Starting phenix.real_space_refine on Fri Jul 3 18:14:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o7s_70207/07_2026/9o7s_70207.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o7s_70207/07_2026/9o7s_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_70207/07_2026/9o7s_70207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o7s_70207/07_2026/9o7s_70207.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o7s_70207/07_2026/9o7s_70207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o7s_70207/07_2026/9o7s_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 0 Ad-hoc single atom residues: {' K': 2} Chain breaks: 2 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'1KP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'1KP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "G" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'1KP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'1KP': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 4.08, per 1000 atoms: 0.26 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: 1.16 Conformation dependent library (CDL) restraints added in 752.8 milliseconds 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: 0.57 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: 2.53 Time building geometry restraints manager: 1.62 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: 12.800 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.410 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 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 are 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/Z covalent geometry : bond 0.00593 / 0.24 (15804) covalent geometry : angle 0.56159 / 0.30 (21408) SS BOND : bond 0.00158 / 0.07 ( 4) SS BOND : angle 1.48933 / 0.80 ( 8) hydrogen bonds : bond 0.10330 / 6.63 ( 1158) hydrogen bonds : angle 4.34285 / 3.19 ( 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 : 0.585 Fit side-chains 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: 0.8666 (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: 0.6425 time to fit residues: 271.3674 Evaluate side-chains 317 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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... 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 = 0.143126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.095577 restraints weight = 18042.393| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.73 r_work: 0.2949 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15808 Z= 0.138 Angle : 0.475 6.576 21416 Z= 0.257 Chirality : 0.036 0.141 2544 Planarity : 0.004 0.033 2648 Dihedral : 3.825 18.731 2172 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.59 % Allowed : 9.32 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.02 (0.19), residues: 2008 helix: 2.80 (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 0.016 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/Z covalent geometry : bond 0.00316 / 0.14 (15804) covalent geometry : angle 0.47486 / 0.26 (21408) SS BOND : bond 0.00079 / 0.04 ( 4) SS BOND : angle 0.97476 / 0.51 ( 8) hydrogen bonds : bond 0.04111 / 2.73 ( 1158) hydrogen bonds : angle 3.47269 / 2.53 ( 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 364 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 339 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8468 (t0) cc_final: 0.7897 (p0) REVERT: A 279 LYS cc_start: 0.7050 (mppt) cc_final: 0.6804 (mptt) REVERT: A 341 ASP cc_start: 0.7876 (t70) cc_final: 0.7541 (t70) REVERT: B 134 ARG cc_start: 0.7790 (mtm110) cc_final: 0.7509 (mtm-85) REVERT: B 162 ASP cc_start: 0.8340 (t70) cc_final: 0.7606 (p0) REVERT: B 279 LYS cc_start: 0.7105 (mppt) cc_final: 0.6858 (mptt) REVERT: B 399 GLU cc_start: 0.8177 (tt0) cc_final: 0.7715 (pt0) REVERT: B 411 MET cc_start: 0.8699 (mmm) cc_final: 0.8473 (mmp) REVERT: C 162 ASP cc_start: 0.8493 (t0) cc_final: 0.7919 (p0) REVERT: C 279 LYS cc_start: 0.7123 (mppt) cc_final: 0.6903 (mptt) REVERT: C 341 ASP cc_start: 0.7848 (t70) cc_final: 0.7543 (t70) REVERT: C 411 MET cc_start: 0.8674 (mmm) cc_final: 0.8461 (mmp) REVERT: D 134 ARG cc_start: 0.7986 (mtm-85) cc_final: 0.7229 (mmt-90) REVERT: D 279 LYS cc_start: 0.8432 (ttmt) cc_final: 0.7691 (mptt) REVERT: D 411 MET cc_start: 0.8743 (mmm) cc_final: 0.8539 (mmp) REVERT: E 22 ASP cc_start: 0.8857 (p0) cc_final: 0.8604 (p0) REVERT: E 24 ASP cc_start: 0.8637 (m-30) cc_final: 0.8424 (m-30) REVERT: E 49 GLN cc_start: 0.8645 (tp-100) cc_final: 0.8281 (mm-40) REVERT: E 53 ASN cc_start: 0.8313 (m110) cc_final: 0.7962 (m110) REVERT: E 78 ASP cc_start: 0.8027 (m-30) cc_final: 0.7760 (p0) REVERT: E 124 MET cc_start: 0.8150 (ttt) cc_final: 0.7927 (ttp) REVERT: F 37 ARG cc_start: 0.8640 (mpp-170) cc_final: 0.8397 (mpp80) REVERT: F 53 ASN cc_start: 0.8515 (m110) cc_final: 0.8203 (m110) REVERT: F 63 ILE cc_start: 0.7804 (mm) cc_final: 0.7601 (mp) REVERT: G 49 GLN cc_start: 0.8634 (tp-100) cc_final: 0.8419 (mm-40) REVERT: G 53 ASN cc_start: 0.8797 (m-40) cc_final: 0.8531 (m-40) REVERT: H 53 ASN cc_start: 0.8169 (m-40) cc_final: 0.7766 (m110) REVERT: H 64 ASP cc_start: 0.7079 (m-30) cc_final: 0.6867 (m-30) REVERT: H 67 GLU cc_start: 0.8182 (mp0) cc_final: 0.7430 (mt-10) REVERT: H 78 ASP cc_start: 0.8074 (m-30) cc_final: 0.7738 (p0) outliers start: 25 outliers final: 13 residues processed: 349 average time/residue: 0.6323 time to fit residues: 242.1018 Evaluate side-chains 331 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 318 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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: 5.9990 chunk 38 optimal weight: 0.8980 chunk 178 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 GLN A 458 GLN B 195 GLN C 195 GLN D 195 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.142399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.094503 restraints weight = 18146.899| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.74 r_work: 0.2935 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15808 Z= 0.149 Angle : 0.472 9.359 21416 Z= 0.254 Chirality : 0.037 0.151 2544 Planarity : 0.003 0.032 2648 Dihedral : 3.825 28.937 2172 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.98 % Allowed : 12.11 % 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 are not related in a simple way. whole: 3.04 (0.19), residues: 2008 helix: 2.82 (0.13), residues: 1428 sheet: 1.50 (0.64), residues: 64 loop : -0.33 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 331 TYR 0.010 0.001 TYR B 362 PHE 0.015 0.001 PHE F 89 TRP 0.012 0.001 TRP D 328 HIS 0.003 0.001 HIS C 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (15804) covalent geometry : angle 0.47134 / 0.25 (21408) SS BOND : bond 0.00090 / 0.04 ( 4) SS BOND : angle 0.80661 / 0.42 ( 8) hydrogen bonds : bond 0.04027 / 2.68 ( 1158) hydrogen bonds : angle 3.37546 / 2.46 ( 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 373 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 326 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8473 (t0) cc_final: 0.7889 (p0) REVERT: A 279 LYS cc_start: 0.7030 (mppt) cc_final: 0.6799 (mptt) REVERT: A 341 ASP cc_start: 0.7897 (t70) cc_final: 0.7558 (t70) REVERT: B 134 ARG cc_start: 0.7793 (mtm110) cc_final: 0.7513 (mtm-85) REVERT: B 162 ASP cc_start: 0.8352 (t70) cc_final: 0.7616 (p0) REVERT: B 279 LYS cc_start: 0.7062 (mppt) cc_final: 0.6847 (mptt) REVERT: B 399 GLU cc_start: 0.8186 (tt0) cc_final: 0.7727 (pt0) REVERT: B 411 MET cc_start: 0.8698 (mmm) cc_final: 0.8468 (mmp) REVERT: C 162 ASP cc_start: 0.8497 (t0) cc_final: 0.7915 (p0) REVERT: C 279 LYS cc_start: 0.7160 (mppt) cc_final: 0.6928 (mptt) REVERT: C 341 ASP cc_start: 0.7888 (t70) cc_final: 0.7558 (t70) REVERT: D 279 LYS cc_start: 0.8413 (ttmt) cc_final: 0.7706 (mptt) REVERT: E 22 ASP cc_start: 0.8778 (p0) cc_final: 0.8497 (p0) REVERT: E 24 ASP cc_start: 0.8612 (m-30) cc_final: 0.8344 (m-30) REVERT: E 49 GLN cc_start: 0.8626 (tp-100) cc_final: 0.8259 (mm-40) REVERT: E 53 ASN cc_start: 0.8253 (m110) cc_final: 0.7898 (m110) REVERT: E 75 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7369 (mptm) REVERT: E 78 ASP cc_start: 0.8061 (m-30) cc_final: 0.7774 (p0) REVERT: E 124 MET cc_start: 0.8154 (ttt) cc_final: 0.7935 (ttp) REVERT: F 53 ASN cc_start: 0.8444 (m110) cc_final: 0.8112 (m110) REVERT: F 75 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.7572 (mptm) REVERT: G 49 GLN cc_start: 0.8639 (tp-100) cc_final: 0.8284 (mm-40) REVERT: G 53 ASN cc_start: 0.8787 (m-40) cc_final: 0.8479 (m-40) REVERT: H 53 ASN cc_start: 0.8221 (m-40) cc_final: 0.7812 (m110) REVERT: H 67 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7349 (mt-10) REVERT: H 78 ASP cc_start: 0.8094 (m-30) cc_final: 0.7719 (p0) REVERT: H 109 MET cc_start: 0.8247 (mmm) cc_final: 0.7944 (mmt) outliers start: 47 outliers final: 28 residues processed: 348 average time/residue: 0.6260 time to fit residues: 239.3540 Evaluate side-chains 347 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 317 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 378 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 193 GLU 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 E residue 18 LEU 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 52 ILE Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 44 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 44 