Starting phenix.real_space_refine on Wed Jul 30 22:32:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pe2_20321/07_2025/6pe2_20321.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pe2_20321/07_2025/6pe2_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_20321/07_2025/6pe2_20321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pe2_20321/07_2025/6pe2_20321.map" model { file = "/net/cci-nas-00/data/ceres_data/6pe2_20321/07_2025/6pe2_20321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pe2_20321/07_2025/6pe2_20321.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'TYR:plan': 1, 'GLU:plan': 6, '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: {'GLN:plan1': 1, 'GLU:plan': 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: {'TYR:plan': 1, 'GLU:plan': 7, '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: {'GLN:plan1': 1, 'GLU:plan': 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: 7.71, per 1000 atoms: 0.60 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: 3.17 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 4.63 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: 5.13 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3144 1.34 - 1.45: 3386 1.45 - 1.57: 6409 1.57 - 1.69: 342 1.69 - 1.81: 56 Bond restraints: 13337 Sorted by residual: bond pdb=" N GLU G 458 " pdb=" CA GLU G 458 " ideal model delta sigma weight residual 1.454 1.490 -0.035 1.17e-02 7.31e+03 9.09e+00 bond pdb=" N ILE G 457 " pdb=" CA ILE G 457 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.29e-02 6.01e+03 7.50e+00 bond pdb=" N CYS G 456 " pdb=" CA CYS G 456 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.31e+00 bond pdb=" N ARG A 540 " pdb=" CA ARG A 540 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.28e-02 6.10e+03 6.06e+00 bond pdb=" C3' DG K -33 " pdb=" O3' DG K -33 " ideal model delta sigma weight residual 1.422 1.494 -0.072 3.00e-02 1.11e+03 5.77e+00 ... (remaining 13332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 18544 2.17 - 4.35: 195 4.35 - 6.52: 11 6.52 - 8.69: 0 8.69 - 10.86: 3 Bond angle restraints: 18753 Sorted by residual: angle pdb=" N CYS G 459 " pdb=" CA CYS G 459 " pdb=" C CYS G 459 " ideal model delta sigma weight residual 112.97 104.08 8.89 1.06e+00 8.90e-01 7.03e+01 angle pdb=" CA GLY A 541 " pdb=" C GLY A 541 " pdb=" O GLY A 541 " ideal model delta sigma weight residual 122.24 118.22 4.02 8.70e-01 1.32e+00 2.13e+01 angle pdb=" O3' DG K -33 " pdb=" P DC K -32 " pdb=" OP1 DC K -32 " ideal model delta sigma weight residual 108.00 118.86 -10.86 3.00e+00 1.11e-01 1.31e+01 angle pdb=" N GLU G 458 " pdb=" CA GLU G 458 " pdb=" C GLU G 458 " ideal model delta sigma weight residual 110.17 104.65 5.52 1.61e+00 3.86e-01 1.18e+01 angle pdb=" O3' DG K -33 " pdb=" P DC K -32 " pdb=" OP2 DC K -32 " ideal model delta sigma weight residual 108.00 99.16 8.84 3.00e+00 1.11e-01 8.68e+00 ... (remaining 18748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 6880 35.69 - 71.37: 634 71.37 - 107.06: 7 107.06 - 142.75: 6 142.75 - 178.44: 7 Dihedral angle restraints: 7534 sinusoidal: 4144 harmonic: 3390 Sorted by residual: dihedral pdb=" C8 GTP G 601 " pdb=" C1' GTP G 601 " pdb=" N9 GTP G 601 " pdb=" O4' GTP G 601 " ideal model delta sinusoidal sigma weight residual 104.59 -31.58 136.18 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" C8 GTP A 601 " pdb=" C1' GTP A 601 " pdb=" N9 GTP A 601 " pdb=" O4' GTP A 601 " ideal model delta sinusoidal sigma weight residual 104.59 -30.62 135.21 1 2.00e+01 2.50e-03 4.10e+01 dihedral pdb=" CA ALA A 155 " pdb=" C ALA A 155 " pdb=" N THR A 156 " pdb=" CA THR A 156 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 7531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1797 0.049 - 0.097: 254 0.097 - 0.146: 53 0.146 - 0.194: 5 0.194 - 0.243: 1 Chirality restraints: 2110 Sorted by residual: chirality pdb=" CA CYS G 459 " pdb=" N CYS G 459 " pdb=" C CYS G 459 " pdb=" CB CYS G 459 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA MET A 537 " pdb=" N MET A 537 " pdb=" C MET A 537 " pdb=" CB MET A 537 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" P DG D 14 " pdb=" OP1 DG D 14 " pdb=" OP2 DG D 14 " pdb=" O5' DG D 14 " both_signs ideal model delta sigma weight residual True 2.35 -2.51 -0.16 2.00e-01 2.50e+01 6.71e-01 ... (remaining 