Starting phenix.real_space_refine on Wed Mar 4 08:40:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ahh_11786/03_2026/7ahh_11786.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ahh_11786/03_2026/7ahh_11786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ahh_11786/03_2026/7ahh_11786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ahh_11786/03_2026/7ahh_11786.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ahh_11786/03_2026/7ahh_11786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ahh_11786/03_2026/7ahh_11786.map" } resolution = 3.5 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= 0.006 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 60 5.16 5 C 7763 2.51 5 N 2024 2.21 5 O 2270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12125 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4011 Classifications: {'peptide': 526} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 504} Chain breaks: 1 Chain: "B" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2016 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain: "C" Number of atoms: 2992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2992 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 14, 'TRANS': 367} Chain breaks: 1 Chain: "D" Number of atoms: 2992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2992 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 14, 'TRANS': 367} Chain breaks: 1 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'BET': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'2BA': 1, 'ANP': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Link IDs: {None: 1} Time building chain proxies: 2.79, per 1000 atoms: 0.23 Number of scatterers: 12125 At special positions: 0 Unit cell: (93.104, 100.188, 150.788, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 8 15.00 O 2270 8.00 N 2024 7.00 C 7763 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=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 521.4 milliseconds 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2894 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 16 sheets defined 63.6% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 10 through 26 Processing helix chain 'A' and resid 26 through 51 Processing helix chain 'A' and resid 52 through 68 Processing helix chain 'A' and resid 72 through 89 Processing helix chain 'A' and resid 91 through 121 Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 122 through 138 removed outlier: 3.929A pdb=" N ALA A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Proline residue: A 131 - end of helix removed outlier: 3.662A pdb=" N THR A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 152 removed outlier: 4.155A pdb=" N TYR A 144 " --> pdb=" O PRO A 140 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 156 through 180 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 183 through 193 removed outlier: 3.565A pdb=" N VAL A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 204 through 232 removed outlier: 3.543A pdb=" N LEU A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLY A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N THR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 249 removed outlier: 3.860A pdb=" N GLY A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 275 Processing helix chain 'A' and resid 330 through 347 removed outlier: 3.582A pdb=" N ALA A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 346 " --> pdb=" O GLN A 342 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 368 removed outlier: 3.687A pdb=" N GLY A 368 " --> pdb=" O THR A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 390 Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 423 through 426 removed outlier: 4.097A pdb=" N ASN A 426 " --> pdb=" O ASN A 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 423 through 426' Processing helix chain 'A' and resid 437 through 447 Processing helix chain 'A' and resid 450 through 455 removed outlier: 4.191A pdb=" N ASP A 454 " --> pdb=" O ASN A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 476 removed outlier: 3.580A pdb=" N VAL A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 518 through 522 Processing helix chain 'A' and resid 523 through 533 Processing helix chain 'A' and resid 539 through 549 removed outlier: 4.265A pdb=" N VAL A 543 " --> pdb=" O ASP A 539 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 564 removed outlier: 3.576A pdb=" N ILE A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 573 removed outlier: 3.680A pdb=" N TRP A 571 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 572 " --> pdb=" O VAL A 568 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A 573 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 26 Processing helix chain 'B' and resid 26 through 51 removed outlier: 3.629A pdb=" N