Starting phenix.real_space_refine on Wed Mar 4 10:15:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pe2_20321/03_2026/6pe2_20321.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pe2_20321/03_2026/6pe2_20321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pe2_20321/03_2026/6pe2_20321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pe2_20321/03_2026/6pe2_20321.map" model { file = "/net/cci-nas-00/data/ceres_data/6pe2_20321/03_2026/6pe2_20321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pe2_20321/03_2026/6pe2_20321.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 176 5.49 5 Mg 4 5.21 5 S 36 5.16 5 C 7547 2.51 5 N 2222 2.21 5 O 2761 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12746 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3611 Classifications: {'peptide': 456} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 13, 'TRANS': 442} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'TYR:plan': 1, 'ARG:plan': 5, 'GLN:plan1': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 980 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 116} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 184 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "D" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 557 Classifications: {'DNA': 27} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 26} Chain: "E" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1143 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain breaks: 1 Chain: "G" Number of atoms: 3626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3626 Classifications: {'peptide': 456} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 13, 'TRANS': 442} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'TYR:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 62 Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 980 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 116} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 184 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "J" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 416 Classifications: {'DNA': 20} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 19} Chain: "K" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 997 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.63, per 1000 atoms: 0.21 Number of scatterers: 12746 At special positions: 0 Unit cell: (126.44, 110.2, 136.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 176 15.00 Mg 4 11.99 O 2761 8.00 N 2222 7.00 C 7547 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 382.9 milliseconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 6 sheets defined 59.9% alpha, 8.0% beta 74 base pairs and 108 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 114 through 129 removed outlier: 3.583A pdb=" N SER A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 removed outlier: 3.843A pdb=" N GLU A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU A 134 " --> pdb=" O GLN A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 158 through 170 Processing helix chain 'A' and resid 172 through 183 removed outlier: 3.603A pdb=" N HIS A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 206 through 213 removed outlier: 3.678A pdb=" N ILE A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 294 Processing helix chain 'A' and resid 305 through 315 Processing helix chain 'A' and resid 339 through 354 Processing helix chain 'A' and resid 365 through 376 Processing helix chain 'A' and resid 387 through 392 removed outlier: 3.879A pdb=" N ILE A 391 " --> pdb=" O ASN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 408 removed outlier: 3.841A pdb=" N ALA A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 422 Processing helix chain 'A' and resid 428 through 447 Processing helix chain 'A' and resid 465 through 480 removed outlier: 3.842A pdb=" N ASP A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 515 Processing helix chain 'A' and resid 521 through 526 removed outlier: 3.970A pdb=" N ASN A 526 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 540 Processing helix chain 'A' and resid 548 through 563 removed outlier: 3.552A pdb=" N ARG A 563 " --> pdb=" O TYR A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 568 removed outlier: 3.851A pdb=" N MET A 567 " --> pdb=" O ASN A 564 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 568 " --> pdb=" O THR A 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 564 through 568' Processing helix chain 'B' and resid 620 through 639 Processing helix chain 'B' and resid 652 through 657 removed outlier: 3.641A pdb=" N SER B 657 " --> pdb=" O VAL B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 682 Processing helix chain 'B' and resid 693 through 702 Processing helix chain 'B' and resid 708 through 734 Processing helix chain 'G' and resid 116 through 141 removed outlier: 3.974A pdb=" N LEU G 133 " --> pdb=" O GLU G 129 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU G 134 " --> pdb=" O SER G 130 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU G 135 " --> pdb=" O GLN G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 150 Processing helix chain 'G' and resid 159 through 171 removed outlier: 3.619A pdb=" N ILE G 163 " --> pdb=" O ASN G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 184 removed outlier: 3.570A pdb=" N HIS G 179 " --> pdb=" O ARG G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 198 Processing helix chain 'G' and resid 207 through 214 removed outlier: 3.725A pdb=" N ILE G 211 