Starting phenix.real_space_refine on Sat Jul 4 10:16:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p99_71403/07_2026/9p99_71403_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p99_71403/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9p99_71403/07_2026/9p99_71403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p99_71403/07_2026/9p99_71403.map" model { file = "/net/cci-nas-00/data/ceres_data/9p99_71403/07_2026/9p99_71403_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p99_71403/07_2026/9p99_71403_trim.cif" } 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-dev-6108/lib/python3.11/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, 28 Ad-hoc single atom residues: {' CA': 3, ' MN': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 4 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, 14 Ad-hoc single atom residues: {' MN': 3} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 2.31, per 1000 atoms: 0.12 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: 1.41 Conformation dependent library (CDL) restraints added in 566.2 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: 0.30 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: 3.26 Time building geometry restraints manager: 2.00 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 2.590 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 2.940 nonbonded pdb=" OG1 THR A 261 " pdb="MN MN A1206 " model vdw 1.848 2.940 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: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 14.370 Find NCS groups from input model: 0.050 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 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/Z covalent geometry : bond 0.00529 / 0.24 ( 9989) covalent geometry : angle 0.67931 / 0.39 (13555) SS BOND : bond 0.00294 / 0.15 ( 5) SS BOND : angle 0.74653 / 0.45 ( 10) hydrogen bonds : bond 0.20554 / 13.73 ( 312) hydrogen bonds : angle 9.35216 / 6.89 ( 858) link_BETA1-4 : bond 0.00629 / 0.32 ( 5) link_BETA1-4 : angle 3.89814 / 2.23 ( 15) link_NAG-ASN : bond 0.00355 / 0.21 ( 6) link_NAG-ASN : angle 2.22406 / 1.33 ( 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 : 0.353 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: 0.2489 time to fit residues: 71.4045 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 : 0.479 ------------------------------------------------------------------------------- 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: 0.4980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.173789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.138689 restraints weight = 39594.669| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.52 r_work: 0.3440 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.0593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10005 Z= 0.126 Angle : 0.569 5.380 13598 Z= 0.296 Chirality : 0.045 0.362 1547 Planarity : 0.005 0.051 1774 Dihedral : 7.999 59.132 1605 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.51 % Favored : 95.41 % Rotamer: Outliers : 1.04 % Allowed : 9.66 % 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: -1.43 (0.23), residues: 1242 helix: 0.32 (0.40), residues: 182 sheet: -0.87 (0.27), residues: 376 loop : -1.32 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 171 TYR 0.009 0.001 TYR B 131 PHE 0.012 0.001 PHE A 236 TRP 0.008 0.001 TRP A 408 HIS 0.003 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 9989) covalent geometry : angle 0.55847 / 0.29 (13555) SS BOND : bond 0.00275 / 0.14 ( 5) SS BOND : angle 0.59931 / 0.35 ( 10) hydrogen bonds : bond 0.04355 / 2.80 ( 312) hydrogen bonds : angle 6.74277 / 4.86 ( 858) link_BETA1-4 : bond 0.00276 / 0.16 ( 5) link_BETA1-4 : angle 2.52600 / 1.44 ( 15) link_NAG-ASN : bond 0.00294 / 0.15 ( 6) link_NAG-ASN : angle 1.97459 / 1.15 ( 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 211 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 200 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 SER cc_start: 0.8418 (p) cc_final: 0.8164 (m) REVERT: A 51 ARG cc_start: 0.7907 (ptt-90) cc_final: 0.7643 (ptt90) REVERT: A 58 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6744 (mm-30) REVERT: A 78 THR cc_start: 