Starting phenix.real_space_refine on Fri Jul 3 13:13:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pm4_13520/07_2026/7pm4_13520.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pm4_13520/07_2026/7pm4_13520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pm4_13520/07_2026/7pm4_13520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pm4_13520/07_2026/7pm4_13520.map" model { file = "/net/cci-nas-00/data/ceres_data/7pm4_13520/07_2026/7pm4_13520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pm4_13520/07_2026/7pm4_13520.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7pm4_13520/07_2026/7pm4_13520.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pm4_13520/07_2026/7pm4_13520.cif" } resolution = 2.49 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= 0.002 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 9276 2.51 5 N 2340 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14288 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3533 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 30, 'TRANS': 400} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'DFU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Restraints were copied for chains: B, C, D Time building chain proxies: 3.02, per 1000 atoms: 0.21 Number of scatterers: 14288 At special positions: 0 Unit cell: (159.408, 113.488, 59.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 2632 8.00 N 2340 7.00 C 9276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS D 266 " - pdb=" SG CYS D 274 " 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 236 " " NAG B 501 " - " ASN B 236 " " NAG C 501 " - " ASN C 236 " " NAG D 501 " - " ASN D 236 " Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 662.6 milliseconds 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3200 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 12 sheets defined 36.0% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 35 through 40 Processing helix chain 'A' and resid 45 through 52 removed outlier: 4.197A pdb=" N ASP A 49 " --> pdb=" O PRO A 45 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 71 through 77 Processing helix chain 'A' and resid 81 through 92 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 100 through 105 removed outlier: 4.476A pdb=" N GLN A 104 " --> pdb=" O ASP A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 158 through 169 Processing helix chain 'A' and resid 185 through 194 Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'A' and resid 343 through 361 removed outlier: 3.668A pdb=" N ILE A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'B' and resid 35 through 40 Processing helix chain 'B' and resid 45 through 52 removed outlier: 4.197A pdb=" N ASP B 49 " --> pdb=" O PRO B 45 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 64 Processing helix chain 'B' and resid 71 through 77 Processing helix chain 'B' and resid 81 through 92 Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 100 through 105 removed outlier: 4.476A pdb=" N GLN B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 122 Processing helix chain 'B' and resid 158 through 169 Processing helix chain 'B' and resid 185 through 194 Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 312 through 326 Processing helix chain 'B' and resid 343 through 361 removed outlier: 3.668A pdb=" N ILE B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'C' and resid 35 through 40 Processing helix chain 'C' and resid 45 through 52 removed outlier: 4.197A pdb=" N ASP C 49 " --> pdb=" O PRO C 45 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS C 52 " --> pdb=" O PHE C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 64 Processing helix chain 'C' and resid 71 through 77 Processing helix chain 'C' and resid 81 through 92 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 100 through 105 removed outlier: 4.476A pdb=" N GLN C 104 " --> pdb=" O ASP C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 122 Processing helix chain 'C' and resid 158 through 169 Processing helix chain 'C' and resid 185 through 194 Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 205 through 216 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 236 through 247 Processing helix chain 'C' and resid 312 through 326 Processing helix chain 'C' and resid 343 through 361 removed outlier: 3.668A pdb=" N ILE C 359 " --> pdb=" O LYS C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'D' and resid 35 through 40 Processing helix chain 'D' and resid 45 through 52 removed outlier: 4.197A pdb=" N ASP D 49 " --> pdb=" O PRO D 45 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS D 52 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 64 Processing helix chain 'D' and resid 71 through 77 Processing helix chain 'D' and resid 81 through 92 Processing helix chain 'D' and resid 97 through 99 No H-bonds generated for 'chain 'D' and resid 97 through 99' Processing helix chain 'D' and resid 100 through 105 