 6, 'TRANS': 354} Chain: "D" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2884 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 6, 'TRANS': 354} Chain: "E" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 982 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 16, 'ASP:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 131 Chain: "F" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 982 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 16, 'ASP:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 131 Chain: "G" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 986 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 16, 'ASP:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 131 Chain: "H" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 982 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 16, 'ASP:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 131 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' CA': 2, '1KP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' CA': 2, '1KP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' CA': 2, '1KP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' CA': 2, '1KP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.27, per 1000 atoms: 0.27 Number of scatterers: 15539 At special positions: 0 Unit cell: (120.384, 121.114, 95.5776, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 8 19.99 K 3 19.00 Cl 8 17.00 S 120 16.00 O 2752 8.00 N 2661 7.00 C 9987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 371 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 371 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 371 " distance=2.03 Simple disulfide: pdb=" SG CYS D 333 " - pdb=" SG CYS D 371 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 766.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3816 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 8 sheets defined 76.3% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 123 through 159 removed outlier: 3.755A pdb=" N TRP A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 201 removed outlier: 3.707A pdb=" N LEU A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 212 through 227 removed outlier: 3.633A pdb=" N ILE A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 261 removed outlier: 3.571A pdb=" N LEU A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 266 Processing helix chain 'A' and resid 267 through 277 removed outlier: 3.919A pdb=" N ALA A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.816A pdb=" N THR A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 291 Processing helix chain 'A' and resid 298 through 310 Processing helix chain 'A' and resid 310 through 335 Processing helix chain 'A' and resid 345 through 358 Processing helix chain 'A' and resid 369 through 398 removed outlier: 3.701A pdb=" N GLY A 385 " --> pdb=" O ILE A 381 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 439 removed outlier: 3.506A pdb=" N TYR A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 477 Processing helix chain 'B' and resid 120 through 159 removed outlier: 3.762A pdb=" N TRP B 158 " --> pdb=" O THR B 154 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 201 removed outlier: 3.725A pdb=" N LEU B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 213 through 227 removed outlier: 3.623A pdb=" N ILE B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 261 removed outlier: 3.559A pdb=" N LEU B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 266 Processing helix chain 'B' and resid 267 through 277 removed outlier: 3.883A pdb=" N ALA B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 283 removed outlier: 3.605A pdb=" N THR B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 291 Processing helix chain 'B' and resid 298 through 310 Processing helix chain 'B' and resid 310 through 335 Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 369 through 398 removed outlier: 3.700A pdb=" N GLY B 385 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 440 Processing helix chain 'B' and resid 445 through 477 Processing helix chain 'C' and resid 120 through 159 removed outlier: 3.761A pdb=" N TRP C 158 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 201 removed outlier: 3.548A pdb=" N LEU C 169 " --> pdb=" O SER C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 213 through 227 removed outlier: 3.630A pdb=" N ILE C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 261 removed outlier: 3.584A pdb=" N LEU C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 266 Processing helix chain 'C' and resid 267 through 277 removed outlier: 3.900A pdb=" N ALA C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 291 Processing helix chain 'C' and resid 298 through 310 Processing helix chain 'C' and resid 310 through 335 Processing helix chain 'C' and resid 345 through 358 Processing helix chain 'C' and resid 369 through 398 removed outlier: 3.701A pdb=" N GLY C 385 " --> pdb=" O ILE C 381 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA C 388 " --> pdb=" O ALA C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 439 removed outlier: 3.582A pdb=" N TYR C 435 " --> pdb=" O THR C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 477 Processing helix chain 'D' and resid 119 through 159 removed outlier: 3.545A pdb=" N ARG D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TRP D 158 " --> pdb=" O THR D 154 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 201 Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 211 through 227 removed outlier: 3.640A pdb=" N ILE D 227 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 261 removed outlier: 3.574A pdb=" N LEU D 259 " --> pdb=" O VAL D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 266 Processing helix chain 'D' and resid 267 through 277 removed outlier: 3.902A pdb=" N ALA D 271 " --> pdb=" O LEU D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 283 removed outlier: 3.640A pdb=" N THR D 282 " --> pdb=" O SER D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 294 removed outlier: 3.808A pdb=" N LEU D 292 " --> pdb=" O SER D 288 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN D 293 " --> pdb=" O ILE D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 310 Processing helix chain 'D' and resid 310 through 