optimal weight: 0.5980 chunk 159 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 GLN A 458 GLN B 195 GLN C 195 GLN D 195 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.142837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.095064 restraints weight = 18112.403| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.74 r_work: 0.2950 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1451 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= 0.134 Angle : 0.470 10.332 21416 Z= 0.250 Chirality : 0.036 0.156 2544 Planarity : 0.003 0.032 2648 Dihedral : 3.792 32.152 2172 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.92 % Allowed : 14.14 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.16 (0.19), residues: 2008 helix: 2.91 (0.14), residues: 1428 sheet: 1.53 (0.65), residues: 64 loop : -0.29 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 207 TYR 0.021 0.001 TYR A 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/Z covalent geometry : bond 0.00314 / 0.13 (15804) covalent geometry : angle 0.46952 / 0.25 (21408) SS BOND : bond 0.00067 / 0.03 ( 4) SS BOND : angle 0.70023 / 0.35 ( 8) hydrogen bonds : bond 0.03812 / 2.53 ( 1158) hydrogen bonds : angle 3.29860 / 2.41 ( 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 371 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 325 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8453 (t0) cc_final: 0.7915 (p0) REVERT: A 279 LYS cc_start: 0.7065 (mppt) cc_final: 0.6828 (mptt) REVERT: B 134 ARG cc_start: 0.7812 (mtm110) cc_final: 0.7227 (mpt180) REVERT: B 279 LYS cc_start: 0.7133 (mppt) cc_final: 0.6907 (mptt) REVERT: B 303 MET cc_start: 0.7150 (mtm) cc_final: 0.6421 (tmm) REVERT: B 399 GLU cc_start: 0.8176 (tt0) cc_final: 0.7730 (pt0) REVERT: B 411 MET cc_start: 0.8716 (mmm) cc_final: 0.8475 (mmp) REVERT: C 162 ASP cc_start: 0.8503 (t0) cc_final: 0.7962 (p0) REVERT: C 279 LYS cc_start: 0.7197 (mppt) cc_final: 0.6945 (mptt) REVERT: D 279 LYS cc_start: 0.8416 (ttmt) cc_final: 0.7727 (mptt) REVERT: E 49 GLN cc_start: 0.8599 (tp-100) cc_final: 0.8246 (mm-40) REVERT: E 53 ASN cc_start: 0.8268 (m110) cc_final: 0.7864 (m110) REVERT: E 75 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.7610 (mptm) REVERT: E 78 ASP cc_start: 0.8028 (m-30) cc_final: 0.7762 (p0) REVERT: F 37 ARG cc_start: 0.8610 (mpp-170) cc_final: 0.8349 (mpp80) REVERT: F 53 ASN cc_start: 0.8473 (m110) cc_final: 0.8190 (m-40) REVERT: F 75 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.7629 (mptm) REVERT: G 49 GLN cc_start: 0.8674 (tp-100) cc_final: 0.8275 (mm-40) REVERT: G 53 ASN cc_start: 0.8799 (m-40) cc_final: 0.8486 (m-40) REVERT: H 37 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8390 (mtm-85) REVERT: H 53 ASN cc_start: 0.8228 (m-40) cc_final: 0.7847 (m110) REVERT: H 54 GLU cc_start: 0.8571 (pt0) cc_final: 0.8348 (pt0) REVERT: H 67 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7727 (mt-10) REVERT: H 78 ASP cc_start: 0.8012 (m-30) cc_final: 0.7672 (p0) REVERT: H 109 MET cc_start: 0.8256 (mmm) cc_final: 0.8038 (mmt) outliers start: 46 outliers final: 30 residues processed: 347 average time/residue: 0.6149 time to fit residues: 234.4344 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 : 0.620 ------------------------------------------------------------------------------- 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 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 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 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 52 ILE Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 86 optimal weight: 0.7980 chunk 71 optimal weight: 0.4980 chunk 139 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 146 optimal weight: 0.0470 chunk 188 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 GLN A 458 GLN B 195 GLN C 195 GLN D 195 GLN F 53 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.143807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.096313 restraints weight = 18080.119| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.74 r_work: 0.2962 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1649 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= 0.113 Angle : 0.448 9.512 21416 Z= 0.240 Chirality : 0.035 0.145 2544 Planarity : 0.003 0.031 2648 Dihedral : 3.705 34.175 2172 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.17 % Allowed : 14.84 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.19), residues: 2008 helix: 2.90 (0.14), residues: 1456 sheet: 1.71 (0.67), residues: 64 loop : -0.35 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 207 TYR 0.021 0.001 TYR B 435 PHE 0.013 0.001 PHE F 89 TRP 0.012 0.001 TRP D 328 