removed outlier: 4.476A pdb=" N GLN D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 122 Processing helix chain 'D' and resid 158 through 169 Processing helix chain 'D' and resid 185 through 194 Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 236 through 247 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'D' and resid 343 through 361 removed outlier: 3.668A pdb=" N ILE D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing sheet with id=AA1, first strand: chain 'A' and resid 255 through 256 removed outlier: 6.314A pdb=" N VAL A 127 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR A 177 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU A 129 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N SER A 179 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N THR A 131 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR A 126 " --> pdb=" O PHE A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 368 through 374 removed outlier: 4.258A pdb=" N TRP A 370 " --> pdb=" O TYR A 383 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N TYR A 383 " --> pdb=" O TRP A 370 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N VAL A 372 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N VAL A 381 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL A 460 " --> pdb=" O THR A 413 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N THR A 413 " --> pdb=" O VAL A 460 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 402 through 405 removed outlier: 4.371A pdb=" N LYS A 426 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 255 through 256 removed outlier: 6.314A pdb=" N VAL B 127 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR B 177 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU B 129 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N SER B 179 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N THR B 131 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR B 126 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 368 through 374 removed outlier: 4.258A pdb=" N TRP B 370 " --> pdb=" O TYR B 383 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N TYR B 383 " --> pdb=" O TRP B 370 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N VAL B 372 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N VAL B 381 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL B 460 " --> pdb=" O THR B 413 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N THR B 413 " --> pdb=" O VAL B 460 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 402 through 405 removed outlier: 4.371A pdb=" N LYS B 426 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 255 through 256 removed outlier: 6.314A pdb=" N VAL C 127 " --> pdb=" O GLY C 175 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR C 177 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU C 129 " --> pdb=" O TYR C 177 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N SER C 179 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N THR C 131 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR C 126 " --> pdb=" O PHE C 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 368 through 374 removed outlier: 4.258A pdb=" N TRP C 370 " --> pdb=" O TYR C 383 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N TYR C 383 " --> pdb=" O TRP C 370 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N VAL C 372 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N VAL C 381 " --> pdb=" O VAL C 372 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL C 460 " --> pdb=" O THR C 413 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N THR C 413 " --> pdb=" O VAL C 460 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 402 through 405 removed outlier: 4.371A pdb=" N LYS C 426 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 255 through 256 removed outlier: 6.314A pdb=" N VAL D 127 " --> pdb=" O GLY D 175 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR D 177 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU D 129 " --> pdb=" O TYR D 177 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N SER D 179 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N THR D 131 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR D 126 " --> pdb=" O PHE D 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 368 through 374 removed outlier: 4.258A pdb=" N TRP D 370 " --> pdb=" O TYR D 383 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N TYR D 383 " --> pdb=" O TRP D 370 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N VAL D 372 " --> pdb=" O VAL D 381 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N VAL D 381 " --> pdb=" O VAL D 372 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL D 460 " --> pdb=" O THR D 413 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N THR D 413 " --> pdb=" O VAL D 460 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 402 through 405 removed outlier: 4.371A pdb=" N LYS D 426 " --> pdb=" O SER D 438 " (cutoff:3.500A) 508 hydrogen bonds defined for protein. 