335 Processing helix chain 'D' and resid 345 through 358 Processing helix chain 'D' and resid 369 through 398 removed outlier: 3.699A pdb=" N GLY D 385 " --> pdb=" O ILE D 381 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA D 388 " --> pdb=" O ALA D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 440 Processing helix chain 'D' and resid 445 through 477 Processing helix chain 'E' and resid 5 through 18 Processing helix chain 'E' and resid 28 through 39 removed outlier: 3.622A pdb=" N LEU E 32 " --> pdb=" O THR E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 53 Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.800A pdb=" N ARG E 74 " --> pdb=" O THR E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 93 removed outlier: 3.586A pdb=" N GLU E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 112 Processing helix chain 'E' and resid 117 through 128 Processing helix chain 'E' and resid 129 through 132 removed outlier: 4.197A pdb=" N GLY E 132 " --> pdb=" O ASP E 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 129 through 132' Processing helix chain 'E' and resid 138 through 147 removed outlier: 3.722A pdb=" N MET E 145 " --> pdb=" O PHE E 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 20 removed outlier: 3.876A pdb=" N PHE F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 39 removed outlier: 3.586A pdb=" N LEU F 32 " --> pdb=" O THR F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 53 Processing helix chain 'F' and resid 64 through 76 removed outlier: 3.697A pdb=" N ARG F 74 " --> pdb=" O THR F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 93 removed outlier: 3.749A pdb=" N PHE F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 112 Processing helix chain 'F' and resid 117 through 129 Processing helix chain 'F' and resid 138 through 147 removed outlier: 3.686A pdb=" N MET F 145 " --> pdb=" O PHE F 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 18 Processing helix chain 'G' and resid 29 through 39 removed outlier: 3.813A pdb=" N VAL G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 54 Processing helix chain 'G' and resid 64 through 76 removed outlier: 3.743A pdb=" N ARG G 74 " --> pdb=" O THR G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 93 removed outlier: 3.693A pdb=" N PHE G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 111 Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'G' and resid 138 through 145 removed outlier: 3.623A pdb=" N MET G 145 " --> pdb=" O PHE G 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 18 Processing helix chain 'H' and resid 30 through 39 Processing helix chain 'H' and resid 44 through 53 Processing helix chain 'H' and resid 64 through 76 removed outlier: 3.737A pdb=" N ARG H 74 " --> pdb=" O THR H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 93 removed outlier: 3.762A pdb=" N PHE H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 97 Processing helix chain 'H' and resid 102 through 112 Processing helix chain 'H' and resid 122 through 128 Processing helix chain 'H' and resid 138 through 146 removed outlier: 3.750A pdb=" N MET H 145 " --> pdb=" O PHE H 141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 241 Processing sheet with id=AA2, first strand: chain 'B' and resid 235 through 241 Processing sheet with id=AA3, first strand: chain 'C' and resid 235 through 241 Processing sheet with id=AA4, first strand: chain 'D' and resid 235 through 241 Processing sheet with id=AA5, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=AA6, first strand: chain 'F' and resid 99 through 100 Processing sheet with id=AA7, first strand: chain 'G' and resid 99 through 101 Processing sheet with id=AA8, first strand: chain 'H' and resid 99 through 101 1158 hydrogen bonds defined for protein. 3417 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2855 1.33 - 1.45: 3828 1.45 - 1.57: 8905 1.57 - 1.69: 0 1.69 - 1.82: 216 Bond restraints: 15804 Sorted by residual: bond pdb=" C ILE B 360 " pdb=" N GLY B 361 " ideal model delta sigma weight residual 1.327 1.314 0.012 8.10e-03 1.52e+04 2.29e+00 bond pdb=" CB THR D 329 " pdb=" CG2 THR D 329 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.16e+00 bond pdb=" CB THR C 329 " pdb=" CG2 THR C 329 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.07e+00 bond pdb=" CG LEU B 242 " pdb=" CD1 LEU B 242 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.95e+00 bond pdb=" CG LEU A 242 " pdb=" CD1 LEU A 242 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.94e+00 ... (remaining 15799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 20878 1.49 - 2.98: 436 2.98 - 4.47: 69 4.47 - 5.97: 18 5.97 - 7.46: 7 Bond angle restraints: 21408 Sorted by residual: angle pdb=" N ILE B 360 " pdb=" CA ILE B 360 " pdb=" C ILE B 360 " ideal model delta sigma weight residual 110.53 106.84 3.69 9.40e-01 1.13e+00 1.54e+01 angle pdb=" N VAL G 55 " pdb=" CA VAL G 55 " pdb=" C VAL G 55 " ideal model delta sigma weight residual 113.53 109.80 3.73 9.80e-01 1.04e+00 1.45e+01 angle pdb=" N ILE A 360 " pdb=" CA ILE A 360 " pdb=" C ILE A 360 " ideal model delta sigma weight residual 110.53 107.47 3.06 9.40e-01 1.13e+00 1.06e+01 angle pdb=" N ILE C 360 " pdb=" CA ILE C 360 " pdb=" C ILE C 360 " ideal model delta sigma weight residual 110.53 107.57 2.96 9.40e-01 1.13e+00 9.89e+00 angle pdb=" C VAL H 121 " pdb=" N ASP H 122 " pdb=" CA ASP H 122 " ideal model delta sigma weight residual 121.54 126.88 -5.34 1.91e+00 2.74e-01 7.82e+00 ... (remaining 21403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 8495 17.48 - 34.96: 766 34.96 - 52.44: 111 52.44 - 69.92: 21 69.92 - 87.40: 7 Dihedral angle restraints: 9400 sinusoidal: 3512 harmonic: 5888 Sorted by residual: dihedral pdb=" CA GLY C 363 " pdb=" C GLY C 363 " pdb=" N ASP C 364 " pdb=" CA ASP C 364 " ideal model delta harmonic sigma weight residual 180.00 158.45 21.55 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA GLY A 363 " pdb=" C GLY A 363 " pdb=" N ASP A 364 " pdb=" CA ASP A 364 " ideal model delta harmonic sigma weight residual 180.00 158.91 21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA GLY B 363 " pdb=" C GLY B 363 " pdb=" N ASP B 364 " pdb=" CA ASP B 364 " ideal model delta harmonic sigma weight residual 180.00 159.54 20.46 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 