0.8224 (m) cc_final: 0.7781 (p) REVERT: A 183 THR cc_start: 0.7964 (t) cc_final: 0.7341 (p) REVERT: A 240 ASP cc_start: 0.6961 (m-30) cc_final: 0.6610 (t0) REVERT: A 272 ASP cc_start: 0.6685 (m-30) cc_final: 0.6345 (m-30) REVERT: A 302 LEU cc_start: 0.8206 (mt) cc_final: 0.7984 (mp) REVERT: A 335 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7015 (mt-10) REVERT: A 408 TRP cc_start: 0.8196 (m100) cc_final: 0.7864 (m-90) REVERT: A 457 SER cc_start: 0.7888 (t) cc_final: 0.7498 (p) REVERT: A 476 LYS cc_start: 0.7704 (tttt) cc_final: 0.7444 (tttt) REVERT: A 527 GLU cc_start: 0.7481 (mp0) cc_final: 0.7241 (mp0) REVERT: A 554 PHE cc_start: 0.8430 (m-80) cc_final: 0.7882 (m-80) REVERT: A 663 ARG cc_start: 0.7762 (mtm180) cc_final: 0.7250 (mtm110) REVERT: A 736 GLU cc_start: 0.6782 (pp20) cc_final: 0.6463 (tm-30) REVERT: A 769 VAL cc_start: 0.8028 (t) cc_final: 0.7728 (p) REVERT: B 271 ASP cc_start: 0.7509 (m-30) cc_final: 0.7166 (m-30) REVERT: B 285 PHE cc_start: 0.8569 (p90) cc_final: 0.8343 (p90) outliers start: 11 outliers final: 9 residues processed: 207 average time/residue: 0.2766 time to fit residues: 76.6728 Evaluate side-chains 208 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 199 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 495 TYR 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: 0.9990 chunk 62 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 82 optimal weight: 0.0980 chunk 8 optimal weight: 0.4980 chunk 85 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.170748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.136060 restraints weight = 39568.812| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.52 r_work: 0.3421 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10005 Z= 0.159 Angle : 0.555 5.390 13598 Z= 0.289 Chirality : 0.045 0.367 1547 Planarity : 0.004 0.047 1774 Dihedral : 7.191 59.866 1583 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.15 % Favored : 94.77 % Rotamer: Outliers : 1.23 % Allowed : 9.85 % Favored : 88.92 % 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: 0.57 (0.42), residues: 176 sheet: -0.82 (0.26), residues: 395 loop : -1.32 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 479 TYR 0.010 0.001 TYR A 445 PHE 0.013 0.001 PHE A 236 TRP 0.008 0.001 TRP A 34 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 9989) covalent geometry : angle 0.54619 / 0.29 (13555) SS BOND : bond 0.00243 / 0.13 ( 5) SS BOND : angle 0.68768 / 0.41 ( 10) hydrogen bonds : bond 0.03853 / 2.49 ( 312) hydrogen bonds : angle 6.22619 / 4.47 ( 858) link_BETA1-4 : bond 0.00300 / 0.16 ( 5) link_BETA1-4 : angle 2.33545 / 1.36 ( 15) link_NAG-ASN : bond 0.00173 / 0.10 ( 6) link_NAG-ASN : angle 1.80619 / 1.07 ( 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 215 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 0.530 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: 0.8339 (p) cc_final: 0.8104 (m) REVERT: A 51 ARG cc_start: 0.7954 (ptt-90) cc_final: 0.7688 (ptt90) REVERT: A 58 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6952 (mt-10) REVERT: A 78 THR cc_start: 0.8262 (m) cc_final: 0.7796 (p) REVERT: A 183 THR cc_start: 0.7990 (t) cc_final: 0.7380 (p) REVERT: A 240 ASP cc_start: 0.7002 (m-30) cc_final: 0.6623 (t0) REVERT: A 272 ASP cc_start: 0.6722 (m-30) cc_final: 0.6417 (m-30) REVERT: A 302 LEU cc_start: 0.8189 (mt) cc_final: 0.7938 (mp) REVERT: A 335 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7026 (mt-10) REVERT: A 408 TRP cc_start: 0.8204 (m100) cc_final: 0.7836 (m-90) REVERT: A 457 SER cc_start: 0.7927 (t) cc_final: 0.7556 (p) REVERT: A 526 GLU cc_start: 0.7743 (pt0) cc_final: 0.7417 (pt0) REVERT: A 527 GLU cc_start: 0.7539 (mp0) cc_final: 0.7248 (mp0) REVERT: A 554 PHE cc_start: 0.8403 (m-80) cc_final: 0.7876 (m-80) REVERT: A 769 VAL cc_start: 0.8047 (t) cc_final: 0.7766 (p) REVERT: B 271 ASP cc_start: 0.7440 (m-30) cc_final: 0.7066 (m-30) outliers start: 13 outliers final: 12 residues processed: 212 average time/residue: 0.2495 time to fit residues: 70.8995 Evaluate side-chains 207 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 495 TYR 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 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: 