1440 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4368 1.34 - 1.46: 4052 1.46 - 1.58: 6300 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 14780 Sorted by residual: bond pdb=" C1 DFU A 502 " pdb=" N5 DFU A 502 " ideal model delta sigma weight residual 1.459 1.503 -0.044 2.00e-02 2.50e+03 4.74e+00 bond pdb=" C1 DFU D 502 " pdb=" N5 DFU D 502 " ideal model delta sigma weight residual 1.459 1.503 -0.044 2.00e-02 2.50e+03 4.74e+00 bond pdb=" C1 DFU B 502 " pdb=" N5 DFU B 502 " ideal model delta sigma weight residual 1.459 1.503 -0.044 2.00e-02 2.50e+03 4.74e+00 bond pdb=" C1 DFU C 502 " pdb=" N5 DFU C 502 " ideal model delta sigma weight residual 1.459 1.503 -0.044 2.00e-02 2.50e+03 4.74e+00 bond pdb=" C5 DFU D 502 " pdb=" N5 DFU D 502 " ideal model delta sigma weight residual 1.465 1.500 -0.035 2.00e-02 2.50e+03 3.10e+00 ... (remaining 14775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 19740 1.38 - 2.77: 332 2.77 - 4.15: 100 4.15 - 5.54: 32 5.54 - 6.92: 16 Bond angle restraints: 20220 Sorted by residual: angle pdb=" C THR D 410 " pdb=" N THR D 411 " pdb=" CA THR D 411 " ideal model delta sigma weight residual 122.44 117.91 4.53 1.19e+00 7.06e-01 1.45e+01 angle pdb=" C THR B 410 " pdb=" N THR B 411 " pdb=" CA THR B 411 " ideal model delta sigma weight residual 122.44 117.91 4.53 1.19e+00 7.06e-01 1.45e+01 angle pdb=" C THR C 410 " pdb=" N THR C 411 " pdb=" CA THR C 411 " ideal model delta sigma weight residual 122.44 117.91 4.53 1.19e+00 7.06e-01 1.45e+01 angle pdb=" C THR A 410 " pdb=" N THR A 411 " pdb=" CA THR A 411 " ideal model delta sigma weight residual 122.44 117.91 4.53 1.19e+00 7.06e-01 1.45e+01 angle pdb=" CG LYS D 426 " pdb=" CD LYS D 426 " pdb=" CE LYS D 426 " ideal model delta sigma weight residual 111.30 117.30 -6.00 2.30e+00 1.89e-01 6.80e+00 ... (remaining 20215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 7312 17.61 - 35.21: 748 35.21 - 52.82: 220 52.82 - 70.42: 76 70.42 - 88.03: 24 Dihedral angle restraints: 8380 sinusoidal: 3384 harmonic: 4996 Sorted by residual: dihedral pdb=" CB CYS D 266 " pdb=" SG CYS D 266 " pdb=" SG CYS D 274 " pdb=" CB CYS D 274 " ideal model delta sinusoidal sigma weight residual 93.00 161.31 -68.31 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CB CYS C 266 " pdb=" SG CYS C 266 " pdb=" SG CYS C 274 " pdb=" CB CYS C 274 " ideal model delta sinusoidal sigma weight residual 93.00 161.31 -68.31 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CB CYS B 266 " pdb=" SG CYS B 266 " pdb=" SG CYS B 274 " pdb=" CB CYS B 274 " ideal model delta sinusoidal sigma weight residual 93.00 161.31 -68.31 1 1.00e+01 1.00e-02 6.05e+01 ... (remaining 8377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1172 0.029 - 0.058: 540 0.058 - 0.087: 196 0.087 - 0.115: 124 0.115 - 0.144: 20 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CA ILE C 455 " pdb=" N ILE C 455 " pdb=" C ILE C 455 " pdb=" CB ILE C 455 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA ILE B 455 " pdb=" N ILE B 455 " pdb=" C ILE B 455 " pdb=" CB ILE B 455 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA ILE A 455 " pdb=" N ILE A 455 " pdb=" C ILE A 455 " pdb=" CB ILE A 455 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 2049 not shown) Planarity restraints: 2552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 418 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.25e+00 pdb=" C MET A 418 " 0.031 2.00e-02 2.50e+03 pdb=" O MET A 418 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 419 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 418 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.25e+00 pdb=" C MET C 418 " -0.031 2.00e-02 2.50e+03 pdb=" O MET C 418 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU C 419 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 418 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.25e+00 pdb=" C MET B 418 " 0.031 2.00e-02 2.50e+03 pdb=" O MET B 418 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU B 419 " -0.010 2.00e-02 2.50e+03 ... (remaining 2549 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2536 2.77 - 3.30: 13354 3.30 - 3.83: 26460 3.83 - 4.37: 32936 4.37 - 4.90: 52980 Nonbonded interactions: 128266 Sorted by model distance: nonbonded pdb=" OG1 THR C 378 " pdb=" N THR C 379 " model vdw 2.237 3.120 nonbonded pdb=" OG1 THR D 378 " pdb=" N THR D 379 " model vdw 2.237 3.120 nonbonded pdb=" OG1 THR A 378 " pdb=" N THR A 379 " model vdw 2.237 3.120 nonbonded pdb=" OG1 THR B 378 " pdb=" N THR B 379 " model vdw 2.237 3.120 nonbonded pdb=" O SER B 445 " pdb=" OG SER B 445 " model vdw 2.253 3.040 ... (remaining 128261 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.710 Find NCS groups from input model: 0.140 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:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 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 : 0.003 0.044 