Starting phenix.real_space_refine on Sat Sep 12 01:23:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pe2_20321/09_2026/6pe2_20321.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pe2_20321/09_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_20321/09_2026/6pe2_20321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pe2_20321/09_2026/6pe2_20321.map" model { file = "/net/cci-nas-00/data/ceres_data/6pe2_20321/09_2026/6pe2_20321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pe2_20321/09_2026/6pe2_20321.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6pe2_20321/09_2026/6pe2_20321.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pe2_20321/09_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-2.2.1-6174/lib/python3.11/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: 2.81, per 1000 atoms: 0.22 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: 1.00 Conformation dependent library (CDL) restraints added in 330.1 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: 1.62 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: 2.47 Time building geometry restraints manager: 1.30 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=" C3' DG K -33 " pdb=" O3' DG K -33 " ideal model delta sigma weight residual 1.435 1.494 -0.059 1.30e-02 5.92e+03 2.06e+01 bond pdb=" C3' DA D 24 " pdb=" C2' DA D 24 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.41e+01 bond pdb=" C3' DT E 20 " pdb=" C2' DT E 20 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DC K -23 " pdb=" C2' DC K -23 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DT E 55 " pdb=" C2' DT E 55 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 ... (remaining 13332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 18402 2.17 - 4.35: 336 4.35 - 6.52: 12 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=" O4' DA E 15 " pdb=" C1' DA E 15 " pdb=" N9 DA E 15 " ideal model delta sigma weight residual 108.00 111.25 -3.25 7.00e-01 2.04e+00 2.16e+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=" N3 DT J 7 " pdb=" C4 DT J 7 " pdb=" O4 DT J 7 " ideal model delta sigma weight residual 119.90 122.66 -2.76 6.00e-01 2.78e+00 2.11e+01 angle pdb=" N3 DT D 7 " pdb=" C4 DT D 7 " pdb=" O4 DT D 7 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.07e+01 ... (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: 1629 0.049 - 0.097: 386 0.097 - 0.146: 89 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=" 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 2.34 -2.51 -0.17 2.00e-01 2.50e+01 7.57e-01 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 ... (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: 1.320 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.860 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13340 Z= 0.400 Angle : 0.644 10.863 18753 Z= 0.541 Chirality : 0.044 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/Z covalent geometry : bond 0.00435 / 0.40 (13337) covalent geometry : angle 0.64351 / 0.54 (18753) hydrogen bonds : bond 0.13622 / 8.82 ( 697) hydrogen bonds : angle 4.97251 / 3.43 ( 1847) Misc. bond : bond 0.02472 / 1.30 ( 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 : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 LEU cc_start: 0.9349 (mt) cc_final: 0.9101 (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: 0.8085 (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: 0.8622 (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: 0.7941 (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: 0.1105 time to fit residues: 24.7524 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 : 0.359 ------------------------------------------------------------------------------- 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: 0.1980 chunk 97 optimal weight: 8.9990 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: 20.