1.9990 chunk 79 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 94 optimal weight: 0.1980 chunk 118 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 114 optimal weight: 0.0370 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.172438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.136647 restraints weight = 39345.047| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.55 r_work: 0.3422 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10005 Z= 0.166 Angle : 0.549 5.239 13598 Z= 0.286 Chirality : 0.044 0.367 1547 Planarity : 0.004 0.049 1774 Dihedral : 6.971 58.692 1581 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.23 % Favored : 94.69 % Rotamer: Outliers : 1.80 % Allowed : 10.32 % Favored : 87.88 % 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: -1.34 (0.23), residues: 1242 helix: 0.54 (0.41), residues: 184 sheet: -0.77 (0.25), residues: 399 loop : -1.37 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 200 TYR 0.010 0.001 TYR A 531 PHE 0.013 0.001 PHE A 236 TRP 0.008 0.002 TRP B 258 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 9989) covalent geometry : angle 0.54124 / 0.28 (13555) SS BOND : bond 0.00250 / 0.13 ( 5) SS BOND : angle 0.55235 / 0.35 ( 10) hydrogen bonds : bond 0.03488 / 2.26 ( 312) hydrogen bonds : angle 5.95825 / 4.26 ( 858) link_BETA1-4 : bond 0.00245 / 0.13 ( 5) link_BETA1-4 : angle 2.16250 / 1.27 ( 15) link_NAG-ASN : bond 0.00155 / 0.08 ( 6) link_NAG-ASN : angle 1.71598 / 1.02 ( 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 221 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.310 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: 0.7955 (ptt-90) cc_final: 0.7686 (ptt90) REVERT: A 58 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6725 (mm-30) REVERT: A 78 THR cc_start: 0.8271 (m) cc_final: 0.7852 (p) REVERT: A 183 THR cc_start: 0.7934 (t) cc_final: 0.7352 (p) REVERT: A 236 PHE cc_start: 0.8043 (p90) cc_final: 0.7563 (p90) REVERT: A 240 ASP cc_start: 0.6949 (m-30) cc_final: 0.6531 (t0) REVERT: A 272 ASP cc_start: 0.6719 (m-30) cc_final: 0.6425 (m-30) REVERT: A 302 LEU cc_start: 0.8163 (mt) cc_final: 0.7917 (mp) REVERT: A 335 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7009 (mt-10) REVERT: A 372 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7182 (tm-30) REVERT: A 408 TRP cc_start: 0.8210 (m100) cc_final: 0.7856 (m-90) REVERT: A 457 SER cc_start: 0.7956 (t) cc_final: 0.7582 (p) REVERT: A 526 GLU cc_start: 0.7719 (pt0) cc_final: 0.7400 (pt0) REVERT: A 527 GLU cc_start: 0.7564 (mp0) cc_final: 0.7277 (mp0) REVERT: A 554 PHE cc_start: 0.8417 (m-80) cc_final: 0.7848 (m-80) REVERT: A 736 GLU cc_start: 0.6804 (tm-30) cc_final: 0.6538 (tm-30) REVERT: A 769 VAL cc_start: 0.8047 (t) cc_final: 0.7762 (p) REVERT: B 224 GLU cc_start: 0.7331 (mm-30) cc_final: 0.7124 (mm-30) REVERT: B 271 ASP cc_start: 0.7462 (m-30) cc_final: 0.7018 (m-30) outliers start: 19 outliers final: 18 residues processed: 216 average time/residue: 0.2275 time to fit residues: 66.6599 Evaluate side-chains 218 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 245 MET Chi-restraints excluded: chain A residue 372 GLU 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 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 299 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 40 optimal weight: 0.9980 chunk 77 optimal weight: 0.1980 chunk 88 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 100 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 chunk 83 optimal weight: 0.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.172617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.136978 restraints weight = 39300.492| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.53 r_work: 0.3400 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10005 Z= 0.144 Angle : 0.532 5.049 13598 Z= 0.276 Chirality : 0.044 0.365 1547 Planarity : 0.004 0.047 1774 Dihedral : 6.832 57.850 1581 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.72 % Favored : 94.20 % Rotamer: Outliers : 1.89 % Allowed : 10.70 % Favored : 87.41 % 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: -1.29 (0.23), residues: 1242 helix: 0.61 (0.41), residues: 184 sheet: -0.71 (0.25), residues: 399 loop : -1.36 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 171 TYR 0.009 0.001 TYR A 415 PHE 0.012 0.001 PHE A 627 TRP 0.008 0.001 TRP A 34 HIS 0.003 0.001 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 9989) covalent geometry : angle 0.52420 / 0.27 (13555) SS BOND : bond 0.00113 / 0.06 ( 5) SS BOND : angle 1.20965 / 0.72 ( 10) hydrogen bonds : bond 0.03190 / 2.07 ( 312) hydrogen bonds : angle 5.75123 / 4.11 ( 858) link_BETA1-4 : bond 0.00387 / 0.22 ( 5) link_BETA1-4 : angle 2.03174 / 1.21 ( 15) link_NAG-ASN : bond 0.00151 / 0.08 ( 6) link_NAG-ASN : angle 1.61625 / 0.96 ( 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 226 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 0.328 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: 0.7945 (ptt-90) cc_final: 0.7640 (ptt90) REVERT: A 58 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6690 (mm-30) REVERT: A 78 THR cc_start: 0.8289 (m) cc_final: 0.7864 (p) REVERT: A 183 THR cc_start: 0.7934 (t) cc_final: 0.7342 (p) REVERT: A 240 ASP cc_start: 0.6956 (m-30) cc_final: 0.6512 (t0) REVERT: A 272 ASP cc_start: 0.6677 (m-30) cc_final: 0.6384 (m-30) REVERT: A 302 LEU cc_start: 0.8148 (mt) cc_final: 0.7911 (mp) REVERT: A 313 MET cc_start: 0.7101 (tpp) cc_final: 0.6579 (ttm) REVERT: A 335 GLU cc_start: 0.7396 (mt-10) cc_final: 0.6970 (mt-10) REVERT: A 372 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7033 (tm-30) REVERT: A 408 TRP cc_start: 0.8200 (m100) cc_final: 0.7864 (m-90) REVERT: A 457 SER cc_start: 0.7948 (t) cc_final: 0.7565 (p) REVERT: A 526 GLU cc_start: 0.7734 (pt0) cc_final: 0.7428 (pt0) REVERT: A 527 GLU cc_start: 0.7557 (mp0) cc_final: 0.7230 (mp0) REVERT: A 554 PHE cc_start: 0.8413 (m-80) cc_final: 0.7873 (m-80) REVERT: A 572 ASP cc_start: 0.6834 (p0) cc_final: 0.6595 (p0) REVERT: A 769 VAL cc_start: 0.8037 (t) cc_final: 0.7752 (p) REVERT: B 271 ASP cc_start: 0.7444 (m-30) cc_final: 0.6971 (m-30) outliers start: 20 outliers final: 18 residues processed: 220 average time/residue: 0.2417 time to fit residues: 71.6625 Evaluate side-chains 221 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 245 MET Chi-restraints excluded: chain A residue 372 GLU 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 299 LEU 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: 0.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.0670 chunk 48 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 0.0040 chunk 58 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.4330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.171855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.136070 restraints weight = 39406.641| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.55 r_work: 0.3409 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10005 Z= 0.154 Angle : 0.539 5.048 13598 Z= 0.280 Chirality : 0.044 0.367 1547 Planarity : 0.004 0.049 1774 Dihedral : 6.798 57.447 1581 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.56 % Favored : 94.36 % Rotamer: Outliers : 2.08 % Allowed : 11.08 % 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: -1.29 (0.23), residues: 1242 helix: 0.47 (0.40), residues: 190 sheet: -0.68 (0.25), residues: 404 loop : -1.35 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 171 TYR 0.010 0.001 TYR A 415 PHE 0.013 0.001 PHE A 627 TRP 0.008 0.001 TRP A 34 HIS 0.004 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 ( 9989) covalent geometry : angle 0.53211 / 0.28 (13555) SS BOND : bond 0.00418 / 0.21 ( 5) SS BOND : angle 1.06818 / 0.64 ( 10) hydrogen bonds : bond 0.03156 / 2.05 ( 312) hydrogen bonds : angle 5.66723 / 4.06 ( 858) link_BETA1-4 : bond 0.00228 / 0.12 ( 5) link_BETA1-4 : angle 1.96068 / 1.16 ( 15) link_NAG-ASN : bond 0.00162 / 0.09 ( 6) link_NAG-ASN : angle 1.60415 / 0.96 ( 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 227 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.526 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: 0.7961 (ptt-90) cc_final: 0.7676 (ptt90) REVERT: A 58 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6712 (mm-30) REVERT: A 78 THR cc_start: 0.8261 (m) cc_final: 0.7867 (p) REVERT: A 183 THR cc_start: 0.7937 (t) cc_final: 0.7360 (p) REVERT: A 240 ASP cc_start: 0.6949 (m-30) cc_final: 0.6534 (t0) REVERT: A 272 ASP cc_start: 0.6690 (m-30) cc_final: 0.6410 (m-30) REVERT: A 302 LEU cc_start: 0.8157 (mt) cc_final: 0.7925 (mp) REVERT: A 335 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7018 (mt-10) REVERT: A 372 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7089 (tm-30) REVERT: A 408 TRP cc_start: 0.8218 (m100) cc_final: 0.7840 (m-90) REVERT: A 457 SER cc_start: 0.7960 (t) cc_final: 0.7583 (p) REVERT: A 526 GLU cc_start: 0.7694 (pt0) cc_final: 0.7391 (pt0) REVERT: A 527 GLU cc_start: 0.7584 (mp0) cc_final: 0.7291 (mp0) REVERT: A 554 PHE cc_start: 0.8415 (m-80) cc_final: 0.7891 (m-80) REVERT: A 572 ASP cc_start: 0.6744 (p0) cc_final: 0.6530 (p0) REVERT: A 735 ARG cc_start: 0.6973 (mmm-85) cc_final: 0.6601 (mtt-85) REVERT: A 736 GLU cc_start: 0.6784 (tm-30) cc_final: 0.6550 (tm-30) REVERT: A 769 VAL cc_start: 0.8065 (t) cc_final: 0.7780 (p) REVERT: B 271 ASP cc_start: 0.7454 (m-30) cc_final: 0.6985 (m-30) REVERT: B 354 GLU cc_start: 0.6924 (mp0) cc_final: 0.6589 (mp0) outliers start: 22 outliers final: 20 residues processed: 220 average time/residue: 0.2713 time to fit residues: 80.2605 Evaluate side-chains 223 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 245 MET Chi-restraints excluded: chain A residue 372 GLU 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 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: 0.9980 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 114 optimal weight: 0.0170 chunk 59 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 41 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 = 0.4022 r_free = 0.4022 target = 0.167816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.132471 restraints weight = 39533.584| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.55 r_work: 0.3357 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 10005 Z= 0.228 Angle : 0.581 5.878 13598 Z= 0.303 Chirality : 0.045 0.372 1547 Planarity : 0.005 0.046 1774 Dihedral : 6.903 56.906 1581 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.36 % Favored : 93.56 % Rotamer: Outliers : 2.27 % Allowed : 10.98 % Favored : 86.74 % 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: -1.39 (0.23), residues: 1242 helix: 0.44 (0.40), residues: 189 sheet: -0.74 (0.25), residues: 409 loop : -1.43 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 703 TYR 0.014 0.002 TYR A 445 PHE 0.015 0.002 PHE A 236 TRP 0.008 0.002 TRP A 408 HIS 0.004 0.001 HIS B 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 ( 9989) covalent geometry : angle 0.57304 / 0.30 (13555) SS BOND : bond 0.00130 / 0.07 ( 5) SS BOND : angle 1.75028 / 1.04 ( 10) hydrogen bonds : bond 0.03473 / 2.26 ( 312) hydrogen bonds : angle 5.73707 / 4.11 ( 858) link_BETA1-4 : bond 0.00256 / 0.14 ( 5) link_BETA1-4 : angle 1.97584 / 1.17 ( 15) link_NAG-ASN : bond 0.00213 / 0.12 ( 6) link_NAG-ASN : angle 1.65423 / 0.99 ( 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 234 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 210 time to evaluate : 0.440 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: symmetry clash REVERT: A 51 ARG cc_start: 0.7968 (ptt-90) cc_final: 0.7650 (ptt90) REVERT: A 58 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6712 (mm-30) REVERT: A 78 THR cc_start: 0.8295 (m) cc_final: 0.7853 (p) REVERT: A 183 THR cc_start: 0.7902 (t) cc_final: 0.7318 (p) REVERT: A 240 ASP cc_start: 0.6970 (m-30) cc_final: 0.6595 (t0) REVERT: A 272 ASP cc_start: 0.6652 (m-30) cc_final: 0.6374 (m-30) REVERT: A 302 LEU cc_start: 0.8129 (mt) cc_final: 0.7898 (mp) REVERT: A 313 MET cc_start: 0.7112 (tpp) cc_final: 0.6565 (ttm) REVERT: A 335 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6985 (mt-10) REVERT: A 372 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7132 (tm-30) REVERT: A 408 TRP cc_start: 0.8234 (m100) cc_final: 0.7821 (m-90) REVERT: A 457 SER cc_start: 0.7988 (t) cc_final: 0.7596 (p) REVERT: A 527 GLU cc_start: 0.7588 (mp0) cc_final: 0.7286 (mp0) REVERT: A 554 PHE cc_start: 0.8396 (m-80) cc_final: 0.7894 (m-80) REVERT: A 572 ASP cc_start: 0.6700 (p0) cc_final: 0.6491 (p0) REVERT: A 736 GLU cc_start: 0.6826 (tm-30) cc_final: 0.6570 (tm-30) REVERT: A 769 VAL cc_start: 0.8077 (t) cc_final: 0.7789 (p) REVERT: B 200 ARG cc_start: 0.8018 (mtp180) cc_final: 0.7738 (mmm160) REVERT: B 271 ASP cc_start: 0.7424 (m-30) cc_final: 0.6955 (m-30) REVERT: B 302 ARG cc_start: 0.7280 (mtp180) cc_final: 0.7068 (mtp85) REVERT: B 354 GLU cc_start: 0.6968 (mp0) cc_final: 0.6627 (mp0) outliers start: 24 outliers final: 22 residues processed: 226 average time/residue: 0.2684 time to fit residues: 81.0715 Evaluate side-chains 226 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 245 MET Chi-restraints excluded: chain A residue 372 GLU 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 215 SER Chi-restraints excluded: chain B residue 229 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 40 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 522 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.167733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.132203 restraints weight = 39810.192| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.58 r_work: 0.3350 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 10005 Z= 0.267 Angle : 0.609 6.031 13598 Z= 0.319 Chirality : 0.046 0.372 1547 Planarity : 0.005 0.073 1774 Dihedral : 7.008 56.797 1581 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.46 % Allowed : 11.93 % Favored : 85.61 % 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: -1.52 (0.23), residues: 1242 helix: 0.31 (0.40), residues: 188 sheet: -0.75 (0.25), residues: 405 loop : -1.57 (0.22), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 479 TYR 0.016 0.002 TYR A 445 PHE 0.019 0.002 PHE B 223 TRP 0.012 0.002 TRP C 59 HIS 0.006 0.001 HIS B 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.27 ( 9989) covalent geometry : angle 0.60180 / 0.32 (13555) SS BOND : bond 0.00330 / 0.23 ( 5) SS BOND : angle 1.75378 / 1.04 ( 10) hydrogen bonds : bond 0.03683 / 2.40 ( 312) hydrogen bonds : angle 5.79418 / 4.15 ( 858) link_BETA1-4 : bond 0.00221 / 0.12 ( 5) link_BETA1-4 : angle 1.96808 / 1.17 ( 15) link_NAG-ASN : bond 0.00258 / 0.14 ( 6) link_NAG-ASN : angle 1.72314 / 1.04 ( 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 234 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 0.486 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: 0.7947 (ptt-90) cc_final: 0.7626 (ptt90) REVERT: A 58 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6708 (mm-30) REVERT: A 78 THR cc_start: 0.8230 (m) cc_final: 0.7758 (p) REVERT: A 183 THR cc_start: 0.7885 (t) cc_final: 0.7313 (p) REVERT: A 240 ASP cc_start: 0.6969 (m-30) cc_final: 0.6614 (t0) REVERT: A 272 ASP cc_start: 0.6629 (m-30) cc_final: 0.6360 (m-30) REVERT: A 302 LEU cc_start: 0.8139 (mt) cc_final: 0.7910 (mp) REVERT: A 313 MET cc_start: 0.7117 (tpp) cc_final: 0.6578 (ttm) REVERT: A 335 GLU cc_start: 0.7415 (mt-10) cc_final: 0.6998 (mt-10) REVERT: A 372 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7193 (tm-30) REVERT: A 408 TRP cc_start: 0.8242 (m100) cc_final: 0.7844 (m-90) REVERT: A 457 SER cc_start: 0.8001 (t) cc_final: 0.7609 (p) REVERT: A 527 GLU cc_start: 0.7599 (mp0) cc_final: 0.7306 (mp0) REVERT: A 554 PHE cc_start: 0.8374 (m-80) cc_final: 0.7878 (m-80) REVERT: A 736 GLU cc_start: 0.6831 (tm-30) cc_final: 0.6571 (tm-30) REVERT: A 750 MET cc_start: 0.5368 (mtm) cc_final: 0.5149 (mtm) REVERT: A 769 VAL cc_start: 0.8092 (t) cc_final: 0.7802 (p) REVERT: B 200 ARG cc_start: 0.8022 (mtp180) cc_final: 0.7722 (mmm160) REVERT: B 271 ASP cc_start: 0.7343 (m-30) cc_final: 0.6918 (m-30) REVERT: B 280 LYS cc_start: 0.8202 (tptm) cc_final: 0.7965 (tttm) REVERT: B 302 ARG cc_start: 0.7287 (mtp180) cc_final: 0.7038 (mtp85) REVERT: B 354 GLU cc_start: 0.6910 (mp0) cc_final: 0.6547 (mp0) outliers start: 26 outliers final: 21 residues processed: 224 average time/residue: 0.2554 time to fit residues: 77.2438 Evaluate side-chains 226 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 245 MET Chi-restraints excluded: chain A residue 372 GLU 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 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 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: 0.9990 chunk 104 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.170500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.135132 