Starting phenix.real_space_refine on Thu Feb 5 20:12:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p99_71403/02_2026/9p99_71403_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p99_71403/02_2026/9p99_71403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9p99_71403/02_2026/9p99_71403_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p99_71403/02_2026/9p99_71403_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p99_71403/02_2026/9p99_71403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p99_71403/02_2026/9p99_71403.map" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 Mn 4 7.51 5 S 47 5.16 5 C 6141 2.51 5 N 1692 2.21 5 O 1903 1.98 5 H 9434 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19224 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 11652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 11652 Classifications: {'peptide': 768} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 731} Chain breaks: 1 Chain: "B" Number of atoms: 5819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 5819 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 21, 'TRANS': 357} Chain: "C" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1598 Classifications: {'peptide': 103} Link IDs: {'PCIS': 3, 'PTRANS': 6, 'TRANS': 93} Chain: "D" 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: "E" 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: "F" 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: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 32 Unusual residues: {' CA': 3, ' MN': 1, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' MN': 3, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.39, per 1000 atoms: 0.18 Number of scatterers: 19224 At special positions: 0 Unit cell: (74.052, 126.786, 199.716, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 Ca 3 19.99 S 47 16.00 O 1903 8.00 N 1692 7.00 C 6141 6.00 H 9434 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 61 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 221 " distance=2.03 Simple disulfide: pdb=" SG CYS A 688 " - pdb=" SG CYS A 744 " distance=2.03 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 204 " distance=2.02 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 455 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1201 " - " ASN A 303 " " NAG A1202 " - " ASN A 253 " " NAG B 801 " - " ASN B 260 " " NAG D 1 " - " ASN A 31 " " NAG E 1 " - " ASN A 426 " " NAG F 1 " - " ASN A 708 " Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 601.3 milliseconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2294 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 20 sheets defined 20.1% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.800A pdb=" N LEU A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 218 Processing helix chain 'A' and resid 239 through 242 removed outlier: 3.546A pdb=" N GLN A 242 " --> pdb=" O ARG A 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 239 through 242' Processing helix chain 'A' and resid 243 through 252 removed outlier: 4.165A pdb=" N GLN A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 303 through 309 Processing helix chain 'A' and resid 329 through 340 removed outlier: 3.872A pdb=" N ALA A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 removed outlier: 4.461A pdb=" N LEU A 357 " --> pdb=" O TYR A 354 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP A 358 " --> pdb=" O MET A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 435 through 439 Processing helix chain 'A' and resid 464 through 468 Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 695 through 702 Processing helix chain 'A' and resid 726 through 731 Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 148 through 167 removed outlier: 3.720A pdb=" N HIS B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 195 Processing helix chain 'B' and resid 219 through 228 Processing helix chain 'B' and resid 242 through 252 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 300 through 306 removed outlier: 4.296A pdb=" N THR B 304 " --> pdb=" O SER B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 322 Processing helix chain 'B' and resid 333 through 344 removed outlier: 3.913A pdb=" N GLU B 339 " --> pdb=" O PRO B 335 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS B 342 " --> pdb=" O GLN B 338 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 368 Processing helix chain 'B' and resid 402 through 406 Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.992A pdb=" N LYS C 30 " --> pdb=" O ASN C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 removed outlier: 3.738A pdb=" N ARG C 70 " --> pdb=" O ASP C 67 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 10 removed outlier: 5.529A pdb=" N ASP A 644 " --> pdb=" O GLY A 634 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 630 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 26 removed outlier: 3.923A pdb=" N SER A 21 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N THR A 33 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU A 54 " --> pdb=" O THR A 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 82 removed outlier: 3.540A pdb=" N THR A 105 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLY A 106 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASN A 122 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N