14788 Z= 0.141 Angle : 0.564 6.924 20240 Z= 0.287 Chirality : 0.043 0.144 2052 Planarity : 0.004 0.034 2548 Dihedral : 16.918 88.029 5168 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.06 % Allowed : 16.22 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.21), residues: 1716 helix: 1.44 (0.23), residues: 512 sheet: 0.06 (0.29), residues: 284 loop : 0.23 (0.23), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 108 TYR 0.010 0.001 TYR D 177 PHE 0.010 0.001 PHE A 394 TRP 0.008 0.001 TRP C 223 HIS 0.002 0.000 HIS A 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (14780) covalent geometry : angle 0.56031 / 0.29 (20220) SS BOND : bond 0.00151 / 0.08 ( 4) SS BOND : angle 0.86715 / 0.52 ( 8) hydrogen bonds : bond 0.12488 / 8.05 ( 508) hydrogen bonds : angle 5.22545 / 3.78 ( 1440) link_NAG-ASN : bond 0.00357 / 0.18 ( 4) link_NAG-ASN : angle 2.48175 / 1.75 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.567 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 116 average time/residue: 0.5826 time to fit residues: 74.9833 Evaluate side-chains 108 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.0980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 ASN B 273 ASN C 273 ASN D 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.117183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.086987 restraints weight = 15886.343| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.49 r_work: 0.2803 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.0528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14788 Z= 0.109 Angle : 0.520 5.832 20240 Z= 0.269 Chirality : 0.043 0.142 2052 Planarity : 0.004 0.033 2548 Dihedral : 4.816 37.549 1940 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.86 % Allowed : 14.10 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.22), residues: 1716 helix: 1.42 (0.23), residues: 560 sheet: 0.13 (0.29), residues: 284 loop : 0.06 (0.24), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 86 TYR 0.009 0.001 TYR C 92 PHE 0.009 0.001 PHE D 96 TRP 0.008 0.001 TRP B 183 HIS 0.001 0.000 HIS B 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (14780) covalent geometry : angle 0.51824 / 0.27 (20220) SS BOND : bond 0.00183 / 0.09 ( 4) SS BOND : angle 0.65380 / 0.38 ( 8) hydrogen bonds : bond 0.03814 / 2.48 ( 508) hydrogen bonds : angle 4.56837 / 3.22 ( 1440) link_NAG-ASN : bond 0.00192 / 0.10 ( 4) link_NAG-ASN : angle 1.78279 / 1.28 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.597 Fit side-chains REVERT: A 315 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7989 (tp30) REVERT: B 315 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7993 (tp30) REVERT: C 315 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7996 (tp30) REVERT: D 315 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7990 (tp30) outliers start: 28 outliers final: 8 residues processed: 132 average time/residue: 0.5466 time to fit residues: 80.3916 Evaluate side-chains 108 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 123 optimal weight: 0.0040 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 ASN B 273 ASN C 273 ASN D 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.114233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.083780 restraints weight = 15985.282| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.49 r_work: 0.2747 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.0659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14788 Z= 0.190 Angle : 0.598 6.143 20240 Z= 0.312 Chirality : 0.047 0.146 2052 Planarity : 0.005 0.035 2548 Dihedral : 5.017 37.840 1928 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.93 % Allowed : 12.50 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.21), residues: 1716 helix: 1.20 (0.23), residues: 560 sheet: 0.11 (0.30), residues: 284 loop : -0.10 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 108 TYR 0.013 0.001 TYR C 92 PHE 0.013 0.002 PHE B 96 TRP 0.011 0.002 TRP A 260 HIS 0.002 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (14780) covalent geometry : angle 0.59422 / 0.31 (20220) SS BOND : bond 0.00439 / 0.22 ( 4) SS BOND : angle 1.03275 / 0.61 ( 8) hydrogen bonds : bond 0.04890 / 3.21 ( 508) hydrogen bonds : angle 4.83155 / 3.40 ( 1440) link_NAG-ASN : bond 0.00537 / 0.27 ( 4) link_NAG-ASN : angle 2.89499 / 2.