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 HIS A 308 ASN ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 GLN B 681 HIS B 704 ASN G 170 HIS H 669 GLN H 681 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.050327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.036918 restraints weight = 76331.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.038194 restraints weight = 33884.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.039003 restraints weight = 20279.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.039555 restraints weight = 14682.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.039868 restraints weight = 11915.507| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13340 Z= 0.184 Angle : 0.624 7.067 18753 Z= 0.357 Chirality : 0.040 0.329 2110 Planarity : 0.004 0.046 1783 Dihedral : 26.317 173.137 3100 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.40 % Allowed : 9.51 % Favored : 89.09 % 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: 0.33 (0.25), residues: 1140 helix: 1.16 (0.20), residues: 657 sheet: -0.21 (0.53), residues: 65 loop : -1.21 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 719 TYR 0.015 0.001 TYR G 249 PHE 0.017 0.002 PHE H 679 TRP 0.006 0.001 TRP A 323 HIS 0.013 0.001 HIS A 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.18 (13337) covalent geometry : angle 0.62439 / 0.36 (18753) hydrogen bonds : bond 0.05028 / 3.34 ( 697) hydrogen bonds : angle 4.01676 / 2.74 ( 1847) Misc. bond : bond 0.00210 / 0.09 ( 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 108 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 196 LEU cc_start: 0.9296 (mt) cc_final: 0.9069 (tp) REVERT: A 382 ILE cc_start: 0.9549 (pt) cc_final: 0.9143 (mt) REVERT: A 476 MET cc_start: 0.9451 (mmm) cc_final: 0.9106 (mmm) REVERT: A 480 MET cc_start: 0.9182 (mmm) cc_final: 0.8884 (mmm) REVERT: A 517 MET cc_start: 0.7696 (tpp) cc_final: 0.7409 (tpp) REVERT: B 647 ASN cc_start: 0.9011 (t0) cc_final: 0.8756 (t0) REVERT: B 693 ASN cc_start: 0.9526 (m-40) cc_final: 0.9261 (p0) REVERT: G 197 LEU cc_start: 0.9174 (mt) cc_final: 0.8956 (tt) REVERT: G 481 MET cc_start: 0.8843 (mmm) cc_final: 0.8394 (mmp) REVERT: G 568 MET cc_start: 0.8222 (mmm) cc_final: 0.7865 (mmm) REVERT: H 627 MET cc_start: 0.9541 (ttt) cc_final: 0.8979 (ppp) REVERT: H 650 PHE cc_start: 0.8667 (t80) cc_final: 0.8376 (t80) outliers start: 14 outliers final: 3 residues processed: 103 average time/residue: 0.0944 time to fit residues: 15.0703 Evaluate side-chains 80 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain H residue 700 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 113 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 399 GLN ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 502 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.050096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.037046 restraints weight = 76793.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.038324 restraints weight = 34220.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.039132 restraints weight = 20480.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.039670 restraints weight = 14696.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.040012 restraints weight = 11871.586| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13340 Z= 0.159 Angle : 0.574 8.714 18753 Z= 0.333 Chirality : 0.040 0.347 2110 Planarity : 0.003 0.043 1783 Dihedral : 26.293 172.798 3100 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.70 % Allowed : 9.01 % Favored : 89.29 % 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: 0.88 (0.25), residues: 1140 helix: 1.60 (0.21), residues: 657 sheet: 0.01 (0.54), residues: 53 loop : -0.93 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 703 TYR 0.014 0.001 TYR B 652 PHE 0.023 0.001 PHE H 668 TRP 0.005 0.001 TRP A 323 HIS 0.003 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.16 (13337) covalent geometry : angle 0.57401 / 0.33 (18753) hydrogen bonds : bond 0.04572 / 3.00 ( 697) hydrogen