VAL B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 68 Processing helix chain 'B' and resid 72 through 89 Processing helix chain 'B' and resid 91 through 122 Proline residue: B 114 - end of helix Processing helix chain 'B' and resid 122 through 138 removed outlier: 3.577A pdb=" N ALA B 126 " --> pdb=" O SER B 122 " (cutoff:3.500A) Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 140 through 152 removed outlier: 4.206A pdb=" N TYR B 144 " --> pdb=" O PRO B 140 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Proline residue: B 147 - end of helix Processing helix chain 'B' and resid 156 through 181 Proline residue: B 169 - end of helix Processing helix chain 'B' and resid 183 through 193 Processing helix chain 'B' and resid 196 through 204 Processing helix chain 'B' and resid 204 through 232 removed outlier: 3.698A pdb=" N LEU B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLY B 211 " --> pdb=" O PRO B 207 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N THR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 250 removed outlier: 4.006A pdb=" N GLY B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 275 Processing helix chain 'C' and resid 18 through 26 Processing helix chain 'C' and resid 30 through 39 Processing helix chain 'C' and resid 67 through 75 Processing helix chain 'C' and resid 96 through 107 Processing helix chain 'C' and resid 122 through 133 removed outlier: 4.679A pdb=" N GLY C 130 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU C 131 " --> pdb=" O THR C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 151 Processing helix chain 'C' and resid 152 through 153 No H-bonds generated for 'chain 'C' and resid 152 through 153' Processing helix chain 'C' and resid 154 through 158 Processing helix chain 'C' and resid 161 through 165 Processing helix chain 'C' and resid 166 through 181 removed outlier: 4.316A pdb=" N ASN C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 removed outlier: 3.950A pdb=" N ALA C 194 " --> pdb=" O ALA C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 214 Processing helix chain 'C' and resid 224 through 230 Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 260 through 265 Processing helix chain 'C' and resid 292 through 304 Processing helix chain 'C' and resid 323 through 333 Processing helix chain 'C' and resid 356 through 363 removed outlier: 3.921A pdb=" N TYR C 361 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.884A pdb=" N GLU C 387 " --> pdb=" O GLY C 383 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 26 Processing helix chain 'D' and resid 30 through 39 Processing helix chain 'D' and resid 67 through 75 Processing helix chain 'D' and resid 96 through 107 Processing helix chain 'D' and resid 122 through 133 removed outlier: 4.680A pdb=" N GLY D 130 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU D 131 " --> pdb=" O THR D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 151 Processing helix chain 'D' and resid 152 through 153 No H-bonds generated for 'chain 'D' and resid 152 through 153' Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 161 through 165 Processing helix chain 'D' and resid 166 through 181 removed outlier: 4.316A pdb=" N ASN D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 195 removed outlier: 3.950A pdb=" N ALA D 194 " --> pdb=" O ALA D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 214 Processing helix chain 'D' and resid 224 through 230 Processing helix chain 'D' and resid 250 through 255 Processing helix chain 'D' and resid 260 through 265 Processing helix chain 'D' and resid 292 through 304 Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 356 through 363 removed outlier: 3.921A pdb=" N TYR D 361 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 389 removed outlier: 3.885A pdb=" N GLU D 387 " --> pdb=" O GLY D 383 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU D 389 " --> pdb=" O VAL D 385 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 322 through 327 Processing sheet with id=AA2, first strand: chain 'A' and resid 372 through 378 removed outlier: 5.607A pdb=" N VAL A 374 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE A 514 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 376 " --> pdb=" O ASN A 512 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 400 " --> pdb=" O ILE A 511 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 481 through 484 removed outlier: 3.612A pdb=" N GLY A 406 " --> pdb=" O GLY A 483 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 428 through 430 removed outlier: 6.104A pdb=" N ILE A 429 " --> pdb=" O VAL A 458 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 42 through 47 removed outlier: 5.618A pdb=" N TYR C 45 " --> pdb=" O LYS C 12 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LYS C 12 " --> pdb=" O TYR C 45 