Starting phenix.real_space_refine on Mon Jul 6 01:51:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hqx_52349/07_2026/9hqx_52349.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hqx_52349/07_2026/9hqx_52349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hqx_52349/07_2026/9hqx_52349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hqx_52349/07_2026/9hqx_52349.map" model { file = "/net/cci-nas-00/data/ceres_data/9hqx_52349/07_2026/9hqx_52349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hqx_52349/07_2026/9hqx_52349.cif" } resolution = 3.08 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 58 5.49 5 S 52 5.16 5 C 9620 2.51 5 N 2749 2.21 5 O 3051 1.98 5 H 15217 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30747 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 10209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 10209 Classifications: {'peptide': 630} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 606} Chain breaks: 2 Chain: "f" Number of atoms: 10168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 10168 Classifications: {'peptide': 627} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 604} Chain breaks: 2 Chain: "A" Number of atoms: 5878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5878 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 354} Chain breaks: 1 Chain: "d" Number of atoms: 2645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2645 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain: "E" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 918 Classifications: {'DNA': 29} Modifications used: {'3*END': 1, 'p5*END': 1} Link IDs: {'rna3p': 28} Chain: "F" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 929 Classifications: {'DNA': 29} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 28} Time building chain proxies: 4.17, per 1000 atoms: 0.14 Number of scatterers: 30747 At special positions: 0 Unit cell: (91.476, 120.516, 202.554, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 52 16.00 P 58 15.00 O 3051 8.00 N 2749 7.00 C 9620 6.00 H 15217 1.00 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: 2.34 Conformation dependent library (CDL) restraints added in 737.9 milliseconds 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3426 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 9 sheets defined 61.2% alpha, 6.6% beta 23 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 4.44 Creating SS restraints... Processing helix chain 'B' and resid 42 through 51 Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 151 through 158 removed outlier: 3.977A pdb=" N ALA B 156 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 167 removed outlier: 4.071A pdb=" N ALA B 166 " --> pdb=" O GLN B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 192 Proline residue: B 189 - end of helix Processing helix chain 'B' and resid 196 through 233 removed outlier: 3.604A pdb=" N ASP B 233 " --> pdb=" O GLN B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 255 through 269 removed outlier: 3.613A pdb=" N ARG B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 342 removed outlier: 3.706A pdb=" N VAL B 317 " --> pdb=" O ASN B 313 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE B 335 " --> pdb=" O ASP B 331 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TRP B 338 " --> pdb=" O LYS B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 378 Processing helix chain 'B' and resid 383 through 421 removed outlier: 3.849A pdb=" N ALA B 387 " --> pdb=" O LYS B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 451 Processing helix chain 'B' and resid 455 through 478 removed outlier: 3.811A pdb=" N LYS B 478 " --> pdb=" O GLU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 502 removed outlier: 4.015A pdb=" N GLY B 501 " --> pdb=" O ASN B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 558 Processing helix chain 'B' and resid 598 through 616 removed outlier: 3.813A pdb=" N GLU B 616 " --> pdb=" O VAL B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 633 Processing helix chain 'f' and resid 42 through 51 Processing helix chain 'f' and resid 117 through 130 Processing helix chain 'f' and resid 151 through 157 removed outlier: 4.188A pdb=" N ALA f 156 " --> pdb=" O ASP f 153 " (cutoff:3.500A) Processing helix chain 'f' and resid 161 through 166 removed outlier: 4.139A pdb=" N ALA f 166 " --> pdb=" O GLN f 162 " (cutoff:3.500A) Processing helix chain 'f' and resid 177 through 192 Proline residue: f 189 - end of helix Processing helix chain 'f' and resid 196 through 225 Processing helix chain 'f' and resid 227 through 244 Processing helix chain 'f' and resid 255 through 269 Processing helix chain 'f' and resid 277 through 323 removed outlier: 3.665A pdb=" N HIS f 320 " --> pdb=" O ARG f 316 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU f 323 " --> pdb=" O MET f 319 " (cutoff:3.500A) Processing helix chain 'f' and resid 334 through 342 removed outlier: 3.902A pdb=" N LEU f 340 " --> pdb=" O SER f 336 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN f 342 " --> pdb=" O TRP f 338 " (cutoff:3.500A) Processing helix chain 'f' and resid 356 through 376 removed outlier: 3.575A pdb=" N ALA f 376 " --> pdb=" O ASP f 372 " (cutoff:3.500A) Processing helix chain 'f' and resid 377 through 383 removed outlier: 4.105A pdb=" N ASP f 380 " --> pdb=" O VAL f 377 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS f 383 " --> pdb=" O ASP f 380 " (cutoff:3.500A) Processing helix chain 'f' and resid 389 through 420 Processing helix chain 'f' and resid 430 through 451 removed outlier: 3.887A pdb=" N ARG f 436 " --> pdb=" O ARG f 432 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLU f 446 " --> pdb=" O GLU f 442 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU f 447 " --> pdb=" O SER f 443 " (cutoff:3.500A) Processing helix chain 'f' and resid 455 through 476 Processing helix chain 'f' and resid 479 through 502 removed outlier: 3.684A pdb=" N GLY f 501 " --> pdb=" O ASN f 497 " (cutoff:3.500A) Processing helix chain 'f' and resid 536 through 558 removed outlier: 3.566A pdb=" N GLN f 558 " --> pdb=" O PHE f 554 " (cutoff:3.500A) Processing helix chain 'f' and resid 573 through 577 Processing helix chain 'f' and resid 599 through 616 Processing helix chain 'f' and resid 629 through 635 removed outlier: 3.727A pdb=" N TRP f 633 " --> pdb=" O PRO f 629 " (cutoff:3.500A) Processing helix chain 'f' and resid 647 through 651 removed outlier: 3.713A pdb=" N LYS f 650 " --> pdb=" O ASP f 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 39 Processing helix chain 'A' and resid 80 through 95 removed outlier: 5.489A pdb=" N ASP A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU A 93 " --> pdb=" O ASN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 127 through 143 Processing helix chain 'A' and resid 150 through 155 removed outlier: 3.655A pdb=" N GLY A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 169 removed outlier: 3.891A pdb=" N TYR A 162 " --> pdb=" O GLU A 158 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 169 " --> pdb=" O LYS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 189 through 201 removed outlier: 3.619A pdb=" N HIS A 201 " --> pdb=" O CYS A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 207 through 229 Processing helix chain 'A' and resid 236 through 257 Processing helix chain 'A' and resid 265 through 270 removed outlier: 3.778A pdb=" N GLN A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 287 through 312 Processing helix chain 'A' and resid 319 through 341 Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 345 through 360 Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 392 through 403 Processing helix chain 'd' and resid 3 through 10 Processing helix chain 'd' and resid 11 through 28 removed outlier: 3.505A pdb=" N LYS d 28 " --> pdb=" O CYS d 24 " (cutoff:3.500A) Processing helix chain 'd' and resid 37 through 43 removed outlier: 4.024A pdb=" N PHE d 42 " --> pdb=" O PRO d 39 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 49 Processing helix chain 'd' and resid 50 through 60 Processing helix chain 'd' and resid 64 through 71 removed outlier: 3.938A pdb=" N ALA d 68 " --> pdb=" O SER d 64 " (cutoff:3.500A) Processing helix chain 'd' and resid 80 through 94 removed outlier: 3.623A pdb=" N LEU d 84 " --> pdb=" O LYS d 80 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N HIS d 88 " --> pdb=" O LEU d 84 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU d 89 " --> pdb=" O PHE d 85 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 108 Processing helix chain 'd' and resid 131 through 151 removed outlier: 3.769A pdb=" N LEU d 151 " --> pdb=" O TRP d 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 160 Processing sheet with id=AA1, first strand: chain 'B' and resid 20 through 23 removed outlier: 6.755A pdb=" N ILE B 5 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 74 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY B 7 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE B 72 " --> pdb=" O GLY B 7 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE B 9 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N PHE B 70 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP B 11 " --> pdb=" O GLU B 68 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 86 " --> pdb=" O ASP B 96 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASP B 96 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 566 through 570 removed outlier: 6.591A pdb=" N LEU B 567 " --> pdb=" O ILE B 623 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU B 625 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU B 569 " --> pdb=" O LEU B 625 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 347 through 348 Processing sheet with id=AA4, first strand: chain 'B' and resid 511 through 514 Processing sheet with id=AA5, first strand: chain 'f' and resid 20 through 23 removed outlier: 5.376A pdb=" N