restraints weight = 39295.827| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.53 r_work: 0.3352 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.1692 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 : 0.582 5.884 13598 Z= 0.303 Chirality : 0.045 0.370 1547 Planarity : 0.005 0.048 1774 Dihedral : 6.870 56.849 1580 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.37 % Allowed : 11.93 % 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: -1.53 (0.23), residues: 1242 helix: 0.31 (0.40), residues: 188 sheet: -0.78 (0.25), residues: 406 loop : -1.57 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 479 TYR 0.015 0.002 TYR A 531 PHE 0.014 0.002 PHE A 627 TRP 0.013 0.002 TRP C 59 HIS 0.004 0.001 HIS B 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.21 ( 9989) covalent geometry : angle 0.57418 / 0.30 (13555) SS BOND : bond 0.00116 / 0.06 ( 5) SS BOND : angle 1.67738 / 0.99 ( 10) hydrogen bonds : bond 0.03404 / 2.21 ( 312) hydrogen bonds : angle 5.70359 / 4.09 ( 858) link_BETA1-4 : bond 0.00243 / 0.12 ( 5) link_BETA1-4 : angle 1.87374 / 1.12 ( 15) link_NAG-ASN : bond 0.00190 / 0.10 ( 6) link_NAG-ASN : angle 1.65635 / 0.99 ( 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 237 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 0.303 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: 0.7934 (ptt-90) cc_final: 0.7604 (ptt90) REVERT: A 58 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6693 (mm-30) REVERT: A 78 THR cc_start: 0.8259 (m) cc_final: 0.7792 (p) REVERT: A 183 THR cc_start: 0.7782 (t) cc_final: 0.7269 (p) REVERT: A 214 PHE cc_start: 0.8190 (m-80) cc_final: 0.7850 (m-80) REVERT: A 240 ASP cc_start: 0.6955 (m-30) cc_final: 0.6629 (t0) REVERT: A 272 ASP cc_start: 0.6599 (m-30) cc_final: 0.6329 (m-30) REVERT: A 302 LEU cc_start: 0.8132 (mt) cc_final: 0.7911 (mp) REVERT: A 313 MET cc_start: 0.7109 (tpp) cc_final: 0.6538 (ttm) REVERT: A 335 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6947 (mt-10) REVERT: A 372 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7144 (tm-30) REVERT: A 408 TRP cc_start: 0.8216 (m100) cc_final: 0.7832 (m-90) REVERT: A 457 SER cc_start: 0.8009 (t) cc_final: 0.7640 (p) REVERT: A 527 GLU cc_start: 0.7569 (mp0) cc_final: 0.7267 (mp0) REVERT: A 554 PHE cc_start: 0.8378 (m-80) cc_final: 0.7898 (m-80) REVERT: A 736 GLU cc_start: 0.6799 (tm-30) cc_final: 0.6563 (tm-30) REVERT: A 750 MET cc_start: 0.5350 (mtm) cc_final: 0.5098 (mtm) REVERT: A 769 VAL cc_start: 0.8069 (t) cc_final: 0.7779 (p) REVERT: B 200 ARG cc_start: 0.8014 (mtp180) cc_final: 0.7785 (mtp180) REVERT: B 271 ASP cc_start: 0.7352 (m-30) cc_final: 0.6913 (m-30) REVERT: B 302 ARG cc_start: 0.7281 (mtp180) cc_final: 0.7045 (mtp85) REVERT: B 354 GLU cc_start: 0.6892 (mp0) cc_final: 0.6562 (mp0) outliers start: 25 outliers final: 23 residues processed: 228 average time/residue: 0.2458 time to fit residues: 76.5979 Evaluate side-chains 234 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 210 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 245 MET Chi-restraints excluded: chain A residue 372 GLU 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 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 229 ARG Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 299 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 32 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 109 optimal weight: 0.0570 chunk 11 optimal weight: 0.4980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.167583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.132302 restraints weight = 39690.114| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.54 r_work: 0.3375 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.1755 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= 0.212 Angle : 0.587 10.727 13598 Z= 0.304 Chirality : 0.045 0.370 1547 Planarity : 0.005 0.048 1774 Dihedral : 6.857 56.754 1580 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.27 % Allowed : 12.50 % 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: -1.55 (0.23), residues: 1242 helix: 0.30 (0.40), residues: 188 sheet: -0.79 (0.25), residues: 406 loop : -1.59 (0.22), residues: 648 