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET G 214 " --> pdb=" O VAL G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 295 Processing helix chain 'G' and resid 306 through 316 Processing helix chain 'G' and resid 340 through 355 Processing helix chain 'G' and resid 366 through 377 Processing helix chain 'G' and resid 388 through 393 removed outlier: 3.884A pdb=" N ILE G 392 " --> pdb=" O ASN G 388 " (cutoff:3.500A) Processing helix chain 'G' and resid 401 through 409 removed outlier: 3.852A pdb=" N ALA G 405 " --> pdb=" O LYS G 401 " (cutoff:3.500A) Processing helix chain 'G' and resid 410 through 423 Processing helix chain 'G' and resid 429 through 448 Processing helix chain 'G' and resid 466 through 481 removed outlier: 3.964A pdb=" N ASP G 472 " --> pdb=" O ASP G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 492 through 516 Processing helix chain 'G' and resid 522 through 526 Processing helix chain 'G' and resid 528 through 541 Processing helix chain 'G' and resid 549 through 564 Processing helix chain 'G' and resid 565 through 570 removed outlier: 3.769A pdb=" N MET G 568 " --> pdb=" O ASN G 565 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU G 569 " --> pdb=" O THR G 566 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG G 570 " --> pdb=" O GLU G 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 565 through 570' Processing helix chain 'H' and resid 620 through 639 Processing helix chain 'H' and resid 652 through 657 removed outlier: 3.641A pdb=" N SER H 657 " --> pdb=" O VAL H 653 " (cutoff:3.500A) Processing helix chain 'H' and resid 667 through 682 Processing helix chain 'H' and resid 693 through 702 Processing helix chain 'H' and resid 708 through 734 Processing sheet with id=AA1, first strand: chain 'A' and resid 204 through 205 removed outlier: 6.624A pdb=" N ALA A 257 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE A 272 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN A 255 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N PHE A 274 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TYR A 253 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU A 227 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE A 300 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N PHE A 229 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N SER A 302 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N GLU A 231 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 9.823A pdb=" N LEU A 296 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 9.847A pdb=" N PHE A 335 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL A 298 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N PHE A 337 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE A 300 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 241 removed outlier: 3.818A pdb=" N ILE A 246 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA4, first strand: chain 'G' and resid 205 through 206 removed outlier: 6.632A pdb=" N ALA G 258 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE G 273 " --> pdb=" O GLN G 256 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLN G 256 " --> pdb=" O PHE G 273 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHE G 275 " --> pdb=" O TYR G 254 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR G 254 " --> pdb=" O PHE G 275 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU G 228 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE G 301 " --> pdb=" O LEU G 228 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE G 230 " --> pdb=" O ILE G 301 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N SER G 303 " --> pdb=" O PHE G 230 " (cutoff:3.500A) removed outlier: 9.413A pdb=" N GLU G 232 " --> pdb=" O SER G 303 " (cutoff:3.500A) removed outlier: 9.891A pdb=" N LEU G 297 " --> pdb=" O LYS G 334 " (cutoff:3.500A) removed outlier: 9.907A pdb=" N PHE G 336 " --> pdb=" O LEU G 297 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL G 299 " --> pdb=" O PHE G 336 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE G 338 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE G 301 " --> pdb=" O PHE G 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 240 through 242 removed outlier: 4.055A pdb=" N ILE G 247 " --> pdb=" O ASP G 242 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 357 through 359 509 hydrogen bonds defined for protein. 1491 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 188 hydrogen bonds 356 hydrogen bond angles 0 basepair planarities 74 basepair parallelities 108 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3144 1.34 - 1.45: 3386 1.45 - 1.57: 6409 1.57 - 1.69: 342 1.69 - 1.81: 56 Bond restraints: 13337 Sorted by residual: bond pdb=" N GLU G 458 " pdb=" CA GLU G 458 " ideal model delta sigma weight residual 1.454 1.490 -0.035 1.17e-02 7.31e+03 9.09e+00 bond pdb=" N ILE G 457 " pdb=" CA ILE G 457 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.29e-02 6.01e+03 7.50e+00 bond pdb=" N CYS G 456 " pdb=" CA CYS G 456 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.31e+00 bond pdb=" N ARG A 540 " pdb=" CA ARG A 540 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.28e-02 6.10e+03 6.06e+00 bond pdb=" C3' DG K -33 " pdb=" O3' DG K -33 " ideal model delta sigma weight residual 1.422 1.494 -0.072 3.00e-02 1.11e+03 5.77e+00 ... (remaining 13332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 18544 2.17 - 4.35: 195 4.35 - 6.52: 11 6.52 - 8.69: 0 8.69 - 10.86: 3 Bond angle restraints: 18753 Sorted by residual: angle pdb=" N CYS G 459 " pdb=" CA CYS G 459 " pdb=" C CYS G 459 " ideal model delta sigma weight residual 112.97 104.08 8.89 1.06e+00 8.90e-01 7.03e+01 angle pdb=" CA GLY A 541 " pdb=" C GLY A 541 " pdb=" O GLY A 541 " ideal model delta sigma weight residual 122.24 118.22 4.02 8.70e-01 1.32e+00 2.13e+01 angle pdb=" O3' DG K -33 " pdb=" P DC K -32 " pdb=" OP1 DC K -32 " ideal model delta sigma weight residual 108.00 118.86 -10.86 3.00e+00 1.11e-01 1.31e+01 angle pdb=" N GLU G 458 " pdb=" CA GLU G 458 " pdb=" C GLU G 458 " ideal model delta sigma weight residual 110.17 104.65 5.52 1.61e+00 3.86e-01 1.18e+01 angle pdb=" O3' DG K -33 " pdb=" P DC K -32 " pdb=" OP2 DC K -32 " ideal model delta sigma weight residual 108.00 99.16 8.84 3.00e+00 1.11e-01 8.68e+00 ... (remaining 18748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 6880 35.69 - 71.37: 634 71.37 - 107.06: 7 107.06 - 142.75: 6 142.75 - 178.44: 7 Dihedral angle restraints: 7534 sinusoidal: 4144 harmonic: 3390 Sorted by residual: dihedral pdb=" C8 GTP G 601 " pdb=" C1' GTP G 601 " pdb=" N9 GTP G 601 " pdb=" O4' GTP G 601 " ideal model delta sinusoidal sigma weight residual 104.59 -31.58 136.18 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" C8 GTP A 601 " pdb=" C1' GTP A 601 " pdb=" N9 GTP A 601 " pdb=" O4' GTP A 601 " ideal model delta sinusoidal sigma weight residual 104.59 -30.62 135.21 1 2.00e+01 2.50e-03 4.10e+01 dihedral pdb=" CA ALA A 155 " pdb=" C ALA A 155 " pdb=" N THR A 156 " pdb=" CA THR A 156 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 7531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1797 0.049 - 0.097: 254 0.097 - 0.146: 53 0.146 - 0.194: 5 0.194 - 0.243: 1 Chirality restraints: 2110 Sorted by residual: chirality pdb=" CA CYS G 459 " pdb=" N CYS G 459 " pdb=" C CYS G 459 " pdb=" CB CYS G 459 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA MET A 537 " pdb=" N MET A 537 " pdb=" C MET A 537 " pdb=" CB MET A 537 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" P DG D 14 " pdb=" OP1 DG D 14 " pdb=" OP2 DG D 14 " pdb=" O5' DG D 14 " both_signs ideal model delta sigma weight residual True 2.35 -2.51 -0.16 2.00e-01 2.50e+01 6.71e-01 ... (remaining 2107 not shown) Planarity restraints: 1783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 172 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO A 173 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 173 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 173 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY G 173 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO G 174 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO G 174 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 174 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 340 " -0.028 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO A 341 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 341 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 341 " -0.024 5.00e-02 4.00e+02 ... (remaining 1780 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 176 2.63 - 3.20: 10418 3.20 - 3.76: 21854 3.76 - 4.33: 28768 4.33 - 4.90: 43563 Nonbonded interactions: 104779 Sorted by model distance: nonbonded pdb=" OG1 THR G 142 " pdb=" OD2 ASP G 162 " model vdw 2.062 3.040 nonbonded pdb=" O1G GTP G 601 " pdb="MG MG G 602 " model vdw 2.072 2.170 nonbonded pdb=" O1G GTP A 601 " pdb="MG MG A 602 " model vdw 2.100 2.170 nonbonded pdb=" O1B GTP A 601 " pdb="MG MG A 602 " model vdw 2.117 2.170 nonbonded pdb=" O1B GTP G 601 " pdb="MG MG G 602 " model vdw 2.122 2.170 ... (remaining 104774 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 'A' and (resid 114 through 456 or (resid 457 and (name N or name CA or na \ me C or name O or name CB )) or resid 458 through 602)) selection = (chain 'G' and (resid 115 through 154 or (resid 155 through 156 and (name N or n \ ame CA or name C or name O or name CB )) or resid 157 through 540 or (resid 541 \ and (name N or name CA or name C or name O or name CB )) or resid 542 through 54 \ 3 or (resid 544 and (name N or name CA or name C or name O or name CB )) or resi \ d 545 or (resid 546 and (name N or name CA or name C or name O or name CB )) or \ resid 547 through 602)) } ncs_group { reference = chain 'B' selection = chain 'H' } ncs_group { reference = (chain 'C' and resid 1 through 9) selection = chain 'I' } ncs_group { reference = (chain 'E' and resid 20 through 74) selection = chain 'K' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.630 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 13340 Z= 0.161 Angle : 0.540 10.863 18753 Z= 0.328 Chirality : 0.036 0.243 2110 Planarity : 0.004 0.048 1783 Dihedral : 21.705 178.437 5334 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.22), residues: 1140 helix: -0.29 (0.18), residues: 652 sheet: -0.93 (0.54), residues: 67 loop : -1.75 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 175 TYR 0.011 0.001 TYR G 511 PHE 0.008 0.001 PHE G 273 TRP 0.004 0.001 TRP G 443 HIS 0.002 0.001 HIS B 681 Details of bonding type rmsd covalent geometry : bond 0.00294 (13337) covalent geometry : angle 0.53963 (18753) hydrogen bonds : bond 0.13622 ( 697) hydrogen bonds : angle 4.97251 ( 1847) Misc. bond : bond 0.02472 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 LEU cc_start: 0.9349 (mt) cc_final: 0.9104 (tp) REVERT: A 425 ASP cc_start: 0.8222 (p0) cc_final: 0.7997 (t0) REVERT: A 522 THR cc_start: 0.9407 (p) cc_final: 0.9194 (p) REVERT: B 647 ASN cc_start: 0.9016 (t0) cc_final: 0.8731 (t0) REVERT: B 668 PHE cc_start: 0.8504 (t80) cc_final: 0.8086 (t80) REVERT: B 693 ASN cc_start: 