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 88 time to evaluate : 0.606 Fit side-chains REVERT: A 315 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8020 (tp30) REVERT: B 315 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8020 (tp30) REVERT: C 315 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8031 (tp30) REVERT: D 315 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8022 (tp30) outliers start: 44 outliers final: 12 residues processed: 128 average time/residue: 0.6262 time to fit residues: 87.9169 Evaluate side-chains 104 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 73 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 0.0030 chunk 117 optimal weight: 0.6980 chunk 120 optimal weight: 6.9990 chunk 23 optimal weight: 0.0980 chunk 42 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 ASN B 273 ASN C 273 ASN D 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.117544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.087442 restraints weight = 16023.650| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.50 r_work: 0.2808 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.0692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14788 Z= 0.101 Angle : 0.506 5.809 20240 Z= 0.262 Chirality : 0.043 0.140 2052 Planarity : 0.004 0.034 2548 Dihedral : 4.438 34.201 1928 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.86 % Allowed : 13.50 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.22), residues: 1716 helix: 1.46 (0.23), residues: 560 sheet: 0.26 (0.30), residues: 284 loop : 0.04 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 86 TYR 0.009 0.001 TYR B 92 PHE 0.009 0.001 PHE D 394 TRP 0.009 0.001 TRP C 183 HIS 0.001 0.000 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (14780) covalent geometry : angle 0.50471 / 0.26 (20220) SS BOND : bond 0.00137 / 0.07 ( 4) SS BOND : angle 0.61040 / 0.36 ( 8) hydrogen bonds : bond 0.03490 / 2.27 ( 508) hydrogen bonds : angle 4.51114 / 3.16 ( 1440) link_NAG-ASN : bond 0.00116 / 0.06 ( 4) link_NAG-ASN : angle 1.74254 / 1.26 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.483 Fit side-chains REVERT: A 315 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7989 (tp30) REVERT: B 315 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7994 (tp30) REVERT: C 315 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7998 (tp30) REVERT: D 315 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7990 (tp30) outliers start: 28 outliers final: 16 residues processed: 120 average time/residue: 0.4920 time to fit residues: 66.4076 Evaluate side-chains 112 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 13 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 ASN B 273 ASN C 273 ASN D 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.114645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.084252 restraints weight = 16000.861| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.49 r_work: 0.2756 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.0674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14788 Z= 0.169 Angle : 0.576 6.103 20240 Z= 0.300 Chirality : 0.046 0.144 2052 Planarity : 0.005 0.035 2548 Dihedral : 4.848 35.967 1928 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.86 % Allowed : 14.10 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.21), residues: 1716 helix: 1.32 (0.23), residues: 560 sheet: 0.18 (0.30), residues: 284 loop : -0.08 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 108 TYR 0.012 0.001 TYR B 92 PHE 0.011 0.002 PHE A 96 TRP 0.009 0.001 TRP A 260 HIS 0.002 0.001 HIS D 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (14780) covalent geometry : angle 0.57211 / 0.30 (20220) SS BOND : bond 0.00375 / 0.19 ( 4) SS BOND : angle 1.55448 / 0.93 ( 8) hydrogen bonds : bond 0.04542 / 2.98 ( 508) hydrogen bonds : angle 4.72200 / 3.32 ( 1440) link_NAG-ASN : bond 0.00408 / 0.20 ( 4) link_NAG-ASN : angle 2.63029 / 1.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.490 Fit side-chains REVERT: A 315 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8047 (tp30) REVERT: B 315 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8051 (tp30) REVERT: C 315 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8059 (tp30) REVERT: D 315 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8052 (tp30) outliers start: 28 outliers final: 16 residues processed: 104 average time/residue: 0.4723 time to fit residues: 55.3130 Evaluate side-chains 104 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 69 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 ASN B 273 ASN C 273 ASN D 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.114537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.084313 restraints weight = 15994.629| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 1.49 r_work: 0.2758 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14788 Z= 0.163 Angle : 0.575 6.068 20240 Z= 0.299 Chirality : 0.045 0.146 2052 Planarity : 0.005 0.035 2548 Dihedral : 4.864 35.816 1928 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.39 % Allowed : 13.56 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.21), residues: 1716 helix: 1.34 (0.23), residues: 560 sheet: 0.13 (0.30), residues: 284 loop : -0.10 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 108 TYR 0.012 0.001 TYR C 92 PHE 0.011 0.002 PHE A 96 TRP 0.010 0.001 TRP B 260 HIS 0.002 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (14780) covalent geometry : angle 0.57113 / 0.30 (20220) SS BOND : bond 0.00330 / 0.17 ( 4) SS BOND : angle 1.43890 / 0.85 ( 8) hydrogen bonds : bond 0.04470 / 2.93 ( 508) hydrogen bonds : angle 4.74877 / 3.33 ( 1440) link_NAG-ASN : bond 0.00437 / 0.22 ( 4) link_NAG-ASN : angle 2.56274 / 1.