Starting phenix.real_space_refine on Tue Mar 3 18:08:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gjk_51395/03_2026/9gjk_51395.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gjk_51395/03_2026/9gjk_51395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gjk_51395/03_2026/9gjk_51395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gjk_51395/03_2026/9gjk_51395.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gjk_51395/03_2026/9gjk_51395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gjk_51395/03_2026/9gjk_51395.map" } resolution = 3.3 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= 0.002 sd= 0.115 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 69 5.16 5 C 4716 2.51 5 N 1266 2.21 5 O 1526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7577 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 5103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5103 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 17, 'TRANS': 627} Chain breaks: 1 Chain: "L" Number of atoms: 2270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2270 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 16, 'TRANS': 258} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'GAL': 1, 'NDG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.50, per 1000 atoms: 0.20 Number of scatterers: 7577 At special positions: 0 Unit cell: (93.184, 92.352, 111.488, 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 69 16.00 O 1526 8.00 N 1266 7.00 C 4716 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS H 69 " - pdb=" SG CYS H 78 " distance=2.03 Simple disulfide: pdb=" SG CYS H 104 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 395 " - pdb=" SG CYS H 404 " distance=2.03 Simple disulfide: pdb=" SG CYS H 400 " - pdb=" SG CYS H 410 " distance=2.03 Simple disulfide: pdb=" SG CYS H 412 " - pdb=" SG CYS H 425 " distance=2.03 Simple disulfide: pdb=" SG CYS H 415 " - pdb=" SG CYS L 75 " distance=2.03 Simple disulfide: pdb=" SG CYS H 416 " - pdb=" SG CYS H 432 " distance=2.03 Simple disulfide: pdb=" SG CYS H 420 " - pdb=" SG CYS H 456 " distance=2.03 Simple disulfide: pdb=" SG CYS H 446 " - pdb=" SG CYS H 462 " distance=2.03 Simple disulfide: pdb=" SG CYS H 450 " - pdb=" SG CYS H 482 " distance=2.03 Simple disulfide: pdb=" SG CYS H 471 " - pdb=" SG CYS H 492 " distance=2.03 Simple disulfide: pdb=" SG CYS H 477 " - pdb=" SG CYS H 515 " distance=2.03 Simple disulfide: pdb=" SG CYS H 498 " - pdb=" SG CYS H 522 " distance=2.03 Simple disulfide: pdb=" SG CYS H 510 " - pdb=" SG CYS H 544 " distance=2.03 Simple disulfide: pdb=" SG CYS H 532 " - pdb=" SG CYS H 550 " distance=2.03 Simple disulfide: pdb=" SG CYS H 539 " - pdb=" SG CYS H 573 " distance=2.03 Simple disulfide: pdb=" SG CYS H 557 " - pdb=" SG CYS H 580 " distance=2.03 Simple disulfide: pdb=" SG CYS H 568 " - pdb=" SG CYS H 603 " distance=2.03 Simple disulfide: pdb=" SG CYS H 586 " - pdb=" SG CYS H 611 " distance=2.03 Simple disulfide: pdb=" SG CYS H 592 " - pdb=" SG CYS H 630 " distance=2.03 Simple disulfide: pdb=" SG CYS H 601 " - pdb=" SG CYS H 613 " distance=2.03 Simple disulfide: pdb=" SG CYS H 622 " - pdb=" SG CYS H 639 " distance=2.03 Simple disulfide: pdb=" SG CYS H 644 " - pdb=" SG CYS H 658 " distance=2.03 Simple disulfide: pdb=" SG CYS L 71 " - pdb=" SG CYS L 74 " distance=2.03 Simple disulfide: pdb=" SG CYS L 241 " - pdb=" SG CYS L 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 ALPHA1-2 " MAN B 4 " - " MAN B 5 " " MAN B 5 " - " MAN B 6 " ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 7 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NDG D 1 " - " GAL D 2 " NAG-ASN " NAG A 1 " - " ASN H 337 " " NAG B 1 " - " ASN H 390 " " NAG C 1 " - " ASN H 468 " " NAG H 701 " - " ASN H 95 " " NAG H 702 " - " ASN H 198 " Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 299.7 milliseconds 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1748 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 22 sheets defined 17.1% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'H' and resid 30 through 34 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.685A pdb=" N ASP H 93 " --> pdb=" O LYS H 90 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE H 94 " --> pdb=" O VAL H 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 90 through 94' Processing helix chain 'H' and resid 125 through 129 removed outlier: 3.537A pdb=" N ARG H 128 " --> pdb=" O ASP H 125 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE H 129 " --> pdb=" O GLU H 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 125 through 129' Processing helix chain 'H' and resid 188 through 199 removed outlier: 4.052A pdb=" N ILE H 192 " --> pdb=" O ASN H 188 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR H 197 " --> pdb=" O ASP H 193 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN H 198 " --> pdb=" O GLN H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 203 Processing helix chain 'H' and resid 224 through 235 removed outlier: 4.532A pdb=" N LYS H 229 " --> pdb=" O SER H 225 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N SER H 230 " --> pdb=" O THR H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 241 Processing helix chain 'H' and resid 268 through 273 Processing helix chain 'H' and resid 282 through 299 removed outlier: 3.667A pdb=" N ASP H 299 " --> pdb=" O THR H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 328 through 333 Processing helix chain 'H' and resid 334 through 336 No H-bonds generated for 'chain 'H' and resid 334 through 336' Processing helix chain 'H' and resid 350 through 358 removed outlier: 3.670A pdb=" N THR H 354 " --> pdb=" O ASP H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 