2107 not shown) Planarity restraints: 1783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 172 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO A 173 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 173 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 173 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY G 173 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO G 174 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO G 174 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 174 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 340 " -0.028 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO A 341 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 341 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 341 " -0.024 5.00e-02 4.00e+02 ... (remaining 1780 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 176 2.63 - 3.20: 10418 3.20 - 3.76: 21854 3.76 - 4.33: 28768 4.33 - 4.90: 43563 Nonbonded interactions: 104779 Sorted by model distance: nonbonded pdb=" OG1 THR G 142 " pdb=" OD2 ASP G 162 " model vdw 2.062 3.040 nonbonded pdb=" O1G GTP G 601 " pdb="MG MG G 602 " model vdw 2.072 2.170 nonbonded pdb=" O1G GTP A 601 " pdb="MG MG A 602 " model vdw 2.100 2.170 nonbonded pdb=" O1B GTP A 601 " pdb="MG MG A 602 " model vdw 2.117 2.170 nonbonded pdb=" O1B GTP G 601 " pdb="MG MG G 602 " model vdw 2.122 2.170 ... (remaining 104774 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 114 through 456 or (resid 457 and (name N or name CA or na \ me C or name O or name CB )) or resid 458 through 569 or resid 601 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 570 or resid 601 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: 0.780 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: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 34.010 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 13340 Z= 0.161 Angle : 0.540 10.863 18753 Z= 0.328 Chirality : 0.036 0.243 2110 Planarity : 0.004 0.048 1783 Dihedral : 21.705 178.437 5334 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.004 0.001 TRP G 443 HIS 0.002 0.001 HIS B 681 PHE 0.008 0.001 PHE G 273 TYR 0.011 0.001 TYR G 511 ARG 0.002 0.000 ARG G 175 Details of bonding type rmsd hydrogen bonds : bond 0.13622 ( 697) hydrogen bonds : angle 4.97251 ( 1847) covalent geometry : bond 0.00294 (13337) covalent geometry : angle 0.53963 (18753) Misc. bond : bond 0.02472 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 LEU cc_start: 0.9349 (mt) cc_final: 0.9104 (tp) REVERT: A 425 ASP cc_start: 0.8222 (p0) cc_final: 0.7997 (t0) REVERT: A 522 THR cc_start: 0.9407 (p) cc_final: 0.9194 (p) REVERT: B 647 ASN cc_start: 0.9016 (t0) cc_final: 0.8731 (t0) REVERT: B 668 PHE cc_start: 0.8504 (t80) cc_final: 0.8085 (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: 0.7942 (t70) REVERT: G 440 MET cc_start: 0.9352 (mmm) cc_final: 0.9066 (mmp) REVERT: H 650 PHE cc_start: 0.8727 (t80) cc_final: 0.8431 (t80) REVERT: H 668 PHE cc_start: 0.8500 (t80) cc_final: 0.8057 (t80) REVERT: H 706 ASP cc_start: 0.8293 (t0) cc_final: 0.8065 (t0) REVERT: H 718 ILE cc_start: 0.9622 (pt) cc_final: 0.9390 (mm) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2609 time to fit residues: 57.5538 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 : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 52 optimal weight: 0.0020 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 113 optimal weight: 0.0970 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 308 ASN A 399 GLN ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 GLN B 704 ASN G 170 HIS G 502 ASN H 669 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.050725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.037441 restraints weight = 76122.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.038723 restraints weight = 33919.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.039553 restraints weight = 20497.034| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13340 Z= 0.143 Angle : 0.530 6.253 18753 Z= 0.300 Chirality : 0.036 0.153 2110 Planarity : 0.004 0.046 1783 Dihedral : 26.017 176.435 3100 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.20 % Allowed : 9.