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 84 time to evaluate : 0.345 Fit side-chains REVERT: A 315 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8044 (tp30) REVERT: B 315 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8037 (tp30) REVERT: C 315 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8048 (tp30) REVERT: D 315 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8043 (tp30) outliers start: 36 outliers final: 24 residues processed: 112 average time/residue: 0.4607 time to fit residues: 57.7736 Evaluate side-chains 112 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 216 SER Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 457 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 147 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 67 optimal weight: 8.9990 chunk 146 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 ASN B 273 ASN C 273 ASN D 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.115595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.085277 restraints weight = 15848.743| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.49 r_work: 0.2773 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.0680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14788 Z= 0.137 Angle : 0.550 5.980 20240 Z= 0.285 Chirality : 0.044 0.145 2052 Planarity : 0.004 0.035 2548 Dihedral : 4.704 34.741 1928 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.66 % Allowed : 13.56 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.21), residues: 1716 helix: 1.37 (0.23), residues: 560 sheet: 0.16 (0.30), residues: 284 loop : -0.04 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 86 TYR 0.011 0.001 TYR B 92 PHE 0.011 0.002 PHE C 96 TRP 0.009 0.001 TRP B 243 HIS 0.002 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (14780) covalent geometry : angle 0.54666 / 0.28 (20220) SS BOND : bond 0.00261 / 0.13 ( 4) SS BOND : angle 1.10167 / 0.65 ( 8) hydrogen bonds : bond 0.04128 / 2.70 ( 508) hydrogen bonds : angle 4.67467 / 3.28 ( 1440) link_NAG-ASN : bond 0.00307 / 0.15 ( 4) link_NAG-ASN : angle 2.31609 / 1.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 92 time to evaluate : 0.553 Fit side-chains REVERT: A 315 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8028 (tp30) REVERT: B 315 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8024 (tp30) REVERT: C 315 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8032 (tp30) REVERT: D 315 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8032 (tp30) outliers start: 40 outliers final: 24 residues processed: 124 average time/residue: 0.5794 time to fit residues: 79.6185 Evaluate side-chains 116 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 457 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 163 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.115571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.085230 restraints weight = 15920.523| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.49 r_work: 0.2772 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.0703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14788 Z= 0.139 Angle : 0.554 5.981 20240 Z= 0.287 Chirality : 0.044 0.146 2052 Planarity : 0.005 0.035 2548 Dihedral : 4.719 34.440 1928 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.39 % Allowed : 13.56 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.21), residues: 1716 helix: 1.34 (0.23), residues: 560 sheet: 0.15 (0.30), residues: 284 loop : -0.03 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 303 TYR 0.011 0.001 TYR C 92 PHE 0.011 0.002 PHE A 96 TRP 0.009 0.001 TRP D 243 HIS 0.002 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (14780) covalent geometry : angle 0.55099 / 0.29 (20220) SS BOND : bond 0.00278 / 0.14 ( 4) SS BOND : angle 1.07041 / 0.63 ( 8) hydrogen bonds : bond 0.04157 / 2.72 ( 508) hydrogen bonds : angle 4.68222 / 3.28 ( 1440) link_NAG-ASN : bond 0.00317 / 0.16 ( 4) link_NAG-ASN : angle 2.34390 / 1.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 88 time to evaluate : 0.574 Fit side-chains REVERT: A 315 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8024 (tp30) REVERT: B 315 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8024 (tp30) REVERT: C 315 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8029 (tp30) REVERT: D 315 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8028 (tp30) outliers start: 36 outliers final: 24 residues processed: 120 average time/residue: 0.4639 time to fit residues: 62.8149 Evaluate side-chains 112 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 216 SER Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 457 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 116 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 25 optimal weight: 0.0870 chunk 92 