363 through 365 No H-bonds generated for 'chain 'H' and resid 363 through 365' Processing helix chain 'H' and resid 375 through 391 Processing helix chain 'H' and resid 560 through 564 Processing helix chain 'H' and resid 604 through 608 Processing helix chain 'L' and resid 92 through 99 Processing helix chain 'L' and resid 111 through 115 removed outlier: 3.940A pdb=" N VAL L 115 " --> pdb=" O LYS L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 138 removed outlier: 3.620A pdb=" N GLN L 138 " --> pdb=" O ASN L 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 135 through 138' Processing helix chain 'L' and resid 197 through 201 Processing helix chain 'L' and resid 222 through 226 Processing helix chain 'L' and resid 254 through 258 removed outlier: 3.924A pdb=" N LYS L 258 " --> pdb=" O THR L 255 " (cutoff:3.500A) Processing helix chain 'L' and resid 278 through 281 Processing sheet with id=AA1, first strand: chain 'H' and resid 104 through 108 removed outlier: 3.902A pdb=" N HIS H 63 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG H 177 " --> pdb=" O PHE H 173 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N CYS H 169 " --> pdb=" O PHE H 181 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR H 152 " --> pdb=" O CYS H 169 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N MET H 171 " --> pdb=" O TYR H 150 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N TYR H 150 " --> pdb=" O MET H 171 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE H 173 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU H 148 " --> pdb=" O PHE H 173 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 256 through 262 removed outlier: 6.162A pdb=" N THR H 214 " --> pdb=" O LYS H 245 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL H 247 " --> pdb=" O THR H 214 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU H 216 " --> pdb=" O VAL H 247 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU H 249 " --> pdb=" O LEU H 216 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE H 218 " --> pdb=" O LEU H 249 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N TYR H 251 " --> pdb=" O ILE H 218 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N PHE H 220 " --> pdb=" O TYR H 251 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N LYS H 253 " --> pdb=" O PHE H 220 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N HIS H 215 " --> pdb=" O THR H 314 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE H 316 " --> pdb=" O HIS H 215 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA H 217 " --> pdb=" O ILE H 316 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU H 318 " --> pdb=" O ALA H 217 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE H 219 " --> pdb=" O LEU H 318 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLY H 313 " --> pdb=" O SER H 339 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N HIS H 341 " --> pdb=" O GLY H 313 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N MET H 315 " --> pdb=" O HIS H 341 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL H 343 " --> pdb=" O MET H 315 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL H 317 " --> pdb=" O VAL H 343 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU H 345 " --> pdb=" O VAL H 317 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N MET H 319 " --> pdb=" O LEU H 345 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N HIS H 368 " --> pdb=" O VAL H 340 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N THR H 342 " --> pdb=" O HIS H 368 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE H 370 " --> pdb=" O THR H 342 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL H 344 " --> pdb=" O PHE H 370 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 403 through 404 Processing sheet with id=AA4, first strand: chain 'H' and resid 423 through 425 Processing sheet with id=AA5, first strand: chain 'H' and resid 452 through 457 removed outlier: 6.513A pdb=" N SER H 453 " --> pdb=" O THR H 465 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS H 457 " --> pdb=" O GLY H 461 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 478 through 481 Processing sheet with id=AA7, first strand: chain 'H' and resid 512 through 515 removed outlier: 6.150A pdb=" N SER H 512 " --> pdb=" O ASP H 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 540 through 543 Processing sheet with id=AA9, first strand: chain 'H' and resid 569 through 573 Processing sheet with id=AB1, first strand: chain 'H' and resid 589 through 591 Processing sheet with id=AB2, first strand: chain 'H' and resid 601 through 602 Processing sheet with id=AB3, first strand: chain 'H' and resid 628 through 631 Processing sheet with id=AB4, first strand: chain 'H' and resid 650 through 651 removed outlier: 3.531A pdb=" N ASN H 659 " --> pdb=" O THR H 664 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR H 664 " --> pdb=" O ASN H 659 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 41 through 42 removed outlier: 6.226A pdb=" N PHE L 41 " --> pdb=" O ASN L 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'L' and resid 77 through 81 Processing sheet with id=AB7, first strand: chain 'L' and resid 83 through 84 removed outlier: 3.739A pdb=" N THR L 89 " --> pdb=" O ASN L 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 103 through 107 Processing sheet with id=AB9, first strand: chain 'L' and resid 140 through 143 removed outlier: 3.642A pdb=" N MET L 147 " --> pdb=" O ALA L 143 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 157 through 160 Processing sheet with id=AC2, first strand: chain 'L' and resid 191 through 192 Processing sheet with id=AC3, first strand: chain 'L' and resid 207 through 212 Processing sheet with id=AC4, first strand: chain 'L' and resid 240 through 244 188 hydrogen bonds defined for protein. 