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.24), residues: 1140 helix: 1.19 (0.20), residues: 656 sheet: -0.43 (0.52), residues: 75 loop : -1.16 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 324 HIS 0.006 0.001 HIS A 546 PHE 0.012 0.001 PHE B 668 TYR 0.010 0.001 TYR A 519 ARG 0.010 0.001 ARG A 563 Details of bonding type rmsd hydrogen bonds : bond 0.03994 ( 697) hydrogen bonds : angle 3.64620 ( 1847) covalent geometry : bond 0.00304 (13337) covalent geometry : angle 0.52980 (18753) Misc. bond : bond 0.00788 ( 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 115 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 1.359 Fit side-chains revert: symmetry clash REVERT: A 196 LEU cc_start: 0.9257 (mt) cc_final: 0.9046 (tp) REVERT: A 425 ASP cc_start: 0.8206 (p0) cc_final: 0.7979 (t0) REVERT: A 517 MET cc_start: 0.7929 (tpp) cc_final: 0.7490 (tpp) REVERT: A 522 THR cc_start: 0.9418 (p) cc_final: 0.9172 (t) REVERT: A 563 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7812 (ptp90) REVERT: A 567 MET cc_start: 0.8716 (mmm) cc_final: 0.8296 (tpt) REVERT: B 647 ASN cc_start: 0.9072 (t0) cc_final: 0.8816 (t0) REVERT: B 668 PHE cc_start: 0.8493 (t80) cc_final: 0.8271 (t80) REVERT: B 693 ASN cc_start: 0.9509 (m-40) cc_final: 0.9224 (p0) REVERT: B 706 ASP cc_start: 0.8896 (t0) cc_final: 0.8611 (t0) REVERT: G 440 MET cc_start: 0.9381 (mmm) cc_final: 0.9084 (mmp) REVERT: G 568 MET cc_start: 0.8312 (mmm) cc_final: 0.7874 (mmm) REVERT: H 620 ASP cc_start: 0.8457 (p0) cc_final: 0.8013 (p0) REVERT: H 622 LEU cc_start: 0.9647 (mm) cc_final: 0.9439 (pp) REVERT: H 627 MET cc_start: 0.9397 (ttt) cc_final: 0.9051 (tmm) REVERT: H 650 PHE cc_start: 0.8618 (t80) cc_final: 0.8361 (t80) outliers start: 12 outliers final: 5 residues processed: 112 average time/residue: 0.2334 time to fit residues: 40.0153 Evaluate side-chains 90 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain B residue 704 ASN Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain H residue 680 LEU Chi-restraints excluded: chain H residue 711 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 122 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 48 optimal weight: 0.0970 chunk 20 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.049341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.036549 restraints weight = 78374.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.037750 restraints weight = 34670.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.038545 restraints weight = 20863.005| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13340 Z= 0.158 Angle : 0.536 7.495 18753 Z= 0.301 Chirality : 0.035 0.149 2110 Planarity : 0.003 0.043 1783 Dihedral : 26.012 175.507 3100 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.80 % Allowed : 9.41 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.25), residues: 1140 helix: 1.76 (0.20), residues: 656 sheet: 0.14 (0.57), residues: 58 loop : -0.81 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 323 HIS 0.004 0.001 HIS A 546 PHE 0.019 0.001 PHE H 668 TYR 0.021 0.001 TYR B 652 ARG 0.006 0.001 ARG A 563 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 697) hydrogen bonds : angle 3.40828 ( 1847) covalent geometry : bond 0.00336 (13337) covalent geometry : angle 0.53613 (18753) Misc. bond : bond 0.00499 ( 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 100 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: A 196 LEU cc_start: 0.9287 (mt) cc_final: 0.9069 (tp) REVERT: A 425 ASP cc_start: 0.8248 (p0) cc_final: 0.7992 (t0) REVERT: A 439 MET cc_start: 0.9363 (tpp) cc_final: 0.8873 (tpp) REVERT: A 476 MET cc_start: 0.9481 (mmt) cc_final: 0.9198 (mmt) REVERT: A 517 MET cc_start: 0.7861 (tpp) cc_final: 0.7478 (tpp) REVERT: A 563 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7862 (ptp-170) REVERT: B 647 ASN cc_start: 0.9003 (t0) cc_final: 0.8700 (t0) REVERT: B 693 ASN cc_start: 0.9511 (m-40) cc_final: 0.9198 (p0) REVERT: G 213 LEU cc_start: 0.9135 (mp) cc_final: 0.8901 (mp) REVERT: G 233 MET cc_start: 0.8116 (ttp) cc_final: 0.7857 (ttp) REVERT: H 620 ASP cc_start: 0.8401 (p0) cc_final: 0.8054 (p0) REVERT: H 622 LEU cc_start: 0.9634 (mm) cc_final: 0.9422 (pp) REVERT: H 627 MET cc_start: 0.9391 (ttt) cc_final: 0.9015 (tmm) REVERT: H 650 PHE cc_start: 0.8609 (t80) cc_final: 0.8366 (t80) REVERT: H 672 LEU cc_start: 0.9747 (OUTLIER) cc_final: 0.9529 (mm) REVERT: H 686 ASN