CYS A 108 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN A 120 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU A 110 " --> pdb=" O GLN A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 233 through 236 removed outlier: 3.511A pdb=" N GLU A 235 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU A 225 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLU A 184 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL A 290 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA A 186 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU A 292 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE A 188 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 390 through 392 Processing sheet with id=AA6, first strand: chain 'A' and resid 447 through 448 removed outlier: 6.655A pdb=" N VAL A 471 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 500 through 503 removed outlier: 6.526A pdb=" N VAL A 530 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE A 547 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL A 532 " --> pdb=" O ALA A 545 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 563 through 565 removed outlier: 3.860A pdb=" N GLN A 613 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 563 through 565 removed outlier: 7.082A pdb=" N PHE A 594 " --> pdb=" O PHE A 627 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 603 Processing sheet with id=AB2, first strand: chain 'A' and resid 661 through 662 Processing sheet with id=AB3, first strand: chain 'A' and resid 664 through 671 Processing sheet with id=AB4, first strand: chain 'A' and resid 664 through 671 Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 Processing sheet with id=AB6, first strand: chain 'B' and resid 83 through 86 removed outlier: 3.553A pdb=" N GLN B 83 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N SER B 372 " --> pdb=" O HIS B 411 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 119 through 126 Processing sheet with id=AB8, first strand: chain 'B' and resid 211 through 217 removed outlier: 7.150A pdb=" N VAL B 213 " --> pdb=" O SER B 176 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N SER B 176 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER B 215 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N PHE B 174 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR B 217 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 133 " --> pdb=" O ARG B 171 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N GLY B 173 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU B 135 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N GLY B 175 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR B 137 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N PHE B 177 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N MET B 139 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASP B 134 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL B 266 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TYR B 136 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N THR B 268 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU B 138 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN B 324 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 269 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N ALA B 348 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N GLY B 350 " --> pdb=" O PRO B 325 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N PHE B 327 " --> pdb=" O GLY B 350 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 19 through 23 removed outlier: 6.110A pdb=" N ASN C 20 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL C 62 " --> pdb=" O ASN C 20 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL C 22 " --> pdb=" O LEU C 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 35 through 39 removed outlier: 3.644A pdb=" N PHE C 77 " --> pdb=" O THR C 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 73 through 75 328 hydrogen bonds defined for protein. 858 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: 4.60 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9418 1.03 - 1.23: 65 1.23 - 1.42: 4168 1.42 - 1.62: 5704 1.62 - 1.81: 68 Bond restraints: 19423 Sorted by residual: bond pdb=" N PHE A 1 " pdb=" CA PHE A 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.74e+00 bond pdb=" N ASP C 1 " pdb=" H ASP C 1 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" N ASP C 1 " pdb=" CA ASP C 1 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.90e-02 2.77e+03 2.20e+00 bond pdb=" CG PRO A 17 " pdb=" CD PRO A 17 " ideal model delta sigma weight residual 1.512 1.473 0.039 2.70e-02 1.37e+03 2.12e+00 bond pdb=" N PHE A 1 " pdb=" H PHE A 1 " ideal model delta sigma weight residual 0.860 0.888 -0.028 2.00e-02 2.50e+03 2.02e+00 ... (remaining 19418 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.26: 34986 7.26 - 14.51: 0 14.51 - 21.77: 0 21.77 - 29.02: 0 29.02 - 36.28: 3 Bond angle restraints: 34989 Sorted by residual: angle pdb=" C ASN A 426 " pdb=" CA ASN A 426 " pdb=" HA ASN A 426 " ideal model delta sigma weight residual 109.00 72.72 36.28 3.00e+00 1.11e-01 1.46e+02 angle pdb=" N ASN A 426 " pdb=" CA ASN A 426 " pdb=" HA ASN A 426 " ideal model delta sigma weight residual 110.00 76.38 33.62 3.00e+00 1.11e-01 1.26e+02 angle