477 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: 1.14 Time building geometry restraints manager: 0.82 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: 2418 1.34 - 1.46: 1701 1.46 - 1.58: 3529 1.58 - 1.70: 0 1.70 - 1.81: 85 Bond restraints: 7733 Sorted by residual: bond pdb=" C2 MAN B 7 " pdb=" C3 MAN B 7 " ideal model delta sigma weight residual 1.525 1.481 0.044 2.00e-02 2.50e+03 4.79e+00 bond pdb=" C1 MAN B 7 " pdb=" C2 MAN B 7 " ideal model delta sigma weight residual 1.526 1.483 0.043 2.00e-02 2.50e+03 4.59e+00 bond pdb=" CA CYS H 573 " pdb=" CB CYS H 573 " ideal model delta sigma weight residual 1.528 1.498 0.029 1.39e-02 5.18e+03 4.46e+00 bond pdb=" C5 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.413 1.438 -0.025 2.00e-02 2.50e+03 1.58e+00 bond pdb=" C4 MAN B 7 " pdb=" C5 MAN B 7 " ideal model delta sigma weight residual 1.533 1.512 0.021 2.00e-02 2.50e+03 1.08e+00 ... (remaining 7728 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 10340 2.03 - 4.07: 102 4.07 - 6.10: 18 6.10 - 8.13: 3 8.13 - 10.16: 2 Bond angle restraints: 10465 Sorted by residual: angle pdb=" CB MET H 478 " pdb=" CG MET H 478 " pdb=" SD MET H 478 " ideal model delta sigma weight residual 112.70 122.50 -9.80 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CA LEU H 459 " pdb=" CB LEU H 459 " pdb=" CG LEU H 459 " ideal model delta sigma weight residual 116.30 126.46 -10.16 3.50e+00 8.16e-02 8.43e+00 angle pdb=" CA MET H 319 " pdb=" CB MET H 319 " pdb=" CG MET H 319 " ideal model delta sigma weight residual 114.10 119.58 -5.48 2.00e+00 2.50e-01 7.50e+00 angle pdb=" C CYS H 482 " pdb=" N ASP H 483 " pdb=" CA ASP H 483 " ideal model delta sigma weight residual 121.54 126.50 -4.96 1.91e+00 2.74e-01 6.75e+00 angle pdb=" N VAL H 600 " pdb=" CA VAL H 600 " pdb=" C VAL H 600 " ideal model delta sigma weight residual 111.62 109.60 2.02 7.90e-01 1.60e+00 6.54e+00 ... (remaining 10460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.26: 4360 19.26 - 38.51: 445 38.51 - 57.77: 98 57.77 - 77.03: 34 77.03 - 96.28: 21 Dihedral angle restraints: 4958 sinusoidal: 2233 harmonic: 2725 Sorted by residual: dihedral pdb=" CB CYS H 415 " pdb=" SG CYS H 415 " pdb=" SG CYS L 75 " pdb=" CB CYS L 75 " ideal model delta sinusoidal sigma weight residual -86.00 -166.73 80.73 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CB CYS H 622 " pdb=" SG CYS H 622 " pdb=" SG CYS H 639 " pdb=" CB CYS H 639 " ideal model delta sinusoidal sigma weight residual -86.00 -149.37 63.37 1 1.00e+01 1.00e-02 5.30e+01 dihedral pdb=" CB CYS H 601 " pdb=" SG CYS H 601 " pdb=" SG CYS H 613 " pdb=" CB CYS H 613 " ideal model delta sinusoidal sigma weight residual -86.00 -145.45 59.45 1 1.00e+01 1.00e-02 4.72e+01 ... (remaining 4955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1070 0.073 - 0.147: 107 0.147 - 0.220: 0 0.220 - 0.293: 1 0.293 - 0.367: 2 Chirality restraints: 1180 Sorted by residual: chirality pdb=" C1 MAN B 7 " pdb=" O6 BMA B 3 " pdb=" C2 MAN B 7 " pdb=" O5 MAN B 7 " both_signs ideal model delta sigma weight residual False 2.40 2.28 0.12 2.00e-02 2.50e+03 3.65e+01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN H 390 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN H 337 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 1177 not shown) Planarity restraints: 1334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " 0.106 2.00e-02 2.50e+03 8.68e-02 9.41e+01 pdb=" C7 NAG A 1 " -0.029 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " 0.080 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " -0.137 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN H 337 " 0.050 2.00e-02 2.50e+03 5.33e-02 3.55e+01 pdb=" CG ASN H 337 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN H 337 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN H 337 " -0.082 2.00e-02 2.50e+03 pdb=" C1 NAG A 1 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN H 390 " -0.038 2.00e-02 2.50e+03 4.41e-02 2.43e+01 pdb=" CG ASN H 390 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN H 390 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN H 390 " 0.074 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " -0.052 2.00e-02 2.50e+03 ... (remaining 1331 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 28 2.42 - 3.04: 4885 3.04 - 3.66: 11279 3.66 - 4.28: 16769 4.28 - 4.90: 27587 Nonbonded interactions: 60548 Sorted by model distance: nonbonded pdb=" OH TYR H 110 " pdb=" O7 NAG B 1 " model vdw 1.799 3.040 nonbonded pdb=" OD2 ASP H 334 " pdb=" O2 BMA B 3 " model vdw 2.199 3.040 nonbonded pdb=" OG SER H 45 " pdb=" OE1 GLU H 47 " model vdw 2.223 3.040 nonbonded pdb=" OG1 THR H 263 " pdb=" OD1 ASP H 265 " model vdw 2.243 3.040 nonbonded pdb=" OD1 ASN H 659 " pdb=" OG1 THR H 661 " model vdw 2.261 3.040 ... (remaining 60543 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 7.720 Find NCS groups from input model: 0.030 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5273 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 0.044 7774 Z= 0.199 Angle : 0.623 11.137 10562 Z= 0.307 Chirality : 0.045 0.367 1180 Planarity : 0.004 0.087 1329 Dihedral : 17.218 96.285 3132 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.12 % Allowed : 19.88 % Favored : 80.00 % 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: -0.27 (0.28), residues: 914 helix: 0.33 (0.61), residues: 91 sheet: -0.14 (0.36), residues: 202 loop : -0.22 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 409 TYR 0.012 0.001 TYR H 27 PHE 0.008 