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 0.0570 chunk 89 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.117442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.087182 restraints weight = 15925.201| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.50 r_work: 0.2807 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14788 Z= 0.104 Angle : 0.515 5.787 20240 Z= 0.265 Chirality : 0.043 0.142 2052 Planarity : 0.004 0.035 2548 Dihedral : 4.404 32.247 1928 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.33 % Allowed : 14.36 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.22), residues: 1716 helix: 1.46 (0.23), residues: 560 sheet: 0.24 (0.30), residues: 284 loop : 0.07 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 86 TYR 0.008 0.001 TYR C 92 PHE 0.010 0.001 PHE B 96 TRP 0.010 0.001 TRP A 183 HIS 0.001 0.000 HIS C 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (14780) covalent geometry : angle 0.51330 / 0.26 (20220) SS BOND : bond 0.00168 / 0.08 ( 4) SS BOND : angle 0.82267 / 0.48 ( 8) hydrogen bonds : bond 0.03505 / 2.29 ( 508) hydrogen bonds : angle 4.51446 / 3.15 ( 1440) link_NAG-ASN : bond 0.00117 / 0.06 ( 4) link_NAG-ASN : angle 1.76579 / 1.28 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.589 Fit side-chains REVERT: A 315 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7993 (tp30) REVERT: B 315 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7996 (tp30) REVERT: C 315 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8000 (tp30) REVERT: D 315 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7988 (tp30) outliers start: 20 outliers final: 16 residues processed: 116 average time/residue: 0.5268 time to fit residues: 68.0722 Evaluate side-chains 116 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 164 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.115298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.084981 restraints weight = 15893.297| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.49 r_work: 0.2768 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.0712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14788 Z= 0.152 Angle : 0.568 6.032 20240 Z= 0.294 Chirality : 0.045 0.147 2052 Planarity : 0.005 0.035 2548 Dihedral : 4.742 34.049 1928 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.80 % Allowed : 14.16 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.21), residues: 1716 helix: 1.33 (0.23), residues: 560 sheet: 0.17 (0.30), residues: 284 loop : -0.01 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 303 TYR 0.011 0.001 TYR C 92 PHE 0.010 0.002 PHE C 96 TRP 0.009 0.001 TRP C 260 HIS 0.002 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (14780) covalent geometry : angle 0.56492 / 0.29 (20220) SS BOND : bond 0.00319 / 0.16 ( 4) SS BOND : angle 1.08136 / 0.64 ( 8) hydrogen bonds : bond 0.04306 / 2.83 ( 508) hydrogen bonds : angle 4.68702 / 3.29 ( 1440) link_NAG-ASN : bond 0.00347 / 0.17 ( 4) link_NAG-ASN : angle 2.44754 / 1.77 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.581 Fit side-chains REVERT: A 315 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8019 (tp30) REVERT: B 315 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8021 (tp30) REVERT: C 315 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8026 (tp30) REVERT: D 315 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8022 (tp30) outliers start: 27 outliers final: 19 residues processed: 107 average time/residue: 0.5070 time to fit residues: 60.6036 Evaluate side-chains 107 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 216 SER Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 19 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.115445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.085141 restraints weight = 15892.908| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.49 r_work: 0.2771 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.0701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14788 Z= 0.147 Angle : 0.573 7.351 20240 Z= 0.295 Chirality : 0.045 0.147 2052 Planarity : 0.005 0.035 2548 Dihedral : 4.733 34.029 1928 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.86 % Allowed : 13.56 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.21), residues: 1716 helix: 1.31 (0.23), residues: 560 sheet: 0.15 (0.30), residues: 284 loop : -0.02 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 303 TYR 0.011 0.001 TYR C 92 PHE 0.011 0.002 PHE A 96 TRP 0.009 0.001 TRP A 243 HIS 0.002 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (14780) covalent geometry : angle 0.57047 / 0.29 (20220) SS BOND : bond 0.00307 / 0.15 ( 4) SS BOND : angle 1.05610 / 0.63 ( 8) hydrogen bonds : bond 0.04232 / 2.77 ( 508) hydrogen bonds : angle 4.69961 / 3.29 ( 1440) link_NAG-ASN : bond 0.00353 / 0.18 ( 4) link_NAG-ASN : angle 2.37050 / 1.72 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4103.09 seconds wall clock time: 71 minutes 1.66 seconds (4261.66 seconds total)