bonds : angle 3.73321 / 2.56 ( 1847) Misc. bond : bond 0.00229 / 0.11 ( 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 101 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 196 LEU cc_start: 0.9297 (mt) cc_final: 0.9056 (tp) REVERT: A 476 MET cc_start: 0.9413 (mmm) cc_final: 0.9055 (mmt) REVERT: A 480 MET cc_start: 0.9160 (mmm) cc_final: 0.8905 (mmm) REVERT: A 517 MET cc_start: 0.7661 (tpp) cc_final: 0.7439 (tpp) REVERT: B 627 MET cc_start: 0.9535 (ttt) cc_final: 0.9118 (tmm) REVERT: B 647 ASN cc_start: 0.8980 (t0) cc_final: 0.8723 (t0) REVERT: B 693 ASN cc_start: 0.9493 (m-40) cc_final: 0.9201 (p0) REVERT: B 706 ASP cc_start: 0.8514 (t0) cc_final: 0.8209 (t0) REVERT: G 197 LEU cc_start: 0.9206 (mt) cc_final: 0.8987 (tt) REVERT: G 477 MET cc_start: 0.9383 (tpp) cc_final: 0.9068 (mmm) REVERT: H 627 MET cc_start: 0.9538 (ttt) cc_final: 0.8993 (ppp) REVERT: H 650 PHE cc_start: 0.8654 (t80) cc_final: 0.8393 (t80) outliers start: 17 outliers final: 7 residues processed: 94 average time/residue: 0.1054 time to fit residues: 15.1899 Evaluate side-chains 86 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain B residue 704 ASN Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain H residue 634 VAL Chi-restraints excluded: chain H residue 700 LEU Chi-restraints excluded: chain H residue 708 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 79 optimal weight: 0.0770 chunk 97 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 51 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 114 optimal weight: 0.2980 chunk 76 optimal weight: 6.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.050174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.037245 restraints weight = 76400.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.038506 restraints weight = 33913.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.039328 restraints weight = 20355.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.039867 restraints weight = 14548.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.040234 restraints weight = 11856.663| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13340 Z= 0.132 Angle : 0.557 7.871 18753 Z= 0.323 Chirality : 0.039 0.341 2110 Planarity : 0.003 0.041 1783 Dihedral : 26.271 172.415 3100 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.10 % Allowed : 9.91 % 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: 1.07 (0.25), residues: 1140 helix: 1.76 (0.21), residues: 657 sheet: 0.06 (0.51), residues: 58 loop : -0.87 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 137 TYR 0.009 0.001 TYR H 652 PHE 0.026 0.001 PHE B 668 TRP 0.003 0.000 TRP A 323 HIS 0.003 0.000 HIS A 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.13 (13337) covalent geometry : angle 0.55726 / 0.32 (18753) hydrogen bonds : bond 0.04243 / 2.78 ( 697) hydrogen bonds : angle 3.65690 / 2.52 ( 1847) Misc. bond : bond 0.00188 / 0.09 ( 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 95 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 196 LEU cc_start: 0.9302 (mt) cc_final: 0.9059 (tp) REVERT: A 476 MET cc_start: 0.9415 (mmm) cc_final: 0.9073 (tpp) REVERT: A 517 MET cc_start: 0.7718 (tpp) cc_final: 0.7449 (tpp) REVERT: B 627 MET cc_start: 0.9544 (ttt) cc_final: 0.9109 (tmm) REVERT: B 647 ASN cc_start: 0.8976 (t0) cc_final: 0.8697 (t0) REVERT: B 668 PHE cc_start: 0.8378 (t80) cc_final: 0.8087 (t80) REVERT: B 693 ASN cc_start: 0.9515 (m-40) cc_final: 0.9211 (p0) REVERT: B 706 ASP cc_start: 0.8534 (t0) cc_final: 0.8173 (t0) REVERT: G 197 LEU cc_start: 0.9187 (mt) cc_final: 0.8960 (tt) REVERT: G 477 MET cc_start: 0.9374 (tpp) cc_final: 0.9111 (mmt) REVERT: G 481 MET cc_start: 0.9131 (tpp) cc_final: 0.8789 (mmp) REVERT: G 568 MET cc_start: 0.8427 (mmm) cc_final: 0.8126 (mmm) REVERT: H 650 PHE cc_start: 0.8671 (t80) cc_final: 0.8402 (t80) REVERT: H 672 LEU cc_start: 0.9726 (mm) cc_final: 0.9487 (mm) outliers start: 11 outliers final: 8 residues processed: 90 average time/residue: 0.0978 time to fit residues: 13.4871 Evaluate side-chains 89 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 704 ASN Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain H residue 700 LEU Chi-restraints excluded: chain H residue 708 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 121 optimal weight: 30.0000 chunk 107 optimal weight: 0.7980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.049614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.036758 restraints weight = 78097.