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 42 through 47 removed outlier: 5.618A pdb=" N TYR C 45 " --> pdb=" O LYS C 12 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LYS C 12 " --> pdb=" O TYR C 45 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU C 10 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER C 82 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.581A pdb=" N MET C 60 " --> pdb=" O MET C 238 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET C 244 " --> pdb=" O ILE C 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 110 through 111 Processing sheet with id=AA9, first strand: chain 'C' and resid 285 through 287 Processing sheet with id=AB1, first strand: chain 'C' and resid 369 through 370 removed outlier: 4.143A pdb=" N GLY C 378 " --> pdb=" O VAL C 369 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 42 through 47 removed outlier: 5.618A pdb=" N TYR D 45 " --> pdb=" O LYS D 12 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LYS D 12 " --> pdb=" O TYR D 45 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 42 through 47 removed outlier: 5.618A pdb=" N TYR D 45 " --> pdb=" O LYS D 12 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LYS D 12 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU D 10 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N SER D 82 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 60 through 61 removed outlier: 6.581A pdb=" N MET D 60 " --> pdb=" O MET D 238 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET D 244 " --> pdb=" O ILE D 237 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 110 through 111 Processing sheet with id=AB6, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AB7, first strand: chain 'D' and resid 369 through 370 removed outlier: 4.143A pdb=" N GLY D 378 " --> pdb=" O VAL D 369 " (cutoff:3.500A) 675 hydrogen bonds defined for protein. 1941 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3432 1.33 - 1.45: 1700 1.45 - 1.57: 7057 1.57 - 1.69: 16 1.69 - 1.81: 120 Bond restraints: 12325 Sorted by residual: bond pdb=" N3B ANP C 501 " pdb=" PG ANP C 501 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.75e+01 bond pdb=" N3B ANP D 501 " pdb=" PG ANP D 501 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" O3A ANP D 501 " pdb=" PB ANP D 501 " ideal model delta sigma weight residual 1.700 1.598 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" O3A ANP C 501 " pdb=" PB ANP C 501 " ideal model delta sigma weight residual 1.700 1.598 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" C5' 2BA D 502 " pdb=" O5' 2BA D 502 " ideal model delta sigma weight residual 1.433 1.359 0.074 2.00e-02 2.50e+03 1.39e+01 ... (remaining 12320 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 16026 2.05 - 4.10: 526 4.10 - 6.15: 110 6.15 - 8.20: 27 8.20 - 10.25: 18 Bond angle restraints: 16707 Sorted by residual: angle pdb=" N ILE C 252 " pdb=" CA ILE C 252 " pdb=" C ILE C 252 " ideal model delta sigma weight residual 111.00 103.52 7.48 1.09e+00 8.42e-01 4.71e+01 angle pdb=" N LEU C 253 " pdb=" CA LEU C 253 " pdb=" C LEU C 253 " ideal model delta sigma weight residual 112.23 120.87 -8.64 1.26e+00 6.30e-01 4.70e+01 angle pdb=" N ILE D 252 " pdb=" CA ILE D 252 " pdb=" C ILE D 252 " ideal model delta sigma weight residual 111.00 103.64 7.36 1.09e+00 8.42e-01 4.56e+01 angle pdb=" N LEU D 253 " pdb=" CA LEU D 253 " pdb=" C LEU D 253 " ideal model delta sigma weight residual 112.23 120.06 -7.83 1.26e+00 6.30e-01 3.86e+01 angle pdb=" CA THR A 537 " pdb=" CB THR A 537 " pdb=" CG2 THR A 537 " ideal model delta sigma weight residual 110.50 119.06 -8.56 1.70e+00 3.46e-01 2.54e+01 ... (remaining 16702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.56: 6981 19.56 - 39.12: 442 39.12 - 58.68: 97 58.68 - 78.24: 20 78.24 - 97.80: 14 Dihedral angle restraints: 7554 sinusoidal: 3086 harmonic: 4468 Sorted by residual: dihedral pdb=" CA THR A 537 " pdb=" C THR A 537 " pdb=" N LYS A 538 " pdb=" CA LYS A 538 " ideal model delta harmonic sigma weight residual 180.00 -154.02 -25.98 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA SER C 109 " pdb=" C SER C 109 " pdb=" N MET C 110 " pdb=" CA MET C 110 " ideal model delta harmonic sigma weight residual -180.00 -158.92 -21.08 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA SER D 109 " pdb=" C SER D 109 " pdb=" N MET D 110 " pdb=" CA MET D 110 " ideal model delta harmonic sigma weight residual -180.00 -158.94 -21.06 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 7551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.230: 1984 0.230 - 0.460: 7 0.460 - 0.691: 8 0.691 - 0.921: 0 0.921 - 1.151: 1 Chirality restraints: 2000 Sorted by residual: chirality pdb=" CB THR A 537 " pdb=" CA THR A 537 " pdb=" OG1 THR A 537 " pdb=" CG2 THR A 537 " both_signs ideal model delta sigma weight residual