9397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1284 0.027 - 0.055: 805 0.055 - 0.082: 355 0.082 - 0.109: 83 0.109 - 0.136: 17 Chirality restraints: 2544 Sorted by residual: chirality pdb=" CB THR C 282 " pdb=" CA THR C 282 " pdb=" OG1 THR C 282 " pdb=" CG2 THR C 282 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CG LEU D 322 " pdb=" CB LEU D 322 " pdb=" CD1 LEU D 322 " pdb=" CD2 LEU D 322 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CG LEU C 322 " pdb=" CB LEU C 322 " pdb=" CD1 LEU C 322 " pdb=" CD2 LEU C 322 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 2541 not shown) Planarity restraints: 2648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 212 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.19e+00 pdb=" C TYR A 212 " 0.043 2.00e-02 2.50e+03 pdb=" O TYR A 212 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU A 213 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 122 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C ASP H 122 " -0.043 2.00e-02 2.50e+03 pdb=" O ASP H 122 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU H 123 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 446 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.48e+00 pdb=" C HIS A 446 " 0.032 2.00e-02 2.50e+03 pdb=" O HIS A 446 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA A 447 " -0.011 2.00e-02 2.50e+03 ... (remaining 2645 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.28: 25 2.28 - 3.00: 8391 3.00 - 3.71: 28122 3.71 - 4.43: 44228 4.43 - 5.14: 73264 Nonbonded interactions: 154030 Sorted by model distance: nonbonded pdb=" O ALA G 57 " pdb=" OD1 ASP G 58 " model vdw 1.567 3.040 nonbonded pdb=" OD1 ASP H 22 " pdb=" OE2 GLU H 31 " model vdw 1.880 3.040 nonbonded pdb=" ND2 ASN F 60 " pdb=" OD1 ASP F 64 " model vdw 1.963 3.120 nonbonded pdb=" OD2 ASP E 58 " pdb=" OD2 ASP E 64 " model vdw 1.975 3.040 nonbonded pdb=" OD1 ASP E 56 " pdb=" O THR E 62 " model vdw 2.035 3.040 ... (remaining 154025 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 118 through 478) selection = chain 'B' selection = (chain 'C' and resid 118 through 478) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = (chain 'G' and (resid 3 through 114 or (resid 115 and (name N or name CA or name \ C or name O or name CB )) or resid 116 through 203)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.200 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 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 0.049 15808 Z= 0.243 Angle : 0.562 7.458 21416 Z= 0.305 Chirality : 0.040 0.136 2544 Planarity : 0.004 0.041 2648 Dihedral : 13.290 87.400 5572 Min Nonbonded Distance : 1.567 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.68 (0.19), residues: 2008 helix: 2.58 (0.14), residues: 1428 sheet: 1.18 (0.61), residues: 64 loop : -0.51 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 331 TYR 0.019 0.002 TYR B 362 PHE 0.017 0.002 PHE C 346 TRP 0.011 0.001 TRP D 328 HIS 0.005 0.001 HIS D 452 Details of bonding type rmsd covalent geometry : bond 0.00593 (15804) covalent geometry : angle 0.56159 (21408) SS BOND : bond 0.00158 ( 4) SS BOND : angle 1.48933 ( 8) hydrogen bonds : bond 0.10330 ( 1158) hydrogen bonds : angle 4.34285 ( 3417) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8475 (t0) cc_final: 0.7966 (p0) REVERT: A 207 ARG cc_start: 0.8093 (mtt90) cc_final: 0.7875 (mtm180) REVERT: A 279 LYS cc_start: 0.7233 (mppt) cc_final: 0.6919 (mptt) REVERT: A 341 ASP cc_start: 0.7870 (t70) cc_final: 0.7655 (t70) REVERT: A 411 MET cc_start: 0.8767 (mmm) cc_final: 0.8523 (mmp) REVERT: B 134 ARG cc_start: 0.7849 (mtm110) cc_final: 0.7580 (mtm-85) REVERT: B 162 ASP cc_start: 0.8386 (t70) cc_final: 0.7682 (p0) REVERT: B 205 ASP cc_start: 0.8638 (t0) cc_final: 0.8377 (t0) REVERT: B 279 LYS cc_start: 0.7182 (mppt) cc_final: 0.6938 (mptt) REVERT: B 399 GLU cc_start: 0.8289 (tt0) cc_final: 0.7886 (pt0) REVERT: B 411 MET cc_start: 0.8822 (mmm) cc_final: 0.8612 (mmp) REVERT: C 162 ASP cc_start: 0.8498 (t0) cc_final: 0.7988 (p0) REVERT: C 279 LYS cc_start: 0.7226 (mppt) cc_final: 0.6987 (mptt) REVERT: C 341 ASP cc_start: 0.7862 (t70) cc_final: 0.7661 (t70) REVERT: C 399 GLU cc_start: 0.8306 (tt0) cc_final: 0.7868 (pt0) REVERT: C 411 MET cc_start: 0.8823 (mmm) cc_final: 0.8610 (mmp) REVERT: D 162 ASP cc_start: 0.8453 (t70) cc_final: 0.7686 (p0) REVERT: D 279 LYS cc_start: 0.8451 (ttmt) cc_final: 0.7792 (mptt) REVERT: D 411 MET cc_start: 0.8876 (mmm) cc_final: 0.8667 (mmp) REVERT: E 49 GLN cc_start: 0.8697 (tp-100) cc_final: 0.8358 (mm-40) REVERT: E 53 ASN cc_start: 0.8217 (m110) cc_final: 0.7997 (m110) REVERT: E 78 ASP cc_start: 0.8060 (m-30) cc_final: 0.7776 (p0) REVERT: E 124 MET cc_start: 0.8229 (ttt) cc_final: 0.7997 (ttp) REVERT: F 53 ASN cc_start: 0.8495 (m110) cc_final: 0.8266 (m-40) REVERT: F 64 ASP cc_start: 0.5557 (m-30) cc_final: 0.5037 (m-30) REVERT: F 67 GLU cc_start: 0.5349 (mt-10) cc_final: 0.5136 (mt-10) REVERT: G 53 ASN cc_start: 0.8813 (m-40) cc_final: 0.8471 (m-40) REVERT: H 64 ASP cc_start: 0.6873 (m-30) cc_final: 0.6112 (m-30) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.6728 time to fit residues: 283.2779 Evaluate side-chains 318 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 458 GLN B 195 GLN B 277 HIS C 195 GLN D 195 GLN E 111 ASN F 111 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.143355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.095748 restraints weight = 18036.651| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.73 r_work: 0.2950 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15808 Z= 0.134 Angle : 0.463 6.644 21416 Z= 0.250 Chirality : 0.036 0.137 2544 Planarity : 0.003 0.033 2648 Dihedral : 3.754 18.515 2172 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.65 % Allowed : 9.51 % Favored : 88.84 % 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 aren not related in a simple way. whole: 3.05 (0.19), residues: 2008 helix: 2.82 (0.14), residues: 1428 sheet: 1.38 (0.62), residues: 64 loop : -0.28 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 331 TYR 0.017 0.002 TYR B 435 PHE 0.012 0.001 PHE F 89 TRP 0.012 0.001 TRP D 328 HIS 0.003 0.001 HIS D 452 Details of bonding type rmsd covalent geometry : bond 0.00308 (15804) covalent geometry : angle 0.46248 (21408) SS BOND : bond 0.00043 ( 