HIS 0.003 0.001 HIS C 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (15804) covalent geometry : angle 0.44747 / 0.24 (21408) SS BOND : bond 0.00023 / 0.01 ( 4) SS BOND : angle 0.63614 / 0.32 ( 8) hydrogen bonds : bond 0.03531 / 2.34 ( 1158) hydrogen bonds : angle 3.20492 / 2.34 ( 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 380 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 330 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8442 (t0) cc_final: 0.7892 (p0) REVERT: A 279 LYS cc_start: 0.7003 (mppt) cc_final: 0.6767 (mptt) REVERT: B 134 ARG cc_start: 0.7777 (mtm110) cc_final: 0.7175 (mpt180) REVERT: B 279 LYS cc_start: 0.7080 (mppt) cc_final: 0.6858 (mptt) REVERT: B 303 MET cc_start: 0.7124 (mtm) cc_final: 0.6362 (tmm) REVERT: B 399 GLU cc_start: 0.8171 (tt0) cc_final: 0.7696 (pt0) REVERT: B 411 MET cc_start: 0.8657 (mmm) cc_final: 0.8410 (mmp) REVERT: C 162 ASP cc_start: 0.8501 (t0) cc_final: 0.7935 (p0) REVERT: C 279 LYS cc_start: 0.7130 (mppt) cc_final: 0.6884 (mptt) REVERT: C 399 GLU cc_start: 0.8195 (tt0) cc_final: 0.7708 (pt0) REVERT: D 134 ARG cc_start: 0.8004 (mtm-85) cc_final: 0.7226 (mmt-90) REVERT: D 279 LYS cc_start: 0.8401 (ttmt) cc_final: 0.7696 (mptt) REVERT: E 49 GLN cc_start: 0.8536 (tp-100) cc_final: 0.8193 (mm-40) REVERT: E 53 ASN cc_start: 0.8257 (m110) cc_final: 0.7818 (m110) REVERT: E 54 GLU cc_start: 0.8382 (pt0) cc_final: 0.7922 (pt0) REVERT: E 75 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.7659 (mptm) REVERT: E 78 ASP cc_start: 0.8045 (m-30) cc_final: 0.7711 (p0) REVERT: F 37 ARG cc_start: 0.8579 (mpp-170) cc_final: 0.8327 (mpp80) REVERT: F 53 ASN cc_start: 0.8540 (m-40) cc_final: 0.8234 (m-40) REVERT: F 75 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.7624 (mptm) REVERT: G 26 THR cc_start: 0.8254 (p) cc_final: 0.8047 (t) REVERT: G 49 GLN cc_start: 0.8618 (tp-100) cc_final: 0.8232 (mm-40) REVERT: G 53 ASN cc_start: 0.8782 (m-40) cc_final: 0.8472 (m-40) REVERT: G 64 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.6974 (p0) REVERT: H 37 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8362 (mtm-85) REVERT: H 53 ASN cc_start: 0.8243 (m-40) cc_final: 0.7848 (m110) REVERT: H 67 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7527 (mt-10) REVERT: H 78 ASP cc_start: 0.8033 (m-30) cc_final: 0.7654 (p0) outliers start: 50 outliers final: 28 residues processed: 357 average time/residue: 0.6211 time to fit residues: 243.8079 Evaluate side-chains 354 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 322 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 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 B residue 468 MET Chi-restraints excluded: chain C residue 177 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 330 VAL 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 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 55 VAL Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 58 ASP 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: 0.5980 chunk 144 optimal weight: 0.9990 chunk 47 optimal weight: 0.0970 chunk 45 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 146 optimal weight: 0.0060 chunk 129 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 GLN B 195 GLN B 452 HIS C 195 GLN D 195 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 = 0.3712 r_free = 0.3712 target = 0.144846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.097614 restraints weight = 17885.858| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.72 r_work: 0.2982 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15808 Z= 0.102 Angle : 0.434 9.713 21416 Z= 0.234 Chirality : 0.035 0.153 2544 Planarity : 0.003 0.031 2648 Dihedral : 3.633 35.078 2172 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.92 % Allowed : 15.28 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.29 (0.19), residues: 2008 helix: 2.99 (0.14), residues: 1460 sheet: 1.74 (0.67), residues: 64 loop : -0.47 (0.28), residues: 484 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 0.012 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/Z covalent geometry : bond 0.00222 / 0.10 (15804) covalent geometry : angle 0.43406 / 0.23 (21408) SS BOND : bond 0.00034 / 0.01 ( 4) SS BOND : angle 0.57111 / 0.28 ( 8) hydrogen bonds : bond 0.03339 / 2.21 ( 1158) hydrogen bonds : angle 3.14569 / 2.31 ( 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 375 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 329 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7976 (mtm-85) cc_final: 0.7242 (mmt-90) REVERT: A 162 ASP cc_start: 0.8411 (t0) cc_final: 0.7906 (p0) REVERT: A 279 LYS cc_start: 0.6995 (mppt) cc_final: 0.6757 (mptt) REVERT: A 365 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8292 (mtm) REVERT: B 134 ARG cc_start: 0.7783 (mtm110) cc_final: 0.7194 (mpt180) REVERT: B 279 LYS cc_start: 0.7082 (mppt) cc_final: 0.6861 (mptt) REVERT: B 303 MET cc_start: 0.7088 (mtm) cc_final: 0.6357 (tmm) REVERT: B 399 GLU cc_start: 0.8144 (tt0) cc_final: 0.7658 (pt0) REVERT: B 411 MET cc_start: 0.8655 (mmm) cc_final: 0.8383 (mmp) REVERT: C 162 ASP cc_start: 0.8439 (t0) cc_final: 0.7946 (p0) REVERT: C 279 LYS cc_start: 0.7106 (mppt) cc_final: 0.6889 (mptt) REVERT: C 399 GLU cc_start: 0.8174 (tt0) cc_final: 0.7688 (pt0) REVERT: D 134 ARG cc_start: 0.8012 (mtm-85) cc_final: 0.7247 (mmt-90) REVERT: D 279 LYS cc_start: 0.8415 (ttmt) cc_final: 0.7718 (mptt) REVERT: E 53 ASN cc_start: 0.8263 (m110) cc_final: 0.7811 (m110) REVERT: E 54 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7893 (pt0) REVERT: E 75 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.7763 (mptm) REVERT: E 78 ASP cc_start: 0.8021 (m-30) cc_final: 0.7695 (p0) REVERT: F 37 ARG cc_start: 0.8575 (mpp-170) cc_final: 0.8335 (mtm-85) REVERT: F 53 ASN cc_start: 0.8523 (m-40) cc_final: 0.8244 (m-40) REVERT: F 75 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.7698 (mptm) REVERT: G 49 GLN cc_start: 0.8634 (tp-100) cc_final: 0.8272 (mm-40) REVERT: G 53 ASN cc_start: 0.8795 (m-40) cc_final: 0.8501 (m-40) REVERT: G 64 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.7022 (p0) REVERT: H 37 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8335 (mtm-85) REVERT: H 53 ASN cc_start: 0.8265 (m-40) cc_final: 0.7842 (m110) REVERT: H 67 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7675 (mt-10) REVERT: H 75 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.7757 (mptm) REVERT: H 78 ASP cc_start: 0.8000 (m-30) cc_final: 0.7656 (p0) outliers start: 46 outliers final: 25 residues processed: 351 average time/residue: 0.6376 time to fit residues: 245.3037 Evaluate side-chains 356 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 324 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 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 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 322 LEU Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 465 SER 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 44 THR Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 74 ARG 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: 8.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 GLN A 345 ASN B 195 GLN B 452 HIS C 195 GLN D 195 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 = 0.3668 r_free = 0.3668 target = 0.141000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.093057 restraints weight = 17984.620| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.72 r_work: 0.2908 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15808 Z= 0.204 Angle : 0.505 11.144 21416 Z= 0.270 Chirality : 0.039 0.154 2544 Planarity : 0.004 0.041 2648 Dihedral : 3.962 50.399 2172 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.98 % Allowed : 16.36 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.11 (0.19), residues: 2008 helix: 2.83 (0.13), residues: 1428 sheet: 2.10 (0.80), 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 0.022 0.002 TYR B 435 PHE 0.015 0.002 PHE F 89 TRP 0.012 0.001 TRP C 328 HIS 0.004 0.001 HIS C 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.20 (15804) covalent geometry : angle 0.50447 / 0.27 (21408) SS BOND : bond 0.00185 / 0.09 ( 4) SS BOND : angle 0.64619 / 0.32 ( 8) hydrogen bonds : bond 0.04295 / 2.87 ( 1158) hydrogen bonds : angle 3.36101 / 2.45 ( 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 365 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 318 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8462 (t0) cc_final: 0.7963 (p0) REVERT: A 279 LYS cc_start: 0.7020 (mppt) cc_final: 0.6757 (mptt) REVERT: B 134 ARG cc_start: 0.7794 (mtm110) cc_final: 0.7443 (mtm-85) REVERT: B 279 LYS cc_start: 0.7089 (mppt) cc_final: 0.6847 (mptt) REVERT: B 399 GLU cc_start: 0.8217 (tt0) cc_final: 0.7712 (pt0) REVERT: B 411 MET cc_start: 0.8748 (mmm) cc_final: 0.8534 (mmp) REVERT: C 134 ARG cc_start: 0.7993 (mtm-85) cc_final: 0.7264 (mmt-90) REVERT: C 162 ASP cc_start: 0.8523 (t0) cc_final: 0.7960 (p0) REVERT: C 279 LYS cc_start: 0.7163 (mppt) cc_final: 0.6885 (mptt) REVERT: C 468 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7535 (mtt) REVERT: D 279 LYS cc_start: 0.8411 (ttmt) cc_final: 0.7740 (mptt) REVERT: E 53 ASN cc_start: 0.8315 (m110) cc_final: 0.7847 (m110) REVERT: E 54 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8025 (pt0) REVERT: E 64 ASP cc_start: 0.7179 (p0) cc_final: 