False 2.55 1.40 1.15 2.00e-01 2.50e+01 3.31e+01 chirality pdb=" CG LEU C 101 " pdb=" CB LEU C 101 " pdb=" CD1 LEU C 101 " pdb=" CD2 LEU C 101 " both_signs ideal model delta sigma weight residual False -2.59 -1.97 -0.62 2.00e-01 2.50e+01 9.64e+00 chirality pdb=" CG LEU D 101 " pdb=" CB LEU D 101 " pdb=" CD1 LEU D 101 " pdb=" CD2 LEU D 101 " both_signs ideal model delta sigma weight residual False -2.59 -1.97 -0.62 2.00e-01 2.50e+01 9.57e+00 ... (remaining 1997 not shown) Planarity restraints: 2084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 214 " 0.029 2.00e-02 2.50e+03 3.42e-02 2.04e+01 pdb=" CG PHE C 214 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 PHE C 214 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE C 214 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE C 214 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE C 214 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 214 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 214 " 0.028 2.00e-02 2.50e+03 3.38e-02 2.00e+01 pdb=" CG PHE D 214 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 PHE D 214 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE D 214 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE D 214 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE D 214 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE D 214 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 169 " -0.050 5.00e-02 4.00e+02 7.57e-02 9.17e+00 pdb=" N PRO A 170 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " -0.043 5.00e-02 4.00e+02 ... (remaining 2081 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1846 2.75 - 3.29: 13180 3.29 - 3.83: 19435 3.83 - 4.36: 23880 4.36 - 4.90: 40952 Nonbonded interactions: 99293 Sorted by model distance: nonbonded pdb=" O GLU C 250 " pdb=" N LEU C 253 " model vdw 2.213 3.120 nonbonded pdb=" OD1 ASP D 91 " pdb=" N VAL D 92 " model vdw 2.226 3.120 nonbonded pdb=" OD1 ASP C 91 " pdb=" N VAL C 92 " model vdw 2.227 3.120 nonbonded pdb=" N HIS C 9 " pdb=" OD1 ASN C 48 " model vdw 2.228 3.120 nonbonded pdb=" N HIS D 9 " pdb=" OD1 ASN D 48 " model vdw 2.228 3.120 ... (remaining 99288 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 'C' selection = (chain 'D' and resid 3 through 501) } 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: 1.120 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.420 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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 : 0.008 0.164 12325 Z= 0.356 Angle : 0.967 10.253 16707 Z= 0.534 Chirality : 0.067 1.151 2000 Planarity : 0.005 0.076 2084 Dihedral : 14.623 97.804 4660 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.23 % Allowed : 2.27 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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 (0.21), residues: 1548 helix: 0.24 (0.18), residues: 870 sheet: -4.26 (0.33), residues: 124 loop : -2.24 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 234 TYR 0.013 0.002 TYR A 327 PHE 0.077 0.003 PHE C 214 TRP 0.026 0.002 TRP A 535 HIS 0.004 0.001 HIS D 9 Details of bonding type rmsd covalent geometry : bond 0.00800 (12325) covalent geometry : angle 0.96673 (16707) hydrogen bonds : bond 0.17609 ( 671) hydrogen bonds : angle 6.84547 ( 1941) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 238 time to evaluate : 0.479 Fit side-chains REVERT: A 119 MET cc_start: 0.8231 (ttm) cc_final: 0.7932 (mtp) REVERT: A 198 ARG cc_start: 0.7770 (ttp-110) cc_final: 0.7554 (ttp-110) REVERT: D 45 TYR cc_start: 0.7776 (t80) cc_final: 0.7342 (t80) REVERT: D 109 SER cc_start: 0.8889 (t) cc_final: 0.8683 (t) REVERT: D 189 ASP cc_start: 0.7543 (t0) cc_final: 0.7277 (t0) outliers start: 3 outliers final: 0 residues processed: 239 average time/residue: 0.1196 time to fit residues: 40.4397 Evaluate side-chains 153 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.0470 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.0060 overall best weight: 0.4294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS A 387 GLN A 451 ASN B 8 GLN C 126 ASN C 151 ASN D 126 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.135595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.118515 restraints weight = 18826.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.121200 restraints weight = 10807.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.123010 restraints weight = 7346.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.124176 restraints weight = 5597.