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.037963 restraints weight = 34323.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.038771 restraints weight = 20522.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.039293 restraints weight = 14807.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.039602 restraints weight = 12001.841| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13340 Z= 0.168 Angle : 0.585 11.840 18753 Z= 0.333 Chirality : 0.039 0.341 2110 Planarity : 0.004 0.055 1783 Dihedral : 26.285 172.168 3100 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.50 % Allowed : 10.51 % Favored : 87.99 % 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: 1.35 (0.25), residues: 1140 helix: 1.97 (0.21), residues: 655 sheet: 0.13 (0.56), residues: 58 loop : -0.70 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 703 TYR 0.008 0.001 TYR G 511 PHE 0.031 0.001 PHE B 668 TRP 0.005 0.001 TRP A 323 HIS 0.003 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.17 (13337) covalent geometry : angle 0.58524 / 0.33 (18753) hydrogen bonds : bond 0.04281 / 2.82 ( 697) hydrogen bonds : angle 3.64350 / 2.51 ( 1847) Misc. bond : bond 0.00175 / 0.08 ( 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: 15 poor density : 81 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 196 LEU cc_start: 0.9298 (mt) cc_final: 0.9050 (tp) REVERT: A 476 MET cc_start: 0.9394 (mmm) cc_final: 0.9047 (mmt) REVERT: A 480 MET cc_start: 0.9253 (mmm) cc_final: 0.8885 (mmp) REVERT: A 517 MET cc_start: 0.7726 (tpp) cc_final: 0.7480 (tpp) REVERT: B 627 MET cc_start: 0.9525 (ttt) cc_final: 0.9071 (tmm) REVERT: B 647 ASN cc_start: 0.8977 (t0) cc_final: 0.8698 (t0) REVERT: B 693 ASN cc_start: 0.9493 (m-40) cc_final: 0.9193 (p0) REVERT: B 703 ARG cc_start: 0.8969 (mtm110) cc_final: 0.8731 (ptp-110) REVERT: B 706 ASP cc_start: 0.8568 (t0) cc_final: 0.8181 (t0) REVERT: G 197 LEU cc_start: 0.9232 (mt) cc_final: 0.8994 (tt) REVERT: G 481 MET cc_start: 0.9176 (tpp) cc_final: 0.8959 (tpp) REVERT: G 568 MET cc_start: 0.8463 (mmm) cc_final: 0.8181 (mmm) REVERT: H 620 ASP cc_start: 0.8827 (p0) cc_final: 0.8612 (p0) REVERT: H 627 MET cc_start: 0.9472 (ttt) cc_final: 0.9060 (tmm) REVERT: H 650 PHE cc_start: 0.8674 (t80) cc_final: 0.8410 (t80) outliers start: 15 outliers final: 10 residues processed: 90 average time/residue: 0.0975 time to fit residues: 13.3333 Evaluate side-chains 88 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain H residue 634 VAL Chi-restraints excluded: chain H residue 708 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 1 optimal weight: 0.4980 chunk 120 optimal weight: 30.0000 chunk 93 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3327 r_free = 0.3327 target = 0.049398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.036537 restraints weight = 77380.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.037772 restraints weight = 34150.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.038577 restraints weight = 20585.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.039092 restraints weight = 14858.