Starting phenix.real_space_refine on Sun Apr 5 04:06:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z32_73782/04_2026/9z32_73782.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z32_73782/04_2026/9z32_73782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9z32_73782/04_2026/9z32_73782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z32_73782/04_2026/9z32_73782.map" model { file = "/net/cci-nas-00/data/ceres_data/9z32_73782/04_2026/9z32_73782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z32_73782/04_2026/9z32_73782.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 42 5.16 5 C 5061 2.51 5 N 1296 2.21 5 O 1494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7902 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2561 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 324, 2539 Classifications: {'peptide': 324} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 308} Conformer: "B" Number of residues, atoms: 324, 2539 Classifications: {'peptide': 324} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 308} bond proxies already assigned to first conformer: 2579 Chain: "B" Number of atoms: 2561 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 324, 2539 Classifications: {'peptide': 324} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 308} Conformer: "B" Number of residues, atoms: 324, 2539 Classifications: {'peptide': 324} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 308} bond proxies already assigned to first conformer: 2579 Chain: "C" Number of atoms: 2561 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 324, 2539 Classifications: {'peptide': 324} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 308} Conformer: "B" Number of residues, atoms: 324, 2539 Classifications: {'peptide': 324} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 308} bond proxies already assigned to first conformer: 2579 Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Unusual residues: {'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Unusual residues: {'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Unusual residues: {'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ATYR A 59 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 59 " occ=0.50 residue: pdb=" N AHIS A 204 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 204 " occ=0.50 residue: pdb=" N ATYR B 59 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR B 59 " occ=0.50 residue: pdb=" N AHIS B 204 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 204 " occ=0.50 residue: pdb=" N ATYR C 59 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 59 " occ=0.50 residue: pdb=" N AHIS C 204 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 204 " occ=0.50 Time building chain proxies: 3.10, per 1000 atoms: 0.39 Number of scatterers: 7902 At special positions: 0 Unit cell: (84.048, 88.992, 125.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 9 15.00 O 1494 8.00 N 1296 7.00 C 5061 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 176 " distance=2.02 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 270 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 176 " distance=2.02 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 279 " distance=2.03 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 176 " distance=2.02 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 226 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 270 " - pdb=" SG CYS C 279 " 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 194 " " NAG A 502 " - " ASN A 310 " " NAG A 503 " - " ASN A 133 " " NAG B 501 " - " ASN B 194 " " NAG B 502 " - " ASN B 310 " " NAG B 503 " - " ASN B 133 " " NAG C 502 " - " ASN C 194 " " NAG C 503 " - " ASN C 310 " " NAG C 504 " - " ASN C 133 " Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 461.4 milliseconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1794 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 21 sheets defined 22.5% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 45 through 63 removed outlier: 3.629A pdb=" N LEU A 53 " --> pdb=" O GLN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 98 No H-bonds generated for 'chain 'A' and resid 95 through 98' Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.513A pdb=" N HIS A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 338 through 366 Processing helix chain 'B' and resid 45 through 63 removed outlier: 3.628A pdb=" N LEU B 53 " --> pdb=" O GLN B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 98 No H-bonds generated for 'chain 'B' and resid 95 through 98' Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 241 through 248 Processing helix chain 'B' and resid 252 through 258 removed outlier: 3.513A pdb=" N HIS B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 278 No H-bonds generated for 'chain 'B' and resid 276 through 278' Processing helix chain 'B' and resid 338 through 366 Processing helix chain 'C' and resid 45 through 63 removed outlier: 3.628A pdb=" N LEU C 53 " --> pdb=" O GLN C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 98 No H-bonds generated for 'chain 'C' and resid 95 through 98' Processing helix chain 'C' and resid 192 through 194 No H-bonds generated for 'chain 'C' and resid 192 through 194' Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 252 through 258 removed outlier: 3.514A pdb=" N HIS C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 278 No H-bonds generated for 'chain 'C' and resid 276 through 278' Processing helix chain 'C' and resid 338 through 366 Processing sheet with id= A, first strand: chain 'A' and resid 75 through 83 Processing sheet with id= B, first strand: chain 'A' and resid 86 through 88 Processing sheet with id= C, first strand: chain 'A' and resid 183 through 187 removed outlier: 6.727A pdb=" N TYR A 321 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL A 114 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS A 319 