0.6900 (p0) REVERT: E 75 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.7557 (mptm) REVERT: E 78 ASP cc_start: 0.8068 (m-30) cc_final: 0.7721 (p0) REVERT: F 53 ASN cc_start: 0.8520 (m-40) cc_final: 0.8248 (m-40) REVERT: F 64 ASP cc_start: 0.7275 (p0) cc_final: 0.6865 (p0) REVERT: F 75 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.7710 (mptm) REVERT: G 49 GLN cc_start: 0.8633 (tp-100) cc_final: 0.8220 (mm-40) REVERT: G 53 ASN cc_start: 0.8783 (m-40) cc_final: 0.8452 (m-40) REVERT: G 64 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.7202 (p0) REVERT: H 37 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8332 (mtm-85) REVERT: H 53 ASN cc_start: 0.8292 (m-40) cc_final: 0.7913 (m110) REVERT: H 67 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7602 (mt-10) REVERT: H 75 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.7759 (mptm) REVERT: H 78 ASP cc_start: 0.8052 (m-30) cc_final: 0.7665 (p0) outliers start: 47 outliers final: 31 residues processed: 343 average time/residue: 0.6545 time to fit residues: 245.9005 Evaluate side-chains 348 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 310 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 465 SER 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 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 55 VAL Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ARG 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: 6.9990 chunk 9 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3696 r_free = 0.3696 target = 0.143457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.095916 restraints weight = 18087.437| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.74 r_work: 0.2962 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1834 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= 0.122 Angle : 0.457 11.603 21416 Z= 0.245 Chirality : 0.036 0.155 2544 Planarity : 0.003 0.038 2648 Dihedral : 3.813 48.707 2172 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.47 % Allowed : 17.37 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.19), residues: 2008 helix: 2.89 (0.14), residues: 1456 sheet: 1.69 (0.67), residues: 64 loop : -0.27 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 207 TYR 0.023 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/Z covalent geometry : bond 0.00281 / 0.12 (15804) covalent geometry : angle 0.45655 / 0.24 (21408) SS BOND : bond 0.00057 / 0.03 ( 4) SS BOND : angle 0.63582 / 0.31 ( 8) hydrogen bonds : bond 0.03606 / 2.39 ( 1158) hydrogen bonds : angle 3.19710 / 2.34 ( 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 356 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 317 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8445 (t0) cc_final: 0.7945 (p0) REVERT: A 279 LYS cc_start: 0.7039 (mppt) cc_final: 0.6770 (mptt) REVERT: A 365 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8240 (mtm) REVERT: B 134 ARG cc_start: 0.7814 (mtm110) cc_final: 0.7228 (mpt180) REVERT: B 279 LYS cc_start: 0.7135 (mppt) cc_final: 0.6907 (mptt) REVERT: B 303 MET cc_start: 0.7112 (mtm) cc_final: 0.6352 (tmm) REVERT: B 411 MET cc_start: 0.8716 (mmm) cc_final: 0.8496 (mmp) REVERT: B 468 MET cc_start: 0.7713 (mtp) cc_final: 0.7437 (mtt) REVERT: C 162 ASP cc_start: 0.8516 (t0) cc_final: 0.7962 (p0) REVERT: C 279 LYS cc_start: 0.7147 (mppt) cc_final: 0.6905 (mptt) REVERT: C 468 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7567 (mtt) REVERT: D 279 LYS cc_start: 0.8419 (ttmt) cc_final: 0.7765 (mptt) REVERT: E 53 ASN cc_start: 0.8336 (m110) cc_final: 0.7887 (m110) REVERT: E 54 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7887 (pt0) REVERT: E 64 ASP cc_start: 0.7252 (p0) cc_final: 0.6901 (p0) REVERT: E 75 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7709 (mptm) REVERT: E 78 ASP cc_start: 0.8047 (m-30) cc_final: 0.7721 (p0) REVERT: F 37 ARG cc_start: 0.8574 (mpp-170) cc_final: 0.8325 (mtm-85) REVERT: F 53 ASN cc_start: 0.8564 (m-40) cc_final: 0.8269 (m-40) REVERT: F 64 ASP cc_start: 0.7387 (p0) cc_final: 0.7048 (p0) REVERT: G 49 GLN cc_start: 0.8625 (tp-100) cc_final: 0.8230 (mm-40) REVERT: G 53 ASN cc_start: 0.8756 (m-40) cc_final: 0.8441 (m-40) REVERT: H 37 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8349 (mtm-85) REVERT: H 53 ASN cc_start: 0.8327 (m-40) cc_final: 0.7948 (m110) REVERT: H 67 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7385 (mt-10) REVERT: H 75 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.7777 (mptm) REVERT: H 78 ASP cc_start: 0.7981 (m-30) cc_final: 0.7666 (p0) outliers start: 39 outliers final: 20 residues processed: 341 average time/residue: 0.6367 time to fit residues: 238.7254 Evaluate