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.039467 restraints weight = 12170.807| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13340 Z= 0.154 Angle : 0.567 8.375 18753 Z= 0.325 Chirality : 0.039 0.341 2110 Planarity : 0.003 0.038 1783 Dihedral : 26.280 172.036 3100 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.20 % Allowed : 11.41 % 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: 1.48 (0.26), residues: 1140 helix: 2.06 (0.20), residues: 655 sheet: 0.13 (0.58), residues: 58 loop : -0.62 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 703 TYR 0.022 0.001 TYR B 652 PHE 0.031 0.001 PHE B 668 TRP 0.004 0.001 TRP A 323 HIS 0.003 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (13337) covalent geometry : angle 0.56718 / 0.33 (18753) hydrogen bonds : bond 0.04154 / 2.73 ( 697) hydrogen bonds : angle 3.59124 / 2.48 ( 1847) Misc. bond : bond 0.00167 / 0.08 ( 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 91 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 196 LEU cc_start: 0.9292 (mt) cc_final: 0.9022 (tp) REVERT: A 476 MET cc_start: 0.9406 (mmm) cc_final: 0.9003 (mmt) REVERT: A 480 MET cc_start: 0.9276 (mmm) cc_final: 0.8916 (mmp) REVERT: A 517 MET cc_start: 0.7673 (tpp) cc_final: 0.7386 (tpp) REVERT: B 627 MET cc_start: 0.9535 (OUTLIER) cc_final: 0.9104 (tmm) REVERT: B 647 ASN cc_start: 0.9008 (t0) cc_final: 0.8735 (t0) REVERT: B 652 TYR cc_start: 0.9328 (t80) cc_final: 0.9054 (t80) REVERT: B 693 ASN cc_start: 0.9506 (m-40) cc_final: 0.9202 (p0) REVERT: B 706 ASP cc_start: 0.8625 (t0) cc_final: 0.8243 (t0) REVERT: G 197 LEU cc_start: 0.9252 (mt) cc_final: 0.9007 (tt) REVERT: G 233 MET cc_start: 0.8269 (mmm) cc_final: 0.7757 (mmm) REVERT: G 481 MET cc_start: 0.9197 (tpp) cc_final: 0.8982 (tpp) REVERT: H 620 ASP cc_start: 0.8693 (p0) cc_final: 0.8284 (p0) REVERT: H 627 MET cc_start: 0.9465 (ttt) cc_final: 0.9046 (tmm) REVERT: H 650 PHE cc_start: 0.8694 (t80) cc_final: 0.8430 (t80) REVERT: H 693 ASN cc_start: 0.9558 (m-40) cc_final: 0.9148 (p0) outliers start: 12 outliers final: 9 residues processed: 86 average time/residue: 0.1043 time to fit residues: 13.8952 Evaluate side-chains 88 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain H residue 634 VAL Chi-restraints excluded: chain H residue 700 LEU Chi-restraints excluded: chain H residue 708 ASP Chi-restraints excluded: chain H residue 711 VAL 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: 20.0000 chunk 70 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 20.0000 chunk 73 optimal weight: 30.0000 chunk 72 optimal weight: 10.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 429 ASN G 502 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.049427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.036560 restraints weight = 77766.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.037769 restraints weight = 34440.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.038584 restraints weight = 20726.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.039071 restraints weight = 14945.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.039445 restraints weight = 12252.852| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13340 Z= 0.142 Angle : 0.568 10.107 18753 Z= 0.323 Chirality : 0.040 0.340 2110 Planarity : 0.003 0.037 1783 Dihedral : 26.270 172.292 3100 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.10 % Allowed : 12.01 % Favored : 86.89 % 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: 1.56 (0.26), residues: 1140 helix: 2.11 (0.20), residues: 658 sheet: 0.31 (0.60), residues: 58 loop : -0.60 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 703 TYR 0.016 0.001 TYR B 652 PHE 0.044 0.001 PHE B 668 TRP 0.004 0.001 TRP A 323 HIS 0.002 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (13337) covalent geometry : angle 0.56799 / 0.32 (18753) hydrogen bonds : bond 0.04035 / 2.67 ( 697) hydrogen bonds : angle 3.52657 / 2.44 ( 1847) Misc. bond : bond 0.00156 / 0.07 ( 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 89 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 196 LEU cc_start: 0.9314 (mt) cc_final: 0.9050 (tp) REVERT: A 476 MET cc_start: 0.9388 (mmm) cc_final: 0.9021 (mmm) REVERT: A 480 MET cc_start: 0.9208 (mmm) cc_final: 0.8796 (mmp) REVERT: A 517 MET cc_start: 0.7705 (tpp) cc_final: 0.7426 (tpp) REVERT: A 537 MET cc_start: 0.9058 (tpp) cc_final: 0.8821 (tpp) REVERT: B 627 MET cc_start: 0.9518 (ttt) cc_final: 0.9101 (tmm) REVERT: B 647 ASN cc_start: 0.8992 (t0) cc_final: 0.8718 (t0) REVERT: B 693 ASN cc_start: 0.9469 (m-40) cc_final: 0.9214 (p0) REVERT: B 706 ASP cc_start: 0.8649 (t0) cc_final: 0.8291 (t0) REVERT: G 197 LEU cc_start: 0.9267 (mt) cc_final: 0.9030 (tt) REVERT: G 233 MET cc_start: 0.8196 (mmm) cc_final: 0.7855 (mmm) REVERT: G 568 MET cc_start: 0.8584 (mmm) cc_final: 0.8165 (mmm) REVERT: H 627 MET cc_start: 0.9438 (ttt) cc_final: 0.9049 (tmm) REVERT: H 650 PHE cc_start: 0.8700 (t80) cc_final: 0.8435 (t80) REVERT: H 693 ASN cc_start: 0.9543 (m-40) cc_final: 0.9168 (p0) outliers start: 11 outliers final: 8 residues processed: 85 average time/residue: 0.0969 time to fit residues: 12.6278 Evaluate side-chains 85 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain H residue 634 VAL Chi-restraints excluded: chain H residue 708 ASP Chi-restraints excluded: chain H residue 711 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 73 optimal weight: 30.0000 chunk 88 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 48 optimal weight: 0.0870 chunk 4 optimal weight: 0.0040 overall best weight: 0.5970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 400 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.049994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.037158 restraints weight = 76878.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.038386 restraints weight = 34010.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.039206 restraints weight = 20360.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.039755 restraints weight = 14634.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.040064 restraints weight = 11831.425| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13340 Z= 0.124 Angle : 0.570 11.105 18753 Z= 0.321 Chirality : 0.039 0.338 2110 Planarity : 0.003 0.037 1783 Dihedral : 26.240 172.638 3100 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.70 % Allowed : 12.71 % Favored : 86.59 % 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: 1.65 (0.25), residues: 1140 helix: 2.13 (0.20), residues: 658 sheet: 0.67 (0.59), residues: 64 loop : -0.53 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 703 TYR 0.038 0.001 TYR B 652 PHE 0.022 0.001 PHE B 668 TRP 0.002 0.000 TRP A 323 HIS 0.002 0.000 HIS A 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.12 (13337) covalent geometry : angle 0.57020 / 0.32 (18753) hydrogen bonds : bond 0.03857 / 2.53 ( 697) hydrogen bonds : angle 3.40256 / 2.36 ( 1847) Misc. bond : bond 0.00128 / 0.06 ( 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 88 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 196 LEU cc_start: 0.9294 (mt) cc_final: 0.9035 (tp) REVERT: A 232 MET cc_start: 0.8315 (tpp) cc_final: 0.8017 (mtp) REVERT: A 476 MET cc_start: 0.9401 (mmm) cc_final: 0.8970 (mmt) REVERT: A 517 MET cc_start: 0.7734 (tpp) cc_final: 0.7439 (tpp) REVERT: A 537 MET cc_start: 0.8984 (tpp) cc_final: 0.8756 (tpp) REVERT: B 647 ASN cc_start: 0.9012 (t0) cc_final: 0.8763 (t0) REVERT: B 693 ASN cc_start: 0.9443 (m-40) cc_final: 0.9181 (p0) REVERT: B 706 ASP cc_start: 0.8640 (t0) cc_final: 0.8316 (t0) REVERT: G 197 LEU cc_start: 0.9267 (mt) cc_final: 0.9025 (tt) REVERT: G 233 MET cc_start: 0.8276 (mmm) cc_final: 0.7877 (mmm) REVERT: G 568 MET cc_start: 0.8527 (mmm) cc_final: 0.8122 (mmm) REVERT: H 627 MET cc_start: 0.9429 (ttt) cc_final: 0.9022 (tmm) REVERT: H 650 PHE cc_start: 0.8712 (t80) cc_final: 0.8453 (t80) REVERT: H 686 ASN cc_start: 0.9200 (p0) cc_final: 0.8983 (p0) REVERT: H 693 ASN cc_start: 0.9522 (m-40) cc_final: 0.9057 (p0) outliers start: 7 outliers final: 5 residues processed: 83 average time/residue: 0.0945 time to fit residues: 12.1866 Evaluate side-chains 85 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain H residue 622 LEU Chi-restraints excluded: chain H residue 711 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.049443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.036587 restraints weight = 77689.