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA A 116 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU A 317 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY A 260 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ASP A 326 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE A 262 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ILE A 328 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL A 264 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N HIS A 330 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE A 266 " --> pdb=" O HIS A 330 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N GLN A 332 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TRP A 268 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLY A 334 " --> pdb=" O TRP A 268 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N CYS A 270 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 121 through 126 Processing sheet with id= E, first strand: chain 'A' and resid 159 through 161 Processing sheet with id= F, first strand: chain 'A' and resid 202 through 205 removed outlier: 4.167A pdb=" N PHE A 210 " --> pdb=" O TYR A 205 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 300 through 309 Processing sheet with id= H, first strand: chain 'B' and resid 75 through 83 Processing sheet with id= I, first strand: chain 'B' and resid 86 through 88 Processing sheet with id= J, first strand: chain 'B' and resid 183 through 187 removed outlier: 6.727A pdb=" N TYR B 321 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL B 114 " --> pdb=" O LYS B 319 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LYS B 319 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALA B 116 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU B 317 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY B 260 " --> pdb=" O ARG B 324 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ASP B 326 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE B 262 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ILE B 328 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL B 264 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N HIS B 330 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE B 266 " --> pdb=" O HIS B 330 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N GLN B 332 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TRP B 268 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLY B 334 " --> pdb=" O TRP B 268 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N CYS B 270 " --> pdb=" O GLY B 334 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 121 through 126 Processing sheet with id= L, first strand: chain 'B' and resid 159 through 161 Processing sheet with id= M, first strand: chain 'B' and resid 202 through 205 removed outlier: 4.168A pdb=" N PHE B 210 " --> pdb=" O TYR B 205 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 300 through 309 Processing sheet with id= O, first strand: chain 'C' and resid 75 through 83 Processing sheet with id= P, first strand: chain 'C' and resid 86 through 88 Processing sheet with id= Q, first strand: chain 'C' and resid 183 through 187 removed outlier: 6.727A pdb=" N TYR C 321 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL C 114 " --> pdb=" O LYS C 319 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LYS C 319 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA C 116 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU C 317 " --> pdb=" O ALA C 116 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY C 260 " --> pdb=" O ARG C 324 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ASP C 326 " --> pdb=" O GLY C 260 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE C 262 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ILE C 328 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL C 264 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N HIS C 330 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE C 266 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N GLN C 332 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TRP C 268 " --> pdb=" O GLN C 332 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N GLY C 334 " --> pdb=" O TRP C 268 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N CYS C 270 " --> pdb=" O GLY C 334 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 121 through 126 Processing sheet with id= S, first strand: chain 'C' and resid 159 through 161 Processing sheet with id= T, first strand: chain 'C' and resid 202 through 205 removed outlier: 4.166A pdb=" N PHE C 210 " --> pdb=" O TYR C 205 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 300 through 309 300 hydrogen bonds defined for protein. 834 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: 1.21 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2451 1.34 - 1.46: 1905 1.46 - 1.58: 3696 1.58 - 1.69: 15 1.69 - 1.81: 51 Bond restraints: 8118 Sorted by residual: bond pdb=" C1 NAG A 502 " pdb=" O5 NAG A 502 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.22e+00 bond pdb=" C1 NAG B 502 " pdb=" O5 NAG B 502 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C1 NAG C 503 " pdb=" O5 NAG C 503 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" N ASN B 133 " pdb=" CA ASN B 133 " ideal model delta sigma weight residual 1.462 1.483 -0.021 1.46e-02 4.69e+03 2.13e+00 bond pdb=" N ASN C 133 " pdb=" CA ASN C 133 " ideal model delta sigma weight residual 1.462 1.483 -0.021 1.46e-02 4.69e+03 2.12e+00 ... (remaining 8113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 10672 1.09 - 2.19: 303 2.19 - 3.28: 72 3.28 - 4.38: 2 4.38 - 5.47: 9 Bond angle restraints: 11058 Sorted by residual: angle pdb=" CA ASN B 133 " pdb=" C ASN B 133 " pdb=" O ASN B 133 " ideal model delta sigma weight residual 121.65 118.33 3.32 1.17e+00 7.31e-01 8.05e+00 angle pdb=" CA ASN C 133 " pdb=" C ASN C 133 " pdb=" O ASN C 133 " ideal model delta sigma weight residual 