4) SS BOND : angle 0.96191 ( 8) hydrogen bonds : bond 0.04063 ( 1158) hydrogen bonds : angle 3.44241 ( 3417) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 342 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8481 (t0) cc_final: 0.7896 (p0) REVERT: A 279 LYS cc_start: 0.7051 (mppt) cc_final: 0.6806 (mptt) REVERT: A 341 ASP cc_start: 0.7874 (t70) cc_final: 0.7536 (t70) REVERT: A 411 MET cc_start: 0.8635 (mmm) cc_final: 0.8433 (mmp) REVERT: B 134 ARG cc_start: 0.7784 (mtm110) cc_final: 0.7502 (mtm-85) REVERT: B 162 ASP cc_start: 0.8340 (t70) cc_final: 0.7605 (p0) REVERT: B 279 LYS cc_start: 0.7106 (mppt) cc_final: 0.6860 (mptt) REVERT: B 399 GLU cc_start: 0.8147 (tt0) cc_final: 0.7682 (pt0) REVERT: B 411 MET cc_start: 0.8704 (mmm) cc_final: 0.8475 (mmp) REVERT: C 162 ASP cc_start: 0.8503 (t0) cc_final: 0.7924 (p0) REVERT: C 279 LYS cc_start: 0.7119 (mppt) cc_final: 0.6898 (mptt) REVERT: C 341 ASP cc_start: 0.7879 (t70) cc_final: 0.7559 (t70) REVERT: C 411 MET cc_start: 0.8675 (mmm) cc_final: 0.8459 (mmp) REVERT: D 134 ARG cc_start: 0.7997 (mtm-85) cc_final: 0.7235 (mmt-90) REVERT: D 279 LYS cc_start: 0.8436 (ttmt) cc_final: 0.7692 (mptt) REVERT: D 411 MET cc_start: 0.8732 (mmm) cc_final: 0.8524 (mmp) REVERT: E 49 GLN cc_start: 0.8641 (tp-100) cc_final: 0.8281 (mm-40) REVERT: E 53 ASN cc_start: 0.8327 (m110) cc_final: 0.7975 (m110) REVERT: E 78 ASP cc_start: 0.8028 (m-30) cc_final: 0.7756 (p0) REVERT: E 124 MET cc_start: 0.8137 (ttt) cc_final: 0.7913 (ttp) REVERT: F 37 ARG cc_start: 0.8648 (mpp-170) cc_final: 0.8359 (mtm-85) REVERT: F 53 ASN cc_start: 0.8502 (m110) cc_final: 0.8195 (m-40) REVERT: G 49 GLN cc_start: 0.8630 (tp-100) cc_final: 0.8418 (mm-40) REVERT: G 53 ASN cc_start: 0.8800 (m-40) cc_final: 0.8538 (m-40) REVERT: H 53 ASN cc_start: 0.8161 (m-40) cc_final: 0.7758 (m110) REVERT: H 67 GLU cc_start: 0.7559 (mp0) cc_final: 0.7305 (mt-10) REVERT: H 78 ASP cc_start: 0.8073 (m-30) cc_final: 0.7731 (p0) outliers start: 26 outliers final: 13 residues processed: 352 average time/residue: 0.6388 time to fit residues: 245.7399 Evaluate side-chains 334 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 321 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 44 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 88 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 178 optimal weight: 0.9990 chunk 180 optimal weight: 0.1980 chunk 136 optimal weight: 0.0670 chunk 97 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN B 195 GLN C 195 GLN D 195 GLN D 452 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.144838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.097067 restraints weight = 17991.141| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.73 r_work: 0.2974 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15808 Z= 0.105 Angle : 0.434 9.070 21416 Z= 0.235 Chirality : 0.035 0.148 2544 Planarity : 0.003 0.030 2648 Dihedral : 3.625 30.344 2172 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.73 % Allowed : 12.37 % Favored : 84.91 % 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 aren not related in a simple way. whole: 3.11 (0.19), residues: 2008 helix: 2.86 (0.14), residues: 1460 sheet: 1.55 (0.65), residues: 64 loop : -0.47 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 207 TYR 0.007 0.001 TYR D 161 PHE 0.013 0.001 PHE F 89 TRP 0.011 0.001 TRP D 328 HIS 0.003 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00229 (15804) covalent geometry : angle 0.43360 (21408) SS BOND : bond 0.00035 ( 4) SS BOND : angle 0.76030 ( 8) hydrogen bonds : bond 0.03551 ( 1158) hydrogen bonds : angle 3.24862 ( 3417) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 331 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8447 (t0) cc_final: 0.7879 (p0) REVERT: A 279 LYS cc_start: 0.7079 (mppt) cc_final: 0.6847 (mptt) REVERT: A 411 MET cc_start: 0.8651 (mmm) cc_final: 0.8419 (mmp) REVERT: B 134 ARG cc_start: 0.7795 (mtm110) cc_final: 0.7203 (mpt180) REVERT: B 279 LYS cc_start: 0.7117 (mppt) cc_final: 0.6871 (mptt) REVERT: B 303 MET cc_start: 0.7136 (mtm) cc_final: 0.6412 (tmm) REVERT: B 399 GLU cc_start: 0.8162 (tt0) cc_final: 0.7715 (pt0) REVERT: B 411 MET cc_start: 0.8716 (mmm) cc_final: 0.8468 (mmp) REVERT: C 162 ASP cc_start: 0.8506 (t0) cc_final: 0.7968 (p0) REVERT: C 279 LYS cc_start: 0.7139 (mppt) cc_final: 0.6901 (mptt) REVERT: C 399 GLU cc_start: 0.8224 (tt0) cc_final: 0.7776 (pt0) REVERT: C 411 MET cc_start: 0.8697 (mmm) cc_final: 0.8467 (mmp) REVERT: D 134 ARG cc_start: 0.8003 (mtm-85) cc_final: 0.7272 (mmt-90) REVERT: D 279 LYS cc_start: 0.8439 (ttmt) cc_final: 0.7724 (mptt) REVERT: D 411 MET cc_start: 0.8761 (mmm) cc_final: 0.8521 (mmp) REVERT: E 49 GLN cc_start: 0.8666 (tp-100) cc_final: 0.8317 (mm-40) REVERT: E 53 ASN cc_start: 0.8279 (m110) cc_final: 0.7913 (m110) REVERT: E 58 ASP cc_start: 0.7773 (p0) cc_final: 0.7449 (p0) REVERT: E 75 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.7451 (mptm) REVERT: E 78 ASP cc_start: 0.8005 (m-30) cc_final: 0.7751 (p0) REVERT: F 53 ASN cc_start: 0.8494 (m110) cc_final: 0.8150 (m110) REVERT: F 75 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7653 (mptm) REVERT: G 49 GLN cc_start: 0.8664 (tp-100) cc_final: 0.8452 (mm-40) REVERT: G 53 ASN cc_start: 0.8777 (m-40) cc_final: 0.8502 (m-40) REVERT: H 53 ASN cc_start: 0.8230 (m-40) cc_final: 0.7812 (m110) REVERT: H 67 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7226 (mt-10) REVERT: H 78 ASP cc_start: 0.8016 (m-30) cc_final: 0.7678 (p0) outliers start: 43 outliers final: 17 residues processed: 350 average time/residue: 0.6385 time to fit residues: 244.1569 Evaluate side-chains 345 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 326 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 74 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 44 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 174 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN B 195 GLN C 195 GLN D 195 GLN D 452 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.141123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.093144 restraints weight = 18197.909| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.74 r_work: 0.2918 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15808 Z= 0.192 Angle : 0.503 10.069 21416 Z= 0.268 Chirality : 