0.9476 (m-40) cc_final: 0.9126 (p0) REVERT: B 700 LEU cc_start: 0.9757 (tt) cc_final: 0.9462 (pp) REVERT: B 706 ASP cc_start: 0.8827 (t0) cc_final: 0.8623 (t0) REVERT: G 197 LEU cc_start: 0.9056 (mt) cc_final: 0.8790 (tt) REVERT: G 340 ASP cc_start: 0.8249 (t70) cc_final: 0.7942 (t70) REVERT: G 440 MET cc_start: 0.9352 (mmm) cc_final: 0.9066 (mmp) REVERT: H 650 PHE cc_start: 0.8727 (t80) cc_final: 0.8431 (t80) REVERT: H 668 PHE cc_start: 0.8500 (t80) cc_final: 0.8057 (t80) REVERT: H 706 ASP cc_start: 0.8293 (t0) cc_final: 0.8065 (t0) REVERT: H 718 ILE cc_start: 0.9622 (pt) cc_final: 0.9390 (mm) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1134 time to fit residues: 25.1900 Evaluate side-chains 91 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.0270 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 308 ASN A 399 GLN ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 GLN B 704 ASN G 170 HIS G 502 ASN H 669 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.051514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.038590 restraints weight = 75998.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.039908 restraints weight = 32068.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.040771 restraints weight = 18604.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.041315 restraints weight = 13109.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.041683 restraints weight = 10590.248| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13340 Z= 0.155 Angle : 0.542 6.275 18753 Z= 0.306 Chirality : 0.036 0.154 2110 Planarity : 0.004 0.047 1783 Dihedral : 26.037 175.973 3100 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.20 % Allowed : 9.81 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.24), residues: 1140 helix: 1.22 (0.20), residues: 656 sheet: -0.49 (0.52), residues: 75 loop : -1.15 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 563 TYR 0.010 0.001 TYR A 519 PHE 0.012 0.001 PHE B 668 TRP 0.005 0.001 TRP A 323 HIS 0.006 0.001 HIS A 546 Details of bonding type rmsd covalent geometry : bond 0.00331 (13337) covalent geometry : angle 0.54191 (18753) hydrogen bonds : bond 0.04133 ( 697) hydrogen bonds : angle 3.66664 ( 1847) Misc. bond : bond 0.00405 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 196 LEU cc_start: 0.9240 (mt) cc_final: 0.9002 (tp) REVERT: A 425 ASP cc_start: 0.8200 (p0) cc_final: 0.7968 (t0) REVERT: A 476 MET cc_start: 0.9488 (mmm) cc_final: 0.9283 (tpp) REVERT: A 517 MET cc_start: 0.7836 (tpp) cc_final: 0.7373 (tpp) REVERT: A 522 THR cc_start: 0.9452 (p) cc_final: 0.9212 (t) REVERT: A 563 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7806 (ptp90) REVERT: A 567 MET cc_start: 0.8614 (mmm) cc_final: 0.8244 (tpt) REVERT: B 647 ASN cc_start: 0.9015 (t0) cc_final: 0.8751 (t0) REVERT: B 693 ASN cc_start: 0.9529 (m-40) cc_final: 0.9241 (p0) REVERT: B 706 ASP cc_start: 0.8882 (t0) cc_final: 0.8600 (t0) REVERT: G 197 LEU cc_start: 0.9157 (mt) cc_final: 0.8944 (tt) REVERT: G 477 MET cc_start: 0.8904 (tpp) cc_final: 0.8631 (tpp) REVERT: G 568 MET cc_start: 0.8141 (mmm) cc_final: 0.7750 (mmm) REVERT: H 620 ASP cc_start: 0.8459 (p0) cc_final: 0.8007 (p0) REVERT: H 622 LEU cc_start: 0.9630 (mm) cc_final: 0.9408 (pp) REVERT: H 627 MET cc_start: 0.9419 (ttt) cc_final: 0.9032 (tmm) REVERT: H 650 PHE cc_start: 0.8606 (t80) cc_final: 0.8358 (t80) outliers start: 12 outliers final: 5 residues processed: 108 average time/residue: 0.1014 time to fit residues: 16.6365 Evaluate side-chains 90 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain B residue 704 ASN Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain H residue 680 LEU Chi-restraints excluded: chain H residue 711 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 113 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 502 ASN G 565 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.047890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.034497 restraints weight = 80364.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.035748 restraints weight = 36091.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.036548 restraints weight = 22116.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.037067 restraints weight = 16219.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.037395 restraints weight = 13294.485| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13340 Z= 0.191 Angle : 0.564 7.093 18753 Z= 0.316 Chirality : 0.036 0.146 2110 Planarity : 0.004 0.045 1783 Dihedral : 26.099 178.444 3100 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.10 % Allowed : 9.21 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.25), residues: 1140 helix: 1.85 (0.20), residues: 654 sheet: 0.20 (0.60), residues: 60 loop : -0.72 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 563 TYR 0.024 0.001 TYR B 652 PHE 0.015 0.001 PHE A 534 TRP 0.007 0.001 TRP A 195 HIS 0.004 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00409 (13337) covalent geometry : angle 0.56387 (18753) hydrogen bonds : bond 0.04186 ( 697) hydrogen bonds : angle 3.52518 ( 1847) Misc. bond : bond 0.00141 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 196 LEU cc_start: 0.9310 (mt) cc_final: 0.9044 (tp) REVERT: A 425 ASP cc_start: 0.8205 (p0) cc_final: 0.7953 (t0) REVERT: A 476 MET cc_start: 0.9405 (mmm) cc_final: 0.9109 (mmt) REVERT: A 517 MET cc_start: 0.7764 (tpp) cc_final: 0.7436 (tpp) REVERT: A 563 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7775 (ptp90) REVERT: B 627 MET cc_start: 0.9582 (ttt) cc_final: 0.9163 (tmm) REVERT: B 