cc_start: 0.9226 (p0) cc_final: 0.8930 (p0) outliers start: 18 outliers final: 7 residues processed: 94 average time/residue: 0.2502 time to fit residues: 35.5104 Evaluate side-chains 86 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 704 ASN Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain H residue 634 VAL Chi-restraints excluded: chain H residue 672 LEU Chi-restraints excluded: chain H residue 708 ASP Chi-restraints excluded: chain H residue 711 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 86 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 16 optimal weight: 0.0170 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 565 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.047628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.034837 restraints weight = 80082.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.036044 restraints weight = 36005.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.036831 restraints weight = 21888.495| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13340 Z= 0.201 Angle : 0.570 6.174 18753 Z= 0.320 Chirality : 0.037 0.137 2110 Planarity : 0.003 0.042 1783 Dihedral : 26.143 179.521 3100 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.90 % Allowed : 10.61 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.26), residues: 1140 helix: 2.07 (0.20), residues: 652 sheet: -0.23 (0.59), residues: 61 loop : -0.52 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 195 HIS 0.004 0.001 HIS A 390 PHE 0.017 0.001 PHE H 668 TYR 0.018 0.001 TYR B 652 ARG 0.009 0.001 ARG B 703 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 697) hydrogen bonds : angle 3.51127 ( 1847) covalent geometry : bond 0.00433 (13337) covalent geometry : angle 0.56993 (18753) Misc. bond : bond 0.00176 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 1.195 Fit side-chains revert: symmetry clash REVERT: A 196 LEU cc_start: 0.9320 (mt) cc_final: 0.9018 (tp) REVERT: A 232 MET cc_start: 0.8160 (ttt) cc_final: 0.7844 (ttt) REVERT: A 476 MET cc_start: 0.9450 (mmt) cc_final: 0.9159 (mmt) REVERT: A 517 MET cc_start: 0.7796 (tpp) cc_final: 0.7485 (tpp) REVERT: A 563 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7482 (ptp90) REVERT: B 627 MET cc_start: 0.9579 (ttt) cc_final: 0.9128 (tmm) REVERT: B 647 ASN cc_start: 0.8888 (t0) cc_final: 0.8588 (t0) REVERT: B 682 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.8378 (t80) REVERT: B 693 ASN cc_start: 0.9527 (m-40) cc_final: 0.9243 (p0) REVERT: G 213 LEU cc_start: 0.9225 (mp) cc_final: 0.8821 (mp) REVERT: G 440 MET cc_start: 0.9347 (mmm) cc_final: 0.8933 (tpp) REVERT: G 481 MET cc_start: 0.9283 (mmm) cc_final: 0.8979 (tpp) REVERT: G 568 MET cc_start: 0.8547 (mmm) cc_final: 0.7913 (mmm) REVERT: H 627 MET cc_start: 0.9418 (ttt) cc_final: 0.9043 (tmm) REVERT: H 650 PHE cc_start: 0.8628 (t80) cc_final: 0.8391 (t80) REVERT: H 686 ASN cc_start: 0.9262 (p0) cc_final: 0.8941 (p0) outliers start: 19 outliers final: 10 residues processed: 90 average time/residue: 0.2429 time to fit residues: 32.9468 Evaluate side-chains 84 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 704 ASN Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 101 optimal weight: 0.7980 chunk 64 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 116 optimal weight: 0.4980 chunk 124 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 ASN G 502 ASN H 692 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.049078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.036445 restraints weight = 79296.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.037660 restraints weight = 35227.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.038475 restraints weight = 21091.469| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13340 Z= 0.131 Angle : 0.529 7.742 18753 Z= 0.297 Chirality : 0.036 0.185 2110 Planarity : 0.003 0.041 1783 Dihedral : 25.959 177.436 3100 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.50 % Allowed : 11.41 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.26), residues: 1140 helix: 2.18 (0.20), residues: 663 sheet: 0.89 (0.63), residues: 54 loop : -0.53 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 442 HIS 0.002 0.000 HIS A 546 PHE 0.028 0.001 PHE B 668 TYR 0.029 0.001 TYR B 652 ARG 0.006 0.000 ARG B 703 