0.038 0.171 2544 Planarity : 0.004 0.032 2648 Dihedral : 3.831 33.984 2172 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.23 % Allowed : 13.76 % Favored : 83.01 % 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 aren not related in a simple way. whole: 3.04 (0.19), residues: 2008 helix: 2.79 (0.13), residues: 1428 sheet: 1.96 (0.81), residues: 40 loop : -0.17 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 207 TYR 0.021 0.002 TYR A 435 PHE 0.016 0.002 PHE F 89 TRP 0.013 0.001 TRP D 328 HIS 0.004 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00465 (15804) covalent geometry : angle 0.50283 (21408) SS BOND : bond 0.00215 ( 4) SS BOND : angle 0.72918 ( 8) hydrogen bonds : bond 0.04279 ( 1158) hydrogen bonds : angle 3.38974 ( 3417) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 326 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8477 (t0) cc_final: 0.7939 (p0) REVERT: A 279 LYS cc_start: 0.7055 (mppt) cc_final: 0.6815 (mptt) REVERT: B 134 ARG cc_start: 0.7789 (mtm110) cc_final: 0.7452 (mtm-85) REVERT: B 279 LYS cc_start: 0.7119 (mppt) cc_final: 0.6890 (mptt) REVERT: B 399 GLU cc_start: 0.8195 (tt0) cc_final: 0.7698 (pt0) REVERT: B 411 MET cc_start: 0.8724 (mmm) cc_final: 0.8511 (mmp) REVERT: C 134 ARG cc_start: 0.8015 (mtm-85) cc_final: 0.7253 (mmt-90) REVERT: C 162 ASP cc_start: 0.8499 (t0) cc_final: 0.7923 (p0) REVERT: C 279 LYS cc_start: 0.7197 (mppt) cc_final: 0.6946 (mptt) REVERT: D 279 LYS cc_start: 0.8430 (ttmt) cc_final: 0.7700 (mptt) REVERT: E 58 ASP cc_start: 0.7727 (p0) cc_final: 0.7500 (p0) REVERT: E 63 ILE cc_start: 0.7663 (mm) cc_final: 0.7461 (mp) REVERT: E 67 GLU cc_start: 0.7225 (mt-10) cc_final: 0.7013 (mt-10) REVERT: E 75 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.7527 (mptm) REVERT: E 78 ASP cc_start: 0.8050 (m-30) cc_final: 0.7768 (p0) REVERT: F 53 ASN cc_start: 0.8411 (m110) cc_final: 0.8099 (m110) REVERT: F 75 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7640 (mptm) REVERT: G 49 GLN cc_start: 0.8642 (tp-100) cc_final: 0.8270 (mm-40) REVERT: G 53 ASN cc_start: 0.8797 (m-40) cc_final: 0.8497 (m-40) REVERT: G 64 ASP cc_start: 0.7051 (m-30) cc_final: 0.6814 (m-30) REVERT: H 53 ASN cc_start: 0.8185 (m-40) cc_final: 0.7761 (m110) REVERT: H 67 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7221 (mt-10) REVERT: H 78 ASP cc_start: 0.8060 (m-30) cc_final: 0.7668 (p0) outliers start: 51 outliers final: 31 residues processed: 355 average time/residue: 0.5697 time to fit residues: 221.2848 Evaluate side-chains 351 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 318 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 124 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 86 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 155 optimal weight: 8.9990 chunk 128 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 458 GLN B 195 GLN C 195 GLN D 195 GLN E 53 ASN F 53 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.142739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.094995 restraints weight = 18104.826| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.74 r_work: 0.2945 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15808 Z= 0.136 Angle : 0.468 10.351 21416 Z= 0.251 Chirality : 0.036 0.156 2544 Planarity : 0.003 0.032 2648 Dihedral : 3.765 36.139 2172 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.79 % Allowed : 15.47 % Favored : 81.74 % 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 aren not related in a simple way. whole: 3.25 (0.19), residues: 2008 helix: 2.96 (0.13), residues: 1428 sheet: 2.09 (0.81), residues: 40 loop : -0.15 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 207 TYR 0.021 0.001 TYR B 435 PHE 0.014 0.001 PHE F 89 TRP 0.012 0.001 TRP D 328 HIS 0.004 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00322 (15804) covalent geometry : angle 0.46829 (21408) SS BOND : bond 0.00080 ( 4) SS BOND : angle 0.70784 ( 8) hydrogen bonds : bond 0.03830 ( 1158) hydrogen bonds : angle 3.26572 ( 3417) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 322 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8451 (t0) cc_final: 0.7947 (p0) REVERT: A 279 LYS cc_start: 0.7069 (mppt) cc_final: 0.6825 (mptt) REVERT: A 365 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8278 (mtm) REVERT: B 134 ARG cc_start: 0.7815 (mtm110) cc_final: 0.7230 (mpt180) REVERT: B 279 LYS cc_start: 0.7141 (mppt) cc_final: 0.6916 (mptt) REVERT: B 303 MET cc_start: 0.7154 (mtm) cc_final: 0.6428 (tmm) REVERT: B 411 MET cc_start: 0.8728 (mmm) cc_final: 0.8503 (mmp) REVERT: C 162 ASP cc_start: 0.8503 (t0) cc_final: 0.7963 (p0) REVERT: C 279 LYS cc_start: 0.7195 (mppt) cc_final: 0.6932 (mptt) REVERT: C 468 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7572 (mtt) REVERT: D 279 LYS cc_start: 0.8416 (ttmt) cc_final: 0.7735 (mptt) REVERT: E 49 GLN cc_start: 0.8618 (mm-40) cc_final: 0.7714 (tp-100) REVERT: E 53 ASN cc_start: 0.8323 (m-40) cc_final: 0.7716 (m110) REVERT: E 54 GLU cc_start: 0.8367 (pt0) cc_final: 0.7978 (pt0) REVERT: E 63 ILE cc_start: 0.7678 (mm) cc_final: 0.7428 (mp) REVERT: E 75 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.7706 (mptm) REVERT: E 78 ASP cc_start: 0.8001 (m-30) cc_final: 0.7744 (p0) REVERT: F 37 ARG cc_start: 0.8583 (mpp-170) cc_final: 0.8336 (mpp80) REVERT: F 53 ASN cc_start: 0.8581 (m-40) cc_final: 0.8278 (m-40) REVERT: F 75 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7705 (mptm) REVERT: G 49 GLN cc_start: 0.8628 (tp-100) cc_final: 0.8260 (mm-40) REVERT: G 53 ASN cc_start: 0.8786 (m-40) cc_final: 0.8486 (m-40) REVERT: G 64 ASP cc_start: 0.7208 (m-30) cc_final: 0.6959 (m-30) REVERT: H 53 ASN cc_start: 0.8284 (m-40) cc_final: 0.7883 (m110) REVERT: H 54 GLU cc_start: 0.8509 (pt0) cc_final: 0.8263 (pt0) REVERT: H 67 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7274 (mt-10) REVERT: H 78 ASP cc_start: 0.8020 (m-30) cc_final: 0.7674 (p0) outliers start: 44 outliers final: 31 residues processed: 348 average time/residue: 0.5896 time to fit residues: 224.5881 Evaluate side-chains 352 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 317 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 44 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 153 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 144 optimal weight: 0.5980 chunk 