121.65 118.35 3.30 1.17e+00 7.31e-01 7.97e+00 angle pdb=" CA ASN A 133 " pdb=" C ASN A 133 " pdb=" O ASN A 133 " ideal model delta sigma weight residual 121.65 118.41 3.24 1.17e+00 7.31e-01 7.65e+00 angle pdb=" C LEU B 288 " pdb=" N ASP B 289 " pdb=" CA ASP B 289 " ideal model delta sigma weight residual 122.38 116.91 5.47 2.90e+00 1.19e-01 3.56e+00 angle pdb=" C LEU A 288 " pdb=" N ASP A 289 " pdb=" CA ASP A 289 " ideal model delta sigma weight residual 122.38 116.92 5.46 2.90e+00 1.19e-01 3.55e+00 ... (remaining 11053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.57: 4589 14.57 - 29.13: 235 29.13 - 43.70: 75 43.70 - 58.27: 42 58.27 - 72.84: 6 Dihedral angle restraints: 4947 sinusoidal: 2124 harmonic: 2823 Sorted by residual: dihedral pdb=" N LEU A 154 " pdb=" CA LEU A 154 " pdb=" CB LEU A 154 " pdb=" CG LEU A 154 " ideal model delta sinusoidal sigma weight residual -60.00 -116.65 56.65 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" N LEU B 154 " pdb=" CA LEU B 154 " pdb=" CB LEU B 154 " pdb=" CG LEU B 154 " ideal model delta sinusoidal sigma weight residual -60.00 -116.63 56.63 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" N LEU C 154 " pdb=" CA LEU C 154 " pdb=" CB LEU C 154 " pdb=" CG LEU C 154 " ideal model delta sinusoidal sigma weight residual -60.00 -116.62 56.62 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 4944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 802 0.033 - 0.066: 289 0.066 - 0.098: 88 0.098 - 0.131: 66 0.131 - 0.164: 6 Chirality restraints: 1251 Sorted by residual: chirality pdb=" C1 NAG B 501 " pdb=" ND2 ASN B 194 " pdb=" C2 NAG B 501 " pdb=" O5 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 194 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" C1 NAG C 502 " pdb=" ND2 ASN C 194 " pdb=" C2 NAG C 502 " pdb=" O5 NAG C 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.51e-01 ... (remaining 1248 not shown) Planarity restraints: 1377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 133 " -0.054 2.00e-02 2.50e+03 6.28e-02 4.93e+01 pdb=" CG ASN C 133 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN C 133 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN C 133 " 0.104 2.00e-02 2.50e+03 pdb=" C1 NAG C 504 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 133 " 0.054 2.00e-02 2.50e+03 6.27e-02 4.91e+01 pdb=" CG ASN A 133 " -0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN A 133 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN A 133 " -0.103 2.00e-02 2.50e+03 pdb=" C1 NAG A 503 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 133 " -0.054 2.00e-02 2.50e+03 6.25e-02 4.89e+01 pdb=" CG ASN B 133 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN B 133 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN B 133 " 0.103 2.00e-02 2.50e+03 pdb=" C1 NAG B 503 " -0.076 2.00e-02 2.50e+03 ... (remaining 1374 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 2251 2.82 - 3.34: 7050 3.34 - 3.86: 12776 3.86 - 4.38: 14821 4.38 - 4.90: 26579 Nonbonded interactions: 63477 Sorted by model distance: nonbonded pdb=" O LEU A 338 " pdb=" OG1 THR A 341 " model vdw 2.294 3.040 nonbonded pdb=" O LEU B 338 " pdb=" OG1 THR B 341 " model vdw 2.295 3.040 nonbonded pdb=" O LEU C 338 " pdb=" OG1 THR C 341 " model vdw 2.295 3.040 nonbonded pdb=" OE1 GLU A 96 " pdb=" OH TYR B 306 " model vdw 2.301 3.040 nonbonded pdb=" OE1 GLU B 96 " pdb=" OH TYR C 306 " model vdw 2.306 3.040 ... (remaining 63472 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 44 through 58 or resid 60 through 203 or resid 205 through \ 367 or resid 502 through 503)) selection = (chain 'B' and (resid 44 through 58 or resid 60 through 203 or resid 205 through \ 367 or resid 502 through 503)) selection = (chain 'C' and (resid 44 through 58 or resid 60 through 203 or resid 205 through \ 367 or resid 502 through 503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.020 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:8.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8142 Z= 0.175 Angle : 0.486 5.471 11115 Z= 0.252 Chirality : 0.044 0.164 1251 Planarity : 0.004 0.038 1368 Dihedral : 11.194 72.837 3108 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.78 % Allowed : 5.34 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.27), residues: 984 helix: 2.40 (0.34), residues: 219 sheet: 0.20 (0.29), residues: 348 loop : -0.67 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 302 TYR 0.009 0.001 TYR C 98 PHE 0.007 0.001 PHE C 239 TRP 0.008 0.001 TRP C 268 HIS 0.002 0.000 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 8118) covalent geometry : angle 0.47217 (11058) SS BOND : bond 0.00362 ( 15) SS BOND : angle 0.92686 ( 30) hydrogen bonds : bond 0.14930 ( 300) hydrogen bonds : angle 7.53796 ( 834) link_NAG-ASN : bond 0.00477 ( 9) link_NAG-ASN : angle 2.20849 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.279 Fit side-chains REVERT: A 45 TYR cc_start: 0.6001 (OUTLIER) cc_final: 0.5372 (m-80) REVERT: A 68 GLN cc_start: 0.7460 (mt0) cc_final: 0.7259 (mt0) REVERT: A 90 HIS cc_start: 0.8421 (m-70) cc_final: 0.8028 (m90) REVERT: A 127 GLU cc_start: 0.8837 (tp30) cc_final: 0.8594 (tp30) REVERT: A 186 GLN cc_start: 0.8169 (mt0) cc_final: 0.7968 (mt0) REVERT: A 191 MET cc_start: 0.8334 (mtm) cc_final: 0.8120 (mtm) REVERT: A 254 GLU cc_start: 0.8522 (tt0) cc_final: 0.8309 (tm-30) REVERT: A 258 LYS cc_start: 0.8487 (mttp) cc_final: 0.7950 (mmtt) REVERT: B 45 TYR cc_start: 0.6011 (OUTLIER) cc_final: 0.5319 (m-80) REVERT: B 68 GLN cc_start: 0.7591 (mt0) cc_final: 0.7377 (mt0) REVERT: B 90 HIS cc_start: 0.8456 (m-70) cc_final: 0.7878 (m-70) REVERT: B 186 GLN cc_start: 0.8207 (mt0) cc_final: 0.7868 (mt0) REVERT: B 254 GLU cc_start: 0.8584 (tt0) cc_final: 0.8186 (tm-30) REVERT: C 45 TYR cc_start: 0.5992 (OUTLIER) cc_final: 0.5253 (m-80) REVERT: C 186 GLN cc_start: 0.8247 (mt0) cc_final: 0.7995 (mt0) REVERT: C 191 MET cc_start: 0.8333 (mtm) cc_final: 0.7976 (mtm) REVERT: C 254 GLU cc_start: 0.8575 (tt0) cc_final: 0.8317 (tm-30) REVERT: C 258 LYS cc_start: 0.8539 (mttp) cc_final: 0.7993 (mptt) REVERT: C 284 SER cc_start: 0.8386 (m) cc_final: 0.8060 (t) REVERT: C 292 HIS cc_start: 0.8312 (m-70) cc_final: 0.7927 (m-70) outliers start: 9 outliers final: 3 residues processed: 102 average time/residue: 0.4437 time to fit residues: 48.4545 Evaluate side-chains 68 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain C residue 45 TYR Chi-restraints excluded: chain C residue 172 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.0030 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.3980 chunk 74 optimal weight: 4.