647 ASN cc_start: 0.8988 (t0) cc_final: 0.8706 (t0) REVERT: B 668 PHE cc_start: 0.8705 (t80) cc_final: 0.8398 (t80) REVERT: B 693 ASN cc_start: 0.9501 (m-40) cc_final: 0.9208 (p0) REVERT: B 698 LEU cc_start: 0.9690 (mt) cc_final: 0.9485 (mp) REVERT: B 703 ARG cc_start: 0.8962 (ptp-110) cc_final: 0.8729 (ttm110) REVERT: G 481 MET cc_start: 0.9043 (mmm) cc_final: 0.8558 (tpp) REVERT: G 568 MET cc_start: 0.8262 (mmm) cc_final: 0.7869 (mmm) REVERT: H 627 MET cc_start: 0.9373 (ttt) cc_final: 0.9014 (tmm) REVERT: H 650 PHE cc_start: 0.8620 (t80) cc_final: 0.8386 (t80) REVERT: H 672 LEU cc_start: 0.9772 (OUTLIER) cc_final: 0.9520 (mm) REVERT: H 686 ASN cc_start: 0.9246 (p0) cc_final: 0.8901 (p0) outliers start: 21 outliers final: 8 residues processed: 96 average time/residue: 0.1071 time to fit residues: 15.4459 Evaluate side-chains 86 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 704 ASN Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 440 MET Chi-restraints excluded: chain H residue 672 LEU Chi-restraints excluded: chain H residue 708 ASP Chi-restraints excluded: chain H residue 711 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 79 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 34 optimal weight: 0.0670 chunk 67 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.3120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.048743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.036085 restraints weight = 79684.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.037317 restraints weight = 35509.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.038121 restraints weight = 21459.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.038645 restraints weight = 15437.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.038946 restraints weight = 12551.886| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13340 Z= 0.144 Angle : 0.527 6.555 18753 Z= 0.297 Chirality : 0.036 0.146 2110 Planarity : 0.003 0.044 1783 Dihedral : 25.989 176.295 3100 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.70 % Allowed : 10.91 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.26), residues: 1140 helix: 2.14 (0.20), residues: 657 sheet: 0.82 (0.61), residues: 61 loop : -0.60 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 703 TYR 0.024 0.001 TYR B 652 PHE 0.021 0.001 PHE H 668 TRP 0.003 0.001 TRP A 323 HIS 0.003 0.001 HIS A 546 Details of bonding type rmsd covalent geometry : bond 0.00308 (13337) covalent geometry : angle 0.52685 (18753) hydrogen bonds : bond 0.03613 ( 697) hydrogen bonds : angle 3.34401 ( 1847) Misc. bond : bond 0.00166 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 LEU cc_start: 0.9216 (mt) cc_final: 0.8950 (tp) REVERT: A 476 MET cc_start: 0.9390 (mmm) cc_final: 0.8938 (mmt) REVERT: A 517 MET cc_start: 0.7922 (tpp) cc_final: 0.7455 (tpp) REVERT: A 563 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7473 (ptp90) REVERT: B 627 MET cc_start: 0.9665 (ttt) cc_final: 0.9148 (tmm) REVERT: B 647 ASN cc_start: 0.8966 (t0) cc_final: 0.8693 (t0) REVERT: B 668 PHE cc_start: 0.8658 (t80) cc_final: 0.8322 (t80) REVERT: B 682 TYR cc_start: 0.8683 (OUTLIER) cc_final: 0.8390 (t80) REVERT: B 693 ASN cc_start: 0.9470 (m-40) cc_final: 0.9122 (p0) REVERT: H 627 MET cc_start: 0.9431 (ttt) cc_final: 0.9000 (tmm) REVERT: H 650 PHE cc_start: 0.8649 (t80) cc_final: 0.8412 (t80) REVERT: H 686 ASN cc_start: 0.9273 (p0) cc_final: 0.8953 (p0) outliers start: 17 outliers final: 6 residues processed: 91 average time/residue: 0.1042 time to fit residues: 14.1069 Evaluate side-chains 84 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain H residue 711 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 88 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 106 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 692 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.048623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.035928 restraints weight = 80285.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.037181 restraints weight = 35838.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.037990 restraints weight = 21351.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.038517 restraints weight = 15354.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.038832 restraints weight = 12385.617| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13340 Z= 0.146 Angle : 0.532 6.371 18753 Z= 0.297 Chirality : 0.036 0.200 2110 Planarity : 0.003 0.042 1783 Dihedral : 25.996 177.648 3100 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.70 % Allowed : 11.61 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.26), residues: 1140 helix: 2.43 (0.20), residues: 644 sheet: -0.18 (0.55), residues: 72 loop : -0.48 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 639 TYR 0.025 0.001 TYR B 652 PHE 0.017 0.001 PHE H 668 TRP 0.004 0.001 TRP A 195 HIS 0.002 0.000 HIS A 546 Details of bonding type rmsd covalent geometry : bond 0.00313 (13337) covalent geometry : angle 0.53241 (18753) hydrogen bonds : bond 0.03691 ( 697) hydrogen bonds : angle 3.29482 ( 1847) Misc. bond : bond 0.00294 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 196 LEU cc_start: 0.9212 (mt) cc_final: 0.8928 (tp) REVERT: A 232 MET cc_start: 0.8643 (tpp) cc_final: 0.8294 (mtp) REVERT: A 476 MET cc_start: 0.9387 (mmm) cc_final: 0.9160 (tpp) REVERT: A 517 MET cc_start: 0.7995 (tpp) cc_final: 0.7538 (tpp) REVERT: A 563 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7436 (ptp90) REVERT: A 567 MET cc_start: 0.8817 (mmt) cc_final: 0.8584 (tpt) REVERT: B 627 MET cc_start: 0.9611 (ttt) cc_final: 0.9084 (tmm) REVERT: B 647 ASN cc_start: 0.8903 (t0) cc_final: 0.8643 (t0) REVERT: B 668 PHE cc_start: 0.8771 (t80) cc_final: 0.8403 (t80) REVERT: B 682 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.8399 (t80) REVERT: B 693 ASN cc_start: 0.9450 (m-40) cc_final: 0.9169 (p0) REVERT: G 440 MET cc_start: 0.8982 (mmp) cc_final: 0.8755 (tpp) REVERT: G 477 MET cc_start: 0.9302 (OUTLIER) cc_final: 0.8493 (mmm) REVERT: G 568 MET cc_start: 0.8895 (mmm) cc_final: 0.8508 (mmm) REVERT: H 627 MET cc_start: 0.9437 (ttt) cc_final: 0.8979 (tmm) REVERT: H 650 PHE cc_start: 0.8656 (t80) cc_final: 0.8402 (t80) REVERT: H 686 ASN cc_start: 0.9259 (p0) cc_final: 0.8932 (p0) outliers start: 17 outliers final: 8 residues processed: 89 average time/residue: 0.1086 time to fit residues: 14.3617 Evaluate side-chains 84 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 477 MET Chi-restraints excluded: chain H residue 711 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 1 optimal weight: 0.0570 chunk 120 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN A 440 ASN ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.046999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.033596 restraints weight = 82298.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.034843 restraints weight = 37509.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.035651 restraints weight = 23206.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.036114 restraints weight = 17083.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.036468 restraints weight = 14264.143| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13340 Z= 0.203 Angle : 0.591 9.057 18753 Z= 0.324 Chirality : 0.037 0.171 2110 Planarity : 0.003 0.037 1783 Dihedral : 26.175 179.066 3100 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.90 % Allowed : 12.31 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.26), residues: 1140 helix: 2.57 (0.20), residues: 647 sheet: 0.33 (0.55), residues: 79 loop : -0.37 (0.34), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 703 TYR 0.023 0.001 TYR B 652 PHE 0.013 0.001 PHE H 668 TRP 0.008 0.001 TRP A 195 HIS 0.004 0.001 HIS G 391 Details of bonding type rmsd covalent geometry : bond 0.00436 (13337) covalent geometry : angle 0.59124 (18753) hydrogen bonds : bond 0.04301 ( 697) hydrogen bonds : angle 3.49323 ( 1847) Misc. bond : bond 0.00160 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 232 MET cc_start: 0.8370 (tpp) cc_final: 0.8133 (tpp) REVERT: A 507 LEU cc_start: 0.9470 (tp) cc_final: 0.9262 (tt) REVERT: A 517 MET cc_start: 0.7952 (tpp) cc_final: 0.7635 (tpp) REVERT: A 563 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7546 (ptp90) REVERT: B 627 MET cc_start: 0.9562 (ttt) cc_final: 0.9016 (tmm) REVERT: B 647 ASN cc_start: 0.8894 (t0) cc_final: 0.8594 (t0) REVERT: B 693 ASN cc_start: 0.9456 (m-40) cc_final: 0.9151 (p0) REVERT: G 440 MET cc_start: 0.9178 (mmp) cc_final: 0.8797 (tpp) REVERT: G 538 MET cc_start: 0.9114 (tpp) cc_final: 0.8776 (mmt) REVERT: H 650 PHE cc_start: 0.8611 (t80) cc_final: 0.8350 (t80) REVERT: H 686 ASN cc_start: 0.9203 (p0) cc_final: 0.8964 (p0) REVERT: H 693 ASN cc_start: 0.9586 (m-40) cc_final: 0.9083 (p0) outliers start: 19 outliers final: 12 residues processed: 83 average time/residue: 0.1096 time to fit residues: 13.4944 Evaluate side-chains 81 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 704 ASN Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain H residue 708 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 69 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 72 optimal weight: 0.0470 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.048748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.035647 restraints weight = 81300.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.036923 restraints weight = 36912.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.037706 restraints weight = 22275.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.038224 restraints weight = 16313.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.038551 restraints weight = 13365.913| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13340 Z= 0.134 Angle : 0.547 10.159 18753 Z= 0.301 Chirality : 0.036 0.176 2110 Planarity : 0.003 0.036 1783 Dihedral : 26.068 178.320 3100 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.10 % Allowed : 13.91 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.26), residues: 1140 helix: 2.55 (0.20), residues: 657 sheet: 0.89 (0.62), residues: 61 loop : -0.31 (0.33), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 639 TYR 0.023 0.001 TYR B 652 PHE 0.018 0.001 PHE B 668 TRP 0.006 0.000 TRP A 442 HIS 0.002 0.000 HIS G 343 Details of bonding type rmsd covalent geometry : bond 0.00288 (13337) covalent geometry : angle 0.54680 (18753) hydrogen bonds : bond 0.03610 ( 697) hydrogen bonds : angle 3.26326 ( 1847) Misc. bond : bond 0.00187 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 232 MET cc_start: 0.8288 (tpp) cc_final: 0.7982 (tpp) REVERT: A 476 MET cc_start: 0.9313 (tpp) cc_final: 0.9005 (mmt) REVERT: A 517 MET cc_start: 0.8049 (tpp) cc_final: 0.7665 (tpp) REVERT: A 537 MET cc_start: 0.8865 (tpp) cc_final: 0.8660 (tpp) REVERT: A 563 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7587 (ptp90) REVERT: A 567 MET cc_start: 0.8842 (tpt) cc_final: 0.8608 (tpt) REVERT: B 627 MET cc_start: 0.9585 (ttt) cc_final: 0.9073 (tmm) REVERT: B 647 ASN cc_start: 0.8948 (t0) cc_final: 0.8671 (t0) REVERT: B 682 