47 optimal weight: 0.0370 chunk 45 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 458 GLN B 195 GLN C 195 GLN D 195 GLN D 415 GLN D 452 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.143882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.096408 restraints weight = 17921.433| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.74 r_work: 0.2967 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15808 Z= 0.112 Angle : 0.449 10.468 21416 Z= 0.241 Chirality : 0.035 0.148 2544 Planarity : 0.003 0.033 2648 Dihedral : 3.738 49.750 2172 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.60 % Allowed : 16.11 % Favored : 81.29 % 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 aren not related in a simple way. whole: 3.30 (0.19), residues: 2008 helix: 2.96 (0.14), residues: 1456 sheet: 1.89 (0.68), residues: 64 loop : -0.31 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 207 TYR 0.022 0.001 TYR A 435 PHE 0.013 0.001 PHE F 89 TRP 0.012 0.001 TRP D 328 HIS 0.004 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00256 (15804) covalent geometry : angle 0.44893 (21408) SS BOND : bond 0.00027 ( 4) SS BOND : angle 0.63484 ( 8) hydrogen bonds : bond 0.03501 ( 1158) hydrogen bonds : angle 3.17885 ( 3417) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 322 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8442 (t0) cc_final: 0.7945 (p0) REVERT: A 279 LYS cc_start: 0.7042 (mppt) cc_final: 0.6793 (mptt) REVERT: A 365 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8332 (mtm) REVERT: B 134 ARG cc_start: 0.7814 (mtm110) cc_final: 0.7219 (mpt180) REVERT: B 279 LYS cc_start: 0.7131 (mppt) cc_final: 0.6910 (mptt) REVERT: B 303 MET cc_start: 0.7097 (mtm) cc_final: 0.6365 (tmm) REVERT: B 399 GLU cc_start: 0.8150 (tt0) cc_final: 0.7690 (pt0) REVERT: B 411 MET cc_start: 0.8696 (mmm) cc_final: 0.8452 (mmp) REVERT: B 468 MET cc_start: 0.7812 (mtp) cc_final: 0.7533 (mtt) REVERT: C 162 ASP cc_start: 0.8500 (t0) cc_final: 0.7964 (p0) REVERT: C 177 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8269 (OUTLIER) REVERT: C 279 LYS cc_start: 0.7146 (mppt) cc_final: 0.6915 (mptt) REVERT: C 468 MET cc_start: 0.7848 (mtp) cc_final: 0.7572 (mtt) REVERT: D 279 LYS cc_start: 0.8406 (ttmt) cc_final: 0.7727 (mptt) REVERT: E 53 ASN cc_start: 0.8365 (m-40) cc_final: 0.7927 (m110) REVERT: E 54 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8046 (pt0) REVERT: E 63 ILE cc_start: 0.7568 (mm) cc_final: 0.7275 (mp) REVERT: E 75 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.7690 (mptm) REVERT: E 78 ASP cc_start: 0.8007 (m-30) cc_final: 0.7698 (p0) REVERT: F 37 ARG cc_start: 0.8570 (mpp-170) cc_final: 0.8342 (mtm-85) REVERT: F 53 ASN cc_start: 0.8581 (m-40) cc_final: 0.8290 (m-40) REVERT: F 64 ASP cc_start: 0.7263 (p0) cc_final: 0.6992 (p0) REVERT: F 75 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.7711 (mptm) REVERT: G 49 GLN cc_start: 0.8639 (tp-100) cc_final: 0.8249 (mm-40) REVERT: G 53 ASN cc_start: 0.8773 (m-40) cc_final: 0.8462 (m-40) REVERT: G 64 ASP cc_start: 0.7252 (m-30) cc_final: 0.6992 (m-30) REVERT: H 53 ASN cc_start: 0.8305 (m-40) cc_final: 0.7903 (m110) REVERT: H 54 GLU cc_start: 0.8492 (pt0) cc_final: 0.8240 (pt0) REVERT: H 67 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7294 (mt-10) REVERT: H 75 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.7786 (mptm) REVERT: H 78 ASP cc_start: 0.7981 (m-30) cc_final: 0.7661 (p0) outliers start: 41 outliers final: 30 residues processed: 346 average time/residue: 0.5787 time to fit residues: 219.4628 Evaluate side-chains 355 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 320 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 75 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 96 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN B 195 GLN C 195 GLN D 195 GLN D 415 GLN D 452 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.141556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.093688 restraints weight = 17979.560| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.73 r_work: 0.2923 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15808 Z= 0.182 Angle : 0.487 11.141 21416 Z= 0.261 Chirality : 0.038 0.143 2544 Planarity : 0.004 0.039 2648 Dihedral : 3.883 49.338 2172 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.04 % Allowed : 16.23 % Favored : 80.72 % 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 aren not related in a simple way. whole: 3.17 (0.19), residues: 2008 helix: 2.89 (0.13), residues: 1428 sheet: 2.19 (0.81), residues: 40 loop : -0.14 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 207 TYR 0.021 0.002 TYR D 435 PHE 0.015 0.002 PHE F 89 TRP 0.012 0.001 TRP D 328 HIS 0.004 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00442 (15804) covalent geometry : angle 0.48666 (21408) SS BOND : bond 0.00196 ( 4) SS BOND : angle 0.68348 ( 8) hydrogen bonds : bond 0.04131 ( 1158) hydrogen bonds : angle 3.31485 ( 3417) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 319 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8483 (t0) cc_final: 0.7949 (p0) REVERT: A 279 LYS cc_start: 0.7012 (mppt) cc_final: 0.6756 (mptt) REVERT: A 365 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8324 (mtm) REVERT: B 134 ARG cc_start: 0.7800 (mtm110) cc_final: 0.7205 (mpt180) REVERT: B 279 LYS cc_start: 0.7088 (mppt) cc_final: 0.6851 (mptt) REVERT: B 303 MET cc_start: 0.7145 (mtm) cc_final: 0.6403 (tmm) REVERT: B 411 MET cc_start: 0.8742 (mmm) cc_final: 0.8532 (mmp) REVERT: B 468 MET cc_start: 0.7776 (mtp) cc_final: 0.7519 (mtt) REVERT: C 134 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7234 (mmt-90) REVERT: C 162 ASP cc_start: 0.8492 (t0) cc_final: 0.7930 (p0) REVERT: C 279 LYS cc_start: 0.7141 (mppt) cc_final: 0.6876 (mptt) REVERT: C 468 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7535 (mtt) REVERT: D 279 LYS cc_start: 0.8406 (ttmt) cc_final: 0.7715 (mptt) REVERT: E 53 ASN cc_start: 0.8360 (m-40) cc_final: 0.7929 (m110) REVERT: E 54 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8153 (pt0) REVERT: E 75 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7699 (mptm) REVERT: E 78 ASP cc_start: 0.8078 (m-30) cc_final: 0.7720 (p0) REVERT: F 53 ASN cc_start: 0.8494 (m-40) cc_final: 0.8200 (m-40) REVERT: F 64 ASP cc_start: 0.7409 (p0) cc_final: 0.6947 (p0) REVERT: F 75 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7683 (mptm) REVERT: G 49 GLN cc_start: 0.8601 (tp-100) cc_final: 0.8221 (mm-40) REVERT: G 53 ASN cc_start: 0.8789 (m-40) cc_final: 0.8475 (m-40) REVERT: G 64 ASP cc_start: 0.7263 (m-30) cc_final: 0.7018 (m-30) REVERT: H 28 THR cc_start: 0.8791 (t) cc_final: 0.8449 (p) REVERT: H 53 ASN cc_start: 0.8307 (m-40) cc_final: 0.7949 (m110) REVERT: H 54 GLU cc_start: 0.8538 (pt0) cc_final: 0.8324 (pt0) REVERT: H 67 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7287 (mt-10) REVERT: H 75 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.7704 (mptm) REVERT: H 78 ASP cc_start: 0.8074 (m-30) cc_final: 0.7685 (p0) outliers start: 48 outliers final: 35 residues processed: 346 average time/residue: 0.5306 time to fit residues: 201.7566 Evaluate side-chains 356 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 315 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 75 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 148 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 9 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 89 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 458 GLN B 195 GLN C 195 GLN D 195 GLN D 415 GLN D 452 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.142462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.094770 restraints weight = 18111.537| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.74 r_work: 0.2942 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15808 Z= 0.144 Angle : 0.468 11.571 21416 Z= 0.252 Chirality : 0.037 0.148 2544 Planarity : 0.004 0.040 2648 Dihedral : 3.849 50.563 2172 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.79 % Allowed : 17.12 % Favored : 80.09 % 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 aren not related in a simple way. whole: 3.29 (0.19), residues: 2008 helix: 2.97 (0.13), residues: 1428 sheet: 2.20 (0.81), residues: 40 loop : -0.09 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 207 TYR 0.024 0.001 TYR A 435 PHE 0.013 0.001 PHE F 89 TRP 0.012 0.001 TRP D 328 HIS 0.004 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00342 (15804) covalent geometry : angle 0.46823 (21408) SS BOND : bond 0.00121 ( 4) SS BOND : angle 0.64761 ( 8) hydrogen bonds : bond 0.03851 ( 1158) hydrogen bonds : angle 3.25221 ( 3417) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 318 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8484 (t0) cc_final: 0.7960 (p0) REVERT: A 365 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8313 (mtm) REVERT: B 134 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7235 (mpt180) REVERT: B 279 LYS cc_start: 0.7158 (mppt) cc_final: 0.6919 (mptt) REVERT: B 303 MET cc_start: 0.7147 (mtm) cc_final: 0.6423 (tmm) REVERT: B 411 MET cc_start: 0.8754 (mmm) cc_final: 0.8536 (mmp) REVERT: B 468 MET cc_start: 0.7776 (mtp) cc_final: 0.7513 (mtt) REVERT: C 134 ARG cc_start: 0.7921 (mtm-85) cc_final: 0.7196 (mmt-90) REVERT: C 162 ASP cc_start: 0.8509 (t0) cc_final: 0.7964 (p0) REVERT: C 279 LYS cc_start: 0.7174 (mppt) cc_final: 0.6914 (mptt) REVERT: C 468 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7572 (mtt) REVERT: D 279 LYS cc_start: 0.8428 (ttmt) cc_final: 0.7763 (mptt) REVERT: E 53 ASN cc_start: 0.8421 (m-40) cc_final: 0.7976 (m110) REVERT: E 64 ASP cc_start: 0.7083 (p0) cc_final: 0.6830 (p0) REVERT: E 78 ASP cc_start: 0.8036 (m-30) cc_final: 0.7701 (p0) REVERT: F 53 ASN cc_start: 0.8531 (m-40) cc_final: 0.8228 (m-40) REVERT: G 49 GLN cc_start: 0.8638 (tp-100) cc_final: 0.8200 (mm-40) REVERT: G 53 ASN cc_start: 0.8783 (m-40) cc_final: 0.8444 (m-40) REVERT: G 64 ASP cc_start: 0.7313 (m-30) cc_final: 0.7057 (m-30) REVERT: H 28 THR cc_start: 0.8811 (t) cc_final: 0.8510 (p) REVERT: H 53 ASN cc_start: 0.8348 (m-40) cc_final: 0.7997 (m110) REVERT: H 54 GLU cc_start: 0.8501 (pt0) cc_final: 0.8268 (pt0) REVERT: H 67 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7358 (mt-10) REVERT: H 75 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.7792 (mptm) REVERT: H 78 ASP cc_start: 0.8021 (m-30) cc_final: 0.7677 (p0) outliers start: 44 outliers final: 33 residues processed: 346 average time/residue: 0.6029 time to fit residues: 228.6473 Evaluate side-chains 351 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 315 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 124 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 196 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 115 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 152 optimal weight: 10.0000 chunk 192 optimal weight: 0.2980 chunk 157 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 170 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 458 GLN B 195 GLN C 195 GLN C 415 GLN D 195 GLN D 415 GLN D 437 ASN D 452 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.140653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.092823 restraints weight = 18063.832| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.72 r_work: 0.2917 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15808 Z= 0.195 Angle : 0.512 12.254 21416 Z= 0.273 Chirality : 0.038 0.168 2544 Planarity : 0.004 0.040 2648 Dihedral : 3.988 51.152 2172 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.66 % Allowed : 17.50 % Favored : 79.84 % 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 aren not related in a simple way. whole: 3.04 (0.19), residues: 2008 helix: 2.77 (0.13), residues: 1428 sheet: 2.12 (0.80), residues: 40 loop : -0.12 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 207 TYR 0.021 0.002 TYR D 435 PHE 0.014 0.002 PHE F 89 TRP 0.013 0.001 TRP D 328 HIS 0.004 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00476 (15804) covalent geometry : angle 0.51234 (21408) SS BOND : bond 0.00216 ( 4) SS BOND : angle 0.69421 ( 8) hydrogen bonds : bond 0.04304 ( 1158) hydrogen bonds : angle 3.36075 ( 3417) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 316 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8500 (t0) cc_final: 0.7970 (p0) REVERT: A 365 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8327 (mtm) REVERT: B 134 ARG cc_start: 0.7812 (mtm110) cc_final: 0.7220 (mpt180) REVERT: B 279 LYS cc_start: 0.7138 (mppt) cc_final: 0.6875 (mptt) REVERT: B 468 