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS B 90 HIS B 152 ASN C 152 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.133386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.081721 restraints weight = 45260.375| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 5.84 r_work: 0.2771 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8142 Z= 0.113 Angle : 0.506 5.133 11115 Z= 0.268 Chirality : 0.046 0.218 1251 Planarity : 0.004 0.039 1368 Dihedral : 9.447 86.680 1365 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.90 % Allowed : 9.02 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.27), residues: 984 helix: 2.38 (0.35), residues: 219 sheet: 0.29 (0.27), residues: 354 loop : -0.83 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 315 TYR 0.013 0.001 TYR B 98 PHE 0.010 0.001 PHE C 210 TRP 0.009 0.001 TRP A 175 HIS 0.005 0.001 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8118) covalent geometry : angle 0.49101 (11058) SS BOND : bond 0.00261 ( 15) SS BOND : angle 0.66170 ( 30) hydrogen bonds : bond 0.03477 ( 300) hydrogen bonds : angle 5.00412 ( 834) link_NAG-ASN : bond 0.00807 ( 9) link_NAG-ASN : angle 2.51881 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.233 Fit side-chains REVERT: A 45 TYR cc_start: 0.6109 (OUTLIER) cc_final: 0.5469 (m-80) REVERT: A 127 GLU cc_start: 0.8761 (tp30) cc_final: 0.8505 (tp30) REVERT: A 191 MET cc_start: 0.8329 (mtm) cc_final: 0.8102 (mtm) REVERT: A 258 LYS cc_start: 0.8538 (mttp) cc_final: 0.8059 (mmtt) REVERT: A 284 SER cc_start: 0.8630 (m) cc_final: 0.8188 (p) REVERT: A 332 GLN cc_start: 0.6733 (mt0) cc_final: 0.6388 (mp10) REVERT: B 45 TYR cc_start: 0.6148 (OUTLIER) cc_final: 0.5432 (m-80) REVERT: B 254 GLU cc_start: 0.8748 (tt0) cc_final: 0.8380 (tm-30) REVERT: B 284 SER cc_start: 0.8664 (m) cc_final: 0.8200 (p) REVERT: B 332 GLN cc_start: 0.6957 (mt0) cc_final: 0.6574 (mp10) REVERT: C 45 TYR cc_start: 0.6029 (OUTLIER) cc_final: 0.5248 (m-80) REVERT: C 191 MET cc_start: 0.8268 (mtm) cc_final: 0.8034 (mtm) REVERT: C 254 GLU cc_start: 0.8730 (tt0) cc_final: 0.8402 (tm-30) REVERT: C 258 LYS cc_start: 0.8637 (mttp) cc_final: 0.8157 (mptt) REVERT: C 284 SER cc_start: 0.8690 (m) cc_final: 0.8220 (p) REVERT: C 292 HIS cc_start: 0.8223 (m-70) cc_final: 0.7891 (m-70) REVERT: C 332 GLN cc_start: 0.6865 (mt0) cc_final: 0.6451 (mp10) outliers start: 10 outliers final: 6 residues processed: 73 average time/residue: 0.4696 time to fit residues: 36.6828 Evaluate side-chains 65 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 45 TYR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 69 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.133204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.081125 restraints weight = 56202.200| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 6.25 r_work: 0.2710 rms_B_bonded: 5.21 restraints_weight: 2.0000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8142 Z= 0.129 Angle : 0.488 5.285 11115 Z= 0.257 Chirality : 0.046 0.205 1251 Planarity : 0.004 0.034 1368 Dihedral : 9.191 88.247 1365 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.85 % Allowed : 10.20 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.27), residues: 984 helix: 2.27 (0.35), residues: 219 sheet: 0.28 (0.27), residues: 354 loop : -0.84 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 324 TYR 0.010 0.001 TYR A 98 PHE 0.008 0.001 PHE C 301 TRP 0.008 0.001 TRP C 268 HIS 0.003 0.001 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8118) covalent geometry : angle 0.47305 (11058) SS BOND : bond 0.00287 ( 15) SS BOND : angle 0.66714 ( 30) hydrogen bonds : bond 0.03132 ( 300) hydrogen bonds : angle 4.63600 ( 834) link_NAG-ASN : bond 0.00756 ( 9) link_NAG-ASN : angle 2.46775 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 45 TYR cc_start: 0.6076 (OUTLIER) cc_final: 0.5422 (m-80) REVERT: A 89 GLU cc_start: 0.8322 (tp30) cc_final: 0.8121 (tp30) REVERT: A 127 GLU cc_start: 0.8690 (tp30) cc_final: 0.8369 (tp30) REVERT: A 191 MET cc_start: 0.8103 (mtm) cc_final: 0.7813 (mtm) REVERT: A 254 GLU cc_start: 0.8528 (tt0) cc_final: 0.8163 (tm-30) REVERT: A 258 LYS cc_start: 0.8316 (mttp) cc_final: 0.7833 (mmtt) REVERT: A 332 GLN cc_start: 0.6489 (mt0) cc_final: 0.6217 (mp10) REVERT: B 45 TYR cc_start: 0.6203 (OUTLIER) cc_final: 0.5527 (m-80) REVERT: B 230 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8217 (tp30) REVERT: B 254 GLU cc_start: 0.8602 (tt0) cc_final: 0.8178 (tm-30) REVERT: B 284 SER cc_start: 0.8327 (m) cc_final: 0.7754 (p) REVERT: B 332 GLN cc_start: 0.6695 (mt0) cc_final: 0.6393 (mp10) REVERT: C 45 TYR cc_start: 0.6052 (OUTLIER) cc_final: 0.5285 (m-80) REVERT: C 89 GLU cc_start: 0.8574 (tp30) cc_final: 0.7670 (tp30) REVERT: C 90 HIS cc_start: 0.8759 (t70) cc_final: 0.8493 (m90) REVERT: C 191 MET cc_start: 0.7996 (mtm) cc_final: 0.7670 (mtm) REVERT: C 230 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8282 (tp30) REVERT: C 254 GLU cc_start: 0.8569 (tt0) cc_final: 0.8231 (tm-30) REVERT: C 258 LYS cc_start: 0.8370 (mttp) cc_final: 0.7896 (mptt) REVERT: C 284 SER cc_start: 0.8430 (m) cc_final: 0.7846 (p) REVERT: C 292 HIS cc_start: 0.8237 (m-70) cc_final: 0.7880 (m-70) REVERT: C 332 GLN cc_start: 0.6627 (mt0) cc_final: 0.6324 (mp10) outliers start: 18 outliers final: 8 residues processed: 70 average time/residue: 0.4760 time to fit residues: 35.6952 Evaluate side-chains 68 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 90 HIS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain C residue 45 TYR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 32 optimal weight: 40.0000 chunk 5 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 73 optimal weight: 0.0060 chunk 94 optimal weight: 4.