TYR cc_start: 0.8385 (t80) cc_final: 0.7650 (t80) REVERT: B 693 ASN cc_start: 0.9412 (m-40) cc_final: 0.9003 (p0) REVERT: G 440 MET cc_start: 0.9202 (mmp) cc_final: 0.8789 (tpp) REVERT: G 538 MET cc_start: 0.9097 (tpp) cc_final: 0.8762 (mmt) REVERT: H 650 PHE cc_start: 0.8653 (t80) cc_final: 0.8372 (t80) REVERT: H 682 TYR cc_start: 0.8187 (t80) cc_final: 0.7780 (t80) REVERT: H 686 ASN cc_start: 0.9252 (p0) cc_final: 0.9006 (p0) REVERT: H 692 ASN cc_start: 0.9311 (m-40) cc_final: 0.8860 (t0) REVERT: H 693 ASN cc_start: 0.9561 (m-40) cc_final: 0.9006 (p0) outliers start: 11 outliers final: 7 residues processed: 79 average time/residue: 0.0961 time to fit residues: 11.6808 Evaluate side-chains 78 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain H residue 708 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 73 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 98 optimal weight: 0.0570 chunk 38 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 16 optimal weight: 0.0570 chunk 6 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 410 ASN A 527 GLN ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.049768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.037247 restraints weight = 79223.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.038518 restraints weight = 35111.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.039377 restraints weight = 20988.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.039885 restraints weight = 14890.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.040197 restraints weight = 11997.375| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13340 Z= 0.122 Angle : 0.546 10.841 18753 Z= 0.296 Chirality : 0.035 0.248 2110 Planarity : 0.003 0.041 1783 Dihedral : 26.001 176.807 3100 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.10 % Allowed : 13.81 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.26), residues: 1140 helix: 2.70 (0.20), residues: 646 sheet: 1.11 (0.63), residues: 61 loop : -0.37 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 703 TYR 0.009 0.001 TYR G 511 PHE 0.017 0.001 PHE B 668 TRP 0.008 0.001 TRP A 442 HIS 0.002 0.000 HIS A 546 Details of bonding type rmsd covalent geometry : bond 0.00259 (13337) covalent geometry : angle 0.54604 (18753) hydrogen bonds : bond 0.03454 ( 697) hydrogen bonds : angle 3.14797 ( 1847) Misc. bond : bond 0.00093 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.424 Fit side-chains REVERT: A 196 LEU cc_start: 0.9259 (mt) cc_final: 0.9000 (tp) REVERT: A 476 MET cc_start: 0.9307 (tpp) cc_final: 0.8916 (mmt) REVERT: A 517 MET cc_start: 0.8091 (tpp) cc_final: 0.7738 (tpp) REVERT: A 537 MET cc_start: 0.8816 (tpp) cc_final: 0.8612 (tpp) REVERT: B 627 MET cc_start: 0.9573 (ttt) cc_final: 0.9072 (tmm) REVERT: B 647 ASN cc_start: 0.8969 (t0) cc_final: 0.8704 (t0) REVERT: B 682 TYR cc_start: 0.8236 (t80) cc_final: 0.7539 (t80) REVERT: B 693 ASN cc_start: 0.9384 (m-40) cc_final: 0.8724 (p0) REVERT: G 440 MET cc_start: 0.9158 (mmp) cc_final: 0.8947 (tpp) REVERT: G 538 MET cc_start: 0.9034 (tpp) cc_final: 0.8758 (mmt) REVERT: G 568 MET cc_start: 0.9141 (mmm) cc_final: 0.8814 (mmm) REVERT: H 617 THR cc_start: 0.8849 (m) cc_final: 0.8529 (t) REVERT: H 627 MET cc_start: 0.9422 (ttt) cc_final: 0.8711 (tmm) REVERT: H 650 PHE cc_start: 0.8684 (t80) cc_final: 0.8386 (t80) REVERT: H 682 TYR cc_start: 0.8213 (t80) cc_final: 0.7714 (t80) REVERT: H 686 ASN cc_start: 0.9251 (p0) cc_final: 0.8990 (p0) REVERT: H 693 ASN cc_start: 0.9500 (m-40) cc_final: 0.8884 (p0) outliers start: 11 outliers final: 7 residues processed: 84 average time/residue: 0.1094 time to fit residues: 13.9742 Evaluate side-chains 80 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain H residue 708 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 22 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 76 optimal weight: 0.0570 chunk 86 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.049852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.036497 restraints weight = 80867.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.037781 restraints weight = 36555.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.038628 restraints weight = 22435.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.039097 restraints weight = 16415.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.039495 restraints weight = 13557.594| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13340 Z= 0.122 Angle : 0.548 12.949 18753 Z= 0.297 Chirality : 0.035 0.193 2110 Planarity : 0.003 0.035 1783 Dihedral : 26.043 176.977 3100 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.00 % Allowed : 14.31 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.26), residues: 1140 helix: 2.68 (0.20), residues: 652 sheet: 1.06 (0.62), residues: 61 loop : -0.34 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 639 TYR 0.010 0.001 TYR G 511 PHE 0.020 0.001 PHE B 668 TRP 0.007 0.001 TRP A 442 HIS 0.002 0.000 HIS A 546 Details of bonding type rmsd covalent geometry : bond 0.00261 (13337) covalent geometry : angle 0.54812 (18753) hydrogen bonds : bond 0.03462 ( 697) hydrogen bonds : angle 3.14697 ( 1847) Misc. bond : bond 0.00101 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 196 LEU cc_start: 0.9252 (mt) cc_final: 0.8993 (tp) REVERT: A 232 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8413 (mmm) REVERT: A 476 MET cc_start: 0.9313 (tpp) cc_final: 0.8960 (mmt) REVERT: A 517 MET cc_start: 0.8072 (tpp) cc_final: 0.7752 (tpp) REVERT: B 627 MET cc_start: 0.9589 (ttt) cc_final: 