pdb=" CB ASN A 426 " pdb=" CA ASN A 426 " pdb=" HA ASN A 426 " ideal model delta sigma weight residual 109.00 76.00 33.00 3.00e+00 1.11e-01 1.21e+02 angle pdb=" C ALA B 403 " pdb=" CA ALA B 403 " pdb=" CB ALA B 403 " ideal model delta sigma weight residual 116.63 110.74 5.89 1.16e+00 7.43e-01 2.58e+01 angle pdb=" C ASP A 589 " pdb=" CA ASP A 589 " pdb=" CB ASP A 589 " ideal model delta sigma weight residual 116.54 111.05 5.49 1.15e+00 7.56e-01 2.28e+01 ... (remaining 34984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 8341 17.84 - 35.67: 683 35.67 - 53.51: 236 53.51 - 71.35: 91 71.35 - 89.19: 24 Dihedral angle restraints: 9375 sinusoidal: 5226 harmonic: 4149 Sorted by residual: dihedral pdb=" CB CYS B 429 " pdb=" SG CYS B 429 " pdb=" SG CYS B 455 " pdb=" CB CYS B 455 " ideal model delta sinusoidal sigma weight residual -86.00 -136.17 50.17 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CA MET A 371 " pdb=" C MET A 371 " pdb=" N GLU A 372 " pdb=" CA GLU A 372 " ideal model delta harmonic sigma weight residual 180.00 155.81 24.19 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA GLU C 11 " pdb=" C GLU C 11 " pdb=" N ASN C 12 " pdb=" CA ASN C 12 " ideal model delta harmonic sigma weight residual 180.00 156.39 23.61 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 9372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1387 0.074 - 0.148: 155 0.148 - 0.222: 4 0.222 - 0.295: 0 0.295 - 0.369: 1 Chirality restraints: 1547 Sorted by residual: chirality pdb=" CA ASN A 426 " pdb=" N ASN A 426 " pdb=" C ASN A 426 " pdb=" CB ASN A 426 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" C1 NAG A1202 " pdb=" ND2 ASN A 253 " pdb=" C2 NAG A1202 " pdb=" O5 NAG A1202 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 6.88e-01 ... (remaining 1544 not shown) Planarity restraints: 2960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 15 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.16e+00 pdb=" N PRO C 16 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 16 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 16 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 62 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.97e+00 pdb=" N PRO A 63 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 63 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 63 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 675 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO A 676 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 676 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 676 " -0.026 5.00e-02 4.00e+02 ... (remaining 2957 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 446 2.15 - 2.76: 35840 2.76 - 3.37: 50951 3.37 - 3.99: 66800 3.99 - 4.60: 104487 Nonbonded interactions: 258524 Sorted by model distance: nonbonded pdb="HD22 ASN B 235 " pdb="MN MN B 804 " model vdw 1.534 1.850 nonbonded pdb=" H ASN A 426 " pdb=" HA ASN A 426 " model vdw 1.609 1.816 nonbonded pdb=" OD1 ASP B 237 " pdb="MN MN B 804 " model vdw 1.823 2.200 nonbonded pdb=" OG1 THR A 261 " pdb="MN MN A1206 " model vdw 1.848 2.200 nonbonded pdb=" HG1 THR C 57 " pdb=" HD1 TRP C 59 " model vdw 1.854 2.100 ... (remaining 258519 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.360 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: 0.110 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.840 Find NCS groups from input model: 0.060 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 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 : 0.005 0.056 10005 Z= 0.239 Angle : 0.695 9.138 13598 Z= 0.390 Chirality : 0.046 0.369 1547 Planarity : 0.005 0.062 1774 Dihedral : 14.952 89.186 3836 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.99 % Favored : 94.93 % Rotamer: Outliers : 1.52 % Allowed : 9.00 % Favored : 89.49 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 7.58 % 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: -1.68 (0.23), residues: 1242 helix: -0.11 (0.39), residues: 183 sheet: -1.21 (0.26), residues: 369 loop : -1.30 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 263 TYR 0.014 0.002 TYR A 445 PHE 0.014 0.002 PHE A 627 TRP 0.011 0.002 TRP C 59 HIS 0.005 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 9989) covalent geometry : angle 0.67931 (13555) SS BOND : bond 0.00294 ( 5) SS BOND : angle 0.74653 ( 10) hydrogen bonds : bond 0.20554 ( 312) hydrogen bonds : angle 9.35216 ( 858) link_BETA1-4 : bond 0.00629 ( 5) link_BETA1-4 : angle 3.89814 ( 15) link_NAG-ASN : bond 0.00355 ( 6) link_NAG-ASN : angle 2.22406 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 207 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 SER cc_start: 0.8457 (p) cc_final: 0.8245 (t) REVERT: A 51 ARG cc_start: 0.7936 (ptt-90) cc_final: 0.7663 (ptt90) REVERT: A 58 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6675 (mm-30) REVERT: A 78 THR cc_start: 0.8290 (m) cc_final: 0.7840 (p) REVERT: A 183 THR cc_start: 0.8042 (t) cc_final: 0.7402 (p) REVERT: A 272 ASP cc_start: 0.6849 (m-30) cc_final: 0.6590 (m-30) REVERT: A 302 LEU cc_start: 0.8106 (mt) cc_final: 0.7870 (mp) REVERT: A 335 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7029 (mt-10) REVERT: A 408 TRP cc_start: 0.8245 (m100) cc_final: 0.7933 (m-90) REVERT: A 457 SER cc_start: 0.7883 (t) cc_final: 0.7519 (p) REVERT: A 527 GLU cc_start: 0.7455 (mp0) cc_final: 