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.133586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.082152 restraints weight = 46097.148| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 5.87 r_work: 0.2771 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8142 Z= 0.113 Angle : 0.477 8.897 11115 Z= 0.250 Chirality : 0.045 0.202 1251 Planarity : 0.004 0.035 1368 Dihedral : 8.952 89.684 1365 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.32 % Allowed : 9.73 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.27), residues: 984 helix: 2.24 (0.35), residues: 219 sheet: 0.30 (0.27), residues: 354 loop : -0.80 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 324 TYR 0.010 0.001 TYR B 98 PHE 0.007 0.001 PHE C 301 TRP 0.007 0.001 TRP C 268 HIS 0.003 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8118) covalent geometry : angle 0.46165 (11058) SS BOND : bond 0.00269 ( 15) SS BOND : angle 0.64341 ( 30) hydrogen bonds : bond 0.02861 ( 300) hydrogen bonds : angle 4.38862 ( 834) link_NAG-ASN : bond 0.00680 ( 9) link_NAG-ASN : angle 2.41408 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.247 Fit side-chains REVERT: A 45 TYR cc_start: 0.6052 (OUTLIER) cc_final: 0.5446 (m-80) REVERT: A 89 GLU cc_start: 0.8397 (tp30) cc_final: 0.8168 (tp30) REVERT: A 127 GLU cc_start: 0.8781 (tp30) cc_final: 0.8478 (tp30) REVERT: A 133 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8394 (m-40) REVERT: A 191 MET cc_start: 0.8367 (mtm) cc_final: 0.8089 (mtm) REVERT: A 224 LYS cc_start: 0.9072 (mtpp) cc_final: 0.8790 (mttm) REVERT: A 254 GLU cc_start: 0.8664 (tt0) cc_final: 0.8306 (tm-30) REVERT: A 258 LYS cc_start: 0.8600 (mttp) cc_final: 0.8092 (mmtt) REVERT: A 332 GLN cc_start: 0.6799 (mt0) cc_final: 0.6471 (mp10) REVERT: B 45 TYR cc_start: 0.6191 (OUTLIER) cc_final: 0.5588 (m-80) REVERT: B 133 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8396 (m-40) REVERT: B 224 LYS cc_start: 0.9167 (mtpm) cc_final: 0.8861 (mtmm) REVERT: B 230 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8268 (tp30) REVERT: B 254 GLU cc_start: 0.8739 (tt0) cc_final: 0.8347 (tm-30) REVERT: B 332 GLN cc_start: 0.6945 (mt0) cc_final: 0.6590 (mp10) REVERT: C 45 TYR cc_start: 0.6150 (OUTLIER) cc_final: 0.5429 (m-80) REVERT: C 133 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8313 (m-40) REVERT: C 191 MET cc_start: 0.8287 (mtm) cc_final: 0.7976 (mtm) REVERT: C 230 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8300 (tp30) REVERT: C 254 GLU cc_start: 0.8711 (tt0) cc_final: 0.8372 (tm-30) REVERT: C 258 LYS cc_start: 0.8583 (mttp) cc_final: 0.8099 (mptt) REVERT: C 292 HIS cc_start: 0.8237 (m-70) cc_final: 0.7913 (m-70) outliers start: 22 outliers final: 7 residues processed: 72 average time/residue: 0.5030 time to fit residues: 38.5692 Evaluate side-chains 67 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 90 HIS Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 45 TYR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 337 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 85 optimal weight: 0.0060 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.133009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.081306 restraints weight = 41075.942| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 5.67 r_work: 0.2696 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8142 Z= 0.137 Angle : 0.491 7.863 11115 Z= 0.255 Chirality : 0.046 0.193 1251 Planarity : 0.004 0.033 1368 Dihedral : 8.883 89.397 1364 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.86 % Favored : 98.03 % Rotamer: Outliers : 3.32 % Allowed : 10.20 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.27), residues: 984 helix: 2.25 (0.35), residues: 219 sheet: 0.29 (0.27), residues: 354 loop : -0.78 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 324 TYR 0.009 0.001 TYR B 98 PHE 0.008 0.001 PHE C 301 TRP 0.008 0.001 TRP C 268 HIS 0.004 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8118) covalent geometry : angle 0.47746 (11058) SS BOND : bond 0.00301 ( 15) SS BOND : angle 0.65982 ( 30) hydrogen bonds : bond 0.02848 ( 300) hydrogen bonds : angle 4.32613 ( 834) link_NAG-ASN : bond 0.00639 ( 9) link_NAG-ASN : angle 2.34336 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.222 Fit side-chains REVERT: A 45 TYR cc_start: 0.6128 (OUTLIER) cc_final: 0.5440 (m-80) REVERT: A 89 GLU cc_start: 0.8472 (tp30) cc_final: 0.8184 (tp30) REVERT: A 90 HIS cc_start: 0.8609 (OUTLIER) cc_final: 0.8208 (m-70) REVERT: A 127 GLU cc_start: 0.8731 (tp30) cc_final: 0.8386 (tp30) REVERT: A 133 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.8384 (m-40) REVERT: A 191 MET cc_start: 0.8181 (mtm) cc_final: 0.7870 (mtm) REVERT: A 224 LYS cc_start: 0.9045 (mtpp) cc_final: 0.8757 (mttm) REVERT: A 254 GLU cc_start: 0.8598 (tt0) cc_final: 0.8233 (tm-30) REVERT: A 258 LYS cc_start: 0.8476 (mttp) cc_final: 0.7980 (mmtt) REVERT: B 45 TYR cc_start: 0.6293 (OUTLIER) cc_final: 0.5602 (m-80) REVERT: B 133 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8352 (m-40) REVERT: B 224 LYS cc_start: 0.9134 (mtpm) cc_final: 0.8827 (mtmm) REVERT: B 230 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8263 (tp30) REVERT: B 254 GLU cc_start: 0.8666 (tt0) cc_final: 0.8230 (tm-30) REVERT: B 332 GLN cc_start: 0.6704 (mt0) cc_final: 0.6442 (mp10) REVERT: C 89 GLU cc_start: 0.8538 (tp30) cc_final: 0.7906 (tp30) REVERT: C 133 ASN cc_start: 0.8649 (OUTLIER) cc_final: 0.8278 (m-40) REVERT: C 191 MET cc_start: 