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 697) hydrogen bonds : angle 3.26164 ( 1847) covalent geometry : bond 0.00279 (13337) covalent geometry : angle 0.52862 (18753) Misc. bond : bond 0.00252 ( 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 92 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: A 196 LEU cc_start: 0.9270 (mt) cc_final: 0.9010 (tp) REVERT: A 232 MET cc_start: 0.8418 (ttt) cc_final: 0.7978 (ttt) REVERT: A 476 MET cc_start: 0.9431 (mmt) cc_final: 0.9045 (mmt) REVERT: A 517 MET cc_start: 0.8017 (tpp) cc_final: 0.7544 (tpp) REVERT: A 563 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7382 (ptp90) REVERT: B 627 MET cc_start: 0.9590 (ttt) cc_final: 0.9169 (tmm) REVERT: B 647 ASN cc_start: 0.8981 (t0) cc_final: 0.8698 (t0) REVERT: B 668 PHE cc_start: 0.8494 (t80) cc_final: 0.8181 (t80) REVERT: B 682 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.8388 (t80) REVERT: B 693 ASN cc_start: 0.9432 (m-40) cc_final: 0.9142 (p0) REVERT: G 213 LEU cc_start: 0.9243 (mp) cc_final: 0.8854 (mp) REVERT: G 481 MET cc_start: 0.9317 (mmm) cc_final: 0.9032 (tpp) REVERT: G 568 MET cc_start: 0.8600 (mmm) cc_final: 0.7995 (mmm) REVERT: H 627 MET cc_start: 0.9448 (ttt) cc_final: 0.9027 (tmm) REVERT: H 650 PHE cc_start: 0.8666 (t80) cc_final: 0.8407 (t80) REVERT: H 661 LEU cc_start: 0.9087 (mt) cc_final: 0.8832 (mp) REVERT: H 686 ASN cc_start: 0.9293 (p0) cc_final: 0.8979 (p0) outliers start: 15 outliers final: 5 residues processed: 86 average time/residue: 0.2523 time to fit residues: 32.4944 Evaluate side-chains 81 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain H residue 634 VAL Chi-restraints excluded: chain H residue 711 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 52 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 81 optimal weight: 0.0470 chunk 46 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.9284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 399 GLN ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.047783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.035139 restraints weight = 81828.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.036331 restraints weight = 37108.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.037127 restraints weight = 22446.686| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.4068 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= 0.177 Angle : 0.560 8.365 18753 Z= 0.311 Chirality : 0.036 0.186 2110 Planarity : 0.003 0.041 1783 Dihedral : 26.076 179.063 3100 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.70 % Allowed : 11.81 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.26), residues: 1140 helix: 2.37 (0.20), residues: 652 sheet: 0.58 (0.60), residues: 63 loop : -0.27 (0.33), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 195 HIS 0.003 0.001 HIS A 390 PHE 0.034 0.001 PHE B 668 TYR 0.021 0.001 TYR B 652 ARG 0.011 0.001 ARG B 703 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 697) hydrogen bonds : angle 3.41571 ( 1847) covalent geometry : bond 0.00383 (13337) covalent geometry : angle 0.55963 (18753) Misc. bond : bond 0.00139 ( 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 87 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 1.488 Fit side-chains REVERT: A 517 MET cc_start: 0.8031 (tpp) cc_final: 0.7645 (tpp) REVERT: A 563 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7494 (ptp90) REVERT: B 627 MET cc_start: 0.9562 (ttt) cc_final: 0.9189 (tmm) REVERT: B 647 ASN cc_start: 0.8923 (t0) cc_final: 0.8630 (t0) REVERT: B 693 ASN cc_start: 0.9463 (m-40) cc_final: 0.9204 (p0) REVERT: G 213 LEU cc_start: 0.9200 (mp) cc_final: 0.8765 (mp) REVERT: G 440 MET cc_start: 0.9255 (tpp) cc_final: 0.8923 (tpp) REVERT: G 481 MET cc_start: 0.9382 (mmm) cc_final: 0.9074 (tpp) REVERT: G 568 MET cc_start: 0.8620 (mmm) cc_final: 0.7978 (mmm) REVERT: H 627 MET cc_start: 0.9434 (ttt) cc_final: 0.9004 (ppp) REVERT: H 650 PHE cc_start: 0.8640 (t80) cc_final: 0.8361 (t80) REVERT: H 686 ASN cc_start: 0.9244 (p0) cc_final: 0.8990 (p0) outliers start: 17 outliers final: 10 residues processed: 80 average time/residue: 0.2647 time to fit residues: 31.5270 Evaluate side-chains 77 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 456 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 704 ASN Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain H residue 634 VAL 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 0 optimal weight: 110.0000 chunk 13 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 105 optimal weight: 0.0980 chunk 109 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 18 optimal weight: 7.