0.9040 (tmm) REVERT: B 647 ASN cc_start: 0.8956 (t0) cc_final: 0.8677 (t0) REVERT: B 682 TYR cc_start: 0.8320 (t80) cc_final: 0.7593 (t80) REVERT: B 693 ASN cc_start: 0.9398 (m-40) cc_final: 0.8730 (p0) REVERT: G 440 MET cc_start: 0.9185 (mmp) cc_final: 0.8731 (tpp) REVERT: G 538 MET cc_start: 0.9098 (tpp) cc_final: 0.8636 (mmp) REVERT: G 568 MET cc_start: 0.9223 (mmm) cc_final: 0.8895 (mmm) REVERT: H 617 THR cc_start: 0.8949 (m) cc_final: 0.8677 (t) REVERT: H 627 MET cc_start: 0.9434 (ttt) cc_final: 0.8721 (tmm) REVERT: H 650 PHE cc_start: 0.8721 (t80) cc_final: 0.8410 (t80) REVERT: H 682 TYR cc_start: 0.8250 (t80) cc_final: 0.7751 (t80) REVERT: H 686 ASN cc_start: 0.9325 (p0) cc_final: 0.9070 (p0) REVERT: H 693 ASN cc_start: 0.9516 (m-40) cc_final: 0.8931 (p0) outliers start: 10 outliers final: 7 residues processed: 81 average time/residue: 0.0983 time to fit residues: 12.1465 Evaluate side-chains 80 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain H residue 700 LEU Chi-restraints excluded: chain H residue 708 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 82 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 410 ASN A 527 GLN ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.049654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.036694 restraints weight = 80869.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.037989 restraints weight = 35066.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.038843 restraints weight = 20902.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.039370 restraints weight = 14946.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.039713 restraints weight = 12112.139| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13340 Z= 0.145 Angle : 0.563 13.364 18753 Z= 0.305 Chirality : 0.035 0.180 2110 Planarity : 0.003 0.045 1783 Dihedral : 26.105 177.368 3100 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.00 % Allowed : 14.41 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.26), residues: 1140 helix: 2.80 (0.20), residues: 645 sheet: 0.65 (0.64), residues: 59 loop : -0.21 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 703 TYR 0.011 0.001 TYR G 511 PHE 0.020 0.001 PHE B 668 TRP 0.004 0.001 TRP G 443 HIS 0.002 0.001 HIS G 391 Details of bonding type rmsd covalent geometry : bond 0.00312 (13337) covalent geometry : angle 0.56293 (18753) hydrogen bonds : bond 0.03698 ( 697) hydrogen bonds : angle 3.28598 ( 1847) Misc. bond : bond 0.00100 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.412 Fit side-chains REVERT: A 232 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8474 (mmt) REVERT: A 476 MET cc_start: 0.9362 (tpp) cc_final: 0.8966 (mmt) REVERT: A 517 MET cc_start: 0.8057 (tpp) cc_final: 0.7731 (tpp) REVERT: B 627 MET cc_start: 0.9613 (ttt) cc_final: 0.9017 (tmm) REVERT: B 639 ARG cc_start: 0.8781 (mpp80) cc_final: 0.8419 (mpp80) REVERT: B 647 ASN cc_start: 0.9028 (t0) cc_final: 0.8740 (t0) REVERT: B 682 TYR cc_start: 0.8461 (t80) cc_final: 0.7705 (t80) REVERT: B 693 ASN cc_start: 0.9485 (m-40) cc_final: 0.8824 (p0) REVERT: G 233 MET cc_start: 0.8773 (tpt) cc_final: 0.8561 (tpp) REVERT: G 440 MET cc_start: 0.9312 (mmp) cc_final: 0.8869 (tpp) REVERT: G 538 MET cc_start: 0.9142 (tpp) cc_final: 0.8684 (mmp) REVERT: G 568 MET cc_start: 0.9252 (mmm) cc_final: 0.8943 (mmm) REVERT: H 627 MET cc_start: 0.9464 (ttt) cc_final: 0.8769 (tmm) REVERT: H 650 PHE cc_start: 0.8730 (t80) cc_final: 0.8438 (t80) REVERT: H 682 TYR cc_start: 0.8343 (t80) cc_final: 0.7803 (t80) REVERT: H 686 ASN cc_start: 0.9294 (p0) cc_final: 0.9077 (p0) REVERT: H 693 ASN cc_start: 0.9560 (m-40) cc_final: 0.8999 (p0) REVERT: H 706 ASP cc_start: 0.8722 (t70) cc_final: 0.8398 (p0) outliers start: 10 outliers final: 8 residues processed: 78 average time/residue: 0.0964 time to fit residues: 11.7053 Evaluate side-chains 78 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 551 LEU Chi-restraints excluded: chain H residue 708 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 100 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 67 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 GLN ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.050393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.037444 restraints weight = 80891.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.038765 restraints weight = 34882.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.039628 restraints weight = 20725.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.040170 restraints weight = 14772.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.040497 restraints weight = 11954.691| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13340 Z= 0.125 Angle : 0.558 13.276 18753 Z= 0.300 Chirality : 0.035 0.202 2110 Planarity : 0.003 0.045 1783 Dihedral : 26.059 177.707 3100 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.80 % Allowed : 14.51 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.26), residues: 1140 helix: 2.78 (0.20), residues: 647 sheet: 0.77 (0.64), residues: 58 loop : -0.23 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 703 TYR 0.009 0.001 TYR G 511 PHE 0.015 0.001 PHE B 668 TRP 0.006 0.000 TRP A 442 HIS 0.002 0.000 HIS A 546 Details of bonding type rmsd covalent geometry : bond 0.00268 (13337) covalent geometry : angle 0.55837 (18753) hydrogen bonds : bond 0.03485 ( 697) hydrogen bonds : angle 3.19202 ( 1847) Misc. bond : bond 0.00126 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1845.91 seconds wall clock time: 32 minutes 37.54 seconds (1957.54 seconds total)