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.124992 restraints weight = 4634.846| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12325 Z= 0.149 Angle : 0.667 8.592 16707 Z= 0.346 Chirality : 0.045 0.191 2000 Planarity : 0.005 0.053 2084 Dihedral : 7.824 61.257 1753 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.21 % Allowed : 7.79 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -0.57 (0.22), residues: 1548 helix: 0.92 (0.18), residues: 880 sheet: -3.66 (0.35), residues: 130 loop : -1.65 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 173 TYR 0.016 0.001 TYR A 412 PHE 0.014 0.001 PHE A 74 TRP 0.016 0.001 TRP A 535 HIS 0.002 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00318 (12325) covalent geometry : angle 0.66701 (16707) hydrogen bonds : bond 0.04465 ( 671) hydrogen bonds : angle 4.85550 ( 1941) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: B 205 GLU cc_start: 0.7312 (mm-30) cc_final: 0.7062 (mm-30) REVERT: D 45 TYR cc_start: 0.7661 (t80) cc_final: 0.7223 (t80) REVERT: D 189 ASP cc_start: 0.7423 (t0) cc_final: 0.7217 (t0) outliers start: 16 outliers final: 6 residues processed: 194 average time/residue: 0.0902 time to fit residues: 27.2795 Evaluate side-chains 153 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 346 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 14 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.120590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.101204 restraints weight = 19990.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.104057 restraints weight = 10970.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.105932 restraints weight = 7310.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.107187 restraints weight = 5578.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.108035 restraints weight = 4629.658| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12325 Z= 0.212 Angle : 0.664 8.013 16707 Z= 0.339 Chirality : 0.047 0.170 2000 Planarity : 0.004 0.050 2084 Dihedral : 7.060 62.247 1753 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.36 % Allowed : 10.82 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -0.58 (0.22), residues: 1548 helix: 0.77 (0.17), residues: 897 sheet: -3.17 (0.36), residues: 134 loop : -1.56 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 354 TYR 0.014 0.002 TYR A 327 PHE 0.016 0.002 PHE D 49 TRP 0.021 0.002 TRP A 535 HIS 0.003 0.001 HIS C 120 Details of bonding type rmsd covalent geometry : bond 0.00523 (12325) covalent geometry : angle 0.66419 (16707) hydrogen bonds : bond 0.04297 ( 671) hydrogen bonds : angle 4.66142 ( 1941) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 LYS cc_start: 0.8296 (mmtp) cc_final: 0.8083 (ptmt) REVERT: A 356 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7437 (pp) REVERT: C 60 MET cc_start: 0.8244 (mtp) cc_final: 0.7882 (mtp) REVERT: D 45 TYR cc_start: 0.7969 (t80) cc_final: 0.7296 (t80) outliers start: 18 outliers final: 12 residues processed: 169 average time/residue: 0.0941 time to fit residues: 24.4042 Evaluate side-chains 161 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 280 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 0.0040 chunk 113 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 43 optimal weight: 0.0170 chunk 92 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.4230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 338 ASN C 135 ASN C 325 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.129723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111904 restraints weight = 19140.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.114376 restraints weight = 11434.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.116064 restraints weight = 8016.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.117067 restraints weight = 6254.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.117916 restraints weight = 5310.842| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12325 Z= 0.114 Angle : 0.563 7.099 16707 Z= 0.288 Chirality : 0.042 0.151 2000 Planarity : 0.004 0.050 2084 Dihedral : 6.647 61.953 1753 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.04 % Allowed : 12.33 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -0.06 (0.22), residues: 1548 helix: 1.16 (0.18), residues: 897 sheet: -2.78 (0.38), residues: 134 loop : -1.33 (0.29), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 142 TYR 0.018 0.001 TYR A 527 PHE 0.017 0.001 PHE A 349 TRP 0.015 0.001 TRP A 535 HIS 0.001 0.000 HIS A 487 Details of bonding type rmsd covalent geometry : bond 0.00252 (12325) covalent geometry : angle 0.56310 (16707) hydrogen bonds : bond 0.03536 ( 671) hydrogen bonds : angle 4.31720 ( 1941) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8399 (ttm) cc_final: 0.8010 (mtp) REVERT: A 205 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7474 (mm-30) REVERT: A 356 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7424 (pp) REVERT: D 45 TYR cc_start: 0.7768 (t80) cc_final: 0.7172 (t80) REVERT: D 60 MET cc_start: 0.8468 (mtp) cc_final: 0.7787 (mtm) outliers start: 27 outliers final: 16 residues processed: 189 average time/residue: 0.0901 time to fit residues: 26.1119 Evaluate side-chains 169 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 381 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 95 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 147 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 67 optimal weight: 0.1980 chunk 70 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN C 135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.128337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110283 restraints weight = 19385.