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 440 ASN ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 692 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.048069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.035155 restraints weight = 80505.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.036383 restraints weight = 36886.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.037172 restraints weight = 22376.098| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13340 Z= 0.160 Angle : 0.557 9.599 18753 Z= 0.308 Chirality : 0.036 0.214 2110 Planarity : 0.003 0.036 1783 Dihedral : 26.095 179.294 3100 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.20 % Allowed : 13.31 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.26), residues: 1140 helix: 2.59 (0.20), residues: 648 sheet: 0.70 (0.64), residues: 54 loop : -0.17 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 195 HIS 0.002 0.001 HIS A 390 PHE 0.028 0.001 PHE B 668 TYR 0.020 0.001 TYR B 652 ARG 0.007 0.000 ARG B 703 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 697) hydrogen bonds : angle 3.38711 ( 1847) covalent geometry : bond 0.00346 (13337) covalent geometry : angle 0.55667 (18753) Misc. bond : bond 0.00105 ( 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 86 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 1.154 Fit side-chains REVERT: A 517 MET cc_start: 0.8116 (tpp) cc_final: 0.7740 (tpp) REVERT: A 563 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7411 (ptp90) REVERT: B 627 MET cc_start: 0.9547 (ttt) cc_final: 0.8971 (tmm) REVERT: B 647 ASN cc_start: 0.8948 (t0) cc_final: 0.8679 (t0) REVERT: B 653 VAL cc_start: 0.9256 (OUTLIER) cc_final: 0.9031 (p) REVERT: B 682 TYR cc_start: 0.8422 (t80) cc_final: 0.7733 (t80) REVERT: B 693 ASN cc_start: 0.9396 (m-40) cc_final: 0.9055 (p0) REVERT: G 213 LEU cc_start: 0.9228 (mp) cc_final: 0.8779 (mp) REVERT: G 481 MET cc_start: 0.9372 (mmm) cc_final: 0.9033 (tpp) REVERT: G 538 MET cc_start: 0.9146 (tpp) cc_final: 0.8719 (mmt) REVERT: G 568 MET cc_start: 0.8715 (mmm) cc_final: 0.8187 (mmm) REVERT: H 627 MET cc_start: 0.9420 (ttt) cc_final: 0.9023 (tmm) REVERT: H 650 PHE cc_start: 0.8639 (t80) cc_final: 0.8353 (t80) REVERT: H 682 TYR cc_start: 0.8236 (t80) cc_final: 0.7755 (t80) REVERT: H 686 ASN cc_start: 0.9255 (p0) cc_final: 0.9021 (p0) REVERT: H 692 ASN cc_start: 0.9287 (m-40) cc_final: 0.8820 (t0) REVERT: H 693 ASN cc_start: 0.9567 (m-40) cc_final: 0.9056 (p0) outliers start: 12 outliers final: 9 residues processed: 84 average time/residue: 0.2498 time to fit residues: 31.1817 Evaluate side-chains 80 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 203 LYS Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain H residue 634 VAL 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 98 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3263 r_free = 0.3263 target = 0.047458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.034770 restraints weight = 82664.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.035999 restraints weight = 37114.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.036779 restraints weight = 22638.302| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13340 Z= 0.169 Angle : 0.581 11.897 18753 Z= 0.316 Chirality : 0.036 0.218 2110 Planarity : 0.003 0.043 1783 Dihedral : 26.154 179.665 3100 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.20 % Allowed : 13.51 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.26), residues: 1140 helix: 2.51 (0.21), residues: 652 sheet: 1.09 (0.64), residues: 61 loop : -0.17 (0.33), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 195 HIS 0.003 0.001 HIS G 391 PHE 0.030 0.001 PHE B 668 TYR 0.020 0.001 TYR B 652 ARG 0.013 0.001 ARG B 703 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 697) hydrogen bonds : angle 3.41689 ( 1847) covalent geometry : bond 0.00366 (13337) covalent geometry : angle 0.58114 (18753) Misc. bond : bond 0.00155 ( 