side-chains 340 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 314 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 54 GLU Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 75 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 196 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 192 optimal weight: 0.8980 chunk 157 optimal weight: 10.0000 chunk 160 optimal weight: 0.8980 chunk 170 optimal weight: 7.9990 chunk 186 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3688 r_free = 0.3688 target = 0.142850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.095154 restraints weight = 18052.883| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.73 r_work: 0.2948 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15808 Z= 0.139 Angle : 0.480 12.199 21416 Z= 0.253 Chirality : 0.036 0.150 2544 Planarity : 0.003 0.038 2648 Dihedral : 3.841 50.563 2172 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.09 % Allowed : 17.88 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.19), residues: 2008 helix: 2.87 (0.14), residues: 1456 sheet: 1.76 (0.67), residues: 64 loop : -0.25 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 207 TYR 0.022 0.001 TYR B 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/Z covalent geometry : bond 0.00328 / 0.14 (15804) covalent geometry : angle 0.48010 / 0.25 (21408) SS BOND : bond 0.00098 / 0.05 ( 4) SS BOND : angle 0.60560 / 0.29 ( 8) hydrogen bonds : bond 0.03729 / 2.48 ( 1158) hydrogen bonds : angle 3.21793 / 2.35 ( 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 347 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 314 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8439 (t0) cc_final: 0.7953 (p0) REVERT: A 279 LYS cc_start: 0.7026 (mppt) cc_final: 0.6758 (mptt) REVERT: A 365 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8238 (mtm) REVERT: B 134 ARG cc_start: 0.7824 (mtm110) cc_final: 0.7231 (mpt180) REVERT: B 279 LYS cc_start: 0.7106 (mppt) cc_final: 0.6875 (mptt) REVERT: B 303 MET cc_start: 0.7145 (mtm) cc_final: 0.6420 (tmm) REVERT: B 399 GLU cc_start: 0.8185 (tt0) cc_final: 0.7736 (pt0) REVERT: B 411 MET cc_start: 0.8725 (mmm) cc_final: 0.8500 (mmp) REVERT: B 468 MET cc_start: 0.7742 (mtp) cc_final: 0.7472 (mtt) REVERT: C 134 ARG cc_start: 0.7939 (mtm-85) cc_final: 0.7199 (mmt-90) REVERT: C 162 ASP cc_start: 0.8520 (t0) cc_final: 0.7962 (p0) REVERT: C 279 LYS cc_start: 0.7163 (mppt) cc_final: 0.6901 (mptt) REVERT: C 468 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7530 (mtt) REVERT: D 279 LYS cc_start: 0.8439 (ttmt) cc_final: 0.7747 (mptt) REVERT: E 53 ASN cc_start: 0.8346 (m110) cc_final: 0.7899 (m110) REVERT: E 54 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7879 (pt0) REVERT: E 64 ASP cc_start: 0.7372 (p0) cc_final: 0.7141 (p0) REVERT: E 75 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.7707 (mptm) REVERT: E 78 ASP cc_start: 0.8047 (m-30) cc_final: 0.7712 (p0) REVERT: F 53 ASN cc_start: 0.8569 (m-40) cc_final: 0.8306 (m-40) REVERT: F 75 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.7752 (mptm) REVERT: G 49 GLN cc_start: 0.8649 (tp-100) cc_final: 0.8256 (mm-40) REVERT: G 53 ASN cc_start: 0.8767 (m-40) cc_final: 0.8438 (m-40) REVERT: H 37 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7807 (mtp180) REVERT: H 53 ASN cc_start: 0.8345 (m-40) cc_final: 0.7971 (m110) REVERT: H 67 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7653 (mt-10) REVERT: H 75 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.7762 (mptm) REVERT: H 78 ASP cc_start: 0.7988 (m-30) cc_final: 0.7668 (p0) outliers start: 33 outliers final: 23 residues processed: 334 average time/residue: 0.6124 time to fit residues: 224.3479 Evaluate side-chains 344 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 314 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 54 GLU Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 110 THR 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 37 ARG Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 75 LYS 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: 0.6980 chunk 66 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 chunk 186 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 176 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3690 r_free = 0.3690 target = 0.142985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.095377 restraints weight = 18016.507| |-----------------------------------------------------------------------------| r_work (start): 0.3061 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: 3.56 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1863 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= 