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.112719 restraints weight = 11683.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.114378 restraints weight = 8250.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.115465 restraints weight = 6481.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.116099 restraints weight = 5470.880| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12325 Z= 0.118 Angle : 0.546 9.438 16707 Z= 0.278 Chirality : 0.042 0.164 2000 Planarity : 0.004 0.046 2084 Dihedral : 6.483 65.018 1753 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.34 % Allowed : 13.92 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: 0.18 (0.22), residues: 1548 helix: 1.34 (0.18), residues: 897 sheet: -2.48 (0.40), residues: 134 loop : -1.27 (0.29), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 142 TYR 0.013 0.001 TYR A 527 PHE 0.013 0.001 PHE A 349 TRP 0.013 0.001 TRP A 535 HIS 0.001 0.000 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00275 (12325) covalent geometry : angle 0.54622 (16707) hydrogen bonds : bond 0.03428 ( 671) hydrogen bonds : angle 4.21965 ( 1941) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8375 (ttm) cc_final: 0.8027 (mtp) REVERT: A 356 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7444 (pp) REVERT: C 60 MET cc_start: 0.7806 (mtp) cc_final: 0.7344 (mtp) REVERT: D 11 THR cc_start: 0.9060 (t) cc_final: 0.8682 (m) REVERT: D 45 TYR cc_start: 0.7757 (t80) cc_final: 0.7056 (t80) REVERT: D 60 MET cc_start: 0.8406 (mtp) cc_final: 0.7768 (mtm) outliers start: 31 outliers final: 17 residues processed: 185 average time/residue: 0.0937 time to fit residues: 26.6590 Evaluate side-chains 169 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 290 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 122 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 ASN B 274 GLN C 52 ASN C 135 ASN C 245 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.126268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.106887 restraints weight = 19642.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.109499 restraints weight = 11437.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111298 restraints weight = 7955.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.112424 restraints weight = 6180.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.113250 restraints weight = 5215.370| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12325 Z= 0.160 Angle : 0.584 9.022 16707 Z= 0.296 Chirality : 0.044 0.159 2000 Planarity : 0.004 0.044 2084 Dihedral : 6.475 69.711 1753 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.50 % Allowed : 15.13 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: 0.18 (0.22), residues: 1548 helix: 1.31 (0.18), residues: 896 sheet: -2.38 (0.42), residues: 132 loop : -1.25 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 142 TYR 0.010 0.001 TYR A 327 PHE 0.013 0.001 PHE D 49 TRP 0.016 0.001 TRP A 535 HIS 0.002 0.000 HIS A 487 Details of bonding type rmsd covalent geometry : bond 0.00384 (12325) covalent geometry : angle 0.58398 (16707) hydrogen bonds : bond 0.03621 ( 671) hydrogen bonds : angle 4.24249 ( 1941) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 119 MET cc_start: 0.8514 (ttm) cc_final: 0.8150 (mtp) REVERT: A 356 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7442 (pp) REVERT: C 60 MET cc_start: 0.7963 (mtp) cc_final: 0.7475 (mtp) REVERT: D 11 THR cc_start: 0.9112 (t) cc_final: 0.8713 (m) REVERT: D 45 TYR cc_start: 0.7916 (t80) cc_final: 0.7179 (t80) outliers start: 33 outliers final: 23 residues processed: 179 average time/residue: 0.0924 time to fit residues: 25.7183 Evaluate side-chains 176 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 334 GLN Chi-restraints excluded: chain D residue 381 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 21 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 142 optimal weight: 0.4980 chunk 137 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN C 135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.127882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.108907 restraints weight = 19591.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111492 restraints weight = 11539.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.113256 restraints weight = 8041.