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 83 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 1.397 Fit side-chains REVERT: A 232 MET cc_start: 0.8787 (tpp) cc_final: 0.8262 (tpp) REVERT: A 517 MET cc_start: 0.8078 (tpp) cc_final: 0.7729 (tpp) REVERT: A 563 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7475 (ptp90) REVERT: B 627 MET cc_start: 0.9596 (ttt) cc_final: 0.9070 (tmm) REVERT: B 647 ASN cc_start: 0.8982 (t0) cc_final: 0.8720 (t0) REVERT: B 682 TYR cc_start: 0.8448 (t80) cc_final: 0.7825 (t80) REVERT: B 693 ASN cc_start: 0.9454 (m-40) cc_final: 0.9180 (p0) REVERT: B 703 ARG cc_start: 0.9083 (mtm110) cc_final: 0.8850 (ptp-110) REVERT: G 213 LEU cc_start: 0.9223 (mp) cc_final: 0.8744 (mp) REVERT: G 440 MET cc_start: 0.9237 (tpp) cc_final: 0.8795 (tpp) REVERT: G 481 MET cc_start: 0.9459 (mmm) cc_final: 0.9071 (tpp) REVERT: G 538 MET cc_start: 0.9167 (tpp) cc_final: 0.8851 (mmt) REVERT: G 568 MET cc_start: 0.8737 (mmm) cc_final: 0.8182 (mmm) REVERT: H 627 MET cc_start: 0.9409 (ttt) cc_final: 0.9007 (tmm) REVERT: H 650 PHE cc_start: 0.8707 (t80) cc_final: 0.8415 (t80) REVERT: H 682 TYR cc_start: 0.8364 (t80) cc_final: 0.7859 (t80) REVERT: H 686 ASN cc_start: 0.9240 (p0) cc_final: 0.8989 (p0) REVERT: H 693 ASN cc_start: 0.9582 (m-40) cc_final: 0.9017 (p0) outliers start: 12 outliers final: 9 residues processed: 80 average time/residue: 0.2369 time to fit residues: 28.8122 Evaluate side-chains 78 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain H residue 634 VAL Chi-restraints excluded: chain H residue 700 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 65 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 54 optimal weight: 0.1980 chunk 34 optimal weight: 0.0270 chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 8 optimal weight: 0.0970 chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 overall best weight: 1.0238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.048535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.035421 restraints weight = 82067.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.036690 restraints weight = 37112.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.037527 restraints weight = 22826.343| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13340 Z= 0.133 Angle : 0.560 12.629 18753 Z= 0.304 Chirality : 0.036 0.251 2110 Planarity : 0.003 0.049 1783 Dihedral : 26.088 178.011 3100 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.80 % Allowed : 14.21 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.26), residues: 1140 helix: 2.55 (0.21), residues: 654 sheet: 1.21 (0.65), residues: 61 loop : -0.16 (0.33), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 442 HIS 0.002 0.000 HIS A 546 PHE 0.026 0.001 PHE B 668 TYR 0.020 0.001 TYR B 652 ARG 0.012 0.001 ARG B 703 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 697) hydrogen bonds : angle 3.28672 ( 1847) covalent geometry : bond 0.00285 (13337) covalent geometry : angle 0.55959 (18753) Misc. bond : bond 0.00113 ( 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 81 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 1.242 Fit side-chains REVERT: A 196 LEU cc_start: 0.9265 (mt) cc_final: 0.8991 (tp) REVERT: A 232 MET cc_start: 0.8747 (tpp) cc_final: 0.8390 (tpp) REVERT: A 517 MET cc_start: 0.8070 (tpp) cc_final: 0.7725 (tpp) REVERT: A 563 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7519 (ptp90) REVERT: B 627 MET cc_start: 0.9612 (ttt) cc_final: 0.9030 (tmm) REVERT: B 647 ASN cc_start: 0.9014 (t0) cc_final: 0.8753 (t0) REVERT: B 682 TYR cc_start: 0.8403 (t80) cc_final: 0.7788 (t80) REVERT: B 693 ASN cc_start: 0.9434 (m-40) cc_final: 0.9049 (p0) REVERT: G 213 LEU cc_start: 0.9227 (mp) cc_final: 0.8745 (mp) REVERT: G 440 MET cc_start: 0.9209 (tpp) cc_final: 0.8766 (tpp) REVERT: G 481 MET cc_start: 0.9424 (mmm) cc_final: 0.9109 (tpp) REVERT: G 538 MET cc_start: 0.9139 (tpp) cc_final: 0.8732 (mmt) REVERT: G 568 MET cc_start: 0.8765 (mmm) cc_final: 0.8233 (mmm) REVERT: H 627 MET cc_start: 0.9388 (ttt) cc_final: 0.8963 (tmm) REVERT: H 650 PHE cc_start: 0.8746 (t80) cc_final: 0.8436 (t80) REVERT: H 682 TYR cc_start: 0.8250 (t80) cc_final: 0.7758 (t80) REVERT: H 686 ASN cc_start: 0.9279 (p0) cc_final: 0.9049 (p0) REVERT: H 692 ASN cc_start: 0.9316 (m-40) cc_final: 0.8902 (t0) REVERT: H 693 ASN cc_start: 0.9529 (m-40) cc_final: 0.9010 (p0) outliers start: 8 outliers final: 7 residues processed: 79 average time/residue: 0.3062 time to fit residues: 36.9186 Evaluate side-chains 78 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain H residue 634 VAL 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 37 optimal weight: 0.0060 chunk 53 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.048920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.035766 restraints weight = 80882.