0.134 Angle : 0.483 12.857 21416 Z= 0.253 Chirality : 0.036 0.152 2544 Planarity : 0.003 0.040 2648 Dihedral : 3.844 50.829 2172 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.16 % Allowed : 17.88 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.23 (0.19), residues: 2008 helix: 2.89 (0.14), residues: 1456 sheet: 1.75 (0.68), residues: 64 loop : -0.21 (0.29), residues: 488 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 0.012 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/Z covalent geometry : bond 0.00314 / 0.13 (15804) covalent geometry : angle 0.48252 / 0.25 (21408) SS BOND : bond 0.00086 / 0.04 ( 4) SS BOND : angle 0.60400 / 0.29 ( 8) hydrogen bonds : bond 0.03679 / 2.44 ( 1158) hydrogen bonds : angle 3.19046 / 2.34 ( 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 345 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 311 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8434 (t0) cc_final: 0.7956 (p0) REVERT: A 279 LYS cc_start: 0.7020 (mppt) cc_final: 0.6751 (mptt) REVERT: A 365 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8245 (mtm) REVERT: B 134 ARG cc_start: 0.7819 (mtm110) cc_final: 0.7234 (mpt180) REVERT: B 279 LYS cc_start: 0.7105 (mppt) cc_final: 0.6874 (mptt) REVERT: B 303 MET cc_start: 0.7118 (mtm) cc_final: 0.6355 (tmm) REVERT: B 411 MET cc_start: 0.8743 (mmm) cc_final: 0.8521 (mmp) REVERT: B 468 MET cc_start: 0.7747 (mtp) cc_final: 0.7492 (mtt) REVERT: C 162 ASP cc_start: 0.8521 (t0) cc_final: 0.7970 (p0) REVERT: C 279 LYS cc_start: 0.7148 (mppt) cc_final: 0.6892 (mptt) REVERT: C 468 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7556 (mtt) REVERT: D 279 LYS cc_start: 0.8434 (ttmt) cc_final: 0.7748 (mptt) REVERT: E 53 ASN cc_start: 0.8367 (m110) cc_final: 0.7914 (m110) REVERT: E 54 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7858 (pt0) REVERT: E 64 ASP cc_start: 0.7456 (p0) cc_final: 0.7207 (p0) REVERT: E 75 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.7698 (mptm) REVERT: E 78 ASP cc_start: 0.8035 (m-30) cc_final: 0.7706 (p0) REVERT: F 37 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8326 (mtm-85) REVERT: F 53 ASN cc_start: 0.8572 (m-40) cc_final: 0.8281 (m-40) REVERT: F 75 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.7777 (mptm) REVERT: G 49 GLN cc_start: 0.8661 (tp-100) cc_final: 0.8280 (mm-40) REVERT: G 53 ASN cc_start: 0.8793 (m-40) cc_final: 0.8468 (m-40) REVERT: H 37 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7801 (mtp180) REVERT: H 53 ASN cc_start: 0.8356 (m-40) cc_final: 0.7997 (m110) REVERT: H 67 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7664 (mt-10) REVERT: H 75 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.7783 (mptm) REVERT: H 78 ASP cc_start: 0.7974 (m-30) cc_final: 0.7660 (p0) outliers start: 34 outliers final: 26 residues processed: 333 average time/residue: 0.6227 time to fit residues: 227.5358 Evaluate side-chains 344 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 310 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 54 GLU Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 110 THR 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 37 ARG Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 75 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 123 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 82 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 GLN A 458 GLN B 195 GLN C 195 GLN C 415 GLN D 195 GLN D 415 GLN D 437 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.144274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.096219 restraints weight = 18016.824| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.74 r_work: 0.2963 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15808 Z= 0.117 Angle : 0.468 12.940 21416 Z= 0.245 Chirality : 0.036 0.153 2544 Planarity : 0.003 0.038 2648 Dihedral : 3.779 52.703 2172 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.41 % Allowed : 17.82 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.37 (0.19), residues: 2008 helix: 2.99 (0.14), residues: 1456 sheet: 1.73 (0.68), residues: 64 loop : -0.16 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 207 TYR 0.021 0.001 TYR B 435 PHE 0.011 0.001 PHE F 89 TRP 0.012 0.001 TRP D 328 HIS 0.003 0.001 HIS C 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (15804) covalent geometry : angle 0.46784 / 0.24 (21408) SS BOND : bond 0.00041 / 0.02 ( 4) SS BOND : angle 0.59594 / 0.28 ( 8) hydrogen bonds : bond 0.03461 / 2.29 ( 1158) hydrogen bonds : angle 3.13615 / 2.30 ( 3417) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7075.58 seconds wall clock time: 121 minutes 8.81 seconds (7268.81 seconds total)