0.001 PHE H 181 TRP 0.008 0.001 TRP H 511 HIS 0.003 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 7733) covalent geometry : angle 0.58879 (10465) SS BOND : bond 0.00223 ( 26) SS BOND : angle 1.06710 ( 52) hydrogen bonds : bond 0.24621 ( 188) hydrogen bonds : angle 9.45951 ( 477) link_ALPHA1-2 : bond 0.00138 ( 2) link_ALPHA1-2 : angle 1.62938 ( 6) link_ALPHA1-3 : bond 0.00096 ( 1) link_ALPHA1-3 : angle 1.73069 ( 3) link_ALPHA1-6 : bond 0.01903 ( 1) link_ALPHA1-6 : angle 2.10922 ( 3) link_BETA1-4 : bond 0.01108 ( 6) link_BETA1-4 : angle 2.07095 ( 18) link_NAG-ASN : bond 0.01705 ( 5) link_NAG-ASN : angle 4.40411 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 58 MET cc_start: 0.5813 (tpp) cc_final: 0.5178 (ttm) REVERT: H 138 THR cc_start: 0.7361 (p) cc_final: 0.7105 (t) REVERT: H 155 THR cc_start: 0.7255 (t) cc_final: 0.6963 (p) REVERT: H 296 LYS cc_start: 0.7315 (mtpp) cc_final: 0.7049 (mtpp) REVERT: H 377 ASN cc_start: 0.5665 (m110) cc_final: 0.5324 (m-40) REVERT: H 444 LYS cc_start: 0.7859 (ttpt) cc_final: 0.7421 (ptpt) REVERT: H 495 LYS cc_start: 0.6085 (ptmt) cc_final: 0.5852 (pttm) REVERT: H 537 ASN cc_start: 0.5794 (p0) cc_final: 0.5404 (p0) REVERT: H 555 LYS cc_start: 0.6225 (mtpt) cc_final: 0.5653 (mtmt) REVERT: L 100 ASP cc_start: 0.6874 (m-30) cc_final: 0.6620 (m-30) REVERT: L 110 ASP cc_start: 0.7250 (t70) cc_final: 0.6890 (t0) REVERT: L 146 ARG cc_start: 0.5689 (mtt90) cc_final: 0.5484 (mtt90) REVERT: L 196 TYR cc_start: 0.6401 (m-10) cc_final: 0.6196 (m-10) REVERT: L 227 LYS cc_start: 0.6462 (mttt) cc_final: 0.6030 (mmtt) REVERT: L 258 LYS cc_start: 0.7403 (tttt) cc_final: 0.7044 (ttpp) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.1015 time to fit residues: 21.5921 Evaluate side-chains 114 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 574 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.205935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.144954 restraints weight = 8157.925| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 3.02 r_work: 0.3251 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7774 Z= 0.226 Angle : 0.708 11.562 10562 Z= 0.361 Chirality : 0.050 0.205 1180 Planarity : 0.004 0.041 1329 Dihedral : 11.611 79.872 1342 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.46 % Allowed : 17.47 % Favored : 78.07 % 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: -0.49 (0.27), residues: 914 helix: -0.28 (0.57), residues: 91 sheet: -0.15 (0.36), residues: 195 loop : -0.35 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 273 TYR 0.027 0.002 TYR H 27 PHE 0.017 0.002 PHE H 53 TRP 0.013 0.002 TRP H 511 HIS 0.003 0.001 HIS L 229 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 7733) covalent geometry : angle 0.69059 (10465) SS BOND : bond 0.00367 ( 26) SS BOND : angle 1.60421 ( 52) hydrogen bonds : bond 0.04470 ( 188) hydrogen bonds : angle 6.72695 ( 477) link_ALPHA1-2 : bond 0.00526 ( 2) link_ALPHA1-2 : angle 1.71238 ( 6) link_ALPHA1-3 : bond 0.00415 ( 1) link_ALPHA1-3 : angle 2.06425 ( 3) link_ALPHA1-6 : bond 0.00991 ( 1) link_ALPHA1-6 : angle 1.30229 ( 3) link_BETA1-4 : bond 0.00400 ( 6) link_BETA1-4 : angle 2.07110 ( 18) link_NAG-ASN : bond 0.00297 ( 5) link_NAG-ASN : angle 2.00172 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 ASP cc_start: 0.8727 (m-30) cc_final: 0.8451 (m-30) REVERT: H 359 ARG cc_start: 0.8843 (mtt-85) cc_final: 0.8586 (mtt-85) REVERT: H 377 ASN cc_start: 0.7584 (m110) cc_final: 0.7063 (m-40) REVERT: H 521 PHE cc_start: 0.7908 (m-80) cc_final: 0.7419 (m-80) REVERT: H 526 LYS cc_start: 0.7296 (tppp) cc_final: 0.6781 (mmmt) REVERT: H 555 LYS cc_start: 0.7913 (ttpt) cc_final: 0.6578 (pttm) REVERT: H 628 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6953 (mt-10) REVERT: L 91 PHE cc_start: 0.9098 (OUTLIER) cc_final: 0.8622 (m-80) REVERT: L 110 ASP cc_start: 0.8052 (t70) cc_final: 0.7757 (t0) outliers start: 37 outliers final: 21 residues processed: 142 average time/residue: 0.0851 time to fit residues: 16.2992 Evaluate side-chains 124 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 133 ASP Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 283 ASP Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 475 VAL Chi-restraints excluded: chain H residue 491 VAL Chi-restraints excluded: chain H residue 505 SER Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain H residue 647 ASP Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 185 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 46 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 19 optimal weight: 0.1980 chunk 68 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.4295 r_free = 0.4295 target = 0.212888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.150400 restraints weight = 8096.269| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.72 r_work: 0.3305 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7774 Z= 0.152 Angle : 0.640 9.860 10562 Z= 0.324 Chirality : 0.047 0.204 1180 Planarity : 0.004 0.043 1329 Dihedral : 10.176 69.818 1342 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.98 % Allowed : 16.99 % Favored : 79.04 % 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: -0.45 (0.27), residues: 914 helix: 0.07 (0.60), residues: 85 sheet: -0.24 (0.36), residues: 197 loop : -0.33 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 273 TYR 0.021 0.001 TYR H 27 PHE 0.017 0.001 PHE H 258 TRP 0.016 0.001 TRP H 511 HIS 0.003 0.001 HIS H 215 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 7733) covalent geometry : angle 0.62162 (10465) SS BOND : bond 0.00540 ( 26) SS BOND : angle 1.54946 ( 52) hydrogen bonds : bond 0.03883 ( 188) hydrogen bonds : angle 6.12933 ( 477) link_ALPHA1-2 : bond 0.00271 ( 2) link_ALPHA1-2 : angle 1.49415 ( 6) link_ALPHA1-3 : bond 0.00717 ( 1) link_ALPHA1-3 : angle 1.33022 ( 3) link_ALPHA1-6 : bond 0.00169 ( 1) link_ALPHA1-6 : angle 1.51026 ( 3) link_BETA1-4 : bond 0.00376 ( 6) link_BETA1-4 : angle 2.20395 ( 18) link_NAG-ASN : bond 0.00242 ( 5) link_NAG-ASN : angle 1.79242 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: H 24 ASP cc_start: 0.8744 (m-30) cc_final: 0.8450 (m-30) REVERT: H 359 ARG cc_start: 0.8835 (mtt-85) cc_final: 0.8596 (mtt-85) REVERT: H 377 ASN cc_start: 0.7534 (m110) cc_final: 0.7029 (m-40) REVERT: H 526 LYS cc_start: 0.7381 (tppp) cc_final: 0.6868 (mmmt) REVERT: H 555 LYS cc_start: 0.7861 (ttpt) cc_final: 0.6713 (pttm) REVERT: H 628 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7194 (mt-10) REVERT: H 640 LYS cc_start: 0.5685 (mmtt) cc_final: 0.5219 (mmtt) REVERT: H 656 LYS cc_start: 0.6638 (mtpp) cc_final: 0.6409 (tptp) REVERT: L 91 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8637 (m-80) REVERT: L 110 ASP cc_start: 0.8128 (t70) cc_final: 0.7826 (t0) REVERT: L 260 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8390 (tp) outliers start: 33 outliers final: 20 residues processed: 139 average time/residue: 0.0863 time to fit residues: 16.4395 Evaluate side-chains 118 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 133 ASP Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 505 SER Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain H residue 647 ASP Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 260 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 53 optimal weight: 0.3980 chunk 8 optimal weight: 0.2980 chunk 1 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.209080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.159786 restraints weight = 7939.919| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 3.80 r_work: 0.3349 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7774 Z= 0.109 Angle : 0.594 10.034 10562 Z= 0.298 Chirality : 0.046 0.212 1180 Planarity : 0.003 0.044 1329 Dihedral : 8.732 59.824 1342 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.13 % Allowed : 19.76 % Favored : 77.11 % 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: -0.35 (0.27), residues: 914 helix: 0.54 (0.62), residues: 79 sheet: -0.27 (0.35), residues: 211 loop : -0.27 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 583 TYR 0.016 0.001 TYR H 27 PHE 0.014 0.001 PHE H 258 TRP 0.014 0.001 TRP H 511 HIS 0.001 0.000 HIS H 87 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7733) covalent geometry : angle 0.57548 (10465) SS BOND : bond 0.00322 ( 26) SS BOND : angle 1.38183 ( 52) hydrogen bonds : bond 0.03195 ( 188) hydrogen bonds : angle 5.83026 ( 477) link_ALPHA1-2 : bond 0.00306 ( 2) link_ALPHA1-2 : angle 1.44961 ( 6) link_ALPHA1-3 : bond 0.00904 ( 1) link_ALPHA1-3 : angle 1.49116 ( 3) link_ALPHA1-6 : bond 0.00214 ( 1) link_ALPHA1-6 : angle 1.60572 ( 3) link_BETA1-4 : bond 0.00412 ( 6) link_BETA1-4 : angle 2.22022 ( 18) link_NAG-ASN : bond 0.00272 ( 5) link_NAG-ASN : angle 1.77325 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 24 ASP cc_start: 0.8740 (m-30) cc_final: 0.8428 (m-30) REVERT: H 292 ASP cc_start: 0.8229 (t70) cc_final: 0.8029 (t70) REVERT: H 359 ARG cc_start: 0.8828 (mtt-85) cc_final: 0.8612 (mtt-85) REVERT: H 377 ASN cc_start: 0.7475 (m110) cc_final: 0.6999 (m-40) REVERT: H 439 LYS cc_start: 0.8467 (tttt) cc_final: 0.8142 (mtpt) REVERT: H 481 TYR cc_start: 0.7849 (p90) cc_final: 0.7639 (p90) REVERT: H 485 ASP cc_start: 0.6485 (OUTLIER) cc_final: 0.6042 (m-30) REVERT: H 526 LYS cc_start: 0.7493 (tppp) cc_final: 0.6903 (mmmt) REVERT: H 555 LYS cc_start: 0.8010 (ttpt) cc_final: 0.6975 (pttm) REVERT: H 628 GLU cc_start: 0.7495 (mt-10) cc_final: 0.6895 (mt-10) REVERT: H 640 LYS cc_start: 0.5672 (mmtt) cc_final: 0.5458 (mmtm) REVERT: L 91 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8643 (m-80) REVERT: L 110 ASP cc_start: 0.8114 (t70) cc_final: 0.7825 (t0) outliers start: 26 outliers final: 14 residues processed: 127 average time/residue: 0.0901 time to fit residues: 15.4413 Evaluate side-chains 112 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 133 ASP Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 485 ASP Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain H residue 641 VAL Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 185 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 74 optimal weight: 0.5980 chunk 24 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.211431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.155718 restraints weight = 8140.715| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 3.19 r_work: 0.3359 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7774 Z= 0.153 Angle : 0.617 9.679 10562 Z= 0.310 Chirality : 0.047 0.221 1180 Planarity : 0.004 0.045 1329 Dihedral : 8.238 58.989 1342 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.34 % Allowed : 19.40 % Favored : 76.27 % 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: -0.42 (0.27), residues: 914 helix: 0.51 (0.62), residues: 79 sheet: -0.27 (0.35), residues: 211 loop : -0.34 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 146 TYR 0.019 0.001 TYR H 27 PHE 0.014 0.001 PHE H 258 TRP 0.013 0.001 TRP H 511 HIS 0.002 0.001 HIS L 229 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 7733) covalent geometry : angle 0.59603 (10465) SS BOND : bond 0.00426 ( 26) SS BOND : angle 1.64339 ( 52) hydrogen bonds : bond 0.03285 ( 188) hydrogen bonds : angle 5.79622 ( 477) link_ALPHA1-2 : bond 0.00314 ( 2) link_ALPHA1-2 : angle 1.49658 ( 6) link_ALPHA1-3 : bond 0.00785 ( 1) link_ALPHA1-3 : angle 1.53027 ( 3) link_ALPHA1-6 : bond 0.00229 ( 1) link_ALPHA1-6 : angle 1.57740 ( 3) link_BETA1-4 : bond 0.00416 ( 6) link_BETA1-4 : angle 2.19186 ( 18) link_NAG-ASN : bond 0.00193 ( 5) link_NAG-ASN : angle 1.79678 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 ASP cc_start: 0.8650 (m-30) cc_final: 0.8327 (m-30) REVERT: H 292 ASP cc_start: 0.8210 (t70) cc_final: 0.8010 (t70) REVERT: H 377 ASN cc_start: 0.7491 (m110) cc_final: 0.7013 (m-40) REVERT: H 439 LYS cc_start: 0.8443 (tttt) cc_final: 0.8127 (mtpt) REVERT: H 485 ASP cc_start: 0.6546 (OUTLIER) cc_final: 0.6112 (m-30) REVERT: H 499 GLU cc_start: 0.7141 (pm20) cc_final: 0.6265 (tp30) REVERT: H 526 LYS cc_start: 0.7533 (tppp) cc_final: 0.6953 (mmmt) REVERT: H 555 LYS cc_start: 0.8145 (ttpt) cc_final: 0.7555 (ttmm) REVERT: H 612 GLN cc_start: 0.7414 (pt0) cc_final: 0.6998 (pp30) REVERT: H 628 GLU cc_start: 0.7489 (mt-10) cc_final: 0.6910 (mt-10) REVERT: L 91 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.8700 (m-80) REVERT: L 110 ASP cc_start: 0.8058 (t70) cc_final: 0.7765 (t0) outliers start: 36 outliers final: 23 residues processed: 123 average time/residue: 0.0843 time to fit residues: 14.3461 Evaluate side-chains 118 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 485 ASP Chi-restraints excluded: chain H residue 505 SER Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain H residue 564 ILE Chi-restraints excluded: chain H residue 641 VAL Chi-restraints excluded: chain H residue 647 ASP Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 185 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.212231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.156744 restraints weight = 8183.113| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 3.08 r_work: 0.3366 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7774 Z= 0.124 Angle : 0.580 9.838 10562 Z= 0.292 Chirality : 0.046 0.208 1180 Planarity : 0.003 0.045 1329 Dihedral : 7.412 52.111 1342 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.49 % Allowed : 20.36 % Favored : 76.14 % 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: -0.41 (0.27), residues: 914 helix: 0.59 (0.63), residues: 79 sheet: -0.30 (0.35), residues: 211 loop : -0.33 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 146 TYR 0.017 0.001 TYR H 27 PHE 0.014 0.001 PHE H 258 TRP 0.011 0.001 TRP H 511 HIS 0.002 0.000 HIS L 229 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 7733) covalent geometry : angle 0.56063 (10465) SS BOND : bond 0.00332 ( 26) SS BOND : angle 1.48306 ( 52) hydrogen bonds : bond 0.03077 ( 188) hydrogen bonds : angle 5.67588 ( 477) link_ALPHA1-2 : bond 0.00286 ( 2) link_ALPHA1-2 : angle 1.48111 ( 6) link_ALPHA1-3 : bond 0.01002 ( 1) link_ALPHA1-3 : angle 1.52773 ( 3) link_ALPHA1-6 : bond 0.00259 ( 1) link_ALPHA1-6 : angle 1.62976 ( 3) link_BETA1-4 : bond 0.00428 ( 6) link_BETA1-4 : angle 2.08290 ( 18) link_NAG-ASN : bond 0.00238 ( 5) link_NAG-ASN : angle 1.71572 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 292 ASP cc_start: 0.8184 (t70) cc_final: 0.7970 (t70) REVERT: H 377 ASN cc_start: 0.7478 (m110) cc_final: 0.7010 (m-40) REVERT: H 439 LYS cc_start: 0.8423 (tttt) cc_final: 0.8071 (mtpt) REVERT: H 485 ASP cc_start: 0.6601 (OUTLIER) cc_final: 0.6190 (m-30) REVERT: H 555 LYS cc_start: 0.8127 (ttpt) cc_final: 0.7531 (ttmm) REVERT: H 612 GLN cc_start: 0.7317 (pt0) cc_final: 0.6955 (pp30) REVERT: H 628 GLU cc_start: 0.7554 (mt-10) cc_final: 0.6932 (mt-10) REVERT: H 640 LYS cc_start: 0.5845 (mmtt) cc_final: 0.5216 (mmtt) REVERT: L 91 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8702 (m-80) REVERT: L 110 ASP cc_start: 0.8076 (t70) cc_final: 0.7793 (t0) outliers start: 29 outliers final: 17 residues processed: 119 average time/residue: 0.0853 time to fit residues: 14.0369 Evaluate side-chains 111 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 446 CYS Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 485 ASP Chi-restraints excluded: chain H residue 505 SER Chi-restraints excluded: chain H residue 641 VAL Chi-restraints excluded: chain H residue 647 ASP Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 185 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 266 GLN H 659 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.206537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.148195 restraints weight = 8059.864| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 3.04 r_work: 0.3349 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7774 Z= 0.115 Angle : 0.577 9.724 10562 Z= 0.291 Chirality : 0.045 0.186 1180 Planarity : 0.003 0.045 1329 Dihedral : 6.986 50.811 1342 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.98 % Allowed : 19.76 % Favored : 76.27 % 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: -0.44 (0.27), residues: 914 helix: 0.61 (0.63), residues: 79 sheet: -0.30 (0.35), residues: 211 loop : -0.36 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 146 TYR 0.016 0.001 TYR H 27 PHE 0.013 0.001 PHE H 258 TRP 0.010 0.001 TRP H 511 HIS 0.001 0.000 HIS L 229 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7733) covalent geometry : angle 0.56005 (10465) SS BOND : bond 0.00313 ( 26) SS BOND : angle 1.26825 ( 52) hydrogen bonds : bond 0.03006 ( 188) hydrogen bonds : angle 5.58231 ( 477) link_ALPHA1-2 : bond 0.00277 ( 2) link_ALPHA1-2 : angle 1.47355 ( 6) link_ALPHA1-3 : bond 0.01100 ( 1) link_ALPHA1-3 : angle 1.57437 ( 3) link_ALPHA1-6 : bond 0.00354 ( 1) link_ALPHA1-6 : angle 1.67394 ( 3) link_BETA1-4 : bond 0.00440 ( 6) link_BETA1-4 : angle 2.04198 ( 18) link_NAG-ASN : bond 0.00230 ( 5) link_NAG-ASN : angle 1.71994 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 292 ASP cc_start: 0.8203 (t70) cc_final: 