0.8103 (mtm) cc_final: 0.7774 (mtm) REVERT: C 230 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8301 (tp30) REVERT: C 254 GLU cc_start: 0.8624 (tt0) cc_final: 0.8263 (tm-30) REVERT: C 292 HIS cc_start: 0.8239 (m-70) cc_final: 0.7911 (m-70) outliers start: 22 outliers final: 8 residues processed: 71 average time/residue: 0.4960 time to fit residues: 37.8864 Evaluate side-chains 70 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 90 HIS Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 45 TYR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 77 optimal weight: 0.8980 chunk 73 optimal weight: 0.0170 chunk 90 optimal weight: 2.9990 chunk 32 optimal weight: 40.0000 chunk 83 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.133415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.081270 restraints weight = 55300.263| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 6.25 r_work: 0.2770 rms_B_bonded: 5.05 restraints_weight: 2.0000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8142 Z= 0.118 Angle : 0.489 7.417 11115 Z= 0.249 Chirality : 0.046 0.192 1251 Planarity : 0.004 0.036 1368 Dihedral : 8.697 86.891 1364 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.20 % Allowed : 10.56 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.27), residues: 984 helix: 2.84 (0.34), residues: 201 sheet: 0.32 (0.27), residues: 354 loop : -0.57 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 324 TYR 0.010 0.001 TYR A 98 PHE 0.007 0.001 PHE C 301 TRP 0.008 0.001 TRP B 93 HIS 0.004 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8118) covalent geometry : angle 0.47581 (11058) SS BOND : bond 0.00268 ( 15) SS BOND : angle 0.64359 ( 30) hydrogen bonds : bond 0.02744 ( 300) hydrogen bonds : angle 4.21218 ( 834) link_NAG-ASN : bond 0.00651 ( 9) link_NAG-ASN : angle 2.28478 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.186 Fit side-chains REVERT: A 45 TYR cc_start: 0.6202 (OUTLIER) cc_final: 0.5541 (m-80) REVERT: A 89 GLU cc_start: 0.8534 (tp30) cc_final: 0.8242 (tp30) REVERT: A 127 GLU cc_start: 0.8813 (tp30) cc_final: 0.8487 (tp30) REVERT: A 133 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8459 (m-40) REVERT: A 191 MET cc_start: 0.8382 (mtm) cc_final: 0.8076 (mtm) REVERT: A 224 LYS cc_start: 0.9080 (mtpp) cc_final: 0.8806 (mttm) REVERT: A 254 GLU cc_start: 0.8642 (tt0) cc_final: 0.8305 (tm-30) REVERT: A 258 LYS cc_start: 0.8626 (mttp) cc_final: 0.8104 (mmtt) REVERT: B 45 TYR cc_start: 0.6313 (OUTLIER) cc_final: 0.5620 (m-80) REVERT: B 133 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8428 (m-40) REVERT: B 224 LYS cc_start: 0.9182 (mtpm) cc_final: 0.8883 (mtmm) REVERT: B 230 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: B 254 GLU cc_start: 0.8725 (tt0) cc_final: 0.8334 (tm-30) REVERT: B 332 GLN cc_start: 0.6931 (mt0) cc_final: 0.6607 (mp10) REVERT: C 89 GLU cc_start: 0.8181 (tp30) cc_final: 0.7799 (tp30) REVERT: C 90 HIS cc_start: 0.8488 (OUTLIER) cc_final: 0.8086 (m-70) REVERT: C 133 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8351 (m-40) REVERT: C 191 MET cc_start: 0.8267 (mtm) cc_final: 0.7950 (mtm) REVERT: C 230 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8321 (tp30) REVERT: C 254 GLU cc_start: 0.8715 (tt0) cc_final: 0.8321 (tm-30) REVERT: C 292 HIS cc_start: 0.8224 (m-70) cc_final: 0.7912 (m-70) outliers start: 21 outliers final: 10 residues processed: 72 average time/residue: 0.4635 time to fit residues: 35.6484 Evaluate side-chains 72 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 45 TYR Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 15 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 85 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.133543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.081165 restraints weight = 61810.616| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 6.46 r_work: 0.2717 rms_B_bonded: 5.31 restraints_weight: 2.0000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8142 Z= 0.121 Angle : 0.495 8.029 11115 Z= 0.252 Chirality : 0.046 0.235 1251 Planarity : 0.004 0.035 1368 Dihedral : 8.674 86.632 1364 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.08 % Allowed : 10.91 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.27), residues: 984 helix: 2.71 (0.34), residues: 201 sheet: 0.35 (0.27), residues: 354 loop : -0.56 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 324 TYR 0.010 0.001 TYR A 98 PHE 0.007 0.001 PHE A 301 TRP 0.007 0.001 TRP C 268 HIS 0.004 0.001 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8118) covalent geometry : angle 0.48158 (11058) SS BOND : bond 0.00270 ( 15) SS BOND : angle 0.65297 ( 30) hydrogen bonds : bond 0.02734 ( 300) hydrogen bonds : angle 4.18937 ( 834) link_NAG-ASN : bond 0.00680 ( 9) link_NAG-ASN : angle 2.29592 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.279 Fit side-chains REVERT: A 45 TYR cc_start: 0.6278 (OUTLIER) cc_final: 0.5650 (m-80) REVERT: A 89 GLU cc_start: 0.8553 (tp30) cc_final: 0.8219 (tp30) REVERT: A 127 GLU cc_start: 0.8708 (tp30) cc_final: 0.8345 (tp30) REVERT: A 133 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8384 (m-40) REVERT: A 191 MET cc_start: 0.8034 (mtm) cc_final: 0.7718 (mtm) REVERT: A 224 LYS cc_start: 0.9004 (mtpp) cc_final: 0.8740 (mttm) REVERT: A 254 GLU cc_start: 0.8519 (tt0) cc_final: 0.8152 (tm-30) REVERT: A 258 LYS cc_start: 0.8392 (mttp) cc_final: 0.7888 (mmtt) REVERT: B 45 TYR cc_start: 0.6332 (OUTLIER) cc_final: 0.5655 (m-80) REVERT: B 132 HIS cc_start: 0.8507 (t70) cc_final: 0.8302 (t-90) REVERT: B 133 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8331 (m-40) REVERT: B 224 LYS cc_start: 0.9115 (mtpm) cc_final: 0.8819 (mtmm) REVERT: B 230 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7875 (mp0) REVERT: B 254 GLU cc_start: 0.8598 (tt0) cc_final: 0.8176 (tm-30) REVERT: B 332 GLN cc_start: 0.6625 (mt0) cc_final: 0.6387 (mp10) REVERT: C 89 GLU cc_start: 0.8215 (tp30) cc_final: 0.7821 (tp30) REVERT: C 90 HIS cc_start: 0.8501 (OUTLIER) cc_final: 0.8109 (m-70) REVERT: C 133 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.8256 (m-40) REVERT: C 191 MET cc_start: 0.7944 (mtm) cc_final: 0.7602 (mtm) REVERT: C 230 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8302 (tp30) REVERT: C 254 GLU cc_start: 0.8561 (tt0) cc_final: 0.8155 (tm-30) REVERT: C 292 HIS cc_start: 0.8233 (m-70) cc_final: 0.7907 (m-70) outliers start: 20 outliers final: 10 residues processed: 69 average time/residue: 0.4640 time to fit residues: 34.2477 Evaluate side-chains 73 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 45 TYR Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 68 optimal weight: 0.4980 chunk 41 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 64 optimal weight: 40.