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7493 (mtt) REVERT: C 162 ASP cc_start: 0.8510 (t0) cc_final: 0.7932 (p0) REVERT: C 279 LYS cc_start: 0.7189 (mppt) cc_final: 0.6911 (mptt) REVERT: C 468 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7557 (mtt) REVERT: D 279 LYS cc_start: 0.8446 (ttmt) cc_final: 0.7768 (mptt) REVERT: E 53 ASN cc_start: 0.8381 (m-40) cc_final: 0.7966 (m110) REVERT: E 64 ASP cc_start: 0.7295 (p0) cc_final: 0.6844 (p0) REVERT: E 78 ASP cc_start: 0.8083 (m-30) cc_final: 0.7721 (p0) REVERT: F 53 ASN cc_start: 0.8483 (m-40) cc_final: 0.8216 (m-40) REVERT: G 49 GLN cc_start: 0.8639 (tp-100) cc_final: 0.8179 (mm-40) REVERT: G 53 ASN cc_start: 0.8761 (m-40) cc_final: 0.8408 (m-40) REVERT: G 64 ASP cc_start: 0.7345 (m-30) cc_final: 0.6985 (p0) REVERT: H 28 THR cc_start: 0.8815 (t) cc_final: 0.8555 (p) REVERT: H 53 ASN cc_start: 0.8387 (m-40) cc_final: 0.8049 (m110) REVERT: H 54 GLU cc_start: 0.8513 (pt0) cc_final: 0.8287 (pt0) REVERT: H 67 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7422 (mt-10) REVERT: H 75 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.7739 (mptm) REVERT: H 78 ASP cc_start: 0.8041 (m-30) cc_final: 0.7686 (p0) outliers start: 42 outliers final: 33 residues processed: 344 average time/residue: 0.5831 time to fit residues: 220.2673 Evaluate side-chains 348 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 311 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 468 MET Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 124 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 72 optimal weight: 7.9990 chunk 13 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 186 optimal weight: 0.0270 chunk 101 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 199 optimal weight: 6.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 458 GLN B 195 GLN C 195 GLN C 415 GLN D 195 GLN D 415 GLN D 452 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.144140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.096168 restraints weight = 17981.296| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.74 r_work: 0.2961 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15808 Z= 0.113 Angle : 0.474 12.381 21416 Z= 0.251 Chirality : 0.036 0.150 2544 Planarity : 0.003 0.038 2648 Dihedral : 3.824 52.500 2172 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.09 % Allowed : 18.07 % Favored : 79.84 % 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 aren not related in a simple way. whole: 3.23 (0.19), residues: 2008 helix: 2.91 (0.14), residues: 1460 sheet: 1.90 (0.68), residues: 64 loop : -0.34 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 207 TYR 0.013 0.001 TYR H 99 PHE 0.011 0.001 PHE F 89 TRP 0.013 0.001 TRP D 328 HIS 0.003 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00254 (15804) covalent geometry : angle 0.47412 (21408) SS BOND : bond 0.00053 ( 4) SS BOND : angle 0.65894 ( 8) hydrogen bonds : bond 0.03537 ( 1158) hydrogen bonds : angle 3.16859 ( 3417) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 318 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8456 (t0) cc_final: 0.7958 (p0) REVERT: A 279 LYS cc_start: 0.6887 (mptt) cc_final: 0.6522 (mppt) REVERT: A 365 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8298 (mtm) REVERT: B 134 ARG cc_start: 0.7817 (mtm110) cc_final: 0.7227 (mpt180) REVERT: B 279 LYS cc_start: 0.7093 (mppt) cc_final: 0.6856 (mptt) REVERT: B 303 MET cc_start: 0.7079 (mtm) cc_final: 0.6336 (tmm) REVERT: B 468 MET cc_start: 0.7732 (mtp) cc_final: 0.7514 (mtt) REVERT: C 162 ASP cc_start: 0.8490 (t0) cc_final: 0.7942 (p0) REVERT: C 279 LYS cc_start: 0.7154 (mppt) cc_final: 0.6895 (mptt) REVERT: C 468 MET cc_start: 0.7782 (mtp) cc_final: 0.7562 (mtt) REVERT: D 279 LYS cc_start: 0.8455 (ttmt) cc_final: 0.7770 (mptt) REVERT: E 53 ASN cc_start: 0.8443 (m-40) cc_final: 0.8061 (m110) REVERT: E 64 ASP cc_start: 0.7326 (p0) cc_final: 0.6856 (p0) REVERT: E 78 ASP cc_start: 0.8061 (m-30) cc_final: 0.7700 (p0) REVERT: F 53 ASN cc_start: 0.8523 (m-40) cc_final: 0.8264 (m-40) REVERT: G 49 GLN cc_start: 0.8678 (tp-100) cc_final: 0.8210 (mm-40) REVERT: G 53 ASN cc_start: 0.8795 (m-40) cc_final: 0.8470 (m-40) REVERT: G 64 ASP cc_start: 0.7257 (m-30) cc_final: 0.7049 (p0) REVERT: H 28 THR cc_start: 0.8768 (t) cc_final: 0.8521 (p) REVERT: H 53 ASN cc_start: 0.8398 (m-40) cc_final: 0.8051 (m110) REVERT: H 54 GLU cc_start: 0.8437 (pt0) cc_final: 0.8189 (pt0) REVERT: H 67 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7474 (mt-10) REVERT: H 75 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.7767 (mptm) REVERT: H 78 ASP cc_start: 0.7989 (m-30) cc_final: 0.7665 (p0) outliers start: 33 outliers final: 29 residues processed: 341 average time/residue: 0.5546 time to fit residues: 207.5726 Evaluate side-chains 343 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 312 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 124 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 123 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 458 GLN B 195 GLN C 195 GLN C 415 GLN D 195 GLN D 415 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.143214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.095635 restraints weight = 17924.524| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.73 r_work: 0.2955 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15808 Z= 0.122 Angle : 0.475 12.727 21416 Z= 0.250 Chirality : 0.036 0.153 2544 Planarity : 0.003 0.039 2648 Dihedral : 3.789 53.857 2172 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.09 % Allowed : 18.33 % Favored : 79.58 % 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 aren not related in a simple way. whole: 3.30 (0.19), residues: 2008 helix: 2.93 (0.14), residues: 1456 sheet: 1.80 (0.68), residues: 64 loop : -0.18 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 207 TYR 0.024 0.001 TYR A 435 PHE 0.011 0.001 PHE F 89 TRP 0.013 0.001 TRP D 328 HIS 0.004 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00282 (15804) covalent geometry : angle 0.47495 (21408) SS BOND : bond 0.00057 ( 4) SS BOND : angle 0.58069 ( 8) hydrogen bonds : bond 0.03581 ( 1158) hydrogen bonds : angle 3.17105 ( 3417) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6588.71 seconds wall clock time: 112 minutes 45.18 seconds (6765.18 seconds total)