ILE f 5 " --> pdb=" O ALA f 75 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ALA f 75 " --> pdb=" O ILE f 5 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE f 9 " --> pdb=" O GLY f 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 159 through 160 removed outlier: 7.333A pdb=" N GLN f 160 " --> pdb=" O ASP f 570 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU f 567 " --> pdb=" O ILE f 623 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU f 625 " --> pdb=" O LEU f 567 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU f 569 " --> pdb=" O LEU f 625 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASN f 30 " --> pdb=" O VAL f 624 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU f 642 " --> pdb=" O VAL f 29 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL f 31 " --> pdb=" O LEU f 642 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'f' and resid 511 through 514 removed outlier: 3.575A pdb=" N SER f 512 " --> pdb=" O LYS f 521 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 55 removed outlier: 5.961A pdb=" N PHE A 64 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N TYR A 109 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLN A 66 " --> pdb=" O TYR A 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'd' and resid 111 through 114 850 hydrogen bonds defined for protein. 2463 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 7.30 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15198 1.03 - 1.23: 58 1.23 - 1.42: 6530 1.42 - 1.62: 9262 1.62 - 1.81: 85 Bond restraints: 31133 Sorted by residual: bond pdb=" C3' DT E 12 " pdb=" C2' DT E 12 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.82e+00 bond pdb=" C3' DC E 3 " pdb=" C2' DC E 3 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.39e+00 bond pdb=" C3' DT E 20 " pdb=" C2' DT E 20 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.63e+00 bond pdb=" C3' DA E 10 " pdb=" C2' DA E 10 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.59e+00 bond pdb=" C3' DT E 8 " pdb=" C2' DT E 8 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.03e+00 ... (remaining 31128 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 53029 1.15 - 2.31: 3075 2.31 - 3.46: 294 3.46 - 4.62: 44 4.62 - 5.77: 6 Bond angle restraints: 56448 Sorted by residual: angle pdb=" N3 DT F 42 " pdb=" C4 DT F 42 " pdb=" O4 DT F 42 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT F 52 " pdb=" C4 DT F 52 " pdb=" O4 DT F 52 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT F 54 " pdb=" C4 DT F 54 " pdb=" O4 DT F 54 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT F 46 " pdb=" C4 DT F 46 " pdb=" O4 DT F 46 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT F 44 " pdb=" C4 DT F 44 " pdb=" O4 DT F 44 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 56443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 12481 17.95 - 35.90: 1221 35.90 - 53.84: 437 53.84 - 71.79: 108 71.79 - 89.74: 17 Dihedral angle restraints: 14264 sinusoidal: 8306 harmonic: 5958 Sorted by residual: dihedral pdb=" CA ASP B 127 " pdb=" C ASP B 127 " pdb=" N LEU B 128 " pdb=" CA LEU B 128 " ideal model delta harmonic sigma weight residual 180.00 156.08 23.92 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA GLN A 365 " pdb=" C GLN A 365 " pdb=" N ALA A 366 " pdb=" CA ALA A 366 " ideal model delta harmonic sigma weight residual -180.00 -157.91 -22.09 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA TRP A 90 " pdb=" C TRP A 90 " pdb=" N ILE A 91 " pdb=" CA ILE A 91 " ideal model delta harmonic sigma weight residual 180.00 160.91 19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 14261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1781 0.037 - 0.075: 487 0.075 - 0.112: 111 0.112 - 0.150: 70 0.150 - 0.187: 22 Chirality restraints: 2471 Sorted by residual: chirality pdb=" C3' DC F 55 " pdb=" C4' DC F 55 " pdb=" O3' DC F 55 " pdb=" C2' DC F 55 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.74e-01 chirality pdb=" C3' DA E 9 " pdb=" C4' DA E 9 " pdb=" O3' DA E 9 " pdb=" C2' DA E 9 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.38e-01 chirality pdb=" C3' DG F 56 " pdb=" C4' DG F 56 " pdb=" O3' DG F 56 " pdb=" C2' DG F 56 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.79e-01 ... (remaining 2468 not shown) Planarity restraints: 4358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE f 188 " -0.021 2.00e-02 2.50e+03 1.12e-02 3.76e+00 pdb=" CG PHE f 188 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE f 188 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE f 188 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE f 188 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE f 188 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE f 188 " -0.012 2.00e-02 2.50e+03 pdb=" HD1 PHE f 188 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE f 188 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE f 188 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE f 188 