0.7982 (t70) REVERT: H 377 ASN cc_start: 0.7468 (m110) cc_final: 0.6988 (m-40) REVERT: H 439 LYS cc_start: 0.8423 (tttt) cc_final: 0.8078 (mtpt) REVERT: H 485 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.6246 (m-30) REVERT: H 499 GLU cc_start: 0.7047 (pm20) cc_final: 0.6132 (tp30) REVERT: H 555 LYS cc_start: 0.8136 (ttpt) cc_final: 0.7401 (mttp) REVERT: H 612 GLN cc_start: 0.7173 (pt0) cc_final: 0.6867 (pp30) REVERT: H 628 GLU cc_start: 0.7527 (mt-10) cc_final: 0.6953 (mt-10) REVERT: H 640 LYS cc_start: 0.5827 (mmtt) cc_final: 0.5217 (mmtt) REVERT: L 91 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8703 (m-80) REVERT: L 110 ASP cc_start: 0.8157 (t70) cc_final: 0.7851 (t0) REVERT: L 220 THR cc_start: 0.6617 (OUTLIER) cc_final: 0.6110 (t) outliers start: 33 outliers final: 23 residues processed: 118 average time/residue: 0.0791 time to fit residues: 12.9320 Evaluate side-chains 116 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 446 CYS Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 485 ASP Chi-restraints excluded: chain H residue 505 SER Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain H residue 641 VAL Chi-restraints excluded: chain H residue 647 ASP Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 253 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 88 optimal weight: 0.4980 chunk 57 optimal weight: 30.0000 chunk 53 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.214682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.153598 restraints weight = 8234.054| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.76 r_work: 0.3309 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7774 Z= 0.104 Angle : 0.554 9.776 10562 Z= 0.279 Chirality : 0.045 0.186 1180 Planarity : 0.003 0.045 1329 Dihedral : 6.365 50.552 1342 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.13 % Allowed : 20.72 % Favored : 76.14 % 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: -0.38 (0.27), residues: 914 helix: 0.67 (0.62), residues: 79 sheet: -0.24 (0.36), residues: 211 loop : -0.34 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 146 TYR 0.015 0.001 TYR H 27 PHE 0.013 0.001 PHE H 258 TRP 0.008 0.001 TRP H 511 HIS 0.001 0.000 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 7733) covalent geometry : angle 0.53737 (10465) SS BOND : bond 0.00285 ( 26) SS BOND : angle 1.26093 ( 52) hydrogen bonds : bond 0.02856 ( 188) hydrogen bonds : angle 5.48753 ( 477) link_ALPHA1-2 : bond 0.00283 ( 2) link_ALPHA1-2 : angle 1.46705 ( 6) link_ALPHA1-3 : bond 0.00998 ( 1) link_ALPHA1-3 : angle 1.46451 ( 3) link_ALPHA1-6 : bond 0.00466 ( 1) link_ALPHA1-6 : angle 1.59216 ( 3) link_BETA1-4 : bond 0.00432 ( 6) link_BETA1-4 : angle 1.91830 ( 18) link_NAG-ASN : bond 0.00254 ( 5) link_NAG-ASN : angle 1.66778 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 292 ASP cc_start: 0.8229 (t70) cc_final: 0.7992 (t70) REVERT: H 377 ASN cc_start: 0.7468 (m110) cc_final: 0.6987 (m-40) REVERT: H 439 LYS cc_start: 0.8432 (tttt) cc_final: 0.8096 (mtpt) REVERT: H 485 ASP cc_start: 0.6639 (OUTLIER) cc_final: 0.6275 (m-30) REVERT: H 555 LYS cc_start: 0.8091 (ttpt) cc_final: 0.7411 (ttmm) REVERT: H 612 GLN cc_start: 0.7099 (pt0) cc_final: 0.6837 (pp30) REVERT: H 628 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7032 (mt-10) REVERT: L 91 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8690 (m-80) REVERT: L 110 ASP cc_start: 0.8239 (t70) cc_final: 0.7917 (t0) REVERT: L 220 THR cc_start: 0.6644 (OUTLIER) cc_final: 0.6099 (t) outliers start: 26 outliers final: 19 residues processed: 117 average time/residue: 0.0841 time to fit residues: 13.7237 Evaluate side-chains 112 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 347 ARG Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 446 CYS Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 485 ASP Chi-restraints excluded: chain H residue 505 SER Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 253 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 65 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4305 r_free = 0.4305 target = 0.213108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.151166 restraints weight = 8127.164| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.10 r_work: 0.3314 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7774 Z= 0.128 Angle : 0.569 9.716 10562 Z= 0.288 Chirality : 0.046 0.187 1180 Planarity : 0.003 0.044 1329 Dihedral : 6.339 51.544 1342 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.89 % Allowed : 21.33 % Favored : 75.78 % 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: -0.42 (0.27), residues: 914 helix: 0.62 (0.63), residues: 79 sheet: -0.32 (0.36), residues: 213 loop : -0.34 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 146 TYR 0.018 0.001 TYR H 27 PHE 0.014 0.001 PHE H 258 TRP 0.009 0.001 TRP H 511 HIS 0.002 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7733) covalent geometry : angle 0.55227 (10465) SS BOND : bond 0.00283 ( 26) SS BOND : angle 1.28435 ( 52) hydrogen bonds : bond 0.03021 ( 188) hydrogen bonds : angle 5.48356 ( 477) link_ALPHA1-2 : bond 0.00187 ( 2) link_ALPHA1-2 : angle 1.53638 ( 6) link_ALPHA1-3 : bond 0.00922 ( 1) link_ALPHA1-3 : angle 1.59433 ( 3) link_ALPHA1-6 : bond 0.00386 ( 1) link_ALPHA1-6 : angle 1.62563 ( 3) link_BETA1-4 : bond 0.00418 ( 6) link_BETA1-4 : angle 1.96187 ( 18) link_NAG-ASN : bond 0.00234 ( 5) link_NAG-ASN : angle 1.68348 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 292 ASP cc_start: 0.8241 (t70) cc_final: 0.7998 (t70) REVERT: H 377 ASN cc_start: 0.7457 (m110) cc_final: 0.6971 (m-40) REVERT: H 439 LYS cc_start: 0.8427 (tttt) cc_final: 0.8104 (mtpt) REVERT: H 485 ASP cc_start: 