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.114354 restraints weight = 6255.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.115207 restraints weight = 5279.775| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12325 Z= 0.119 Angle : 0.565 10.531 16707 Z= 0.285 Chirality : 0.042 0.163 2000 Planarity : 0.004 0.044 2084 Dihedral : 6.354 69.146 1753 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.04 % Allowed : 16.41 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: 0.39 (0.22), residues: 1548 helix: 1.48 (0.18), residues: 897 sheet: -2.23 (0.43), residues: 132 loop : -1.19 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 142 TYR 0.010 0.001 TYR A 412 PHE 0.011 0.001 PHE C 49 TRP 0.014 0.001 TRP A 535 HIS 0.001 0.000 HIS A 487 Details of bonding type rmsd covalent geometry : bond 0.00277 (12325) covalent geometry : angle 0.56454 (16707) hydrogen bonds : bond 0.03384 ( 671) hydrogen bonds : angle 4.16001 ( 1941) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 119 MET cc_start: 0.8443 (ttm) cc_final: 0.8049 (mtp) REVERT: A 356 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7344 (pp) REVERT: B 214 MET cc_start: 0.7566 (mmm) cc_final: 0.7362 (mmp) REVERT: C 60 MET cc_start: 0.7916 (mtp) cc_final: 0.7389 (mtp) REVERT: D 11 THR cc_start: 0.9094 (t) cc_final: 0.8707 (m) REVERT: D 45 TYR cc_start: 0.7890 (t80) cc_final: 0.7245 (t80) outliers start: 27 outliers final: 23 residues processed: 174 average time/residue: 0.0886 time to fit residues: 24.1009 Evaluate side-chains 174 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 290 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 132 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 113 optimal weight: 0.0470 chunk 107 optimal weight: 0.0870 chunk 78 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN A 347 HIS B 274 GLN C 135 ASN C 245 GLN D 215 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.128717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.109596 restraints weight = 19581.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.112250 restraints weight = 11398.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.114041 restraints weight = 7907.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.115232 restraints weight = 6147.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.115989 restraints weight = 5144.637| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12325 Z= 0.112 Angle : 0.553 9.123 16707 Z= 0.279 Chirality : 0.042 0.138 2000 Planarity : 0.004 0.043 2084 Dihedral : 6.261 68.896 1753 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.12 % Allowed : 16.57 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: 0.54 (0.23), residues: 1548 helix: 1.60 (0.18), residues: 894 sheet: -1.96 (0.43), residues: 142 loop : -1.14 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 142 TYR 0.008 0.001 TYR A 327 PHE 0.010 0.001 PHE C 49 TRP 0.012 0.001 TRP A 535 HIS 0.001 0.000 HIS A 487 Details of bonding type rmsd covalent geometry : bond 0.00258 (12325) covalent geometry : angle 0.55273 (16707) hydrogen bonds : bond 0.03336 ( 671) hydrogen bonds : angle 4.09766 ( 1941) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 119 MET cc_start: 0.8423 (ttm) cc_final: 0.8034 (mtp) REVERT: A 356 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7331 (pp) REVERT: B 42 ASN cc_start: 0.8277 (m110) cc_final: 0.7882 (m110) REVERT: B 254 LYS cc_start: 0.8620 (mtpp) cc_final: 0.8297 (mtpp) REVERT: C 60 MET cc_start: 0.7890 (mtp) cc_final: 0.7334 (mtp) REVERT: C 230 ARG cc_start: 0.8002 (mtp85) cc_final: 0.7751 (mtp85) REVERT: D 11 THR cc_start: 0.9079 (t) cc_final: 0.8703 (m) REVERT: D 45 TYR cc_start: 0.7901 (t80) cc_final: 0.7324 (t80) outliers start: 28 outliers final: 23 residues processed: 174 average time/residue: 0.0849 time to fit residues: 23.2469 Evaluate side-chains 179 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 290 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 77 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 HIS B 274 GLN C 135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.126297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.107236 restraints weight = 19576.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.109854 restraints weight = 11338.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111582 restraints weight = 7831.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.112757 restraints weight = 6092.