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.132677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.080312 restraints weight = 52353.159| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 6.13 r_work: 0.2705 rms_B_bonded: 5.13 restraints_weight: 2.0000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8142 Z= 0.164 Angle : 0.519 8.844 11115 Z= 0.263 Chirality : 0.047 0.186 1251 Planarity : 0.004 0.034 1368 Dihedral : 8.844 87.350 1364 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.20 % Allowed : 11.03 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.27), residues: 984 helix: 2.66 (0.34), residues: 201 sheet: 0.64 (0.27), residues: 336 loop : -0.66 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 302 TYR 0.011 0.001 TYR A 98 PHE 0.009 0.001 PHE C 301 TRP 0.009 0.001 TRP C 268 HIS 0.004 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8118) covalent geometry : angle 0.50704 (11058) SS BOND : bond 0.00329 ( 15) SS BOND : angle 0.69151 ( 30) hydrogen bonds : bond 0.02874 ( 300) hydrogen bonds : angle 4.32020 ( 834) link_NAG-ASN : bond 0.00597 ( 9) link_NAG-ASN : angle 2.28227 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.291 Fit side-chains REVERT: A 45 TYR cc_start: 0.6262 (OUTLIER) cc_final: 0.5635 (m-80) REVERT: A 89 GLU cc_start: 0.8568 (tp30) cc_final: 0.8255 (tp30) REVERT: A 127 GLU cc_start: 0.8743 (tp30) cc_final: 0.8376 (tp30) REVERT: A 133 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8412 (m-40) REVERT: A 191 MET cc_start: 0.8098 (mtm) cc_final: 0.7823 (mtm) REVERT: A 224 LYS cc_start: 0.9015 (mtpp) cc_final: 0.8744 (mttm) REVERT: A 254 GLU cc_start: 0.8498 (tt0) cc_final: 0.8120 (tm-30) REVERT: A 258 LYS cc_start: 0.8419 (mttp) cc_final: 0.7911 (mmtt) REVERT: B 45 TYR cc_start: 0.6307 (OUTLIER) cc_final: 0.5655 (m-80) REVERT: B 54 LEU cc_start: 0.7842 (tm) cc_final: 0.7594 (pp) REVERT: B 80 THR cc_start: 0.9186 (m) cc_final: 0.8843 (p) REVERT: B 133 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8350 (m-40) REVERT: B 224 LYS cc_start: 0.9112 (mtpm) cc_final: 0.8822 (mtmm) REVERT: B 230 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: B 254 GLU cc_start: 0.8616 (tt0) cc_final: 0.8196 (tm-30) REVERT: C 89 GLU cc_start: 0.8290 (tp30) cc_final: 0.7918 (tp30) REVERT: C 90 HIS cc_start: 0.8492 (OUTLIER) cc_final: 0.8072 (m-70) REVERT: C 133 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.8261 (m-40) REVERT: C 149 MET cc_start: 0.8813 (mmm) cc_final: 0.8564 (tpt) REVERT: C 191 MET cc_start: 0.8001 (mtm) cc_final: 0.7647 (mtm) REVERT: C 230 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8275 (tp30) REVERT: C 254 GLU cc_start: 0.8532 (tt0) cc_final: 0.8151 (tm-30) REVERT: C 292 HIS cc_start: 0.8207 (m-70) cc_final: 0.7885 (m-70) outliers start: 21 outliers final: 10 residues processed: 72 average time/residue: 0.4261 time to fit residues: 33.0385 Evaluate side-chains 75 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 45 TYR Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 45 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 13 optimal weight: 0.1980 chunk 53 optimal weight: 0.0270 chunk 23 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 32 optimal weight: 40.0000 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.133112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.080770 restraints weight = 58417.737| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 6.33 r_work: 0.2739 rms_B_bonded: 5.26 restraints_weight: 2.0000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8142 Z= 0.100 Angle : 0.500 8.809 11115 Z= 0.250 Chirality : 0.046 0.188 1251 Planarity : 0.004 0.036 1368 Dihedral : 8.499 84.985 1364 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.61 % Allowed : 11.74 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.27), residues: 984 helix: 2.63 (0.34), residues: 201 sheet: 0.40 (0.27), residues: 354 loop : -0.59 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 302 TYR 0.011 0.001 TYR A 98 PHE 0.016 0.001 PHE C 336 TRP 0.009 0.001 TRP B 93 HIS 0.004 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 8118) covalent geometry : angle 0.48809 (11058) SS BOND : bond 0.00238 ( 15) SS BOND : angle 0.65132 ( 30) hydrogen bonds : bond 0.02689 ( 300) hydrogen bonds : angle 4.12664 ( 834) link_NAG-ASN : bond 0.00668 ( 9) link_NAG-ASN : angle 2.25191 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.228 Fit side-chains REVERT: A 45 TYR cc_start: 0.6291 (OUTLIER) cc_final: 0.5646 (m-80) REVERT: A 54 LEU cc_start: 0.7977 (tm) cc_final: 0.7672 (pp) REVERT: A 89 GLU cc_start: 0.8551 (tp30) cc_final: 0.8209 (tp30) REVERT: A 127 GLU cc_start: 0.8740 (tp30) cc_final: 0.8369 (tp30) REVERT: A 133 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8379 (m-40) REVERT: A 191 MET cc_start: 0.8061 (mtm) cc_final: 0.7741 (mtm) REVERT: A 224 LYS cc_start: 0.9010 (mtpp) cc_final: 0.8678 (mttm) REVERT: A 254 GLU cc_start: 0.8508 (tt0) cc_final: 0.8128 (tm-30) REVERT: A 258 LYS cc_start: 0.8467 (mttp) cc_final: 0.7931 (mmtt) REVERT: B 45 TYR cc_start: 0.6298 (OUTLIER) cc_final: 0.5677 (m-80) REVERT: B 54 LEU cc_start: 