0.6673 (OUTLIER) cc_final: 0.6318 (m-30) REVERT: H 499 GLU cc_start: 0.7059 (pm20) cc_final: 0.6229 (tp30) REVERT: H 555 LYS cc_start: 0.8042 (ttpt) cc_final: 0.7374 (ttmm) REVERT: H 566 MET cc_start: 0.8290 (mtp) cc_final: 0.7954 (mtt) REVERT: H 628 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6883 (mt-10) REVERT: L 91 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8710 (m-80) REVERT: L 110 ASP cc_start: 0.8259 (t70) cc_final: 0.7936 (t0) REVERT: L 220 THR cc_start: 0.6640 (OUTLIER) cc_final: 0.6108 (t) outliers start: 24 outliers final: 20 residues processed: 109 average time/residue: 0.0733 time to fit residues: 11.3232 Evaluate side-chains 113 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 347 ARG Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 446 CYS Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 485 ASP Chi-restraints excluded: chain H residue 505 SER Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 253 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 12 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 84 optimal weight: 10.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 612 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.211908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.156058 restraints weight = 8141.143| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.79 r_work: 0.3300 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7774 Z= 0.142 Angle : 0.580 9.675 10562 Z= 0.295 Chirality : 0.046 0.188 1180 Planarity : 0.003 0.044 1329 Dihedral : 6.376 51.272 1342 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.28 % Favored : 96.61 % Rotamer: Outliers : 3.13 % Allowed : 21.20 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.27), residues: 914 helix: 0.58 (0.62), residues: 79 sheet: -0.36 (0.36), residues: 213 loop : -0.35 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 146 TYR 0.018 0.001 TYR H 27 PHE 0.014 0.001 PHE H 258 TRP 0.010 0.001 TRP H 511 HIS 0.002 0.001 HIS L 229 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7733) covalent geometry : angle 0.56147 (10465) SS BOND : bond 0.00258 ( 26) SS BOND : angle 1.49520 ( 52) hydrogen bonds : bond 0.03088 ( 188) hydrogen bonds : angle 5.51842 ( 477) link_ALPHA1-2 : bond 0.00217 ( 2) link_ALPHA1-2 : angle 1.52341 ( 6) link_ALPHA1-3 : bond 0.00975 ( 1) link_ALPHA1-3 : angle 1.50159 ( 3) link_ALPHA1-6 : bond 0.00393 ( 1) link_ALPHA1-6 : angle 1.65350 ( 3) link_BETA1-4 : bond 0.00426 ( 6) link_BETA1-4 : angle 1.95291 ( 18) link_NAG-ASN : bond 0.00228 ( 5) link_NAG-ASN : angle 1.69688 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 377 ASN cc_start: 0.7482 (m110) cc_final: 0.6992 (m-40) REVERT: H 485 ASP cc_start: 0.6705 (OUTLIER) cc_final: 0.6367 (m-30) REVERT: H 499 GLU cc_start: 0.7146 (pm20) cc_final: 0.6314 (tp30) REVERT: H 555 LYS cc_start: 0.8066 (ttpt) cc_final: 0.7393 (ttmm) REVERT: H 566 MET cc_start: 0.8345 (mtp) cc_final: 0.8056 (mtt) REVERT: H 612 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6933 (pm20) REVERT: H 628 GLU cc_start: 0.7496 (mt-10) cc_final: 0.6989 (mt-10) REVERT: L 91 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.8713 (m-80) REVERT: L 110 ASP cc_start: 0.8261 (t70) cc_final: 0.7947 (t0) REVERT: L 220 THR cc_start: 0.6620 (OUTLIER) cc_final: 0.6122 (t) outliers start: 26 outliers final: 21 residues processed: 109 average time/residue: 0.0810 time to fit residues: 12.2038 Evaluate side-chains 117 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 347 ARG Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 446 CYS Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 485 ASP Chi-restraints excluded: chain H residue 505 SER Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain H residue 586 CYS Chi-restraints excluded: chain H residue 612 GLN Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 253 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 67 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 9 optimal weight: 0.1980 chunk 81 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 612 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.212127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.156666 restraints weight = 8162.032| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 3.10 r_work: 0.3348 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.177 7774 Z= 0.235 Angle : 0.990 59.198 10562 Z= 0.564 Chirality : 0.050 0.736 1180 Planarity : 0.003 0.044 1329 Dihedral : 6.378 51.270 1342 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.28 % Favored : 96.61 % Rotamer: Outliers : 3.25 % Allowed : 21.08 % Favored : 75.66 % Cbeta Deviations : 0.11 % 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: -0.45 (0.27), residues: 914 helix: 0.58 (0.63), residues: 79 sheet: -0.36 (0.36), residues: 213 loop : -0.35 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 146 TYR 0.018 0.001 TYR H 27 PHE 0.014 0.001 PHE H 258 TRP 0.010 0.001 TRP H 511 HIS 0.002 0.001 HIS L 229 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 7733) covalent geometry : angle 0.97949 (10465) SS BOND : bond 0.00483 ( 26) SS BOND : angle 1.79301 ( 52) hydrogen bonds : bond 0.03232 ( 188) hydrogen bonds : angle 5.51152 ( 477) link_ALPHA1-2 : bond 0.00291 ( 2) link_ALPHA1-2 : angle 1.55396 ( 6) link_ALPHA1-3 : bond 0.00993 ( 1) link_ALPHA1-3 : angle 1.52976 ( 3) link_ALPHA1-6 : bond 0.00586 ( 1) link_ALPHA1-6 : angle 1.67400 ( 3) link_BETA1-4 : bond 0.00489 ( 6) link_BETA1-4 : angle 1.93917 ( 18) link_NAG-ASN : bond 0.00223 ( 5) link_NAG-ASN : angle 1.69324 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1856.80 seconds wall clock time: 32 minutes 34.60 seconds (1954.60 seconds total)