0.7251 (mp0) REVERT: A 554 PHE cc_start: 0.8401 (m-80) cc_final: 0.7879 (m-80) REVERT: A 566 MET cc_start: 0.7338 (mmt) cc_final: 0.7133 (mmt) REVERT: A 736 GLU cc_start: 0.6839 (pp20) cc_final: 0.6584 (tm-30) REVERT: A 750 MET cc_start: 0.4794 (mtm) cc_final: 0.4305 (mtm) REVERT: A 769 VAL cc_start: 0.8203 (t) cc_final: 0.7863 (p) REVERT: B 280 LYS cc_start: 0.8380 (tptm) cc_final: 0.8159 (tttm) outliers start: 16 outliers final: 14 residues processed: 215 average time/residue: 0.2415 time to fit residues: 68.3824 Evaluate side-chains 213 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 22 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.0770 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.0970 chunk 113 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.4980 chunk 117 optimal weight: 1.9990 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.170086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.134990 restraints weight = 39625.308| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.49 r_work: 0.3401 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.0627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10005 Z= 0.135 Angle : 0.566 5.302 13598 Z= 0.294 Chirality : 0.045 0.363 1547 Planarity : 0.005 0.052 1774 Dihedral : 7.961 59.154 1605 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.91 % Favored : 95.01 % Rotamer: Outliers : 1.14 % Allowed : 9.56 % Favored : 89.30 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 7.58 % 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: -1.41 (0.23), residues: 1242 helix: 0.32 (0.40), residues: 182 sheet: -0.86 (0.27), residues: 371 loop : -1.31 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 735 TYR 0.010 0.001 TYR A 415 PHE 0.012 0.001 PHE A 236 TRP 0.007 0.001 TRP A 408 HIS 0.003 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9989) covalent geometry : angle 0.55638 (13555) SS BOND : bond 0.00281 ( 5) SS BOND : angle 0.63375 ( 10) hydrogen bonds : bond 0.04079 ( 312) hydrogen bonds : angle 6.64050 ( 858) link_BETA1-4 : bond 0.00296 ( 5) link_BETA1-4 : angle 2.46247 ( 15) link_NAG-ASN : bond 0.00286 ( 6) link_NAG-ASN : angle 1.95813 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 203 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 SER cc_start: 0.8396 (p) cc_final: 0.8146 (m) REVERT: A 51 ARG cc_start: 0.7945 (ptt-90) cc_final: 0.7671 (ptt90) REVERT: A 58 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6712 (mm-30) REVERT: A 78 THR cc_start: 0.8233 (m) cc_final: 0.7779 (p) REVERT: A 183 THR cc_start: 0.7932 (t) cc_final: 0.7309 (p) REVERT: A 240 ASP cc_start: 0.6955 (m-30) cc_final: 0.6591 (t0) REVERT: A 272 ASP cc_start: 0.6701 (m-30) cc_final: 0.6368 (m-30) REVERT: A 302 LEU cc_start: 0.8148 (mt) cc_final: 0.7931 (mp) REVERT: A 335 GLU cc_start: 0.7406 (mt-10) cc_final: 0.6984 (mt-10) REVERT: A 408 TRP cc_start: 0.8175 (m100) cc_final: 0.7819 (m-90) REVERT: A 457 SER cc_start: 0.7934 (t) cc_final: 0.7530 (p) REVERT: A 476 LYS cc_start: 0.7677 (tttt) cc_final: 0.7401 (tttt) REVERT: A 527 GLU cc_start: 0.7485 (mp0) cc_final: 0.7219 (mp0) REVERT: A 554 PHE cc_start: 0.8401 (m-80) cc_final: 0.7785 (m-80) REVERT: A 736 GLU cc_start: 0.6793 (pp20) cc_final: 0.6418 (tm-30) REVERT: A 769 VAL cc_start: 0.8001 (t) cc_final: 0.7704 (p) REVERT: B 285 PHE cc_start: 0.8543 (p90) cc_final: 0.8312 (p90) outliers start: 12 outliers final: 9 residues processed: 211 average time/residue: 0.2680 time to fit residues: 74.3942 Evaluate side-chains 209 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 200 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain C residue 22 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 86 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 82 optimal weight: 0.0980 chunk 8 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.168300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.133120 restraints weight = 39780.282| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.50 r_work: 0.3392 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 10005 Z= 0.218 Angle : 0.585 5.822 13598 Z= 0.306 Chirality : 0.045 0.369 1547 Planarity : 0.005 0.048 1774 Dihedral : 7.315 59.822 1583 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.80 % Favored : 94.12 % Rotamer: Outliers : 1.80 % Allowed : 10.04 % Favored : 88.16 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 7.58 % 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: -1.48 (0.23), residues: 1242 helix: 0.36 (0.41), residues: 182 sheet: -0.88 (0.26), residues: 381 loop : -1.41 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 171 TYR 0.014 0.002 TYR A 445 PHE 0.015 0.002 PHE A 236 TRP 0.009 0.002 TRP B 258 HIS 0.004 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 9989) covalent geometry : angle 0.57580 (13555) SS BOND : bond 0.00249 ( 5) SS BOND : angle 0.66326 ( 10) hydrogen bonds : bond 0.04122 ( 312) hydrogen bonds : angle 6.33748 ( 858) link_BETA1-4 : bond 0.00272 ( 5) link_BETA1-4 : angle 2.39793 ( 15) link_NAG-ASN : bond 0.00206 ( 6) link_NAG-ASN : angle 1.90298 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 207 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 SER cc_start: 0.8352 (p) cc_final: 0.8109 (m) REVERT: A 51 ARG cc_start: 0.7956 (ptt-90) cc_final: 0.7674 (ptt90) REVERT: A 58 