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.037805 restraints weight = 34433.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.038627 restraints weight = 20607.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.039165 restraints weight = 14783.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.039502 restraints weight = 11936.727| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13340 Z= 0.141 Angle : 0.575 11.131 18753 Z= 0.324 Chirality : 0.039 0.338 2110 Planarity : 0.003 0.037 1783 Dihedral : 26.256 172.625 3100 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.10 % Allowed : 12.71 % Favored : 86.19 % 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: 1.77 (0.26), residues: 1140 helix: 2.23 (0.20), residues: 657 sheet: 0.72 (0.60), residues: 64 loop : -0.47 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 703 TYR 0.027 0.001 TYR B 652 PHE 0.034 0.001 PHE B 668 TRP 0.004 0.001 TRP A 323 HIS 0.002 0.000 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (13337) covalent geometry : angle 0.57499 / 0.32 (18753) hydrogen bonds : bond 0.03914 / 2.59 ( 697) hydrogen bonds : angle 3.44939 / 2.39 ( 1847) Misc. bond : bond 0.00137 / 0.06 ( 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 90 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 196 LEU cc_start: 0.9295 (mt) cc_final: 0.9028 (tp) REVERT: A 476 MET cc_start: 0.9417 (mmm) cc_final: 0.8990 (mmt) REVERT: A 517 MET cc_start: 0.7733 (tpp) cc_final: 0.7417 (tpp) REVERT: A 537 MET cc_start: 0.9020 (tpp) cc_final: 0.8787 (tpp) REVERT: B 625 ASP cc_start: 0.9033 (OUTLIER) cc_final: 0.8811 (t0) REVERT: B 627 MET cc_start: 0.9590 (ttt) cc_final: 0.9210 (tmm) REVERT: B 647 ASN cc_start: 0.8976 (t0) cc_final: 0.8723 (t0) REVERT: B 693 ASN cc_start: 0.9458 (m-40) cc_final: 0.9199 (p0) REVERT: B 698 LEU cc_start: 0.9626 (mt) cc_final: 0.9387 (mp) REVERT: B 706 ASP cc_start: 0.8685 (t0) cc_final: 0.8368 (t0) REVERT: G 197 LEU cc_start: 0.9273 (mt) cc_final: 0.9023 (tt) REVERT: G 213 LEU cc_start: 0.9013 (mp) cc_final: 0.8592 (mp) REVERT: G 233 MET cc_start: 0.8241 (mmm) cc_final: 0.7877 (mmm) REVERT: G 568 MET cc_start: 0.8552 (mmm) cc_final: 0.8075 (mmm) REVERT: H 627 MET cc_start: 0.9426 (OUTLIER) cc_final: 0.8961 (tmm) REVERT: H 650 PHE cc_start: 0.8747 (t80) cc_final: 0.8482 (t80) REVERT: H 686 ASN cc_start: 0.9193 (p0) cc_final: 0.8959 (p0) REVERT: H 693 ASN cc_start: 0.9546 (m-40) cc_final: 0.9119 (p0) outliers start: 11 outliers final: 6 residues processed: 85 average time/residue: 0.1010 time to fit residues: 13.2195 Evaluate side-chains 86 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain H residue 627 MET Chi-restraints excluded: chain H residue 711 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 82 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 34 optimal weight: 0.0170 chunk 8 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 overall best weight: 1.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.048821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.035234 restraints weight = 79922.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.036495 restraints weight = 36227.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.037329 restraints weight = 22126.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.037840 restraints weight = 16144.