0.7810 (tm) cc_final: 0.7567 (pp) REVERT: B 133 ASN cc_start: 0.8640 (OUTLIER) cc_final: 0.8310 (m-40) REVERT: B 164 GLN cc_start: 0.8318 (pm20) cc_final: 0.7958 (pm20) REVERT: B 224 LYS cc_start: 0.9136 (mtpm) cc_final: 0.8799 (mtmm) REVERT: B 254 GLU cc_start: 0.8626 (tt0) cc_final: 0.8205 (tm-30) REVERT: B 332 GLN cc_start: 0.6647 (mt0) cc_final: 0.6380 (mp10) REVERT: C 45 TYR cc_start: 0.6316 (OUTLIER) cc_final: 0.5557 (m-80) REVERT: C 54 LEU cc_start: 0.7992 (tm) cc_final: 0.7684 (pp) REVERT: C 89 GLU cc_start: 0.8290 (tp30) cc_final: 0.7929 (tp30) REVERT: C 90 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.8039 (m-70) REVERT: C 132 HIS cc_start: 0.8511 (t70) cc_final: 0.8290 (t-90) REVERT: C 133 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.8228 (m-40) REVERT: C 149 MET cc_start: 0.8825 (mmm) cc_final: 0.8582 (mmt) REVERT: C 191 MET cc_start: 0.8002 (mtm) cc_final: 0.7654 (mtm) REVERT: C 254 GLU cc_start: 0.8594 (tt0) cc_final: 0.8190 (tm-30) REVERT: C 292 HIS cc_start: 0.8229 (m-70) cc_final: 0.7912 (m-70) outliers start: 16 outliers final: 7 residues processed: 66 average time/residue: 0.4536 time to fit residues: 32.1925 Evaluate side-chains 68 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain C residue 45 TYR Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 71 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 chunk 92 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS B 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.134014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.082163 restraints weight = 43983.826| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 5.84 r_work: 0.2792 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8142 Z= 0.123 Angle : 0.503 8.724 11115 Z= 0.254 Chirality : 0.046 0.194 1251 Planarity : 0.004 0.036 1368 Dihedral : 8.524 85.893 1364 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.37 % Allowed : 11.98 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.27), residues: 984 helix: 2.61 (0.35), residues: 201 sheet: 0.38 (0.27), residues: 354 loop : -0.58 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 324 TYR 0.010 0.001 TYR A 98 PHE 0.007 0.001 PHE A 301 TRP 0.008 0.001 TRP C 268 HIS 0.005 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8118) covalent geometry : angle 0.49124 (11058) SS BOND : bond 0.00268 ( 15) SS BOND : angle 0.65380 ( 30) hydrogen bonds : bond 0.02736 ( 300) hydrogen bonds : angle 4.13710 ( 834) link_NAG-ASN : bond 0.00615 ( 9) link_NAG-ASN : angle 2.23665 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.215 Fit side-chains REVERT: A 45 TYR cc_start: 0.6284 (OUTLIER) cc_final: 0.5650 (m-80) REVERT: A 54 LEU cc_start: 0.7960 (tm) cc_final: 0.7745 (pp) REVERT: A 127 GLU cc_start: 0.8805 (tp30) cc_final: 0.8452 (tp30) REVERT: A 133 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8429 (m-40) REVERT: A 191 MET cc_start: 0.8313 (mtm) cc_final: 0.8005 (mtm) REVERT: A 224 LYS cc_start: 0.9066 (mtpp) cc_final: 0.8790 (mttm) REVERT: A 254 GLU cc_start: 0.8594 (tt0) cc_final: 0.8217 (tm-30) REVERT: A 258 LYS cc_start: 0.8603 (mttp) cc_final: 0.8066 (mmtt) REVERT: B 45 TYR cc_start: 0.6286 (OUTLIER) cc_final: 0.5670 (m-80) REVERT: B 132 HIS cc_start: 0.8845 (t70) cc_final: 0.8304 (t70) REVERT: B 133 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8348 (m-40) REVERT: B 164 GLN cc_start: 0.8439 (pm20) cc_final: 0.8056 (pm20) REVERT: B 224 LYS cc_start: 0.9168 (mtpm) cc_final: 0.8836 (mtmm) REVERT: B 254 GLU cc_start: 0.8703 (tt0) cc_final: 0.8307 (tm-30) REVERT: B 332 GLN cc_start: 0.6866 (mt0) cc_final: 0.6562 (mp10) REVERT: C 45 TYR cc_start: 0.6277 (OUTLIER) cc_final: 0.5550 (m-80) REVERT: C 54 LEU cc_start: 0.8004 (tm) cc_final: 0.7694 (pp) REVERT: C 89 GLU cc_start: 0.8300 (tp30) cc_final: 0.7950 (tp30) REVERT: C 90 HIS cc_start: 0.8438 (OUTLIER) cc_final: 0.7978 (m-70) REVERT: C 133 ASN cc_start: 0.8630 (OUTLIER) cc_final: 0.8324 (m-40) REVERT: C 191 MET cc_start: 0.8221 (mtm) cc_final: 0.7883 (mtm) REVERT: C 254 GLU cc_start: 0.8646 (tt0) cc_final: 0.8258 (tm-30) REVERT: C 292 HIS cc_start: 0.8208 (m-70) cc_final: 0.7908 (m-70) outliers start: 14 outliers final: 6 residues processed: 64 average time/residue: 0.4436 time to fit residues: 30.5961 Evaluate side-chains 68 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain C residue 45 TYR Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 chunk 47 optimal weight: 0.6980 chunk 16 optimal weight: 0.0980 chunk 79 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 56 optimal weight: 0.8980 chunk 32 optimal weight: 40.0000 chunk 26 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS C 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.133272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.081210 restraints weight = 50609.142| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 6.08 r_work: 0.2804 rms_B_bonded: 5.00 restraints_weight: 2.0000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8142 Z= 0.099 Angle : 0.506 12.186 11115 Z= 0.249 Chirality : 0.045 0.197 1251 Planarity : 0.004 0.036 1368 Dihedral : 8.331 84.940 1364 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.37 % Allowed : 11.98 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.27), residues: 984 helix: 2.71 (0.35), residues: 198 sheet: 0.39 (0.27), residues: 354 loop : -0.60 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 315 TYR 0.011 0.001 TYR A 98 PHE 0.018 0.001 PHE C 336 TRP 0.007 0.001 TRP A 93 HIS 0.005 0.000 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 8118) covalent geometry : angle 0.49479 (11058) SS BOND : bond 0.00230 ( 15) SS BOND : angle 0.63748 ( 30) hydrogen bonds : bond 0.02623 ( 300) hydrogen bonds : angle 4.03883 ( 834) link_NAG-ASN : bond 0.00648 ( 9) link_NAG-ASN : angle 2.17453 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2906.83 seconds wall clock time: 50 minutes 17.31 seconds (3017.31 seconds total)