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.037024 restraints weight = 36678.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.037800 restraints weight = 22464.872| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13340 Z= 0.131 Angle : 0.565 13.017 18753 Z= 0.304 Chirality : 0.036 0.252 2110 Planarity : 0.003 0.038 1783 Dihedral : 26.084 177.282 3100 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.90 % Allowed : 14.41 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.26), residues: 1140 helix: 2.57 (0.20), residues: 659 sheet: 1.32 (0.66), residues: 61 loop : -0.14 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 442 HIS 0.002 0.000 HIS A 546 PHE 0.025 0.001 PHE B 668 TYR 0.023 0.001 TYR B 652 ARG 0.010 0.000 ARG B 703 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 697) hydrogen bonds : angle 3.28223 ( 1847) covalent geometry : bond 0.00280 (13337) covalent geometry : angle 0.56483 (18753) Misc. bond : bond 0.00135 ( 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 79 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 1.207 Fit side-chains REVERT: A 196 LEU cc_start: 0.9267 (mt) cc_final: 0.8997 (tp) REVERT: A 232 MET cc_start: 0.8768 (tpp) cc_final: 0.8173 (tpp) REVERT: A 517 MET cc_start: 0.8031 (tpp) cc_final: 0.7699 (tpp) REVERT: B 627 MET cc_start: 0.9614 (ttt) cc_final: 0.9086 (tmm) REVERT: B 647 ASN cc_start: 0.9028 (t0) cc_final: 0.8760 (t0) REVERT: B 682 TYR cc_start: 0.8356 (t80) cc_final: 0.7864 (t80) REVERT: B 693 ASN cc_start: 0.9437 (m-40) cc_final: 0.9035 (p0) REVERT: G 213 LEU cc_start: 0.9222 (mp) cc_final: 0.8708 (mp) REVERT: G 440 MET cc_start: 0.9198 (tpp) cc_final: 0.8663 (tpp) REVERT: G 481 MET cc_start: 0.9423 (mmm) cc_final: 0.9089 (tpp) REVERT: G 538 MET cc_start: 0.9123 (tpp) cc_final: 0.8750 (mmt) REVERT: G 568 MET cc_start: 0.8755 (mmm) cc_final: 0.8204 (mmm) REVERT: H 627 MET cc_start: 0.9397 (ttt) cc_final: 0.8949 (tmm) REVERT: H 650 PHE cc_start: 0.8749 (t80) cc_final: 0.8426 (t80) REVERT: H 682 TYR cc_start: 0.8235 (t80) cc_final: 0.7784 (t80) REVERT: H 686 ASN cc_start: 0.9337 (p0) cc_final: 0.9087 (p0) REVERT: H 692 ASN cc_start: 0.9318 (m-40) cc_final: 0.8951 (t0) REVERT: H 693 ASN cc_start: 0.9517 (m-40) cc_final: 0.8983 (p0) outliers start: 9 outliers final: 8 residues processed: 77 average time/residue: 0.2345 time to fit residues: 27.9683 Evaluate side-chains 78 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain H residue 634 VAL 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 77 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.047637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.034833 restraints weight = 81922.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.036059 restraints weight = 37247.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.036857 restraints weight = 22877.440| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13340 Z= 0.165 Angle : 0.587 13.456 18753 Z= 0.315 Chirality : 0.036 0.241 2110 Planarity : 0.003 0.050 1783 Dihedral : 26.152 179.552 3100 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.30 % Allowed : 14.01 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.26), residues: 1140 helix: 2.53 (0.20), residues: 667 sheet: 0.95 (0.69), residues: 56 loop : -0.05 (0.33), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 195 HIS 0.003 0.001 HIS G 391 PHE 0.024 0.001 PHE B 668 TYR 0.019 0.001 TYR B 652 ARG 0.014 0.001 ARG B 703 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 697) hydrogen bonds : angle 3.39454 ( 1847) covalent geometry : bond 0.00356 (13337) covalent geometry : angle 0.58690 (18753) Misc. bond : bond 0.00147 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3675.12 seconds wall clock time: 65 minutes 41.80 seconds (3941.80 seconds total)