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.038211 restraints weight = 13401.304| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13340 Z= 0.164 Angle : 0.608 11.647 18753 Z= 0.338 Chirality : 0.040 0.339 2110 Planarity : 0.003 0.036 1783 Dihedral : 26.287 171.957 3100 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.10 % Allowed : 13.01 % Favored : 85.89 % 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: 1.80 (0.26), residues: 1140 helix: 2.27 (0.20), residues: 653 sheet: 0.63 (0.63), residues: 62 loop : -0.44 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 703 TYR 0.024 0.001 TYR B 652 PHE 0.027 0.001 PHE B 668 TRP 0.007 0.001 TRP A 195 HIS 0.006 0.001 HIS G 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (13337) covalent geometry : angle 0.60805 / 0.34 (18753) hydrogen bonds : bond 0.04115 / 2.74 ( 697) hydrogen bonds : angle 3.53986 / 2.44 ( 1847) Misc. bond : bond 0.00133 / 0.06 ( 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 91 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 196 LEU cc_start: 0.9281 (mt) cc_final: 0.9006 (tp) REVERT: A 232 MET cc_start: 0.8449 (tpp) cc_final: 0.8150 (mtt) REVERT: A 476 MET cc_start: 0.9384 (mmm) cc_final: 0.9025 (mmt) REVERT: A 517 MET cc_start: 0.7694 (tpp) cc_final: 0.7382 (tpp) REVERT: A 537 MET cc_start: 0.9062 (tpp) cc_final: 0.8834 (tpp) REVERT: B 625 ASP cc_start: 0.9017 (OUTLIER) cc_final: 0.8803 (t0) REVERT: B 627 MET cc_start: 0.9582 (ttt) cc_final: 0.9195 (tmm) REVERT: B 647 ASN cc_start: 0.8871 (t0) cc_final: 0.8617 (t0) REVERT: B 693 ASN cc_start: 0.9449 (m-40) cc_final: 0.9156 (p0) REVERT: B 706 ASP cc_start: 0.8710 (t0) cc_final: 0.8416 (t0) REVERT: G 213 LEU cc_start: 0.9077 (mp) cc_final: 0.8662 (mp) REVERT: G 233 MET cc_start: 0.8289 (mmm) cc_final: 0.7927 (mmm) REVERT: G 538 MET cc_start: 0.8967 (mmp) cc_final: 0.8753 (mmt) REVERT: G 568 MET cc_start: 0.8571 (mmm) cc_final: 0.8130 (mmm) REVERT: H 627 MET cc_start: 0.9422 (OUTLIER) cc_final: 0.9012 (tmm) REVERT: H 650 PHE cc_start: 0.8762 (t80) cc_final: 0.8506 (t80) REVERT: H 686 ASN cc_start: 0.9199 (p0) cc_final: 0.8940 (p0) REVERT: H 693 ASN cc_start: 0.9545 (m-40) cc_final: 0.9085 (p0) outliers start: 11 outliers final: 8 residues processed: 85 average time/residue: 0.1005 time to fit residues: 13.1319 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 : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain H residue 622 LEU Chi-restraints excluded: chain H residue 627 MET Chi-restraints excluded: chain H residue 708 ASP Chi-restraints excluded: chain H residue 711 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 100 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 1 optimal weight: 0.0070 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 HIS ** 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 = 0.3323 r_free = 0.3323 target = 0.049226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.036476 restraints weight = 78935.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.037723 restraints weight = 35186.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.038514 restraints weight = 20816.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.039039 restraints weight = 15005.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.039348 restraints weight = 12169.146| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13340 Z= 0.133 Angle : 0.588 12.944 18753 Z= 0.328 Chirality : 0.039 0.339 2110 Planarity : 0.003 0.036 1783 Dihedral : 26.245 172.429 3100 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.20 % Allowed : 12.81 % Favored : 85.99 % 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: 1.96 (0.26), residues: 1140 helix: 2.39 (0.20), residues: 647 sheet: 0.82 (0.63), residues: 62 loop : -0.33 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 703 TYR 0.024 0.001 TYR B 652 PHE 0.030 0.001 PHE B 668 TRP 0.003 0.001 TRP A 323 HIS 0.002 0.000 HIS A 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.13 (13337) covalent geometry : angle 0.58837 / 0.33 (18753) hydrogen bonds : bond 0.03845 / 2.54 ( 697) hydrogen bonds : angle 3.42435 / 2.38 ( 1847) Misc. bond : bond 0.00135 / 0.06 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1768.53 seconds wall clock time: 31 minutes 26.22 seconds (1886.22 seconds total)