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.113461 restraints weight = 5109.615| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12325 Z= 0.138 Angle : 0.573 8.976 16707 Z= 0.289 Chirality : 0.043 0.138 2000 Planarity : 0.004 0.042 2084 Dihedral : 6.256 71.805 1753 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.27 % Allowed : 16.34 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: 0.53 (0.22), residues: 1548 helix: 1.57 (0.18), residues: 894 sheet: -1.87 (0.43), residues: 147 loop : -1.11 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 142 TYR 0.010 0.001 TYR A 412 PHE 0.012 0.001 PHE B 53 TRP 0.015 0.001 TRP A 535 HIS 0.002 0.000 HIS A 487 Details of bonding type rmsd covalent geometry : bond 0.00334 (12325) covalent geometry : angle 0.57312 (16707) hydrogen bonds : bond 0.03489 ( 671) hydrogen bonds : angle 4.13830 ( 1941) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 119 MET cc_start: 0.8492 (ttm) cc_final: 0.8105 (mtp) REVERT: A 356 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7374 (pp) REVERT: B 42 ASN cc_start: 0.8330 (m110) cc_final: 0.7911 (m110) REVERT: B 254 LYS cc_start: 0.8670 (mtpp) cc_final: 0.8377 (mtpp) REVERT: C 60 MET cc_start: 0.7970 (mtp) cc_final: 0.7388 (mtp) REVERT: D 11 THR cc_start: 0.9106 (t) cc_final: 0.8728 (m) REVERT: D 45 TYR cc_start: 0.7955 (t80) cc_final: 0.7368 (t80) outliers start: 30 outliers final: 24 residues processed: 171 average time/residue: 0.0917 time to fit residues: 24.4608 Evaluate side-chains 178 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 290 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 68 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 145 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN C 135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.127291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.107957 restraints weight = 19660.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110555 restraints weight = 11498.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.112318 restraints weight = 8011.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.113393 restraints weight = 6237.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.114275 restraints weight = 5282.518| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12325 Z= 0.123 Angle : 0.568 9.027 16707 Z= 0.285 Chirality : 0.042 0.138 2000 Planarity : 0.004 0.042 2084 Dihedral : 6.222 71.730 1753 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.89 % Allowed : 17.10 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: 0.59 (0.22), residues: 1548 helix: 1.61 (0.18), residues: 894 sheet: -1.87 (0.44), residues: 142 loop : -1.08 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 230 TYR 0.011 0.001 TYR A 412 PHE 0.011 0.001 PHE B 53 TRP 0.013 0.001 TRP A 535 HIS 0.001 0.000 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00293 (12325) covalent geometry : angle 0.56765 (16707) hydrogen bonds : bond 0.03442 ( 671) hydrogen bonds : angle 4.11624 ( 1941) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 119 MET cc_start: 0.8461 (ttm) cc_final: 0.8073 (mtp) REVERT: A 356 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7346 (pp) REVERT: A 545 LEU cc_start: 0.8156 (pp) cc_final: 0.7628 (mt) REVERT: B 42 ASN cc_start: 0.8318 (m110) cc_final: 0.7886 (m110) REVERT: D 11 THR cc_start: 0.9091 (t) cc_final: 0.8722 (m) REVERT: D 45 TYR cc_start: 0.7934 (t80) cc_final: 0.7414 (t80) REVERT: D 244 MET cc_start: 0.7173 (ptp) cc_final: 0.6959 (ptp) outliers start: 25 outliers final: 21 residues processed: 172 average time/residue: 0.0865 time to fit residues: 23.4070 Evaluate side-chains 179 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 290 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 12 optimal weight: 0.0010 chunk 51 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN C 135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.127778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.108807 restraints weight = 19581.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.111437 restraints weight = 11272.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.113186 restraints weight = 7753.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.114381 restraints weight = 6015.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.115076 restraints weight = 5029.189| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12325 Z= 0.116 Angle : 0.568 10.476 16707 Z= 0.283 Chirality : 0.042 0.144 2000 Planarity : 0.004 0.042 2084 Dihedral : 6.162 71.476 1753 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.04 % Allowed : 16.87 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: 0.68 (0.23), residues: 1548 helix: 1.68 (0.18), residues: 894 sheet: -1.80 (0.44), residues: 142 loop : -1.05 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 230 TYR 0.015 0.001 TYR A 412 PHE 0.011 0.001 PHE B 53 TRP 0.012 0.001 TRP A 535 HIS 0.002 0.000 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00273 (12325) covalent geometry : angle 0.56765 (16707) hydrogen bonds : bond 0.03330 ( 671) hydrogen bonds : angle 4.07213 ( 1941) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1884.87 seconds wall clock time: 33 minutes 26.90 seconds (2006.90 seconds total)