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 0.014 0.002 PHE B 223 TRP 0.017 0.002 TRP C 59 HIS 0.005 0.001 HIS B 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 ( 9989) covalent geometry : angle 0.57999 / 0.30 (13555) SS BOND : bond 0.00132 / 0.07 ( 5) SS BOND : angle 1.62860 / 0.97 ( 10) hydrogen bonds : bond 0.03366 / 2.19 ( 312) hydrogen bonds : angle 5.65427 / 4.05 ( 858) link_BETA1-4 : bond 0.00256 / 0.13 ( 5) link_BETA1-4 : angle 1.84189 / 1.11 ( 15) link_NAG-ASN : bond 0.00191 / 0.10 ( 6) link_NAG-ASN : angle 1.64387 / 0.99 ( 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 238 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 0.388 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: 0.7937 (ptt-90) cc_final: 0.7617 (ptt90) REVERT: A 58 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6708 (mm-30) REVERT: A 78 THR cc_start: 0.8258 (m) cc_final: 0.7808 (p) REVERT: A 183 THR cc_start: 0.7830 (t) cc_final: 0.7329 (p) REVERT: A 214 PHE cc_start: 0.8269 (m-80) cc_final: 0.7911 (m-80) REVERT: A 240 ASP cc_start: 0.6978 (m-30) cc_final: 0.6664 (t0) REVERT: A 272 ASP cc_start: 0.6642 (m-30) cc_final: 0.6381 (m-30) REVERT: A 302 LEU cc_start: 0.8151 (mt) cc_final: 0.7929 (mp) REVERT: A 313 MET cc_start: 0.7120 (tpp) cc_final: 0.6547 (ttm) REVERT: A 335 GLU cc_start: 0.7407 (mt-10) cc_final: 0.6981 (mt-10) REVERT: A 372 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7121 (tm-30) REVERT: A 408 TRP cc_start: 0.8233 (m100) cc_final: 0.7846 (m-90) REVERT: A 457 SER cc_start: 0.7998 (t) cc_final: 0.7652 (p) REVERT: A 527 GLU cc_start: 0.7574 (mp0) cc_final: 0.7292 (mp0) REVERT: A 554 PHE cc_start: 0.8383 (m-80) cc_final: 0.7910 (m-80) REVERT: A 704 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7328 (mm-30) REVERT: A 736 GLU cc_start: 0.6821 (tm-30) cc_final: 0.6579 (tm-30) REVERT: A 750 MET cc_start: 0.5341 (mtm) cc_final: 0.5101 (mtm) REVERT: A 766 SER cc_start: 0.8413 (m) cc_final: 0.7746 (p) REVERT: A 769 VAL cc_start: 0.8094 (t) cc_final: 0.7806 (p) REVERT: B 271 ASP cc_start: 0.7370 (m-30) cc_final: 0.6943 (m-30) REVERT: B 302 ARG cc_start: 0.7262 (mtp180) cc_final: 0.7027 (mtp85) REVERT: B 354 GLU cc_start: 0.6905 (mp0) cc_final: 0.6573 (mp0) outliers start: 24 outliers final: 22 residues processed: 229 average time/residue: 0.2574 time to fit residues: 80.0032 Evaluate side-chains 235 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 245 MET Chi-restraints excluded: chain A residue 372 GLU 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 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 229 ARG Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 299 LEU 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: 0.0170 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 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: 1.9990 chunk 68 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.171130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.135668 restraints weight = 39340.901| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.56 r_work: 0.3414 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10005 Z= 0.168 Angle : 0.555 5.421 13598 Z= 0.288 Chirality : 0.045 0.366 1547 Planarity : 0.005 0.049 1774 Dihedral : 6.742 56.668 1580 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.18 % Allowed : 12.97 % Favored : 84.85 % 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: -1.46 (0.23), residues: 1242 helix: 0.38 (0.40), residues: 189 sheet: -0.75 (0.25), residues: 404 loop : -1.51 (0.22), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 479 TYR 0.011 0.001 TYR A 415 PHE 0.013 0.001 PHE A 627 TRP 0.019 0.002 TRP C 59 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 9989) covalent geometry : angle 0.54780 / 0.29 (13555) SS BOND : bond 0.00109 / 0.05 ( 5) SS BOND : angle 1.49866 / 0.89 ( 10) hydrogen bonds : bond 0.03110 / 2.02 ( 312) hydrogen bonds : angle 5.60051 / 4.01 ( 858) link_BETA1-4 : bond 0.00259 / 0.13 ( 5) link_BETA1-4 : angle 1.77421 / 1.07 ( 15) link_NAG-ASN : bond 0.00165 / 0.09 ( 6) link_NAG-ASN : angle 1.58595 / 0.95 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5775.03 seconds wall clock time: 98 minutes 35.62 seconds (5915.62 seconds total)