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6727 (mm-30) REVERT: A 78 THR cc_start: 0.8273 (m) cc_final: 0.7788 (p) REVERT: A 183 THR cc_start: 0.7950 (t) cc_final: 0.7345 (p) REVERT: A 272 ASP cc_start: 0.6721 (m-30) cc_final: 0.6405 (m-30) REVERT: A 302 LEU cc_start: 0.8148 (mt) cc_final: 0.7925 (mp) REVERT: A 335 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6985 (mt-10) REVERT: A 372 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7011 (tm-30) REVERT: A 408 TRP cc_start: 0.8224 (m100) cc_final: 0.7815 (m-90) REVERT: A 457 SER cc_start: 0.7957 (t) cc_final: 0.7591 (p) REVERT: A 526 GLU cc_start: 0.7702 (pt0) cc_final: 0.7375 (pt0) REVERT: A 527 GLU cc_start: 0.7542 (mp0) cc_final: 0.7254 (mp0) REVERT: A 554 PHE cc_start: 0.8409 (m-80) cc_final: 0.7888 (m-80) REVERT: A 750 MET cc_start: 0.4989 (mtm) cc_final: 0.4417 (mtm) REVERT: A 769 VAL cc_start: 0.8051 (t) cc_final: 0.7762 (p) outliers start: 19 outliers final: 16 residues processed: 219 average time/residue: 0.2683 time to fit residues: 77.4903 Evaluate side-chains 218 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain C residue 22 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 15 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 94 optimal weight: 0.1980 chunk 118 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.167922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.132222 restraints weight = 39525.782| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.54 r_work: 0.3408 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 10005 Z= 0.230 Angle : 0.589 5.940 13598 Z= 0.308 Chirality : 0.046 0.371 1547 Planarity : 0.005 0.052 1774 Dihedral : 7.147 58.274 1581 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.36 % Favored : 93.56 % Rotamer: Outliers : 2.27 % Allowed : 10.89 % Favored : 86.84 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 7.58 % 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: -1.49 (0.23), residues: 1242 helix: 0.35 (0.41), residues: 182 sheet: -0.83 (0.25), residues: 399 loop : -1.46 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 479 TYR 0.014 0.002 TYR A 445 PHE 0.016 0.002 PHE A 236 TRP 0.009 0.002 TRP A 408 HIS 0.005 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00544 ( 9989) covalent geometry : angle 0.58100 (13555) SS BOND : bond 0.00327 ( 5) SS BOND : angle 0.64304 ( 10) hydrogen bonds : bond 0.03800 ( 312) hydrogen bonds : angle 6.07035 ( 858) link_BETA1-4 : bond 0.00284 ( 5) link_BETA1-4 : angle 2.20174 ( 15) link_NAG-ASN : bond 0.00184 ( 6) link_NAG-ASN : angle 1.82497 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.7966 (ptt-90) cc_final: 0.7660 (ptt90) REVERT: A 58 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6748 (mm-30) REVERT: A 78 THR cc_start: 0.8270 (m) cc_final: 0.7809 (p) REVERT: A 183 THR cc_start: 0.7951 (t) cc_final: 0.7380 (p) REVERT: A 272 ASP cc_start: 0.6689 (m-30) cc_final: 0.6406 (m-30) REVERT: A 313 MET cc_start: 0.7111 (tpp) cc_final: 0.6626 (ttm) REVERT: A 335 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7003 (mt-10) REVERT: A 408 TRP cc_start: 0.8225 (m100) cc_final: 0.7843 (m-90) REVERT: A 457 SER cc_start: 0.8006 (t) cc_final: 0.7625 (p) REVERT: A 527 GLU cc_start: 0.7593 (mp0) cc_final: 0.7288 (mp0) REVERT: A 554 PHE cc_start: 0.8405 (m-80) cc_final: 0.7855 (m-80) REVERT: A 736 GLU cc_start: 0.6866 (tm-30) cc_final: 0.6592 (tm-30) REVERT: A 769 VAL cc_start: 0.8068 (t) cc_final: 0.7783 (p) REVERT: B 354 GLU cc_start: 0.6898 (mp0) cc_final: 0.6593 (mp0) outliers start: 24 outliers final: 22 residues processed: 224 average time/residue: 0.2681 time to fit residues: 78.7988 Evaluate side-chains 224 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 41 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 40 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 100 optimal weight: 0.2980 chunk 0 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.170896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.135394 restraints weight = 39266.370| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.52 r_work: 0.3405 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10005 Z= 0.215 Angle : 0.583 6.597 13598 Z= 0.304 Chirality : 0.045 0.368 1547 Planarity : 0.005 0.049 1774 Dihedral : 7.074 57.885 1581 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.68 % Favored : 93.24 % Rotamer: Outliers : 2.27 % Allowed : 11.17 % Favored : 86.55 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 7.58 % 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: -1.45 (0.23), residues: 1242 helix: 0.42 (0.41), residues: 182 sheet: -0.77 (0.25), residues: 399 loop : -1.47 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 479 TYR 0.013 0.002 TYR A 445 PHE 0.015 0.002 PHE A 236 TRP 0.009 0.002 TRP A 34 HIS 0.004 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 9989) covalent geometry : angle 0.57511 (13555) SS BOND : bond 0.00405 ( 5) SS BOND : angle 0.76121 ( 10) hydrogen bonds : bond 0.03596 ( 312) hydrogen bonds : angle 5.98934 ( 858) link_BETA1-4 : bond 0.00295 ( 5) link_BETA1-4 : angle 2.10845 ( 15) link_NAG-ASN : bond 0.00169 ( 6) link_NAG-ASN : angle 1.79875 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.7975 (ptt-90) cc_final: 0.7672 (ptt90) REVERT: A 58 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6729 (mm-30) REVERT: A 78 THR cc_start: 