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE f 188 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE f 44 " -0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO f 45 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO f 45 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO f 45 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 212 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.39e+00 pdb=" C THR A 212 " 0.027 2.00e-02 2.50e+03 pdb=" O THR A 212 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN A 213 " -0.009 2.00e-02 2.50e+03 ... (remaining 4355 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 936 2.13 - 2.74: 57494 2.74 - 3.36: 90585 3.36 - 3.98: 113984 3.98 - 4.60: 178778 Nonbonded interactions: 441777 Sorted by model distance: nonbonded pdb=" O SER A 59 " pdb=" H GLU A 100 " model vdw 1.507 2.450 nonbonded pdb=" H SER f 255 " pdb=" OE1 GLN f 258 " model vdw 1.555 2.450 nonbonded pdb=" O ARG A 139 " pdb=" H GLY A 144 " model vdw 1.563 2.450 nonbonded pdb=" O PHE B 157 " pdb=" HE2 HIS B 552 " model vdw 1.574 2.450 nonbonded pdb=" OE2 GLU B 295 " pdb=" H THR f 431 " model vdw 1.586 2.450 ... (remaining 441772 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 'B' and (resid 1 through 133 or resid 148 through 577 or resid 597 throug \ h 626 or (resid 627 and (name N or name CA or name C or name O or name CB or nam \ e CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or nam \ e HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 628 through 660 \ )) selection = chain 'f' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 30.690 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15916 Z= 0.271 Angle : 0.615 5.770 21751 Z= 0.406 Chirality : 0.044 0.187 2471 Planarity : 0.004 0.054 2602 Dihedral : 16.458 89.738 6220 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.19 (0.21), residues: 1775 helix: 1.30 (0.17), residues: 1011 sheet: -0.91 (0.44), residues: 129 loop : -1.60 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 221 TYR 0.023 0.002 TYR f 322 PHE 0.030 0.001 PHE f 188 TRP 0.022 0.001 TRP f 540 HIS 0.008 0.001 HIS f 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.27 (15916) covalent geometry : angle 0.61512 / 0.41 (21751) hydrogen bonds : bond 0.13374 / 9.04 ( 903) hydrogen bonds : angle 6.33246 / 4.51 ( 2569) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 68 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ASN cc_start: 0.7842 (t0) cc_final: 0.6993 (m-40) REVERT: B 186 LYS cc_start: 0.8262 (mmpt) cc_final: 0.7521 (tmtt) REVERT: B 394 GLN cc_start: 0.7638 (tp40) cc_final: 0.7265 (tp40) REVERT: B 426 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8273 (tm-30) REVERT: B 472 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7711 (tp30) REVERT: B 559 LYS cc_start: 0.8179 (mttt) cc_final: 0.7956 (mmtp) REVERT: f 54 ASN cc_start: 0.7817 (m110) cc_final: 0.7433 (p0) REVERT: f 80 GLU cc_start: 0.6157 (tp30) cc_final: 0.5860 (tm-30) REVERT: f 100 LEU cc_start: 0.8315 (tt) cc_final: 0.8063 (tt) REVERT: f 104 ASN cc_start: 0.8108 (t0) cc_final: 0.7345 (m-40) REVERT: f 105 ILE cc_start: 0.8475 (tt) cc_final: 0.7900 (tt) REVERT: f 125 LEU cc_start: 0.9483 (mt) cc_final: 0.9147 (mt) REVERT: f 275 LYS cc_start: 0.8135 (mtpt) cc_final: 0.7800 (mtpp) REVERT: f 316 ARG cc_start: 0.5727 (mmm-85) cc_final: 0.5504 (mtm180) REVERT: f 364 GLN cc_start: 0.7653 (mm110) cc_final: 0.7364 (mm-40) REVERT: f 502 LEU cc_start: 0.7426 (mt) cc_final: 0.7085 (mt) REVERT: f 519 THR cc_start: 0.8381 (t) cc_final: 0.8140 (t) REVERT: f 536 SER cc_start: 0.8271 (m) cc_final: 0.8046 (p) REVERT: f 561 ASN cc_start: 0.7423 (m110) cc_final: 0.7159 (m-40) REVERT: A 243 TRP cc_start: 0.7891 (m-10) cc_final: 0.7503 (m-10) REVERT: A 348 ASP cc_start: 0.8006 (m-30) cc_final: 0.7756 (m-30) REVERT: d 58 LYS cc_start: 0.7370 (tttt) cc_final: 0.7148 (ttpt) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.3340 time to fit residues: 104.4603 Evaluate side-chains 167 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** f 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.204174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.132290 restraints weight = 53518.199| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 3.38 r_work: 0.3613 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15916 Z= 0.183 Angle : 0.591 7.339 21751 Z= 0.336 Chirality : 0.040 0.171 2471 Planarity : 0.005 0.057 2602 Dihedral : 15.559 59.719 2589 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.44 % Allowed : 5.69 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.24 (0.20), residues: 1775 helix: 1.38 (0.16), residues: 1035 sheet: -1.15 (0.43), residues: 129 loop : -1.70 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 221 TYR 0.009 0.001 TYR A 109 PHE 0.016 0.001 PHE B 3 TRP 0.010 0.001 TRP f 633 HIS 0.005 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (15916) covalent geometry : angle 0.59050 / 0.34 (21751) hydrogen bonds : bond 0.06312 / 4.35 ( 903) hydrogen bonds : angle 4.68889 / 3.36 ( 2569) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 68 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 164 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ASN cc_start: 0.8129 (t0) cc_final: 0.7315 (m-40) REVERT: B 186 LYS cc_start: 0.8511 (mmpt) cc_final: 0.7750 (tmtt) REVERT: B 394 GLN cc_start: 0.8085 (tp40) cc_final: 0.7719 (tp40) REVERT: B 408 ARG cc_start: 0.7646 (ttp80) cc_final: 0.7313 (ttp80) REVERT: B 426 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8393 (tm-30) REVERT: B 442 GLU cc_start: 0.8111 (tt0) cc_final: 0.7691 (tp30) REVERT: B 472 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7852 (tp30) REVERT: f 54 ASN cc_start: 0.7792 (m110) cc_final: 0.7427 (p0) REVERT: f 80 GLU cc_start: 0.6252 (tp30) cc_final: 0.5985 (tm-30) REVERT: f 100 LEU cc_start: 0.8284 (tt) cc_final: 0.8028 (tt) REVERT: f 104 ASN cc_start: 0.8117 (t0) cc_final: 0.7367 (m-40) REVERT: f 105 ILE cc_start: 0.8491 (tt) cc_final: 0.7828 (tt) REVERT: f 167 ASN cc_start: 0.7511 (t0) cc_final: 0.6899 (m-40) REVERT: f 275 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7982 (mtpp) REVERT: f 364 GLN cc_start: 0.7631 (mm110) cc_final: 0.7352 (mm-40) REVERT: f 561 ASN cc_start: 0.7474 (m110) cc_final: 0.7221 (m-40) REVERT: A 243 TRP cc_start: 0.8109 (m-10) cc_final: 0.7785 (m-10) REVERT: A 348 ASP cc_start: 0.8141 (m-30) cc_final: 0.7843 (m-30) REVERT: d 58 LYS cc_start: 0.8127 (tttt) cc_final: 0.7898 (ttpt) outliers start: 7 outliers final: 7 residues processed: 168 average time/residue: 0.3179 time to fit residues: 75.0333 Evaluate side-chains 161 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain f residue 51 LEU Chi-restraints excluded: chain f residue 96 ASP Chi-restraints excluded: chain f residue 188 PHE Chi-restraints excluded: chain f residue 520 ILE Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain d residue 152 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 174 optimal weight: 0.0670 chunk 45 optimal weight: 3.9990 chunk 181 optimal weight: 30.0000 chunk 176 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 54 ASN B 115 ASN B 342 ASN ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.204615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.129677 restraints weight = 53452.766| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 3.08 r_work: 0.3629 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15916 Z= 0.159 Angle : 0.552 9.918 21751 Z= 0.312 Chirality : 0.039 0.169 2471 Planarity : 0.004 0.054 2602 Dihedral : 15.804 59.895 2589 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.01 % Allowed : 6.63 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.45 (0.21), residues: 1775 helix: 1.58 (0.16), residues: 1034 sheet: -1.13 (0.43), residues: 129 loop : -1.65 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 425 TYR 0.017 0.001 TYR f 2 PHE 0.014 0.001 PHE B 3 TRP 0.009 0.001 TRP f 645 HIS 0.006 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (15916) covalent geometry : angle 0.55241 / 0.31 (21751) hydrogen bonds : bond 0.05377 / 3.64 ( 903) hydrogen bonds : angle 4.45004 / 3.19 ( 2569) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 68 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7292 (m-40) REVERT: B 186 LYS cc_start: 0.8510 (mmpt) cc_final: 0.7765 (tmtt) REVERT: B 187 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8172 (mp) REVERT: B 394 GLN cc_start: 0.8042 (tp40) cc_final: 0.7685 (tp40) REVERT: B 408 ARG cc_start: 0.7632 (ttp80) cc_final: 0.7324 (ttp80) REVERT: B 426 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8382 (tm-30) REVERT: B 472 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7869 (tp30) REVERT: f 1 MET cc_start: 0.3728 (mtt) cc_final: 0.1261 (ppp) REVERT: f 54 ASN cc_start: 0.7791 (m110) cc_final: 0.7411 (p0) REVERT: f 80 GLU cc_start: 0.6245 (tp30) cc_final: 0.6038 (tm-30) REVERT: f 100 LEU cc_start: 0.8314 (tt) cc_final: 0.8082 (tt) REVERT: f 105 ILE cc_start: 0.8457 (tt) cc_final: 0.8127 (tt) REVERT: f 167 ASN cc_start: 0.7590 (t0) cc_final: 0.6993 (m-40) REVERT: f 275 LYS cc_start: 0.8264 (mtpt) cc_final: 0.7949 (mtpp) REVERT: f 364 GLN cc_start: 0.7668 (mm110) cc_final: 0.7365 (mm-40) REVERT: f 561 ASN cc_start: 0.7507 (m110) cc_final: 0.7200 (m-40) REVERT: A 243 TRP cc_start: 0.8103 (m-10) cc_final: 0.7774 (m-10) REVERT: A 348 ASP cc_start: 0.8140 (m-30) cc_final: 0.7822 (m-30) REVERT: d 58 LYS cc_start: 0.8097 (tttt) cc_final: 0.7863 (ttmt) REVERT: d 163 LYS cc_start: 0.8304 (mtpt) cc_final: 0.8090 (mtpt) outliers start: 16 outliers final: 8 residues processed: 167 average time/residue: 0.3260 time to fit residues: 76.4898 Evaluate side-chains 159 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain f residue 51 LEU Chi-restraints excluded: chain f residue 96 ASP Chi-restraints excluded: chain f residue 188 PHE Chi-restraints excluded: chain f residue 520 ILE Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain d residue 152 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 177 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 138 optimal weight: 20.0000 chunk 72 optimal weight: 0.5980 chunk 179 optimal weight: 20.0000 chunk 136 optimal weight: 0.0980 chunk 46 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... f 440 ASN ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.204880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.130528 restraints weight = 53219.787| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 3.04 r_work: 0.3640 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15916 Z= 0.141 Angle : 0.538 8.051 21751 Z= 0.305 Chirality : 0.039 0.198 2471 Planarity : 0.004 0.043 2602 Dihedral : 15.876 59.856 2589 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.88 % Allowed : 7.83 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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 (0.21), residues: 1775 helix: 1.71 (0.16), residues: 1033 sheet: -1.07 (0.44), residues: 128 loop : -1.64 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 425 TYR 0.012 0.001 TYR f 66 PHE 0.012 0.001 PHE B 3 TRP 0.007 0.001 TRP A 330 HIS 0.006 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (15916) covalent geometry : angle 0.53774 / 0.30 (21751) hydrogen bonds : bond 0.05021 / 3.39 ( 903) hydrogen bonds : angle 4.33149 / 3.10 ( 2569) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 68 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 LYS cc_start: 0.8544 (mmpt) cc_final: 0.7793 (tmtt) REVERT: B 187 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8197 (mp) REVERT: B 264 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8384 (pm20) REVERT: B 394 GLN cc_start: 0.8076 (tp40) cc_final: 0.7741 (tp40) REVERT: B 408 ARG cc_start: 0.7683 (ttp80) cc_final: 0.7383 (ttp80) REVERT: B 426 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8403 (tm-30) REVERT: B 472 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7933 (tp30) REVERT: B 514 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7063 (mp0) REVERT: f 1 MET cc_start: 0.3795 (mtt) cc_final: 0.1328 (ppp) REVERT: f 54 ASN cc_start: 0.7789 (m110) cc_final: 0.7420 (p0) REVERT: f 100 LEU cc_start: 0.8356 (tt) cc_final: 0.8136 (tt) REVERT: f 105 ILE cc_start: 0.8398 (tt) cc_final: 0.8140 (tt) REVERT: f 167 ASN cc_start: 0.7627 (t0) cc_final: 0.7050 (m-40) REVERT: f 275 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7960 (mtpp) REVERT: f 334 LYS cc_start: 0.8641 (mttm) cc_final: 0.7859 (pttm) REVERT: f 364 GLN cc_start: 0.7723 (mm110) cc_final: 0.7421 (mm-40) REVERT: f 561 ASN cc_start: 0.7576 (m110) cc_final: 0.7300 (m-40) REVERT: A 243 TRP cc_start: 0.8110 (m-10) cc_final: 0.7800 (m-10) REVERT: A 348 ASP cc_start: 0.8110 (m-30) cc_final: 0.7769 (m-30) REVERT: d 58 LYS cc_start: 0.8150 (tttt) cc_final: 0.7920 (ttmt) outliers start: 14 outliers final: 11 residues processed: 166 average time/residue: 0.3225 time to fit residues: 75.0351 Evaluate side-chains 163 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain B residue 561 ASN Chi-restraints excluded: chain f residue 51 LEU Chi-restraints excluded: chain f residue 96 ASP Chi-restraints excluded: chain f residue 188 PHE Chi-restraints excluded: chain f residue 520 ILE Chi-restraints excluded: chain f residue 545 LEU Chi-restraints excluded: chain f residue 651 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain d residue 102 ILE Chi-restraints excluded: chain d residue 152 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 47 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.200573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.126447 restraints weight = 54473.983| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 3.04 r_work: 0.3615 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15916 Z= 0.180 Angle : 0.551 7.922 21751 Z= 0.311 Chirality : 0.039 0.163 2471 Planarity : 0.005 0.064 2602 Dihedral : 16.006 59.374 2589 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.01 % Allowed : 8.65 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.51 (0.20), residues: 1775 helix: 1.66 (0.16), residues: 1033 sheet: -1.33 (0.43), residues: 131 loop : -1.64 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG f 425 TYR 0.011 0.001 TYR A 288 PHE 0.018 0.001 PHE B 3 TRP 0.008 0.001 TRP B 11 HIS 0.008 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (15916) covalent geometry : angle 0.55088 / 0.31 (21751) hydrogen bonds : bond 0.04939 / 3.32 ( 903) hydrogen bonds : angle 4.33028 / 3.10 ( 2569) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 68 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 LYS cc_start: 0.8548 (mmpt) cc_final: 0.7786 (tmtt) REVERT: B 187 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8157 (mp) REVERT: B 264 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8403 (pm20) REVERT: B 394 GLN cc_start: 0.8077 (tp40) cc_final: 0.7710 (tp40) REVERT: B 408 ARG cc_start: 0.7647 (ttp80) cc_final: 0.7301 (ttp80) REVERT: B 426 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8383 (tm-30) REVERT: B 472 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7904 (tp30) REVERT: B 514 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7002 (mp0) REVERT: f 1 MET cc_start: 0.3781 (mtt) cc_final: 0.1315 (ppp) REVERT: f 54 ASN cc_start: 0.7784 (m110) cc_final: 0.7384 (p0) REVERT: f 275 LYS cc_start: 0.8274 (mtpt) cc_final: 0.7965 (mtpp) REVERT: f 334 LYS cc_start: 0.8628 (mttm) cc_final: 0.7837 (pttm) REVERT: f 364 GLN cc_start: 0.7755 (mm110) cc_final: 0.7441 (mm-40) REVERT: f 561 ASN cc_start: 0.7540 (m110) cc_final: 0.7237 (m-40) REVERT: A 243 TRP cc_start: 0.8093 (m-10) cc_final: 0.7758 (m-10) REVERT: A 348 ASP cc_start: 0.8125 (m-30) cc_final: 0.7785 (m-30) REVERT: d 58 LYS cc_start: 0.8105 (tttt) cc_final: 0.7868 (ttmt) outliers start: 16 outliers final: 9 residues processed: 160 average time/residue: 0.3141 time to fit residues: 70.5552 Evaluate side-chains 160 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain f residue 188 PHE Chi-restraints excluded: chain f residue 385 VAL Chi-restraints excluded: chain f residue 520 ILE Chi-restraints excluded: chain f residue 651 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain d residue 102 ILE Chi-restraints excluded: chain d residue 152 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 112 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.201427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.127461 restraints weight = 54239.039| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 3.07 r_work: 0.3621 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15916 Z= 0.145 Angle : 0.538 7.894 21751 Z= 0.301 Chirality : 0.039 0.163 2471 Planarity : 0.004 0.055 2602 Dihedral : 16.088 59.902 2589 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.95 % Allowed : 9.22 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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 (0.21), residues: 1775 helix: 1.74 (0.16), residues: 1033 sheet: -1.39 (0.43), residues: 128 loop : -1.62 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG f 425 TYR 0.014 0.001 TYR f 66 PHE 0.014 0.001 PHE B 3 TRP 0.007 0.001 TRP A 330 HIS 0.008 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (15916) covalent geometry : angle 0.53760 / 0.30 (21751) hydrogen bonds : bond 0.04703 / 3.16 ( 903) hydrogen bonds : angle 4.22339 / 3.02 ( 2569) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 68 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 116 THR cc_start: 0.8466 (t) cc_final: 0.8217 (p) REVERT: B 186 LYS cc_start: 0.8553 (mmpt) cc_final: 0.7782 (tmtt) REVERT: B 187 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8149 (mp) REVERT: B 264 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8438 (pm20) REVERT: B 394 GLN cc_start: 0.8049 (tp40) cc_final: 0.7684 (tp40) REVERT: B 408 ARG cc_start: 0.7660 (ttp80) cc_final: 0.7321 (ttp80) REVERT: B 426 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8390 (tm-30) REVERT: B 472 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7895 (tp30) REVERT: f 1 MET cc_start: 0.3840 (mtt) cc_final: 0.1376 (ppp) REVERT: f 54 ASN cc_start: 0.7796 (m110) cc_final: 0.7392 (p0) REVERT: f 275 LYS cc_start: 0.8248 (mtpt) cc_final: 0.7934 (mtpp) REVERT: f 334 LYS cc_start: 0.8625 (mttm) cc_final: 0.7819 (pttm) REVERT: f 561 ASN cc_start: 0.7535 (m110) cc_final: 0.7231 (m-40) REVERT: A 195 GLU cc_start: 0.6302 (mm-30) cc_final: 0.5105 (mt-10) REVERT: A 243 TRP cc_start: 0.8068 (m-10) cc_final: 0.7752 (m-10) REVERT: A 348 ASP cc_start: 0.8105 (m-30) cc_final: 0.7760 (m-30) REVERT: d 58 LYS cc_start: 0.8083 (tttt) cc_final: 0.7842 (ttmt) outliers start: 15 outliers final: 12 residues processed: 162 average time/residue: 0.3196 time to fit residues: 73.3616 Evaluate side-chains 163 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain B residue 561 ASN Chi-restraints excluded: chain f residue 51 LEU Chi-restraints excluded: chain f residue 96 ASP Chi-restraints excluded: chain f residue 188 PHE Chi-restraints excluded: chain f residue 385 VAL Chi-restraints excluded: chain f residue 520 ILE Chi-restraints excluded: chain f residue 651 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain d residue 102 ILE Chi-restraints excluded: chain d residue 152 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 128 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.199039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.124625 restraints weight = 54267.639| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 3.05 r_work: 0.3585 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15916 Z= 0.209 Angle : 0.570 7.590 21751 Z= 0.319 Chirality : 0.040 0.162 2471 Planarity : 0.005 0.047 2602 Dihedral : 16.209 59.445 2589 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.07 % Allowed : 9.92 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.41 (0.20), residues: 1775 helix: 1.62 (0.16), residues: 1035 