0.8278 (m) cc_final: 0.7839 (p) REVERT: A 183 THR cc_start: 0.7953 (t) cc_final: 0.7368 (p) REVERT: A 272 ASP cc_start: 0.6681 (m-30) cc_final: 0.6410 (m-30) REVERT: A 313 MET cc_start: 0.7128 (tpp) cc_final: 0.6468 (ttm) REVERT: A 335 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6997 (mt-10) REVERT: A 408 TRP cc_start: 0.8226 (m100) cc_final: 0.7846 (m-90) REVERT: A 457 SER cc_start: 0.7995 (t) cc_final: 0.7617 (p) REVERT: A 526 GLU cc_start: 0.7728 (pt0) cc_final: 0.7447 (pt0) REVERT: A 527 GLU cc_start: 0.7576 (mp0) cc_final: 0.7285 (mp0) REVERT: A 554 PHE cc_start: 0.8397 (m-80) cc_final: 0.7868 (m-80) REVERT: A 736 GLU cc_start: 0.6828 (tm-30) cc_final: 0.6625 (tm-30) REVERT: A 769 VAL cc_start: 0.8075 (t) cc_final: 0.7791 (p) REVERT: B 354 GLU cc_start: 0.6911 (mp0) cc_final: 0.6617 (mp0) outliers start: 24 outliers final: 23 residues processed: 224 average time/residue: 0.2547 time to fit residues: 75.2388 Evaluate side-chains 229 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain C residue 22 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 60 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.170682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.135305 restraints weight = 39212.290| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.51 r_work: 0.3373 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10005 Z= 0.211 Angle : 0.576 5.744 13598 Z= 0.301 Chirality : 0.045 0.370 1547 Planarity : 0.005 0.052 1774 Dihedral : 6.989 57.339 1581 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.09 % Favored : 92.83 % Rotamer: Outliers : 2.65 % Allowed : 11.36 % Favored : 85.98 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 7.58 % 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: -1.49 (0.23), residues: 1242 helix: 0.27 (0.40), residues: 190 sheet: -0.75 (0.25), residues: 399 loop : -1.52 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 479 TYR 0.013 0.002 TYR A 445 PHE 0.015 0.002 PHE A 236 TRP 0.009 0.002 TRP A 34 HIS 0.004 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 9989) covalent geometry : angle 0.56926 (13555) SS BOND : bond 0.00261 ( 5) SS BOND : angle 0.52061 ( 10) hydrogen bonds : bond 0.03501 ( 312) hydrogen bonds : angle 5.88570 ( 858) link_BETA1-4 : bond 0.00220 ( 5) link_BETA1-4 : angle 2.02598 ( 15) link_NAG-ASN : bond 0.00187 ( 6) link_NAG-ASN : angle 1.75756 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.7971 (ptt-90) cc_final: 0.7655 (ptt90) REVERT: A 58 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6710 (mm-30) REVERT: A 78 THR cc_start: 0.8258 (m) cc_final: 0.7826 (p) REVERT: A 183 THR cc_start: 0.7924 (t) cc_final: 0.7355 (p) REVERT: A 272 ASP cc_start: 0.6638 (m-30) cc_final: 0.6378 (m-30) REVERT: A 302 LEU cc_start: 0.8174 (mt) cc_final: 0.7938 (mp) REVERT: A 335 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6976 (mt-10) REVERT: A 408 TRP cc_start: 0.8212 (m100) cc_final: 0.7824 (m-90) REVERT: A 457 SER cc_start: 0.8009 (t) cc_final: 0.7616 (p) REVERT: A 527 GLU cc_start: 0.7603 (mp0) cc_final: 0.7273 (mp0) REVERT: A 554 PHE cc_start: 0.8377 (m-80) cc_final: 0.7882 (m-80) REVERT: A 769 VAL cc_start: 0.8065 (t) cc_final: 0.7779 (p) REVERT: B 354 GLU cc_start: 0.6839 (mp0) cc_final: 0.6508 (mp0) outliers start: 28 outliers final: 26 residues processed: 227 average time/residue: 0.2531 time to fit residues: 75.5826 Evaluate side-chains 230 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain C residue 22 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 54 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 65 optimal weight: 0.1980 chunk 66 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 9 optimal weight: 0.0170 chunk 11 optimal weight: 0.0980 chunk 103 optimal weight: 0.3980 chunk 114 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.2618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.169019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.133776 restraints weight = 39290.344| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.53 r_work: 0.3388 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10005 Z= 0.114 Angle : 0.528 4.996 13598 Z= 0.273 Chirality : 0.044 0.362 1547 Planarity : 0.004 0.051 1774 Dihedral : 6.716 57.144 1581 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.23 % Favored : 94.69 % Rotamer: Outliers : 2.18 % Allowed : 12.03 % Favored : 85.80 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 7.58 % 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: -1.31 (0.23), residues: 1242 helix: 0.49 (0.41), residues: 190 sheet: -0.70 (0.25), residues: 401 loop : -1.37 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 479 TYR 0.008 0.001 TYR A 415 PHE 0.016 0.001 PHE B 208 TRP 0.009 0.001 TRP A 34 HIS 0.003 0.001 HIS C 79 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9989) covalent geometry : angle 0.52123 (13555) SS BOND : bond 0.00138 ( 5) SS BOND : angle 0.99473 ( 10) hydrogen bonds : bond 0.02956 ( 312) hydrogen bonds : angle 5.63598 ( 858) link_BETA1-4 : bond 0.00273 ( 5) link_BETA1-4 : angle 1.87347 ( 15) link_NAG-ASN : bond 0.00174 ( 6) link_NAG-ASN : angle 1.62023 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.7972 (ptt-90) cc_final: 0.7660 (ptt90) REVERT: A 58 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6696 (mm-30) REVERT: A 183 THR cc_start: 0.7931 (t) cc_final: 0.7358 (p) REVERT: A 272 ASP cc_start: 0.6636 (m-30) cc_final: 0.6368 (m-30) REVERT: A 302 LEU cc_start: 0.8173 (mt) cc_final: 0.7940 (mp) REVERT: A 313 MET cc_start: 0.7061 (tpp) cc_final: 0.6513 (ttm) REVERT: A 335 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6958 (mt-10) REVERT: A 408 TRP cc_start: 0.8216 (m100) cc_final: 0.7824 (m-90) REVERT: A 457 SER cc_start: 0.7995 (t) cc_final: 0.7607 (p) REVERT: A 527 GLU cc_start: 0.7573 (mp0) cc_final: 0.7246 (mp0) REVERT: A 554 PHE cc_start: 0.8367 (m-80) cc_final: 0.7891 (m-80) REVERT: A 735 ARG cc_start: 0.6982 (mmm-85) cc_final: 0.6739 (mtt90) REVERT: A 769 VAL cc_start: 0.8025 (t) cc_final: 0.7735 (p) REVERT: B 354 GLU cc_start: 0.6812 (mp0) cc_final: 0.6486 (mp0) outliers start: 23 outliers final: 23 residues processed: 225 average time/residue: 0.2494 time to fit residues: 74.2360 Evaluate side-chains 229 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain C residue 22 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.169625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.134045 restraints weight = 39665.914| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.58 r_work: 0.3359 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 10005 Z= 0.307 Angle : 0.632 6.369 13598 Z= 0.332 Chirality : 0.047 0.376 1547 Planarity : 0.005 0.068 1774 Dihedral : 7.029 56.581 1581 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.56 % Allowed : 11.74 % Favored : 85.70 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 7.58 % 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: -1.56 (0.23), residues: 1242 helix: 0.30 (0.40), residues: 188 sheet: -0.79 (0.25), residues: 405 loop : -1.60 (0.22), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 703 TYR 0.016 0.002 TYR A 445 PHE 0.022 0.002 PHE B 223 TRP 0.015 0.003 TRP A 737 HIS 0.007 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00731 ( 9989) covalent geometry : angle 0.62424 (13555) SS BOND : bond 0.00297 ( 5) SS BOND : angle 1.79803 ( 10) hydrogen bonds : bond 0.03803 ( 312) hydrogen bonds : angle 5.81760 ( 858) link_BETA1-4 : bond 0.00228 ( 5) link_BETA1-4 : angle 1.99349 ( 15) link_NAG-ASN : bond 0.00316 ( 6) link_NAG-ASN : angle 1.79712 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.7966 (ptt-90) cc_final: 0.7650 (ptt90) REVERT: A 58 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6751 (mm-30) REVERT: A 78 THR cc_start: 0.8243 (m) cc_final: 0.7797 (p) REVERT: A 183 THR cc_start: 0.7905 (t) cc_final: 0.7322 (p) REVERT: A 272 ASP cc_start: 0.6664 (m-30) cc_final: 0.6406 (m-30) REVERT: A 302 LEU cc_start: 0.8174 (mt) cc_final: 0.7931 (mp) REVERT: A 313 MET cc_start: 0.7102 (tpp) cc_final: 0.6552 (ttm) REVERT: A 335 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7012 (mt-10) REVERT: A 408 TRP cc_start: 0.8240 (m100) cc_final: 0.7814 (m-90) REVERT: A 419 SER cc_start: 0.7962 (OUTLIER) cc_final: 0.7736 (p) REVERT: A 457 SER cc_start: 0.8002 (t) cc_final: 0.7615 (p) REVERT: A 527 GLU cc_start: 0.7623 (mp0) cc_final: 0.7313 (mp0) REVERT: A 554 PHE cc_start: 0.8378 (m-80) cc_final: 0.7890 (m-80) REVERT: A 769 VAL cc_start: 0.8120 (t) cc_final: 0.7832 (p) REVERT: B 313 GLN cc_start: 0.8092 (mt0) cc_final: 0.7828 (mt0) REVERT: B 354 GLU cc_start: 0.6884 (mp0) cc_final: 0.6662 (mp0) outliers start: 27 outliers final: 24 residues processed: 228 average time/residue: 0.2361 time to fit residues: 71.7456 Evaluate side-chains 233 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain C residue 22 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 25 optimal weight: 0.9980 chunk 73 optimal weight: 0.4980 chunk 104 optimal weight: 0.8980 chunk 92 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 89 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 723 GLN B 205 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.171028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.135794 restraints weight = 39270.276| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.50 r_work: 0.3415 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10005 Z= 0.185 Angle : 0.575 5.801 13598 Z= 0.299 Chirality : 0.045 0.367 1547 Planarity : 0.005 0.052 1774 Dihedral : 6.874 56.792 1581 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.08 % Allowed : 12.41 % Favored : 85.51 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 7.58 % 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: -1.48 (0.23), residues: 1242 helix: 0.41 (0.40), residues: 188 sheet: -0.77 (0.25), residues: 406 loop : -1.53 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 479 TYR 0.011 0.001 TYR A 415 PHE 0.012 0.001 PHE A 627 TRP 0.011 0.002 TRP C 59 HIS 0.004 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 9989) covalent geometry : angle 0.56700 (13555) SS BOND : bond 0.00104 ( 5) SS BOND : angle 1.85896 ( 10) hydrogen bonds : bond 0.03269 ( 312) hydrogen bonds : angle 5.71221 ( 858) link_BETA1-4 : bond 0.00238 ( 5) link_BETA1-4 : angle 1.86886 ( 15) link_NAG-ASN : bond 0.00155 ( 6) link_NAG-ASN : angle 1.64800 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.7954 (ptt-90) cc_final: 0.7642 (ptt90) REVERT: A 58 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6733 (mm-30) REVERT: A 183 THR cc_start: 0.7832 (t) cc_final: 0.7329 (p) REVERT: A 272 ASP cc_start: 0.6663 (m-30) cc_final: 0.6429 (m-30) REVERT: A 302 LEU cc_start: 0.8190 (mt) cc_final: 0.7954 (mp) REVERT: A 313 MET cc_start: 0.7094 (tpp) cc_final: 0.6496 (ttm) REVERT: A 335 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6970 (mt-10) REVERT: A 408 TRP cc_start: 0.8217 (m100) cc_final: 0.7846 (m-90) REVERT: A 457 SER cc_start: 0.7978 (t) cc_final: 0.7601 (p) REVERT: A 527 GLU cc_start: 0.7596 (mp0) cc_final: 0.7303 (mp0) REVERT: A 554 PHE cc_start: 0.8379 (m-80) cc_final: 0.7904 (m-80) REVERT: A 766 SER cc_start: 0.8385 (m) cc_final: 0.7729 (p) REVERT: A 769 VAL cc_start: 0.8087 (t) cc_final: 0.7800 (p) REVERT: B 354 GLU cc_start: 0.6835 (mp0) cc_final: 0.6539 (mp0) outliers start: 22 outliers final: 21 residues processed: 219 average time/residue: 0.2754 time to fit residues: 79.1798 Evaluate side-chains 226 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 393 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 32 optimal weight: 0.9990 chunk 116 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 96 optimal weight: 0.1980 chunk 30 optimal weight: 0.0970 chunk 20 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 11 optimal weight: 0.2980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.168842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.133650 restraints weight = 39660.873| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.53 r_work: 0.3419 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10005 Z= 0.139 Angle : 0.546 6.972 13598 Z= 0.282 Chirality : 0.044 0.364 1547 Planarity : 0.005 0.049 1774 Dihedral : 6.658 56.623 1580 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.99 % Allowed : 12.78 % Favored : 85.23 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 7.58 % 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: -1.35 (0.23), residues: 1242 helix: 0.52 (0.40), residues: 189 sheet: -0.70 (0.25), residues: 406 loop : -1.45 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 479 TYR 0.010 0.001 TYR A 415 PHE 0.010 0.001 PHE A 627 TRP 0.013 0.002 TRP C 59 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9989) covalent geometry : angle 0.53868 (13555) SS BOND : bond 0.00065 ( 5) SS BOND : angle 1.51565 ( 10) hydrogen bonds : bond 0.02975 ( 312) hydrogen bonds : angle 5.53043 ( 858) link_BETA1-4 : bond 0.00260 ( 5) link_BETA1-4 : angle 1.78219 ( 15) link_NAG-ASN : bond 0.00162 ( 6) link_NAG-ASN : angle 1.59236 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 216 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.7973 (ptt-90) cc_final: 0.7664 (ptt90) REVERT: A 58 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6734 (mm-30) REVERT: A 78 THR cc_start: 0.8241 (m) cc_final: 0.7823 (p) REVERT: A 183 THR cc_start: 0.7840 (t) cc_final: 0.7337 (p) REVERT: A 272 ASP cc_start: 0.6671 (m-30) cc_final: 0.6415 (m-30) REVERT: A 302 LEU cc_start: 0.8188 (mt) cc_final: 0.7953 (mp) REVERT: A 313 MET cc_start: 0.7090 (tpp) cc_final: 0.6522 (ttm) REVERT: A 335 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6985 (mt-10) REVERT: A 408 TRP cc_start: 0.8201 (m100) cc_final: 0.7899 (m-90) REVERT: A 419 SER cc_start: 0.8007 (OUTLIER) cc_final: 0.7727 (p) REVERT: A 457 SER cc_start: 0.8004 (t) cc_final: 0.7638 (p) REVERT: A 554 PHE cc_start: 0.8384 (m-80) cc_final: 0.7919 (m-80) REVERT: A 735 ARG cc_start: 0.6937 (mmm-85) cc_final: 0.6667 (mtt90) REVERT: A 737 TRP cc_start: 0.7040 (t-100) cc_final: 0.5866 (t-100) REVERT: A 766 SER cc_start: 0.8384 (m) cc_final: 0.7728 (p) REVERT: A 769 VAL cc_start: 0.8074 (t) cc_final: 0.7777 (p) REVERT: B 354 GLU cc_start: 0.6871 (mp0) cc_final: 0.6559 (mp0) outliers start: 21 outliers final: 20 residues processed: 230 average time/residue: 0.2565 time to fit residues: 77.6476 Evaluate side-chains 235 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 214 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 393 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 61 optimal weight: 0.0670 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 0 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.170732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.135302 restraints weight = 39443.329| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.53 r_work: 0.3415 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10005 Z= 0.200 Angle : 0.569 5.756 13598 Z= 0.295 Chirality : 0.045 0.368 1547 Planarity : 0.005 0.050 1774 Dihedral : 6.749 56.588 1580 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.27 % Allowed : 12.59 % Favored : 85.13 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 7.58 % 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: -1.41 (0.23), residues: 1242 helix: 0.47 (0.40), residues: 189 sheet: -0.72 (0.25), residues: 406 loop : -1.50 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 479 TYR 0.012 0.002 TYR A 445 PHE 0.015 0.002 PHE A 627 TRP 0.018 0.002 TRP C 59 HIS 0.004 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 9989) covalent geometry : angle 0.56194 (13555) SS BOND : bond 0.00113 ( 5) SS BOND : angle 1.60029 ( 10) hydrogen bonds : bond 0.03247 ( 312) hydrogen bonds : angle 5.55742 ( 858) link_BETA1-4 : bond 0.00259 ( 5) link_BETA1-4 : angle 1.79601 ( 15) link_NAG-ASN : bond 0.00200 ( 6) link_NAG-ASN : angle 1.60923 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5406.10 seconds wall clock time: 92 minutes 10.57 seconds (5530.57 seconds total)