sheet: -1.43 (0.44), residues: 128 loop : -1.74 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG f 425 TYR 0.014 0.002 TYR A 288 PHE 0.022 0.001 PHE B 3 TRP 0.009 0.001 TRP B 11 HIS 0.009 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (15916) covalent geometry : angle 0.56974 / 0.32 (21751) hydrogen bonds : bond 0.04808 / 3.21 ( 903) hydrogen bonds : angle 4.30487 / 3.08 ( 2569) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 68 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 LYS cc_start: 0.8563 (mmpt) cc_final: 0.7790 (tmtt) REVERT: B 187 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8160 (mp) REVERT: B 394 GLN cc_start: 0.8120 (tp40) cc_final: 0.7737 (tp40) REVERT: B 408 ARG cc_start: 0.7723 (ttp80) cc_final: 0.7333 (ttp80) REVERT: B 426 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8410 (tm-30) REVERT: B 472 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7921 (tp30) REVERT: f 1 MET cc_start: 0.3895 (mtt) cc_final: 0.1452 (ppp) REVERT: f 334 LYS cc_start: 0.8632 (mttm) cc_final: 0.7842 (pttm) REVERT: f 364 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7683 (mm-40) REVERT: f 561 ASN cc_start: 0.7507 (m110) cc_final: 0.7175 (m-40) REVERT: A 195 GLU cc_start: 0.6288 (mm-30) cc_final: 0.5094 (mt-10) REVERT: A 243 TRP cc_start: 0.8069 (m-10) cc_final: 0.7721 (m-10) REVERT: A 348 ASP cc_start: 0.8134 (m-30) cc_final: 0.7821 (m-30) REVERT: A 365 GLN cc_start: 0.7911 (tp40) cc_final: 0.7288 (pt0) REVERT: d 58 LYS cc_start: 0.8139 (tttt) cc_final: 0.7903 (ttmt) outliers start: 17 outliers final: 12 residues processed: 165 average time/residue: 0.3163 time to fit residues: 74.1960 Evaluate side-chains 161 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain B residue 561 ASN Chi-restraints excluded: chain f residue 80 GLU Chi-restraints excluded: chain f residue 188 PHE Chi-restraints excluded: chain f residue 385 VAL Chi-restraints excluded: chain f residue 482 LEU Chi-restraints excluded: chain f residue 520 ILE Chi-restraints excluded: chain f residue 651 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain d residue 102 ILE Chi-restraints excluded: chain d residue 152 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 66 optimal weight: 4.9990 chunk 175 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 178 optimal weight: 20.0000 chunk 111 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 130 optimal weight: 20.0000 chunk 165 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.202933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.130950 restraints weight = 53192.715| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 3.39 r_work: 0.3596 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15916 Z= 0.146 Angle : 0.542 8.102 21751 Z= 0.303 Chirality : 0.038 0.161 2471 Planarity : 0.004 0.048 2602 Dihedral : 16.240 59.713 2589 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.95 % Allowed : 10.49 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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 (0.21), residues: 1775 helix: 1.72 (0.16), residues: 1035 sheet: -1.47 (0.43), residues: 128 loop : -1.66 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 604 TYR 0.012 0.001 TYR f 66 PHE 0.013 0.001 PHE B 3 TRP 0.007 0.001 TRP A 330 HIS 0.006 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (15916) covalent geometry : angle 0.54224 / 0.30 (21751) hydrogen bonds : bond 0.04593 / 3.08 ( 903) hydrogen bonds : angle 4.20260 / 3.01 ( 2569) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 68 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 LYS cc_start: 0.8574 (mmpt) cc_final: 0.7805 (tmtt) REVERT: B 394 GLN cc_start: 0.8077 (tp40) cc_final: 0.7703 (tp40) REVERT: B 408 ARG cc_start: 0.7700 (ttp80) cc_final: 0.7321 (ttp80) REVERT: B 426 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8408 (tm-30) REVERT: B 472 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7918 (tp30) REVERT: f 1 MET cc_start: 0.3820 (mtt) cc_final: 0.1407 (ppp) REVERT: f 54 ASN cc_start: 0.7678 (m-40) cc_final: 0.7474 (m110) REVERT: f 275 LYS cc_start: 0.8254 (mtpt) cc_final: 0.7953 (mtpp) REVERT: f 334 LYS cc_start: 0.8627 (mttm) cc_final: 0.7834 (pttm) REVERT: f 364 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7669 (mm-40) REVERT: f 561 ASN cc_start: 0.7496 (m110) cc_final: 0.7162 (m-40) REVERT: A 195 GLU cc_start: 0.6264 (mm-30) cc_final: 0.5093 (mt-10) REVERT: A 243 TRP cc_start: 0.8054 (m-10) cc_final: 0.7626 (m-10) REVERT: A 348 ASP cc_start: 0.8143 (m-30) cc_final: 0.7783 (m-30) REVERT: A 365 GLN cc_start: 0.7882 (tp40) cc_final: 0.7235 (pt0) REVERT: d 58 LYS cc_start: 0.8108 (tttt) cc_final: 0.7865 (ttmt) outliers start: 15 outliers final: 14 residues processed: 159 average time/residue: 0.3100 time to fit residues: 70.6563 Evaluate side-chains 163 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain B residue 561 ASN Chi-restraints excluded: chain f residue 80 GLU Chi-restraints excluded: chain f residue 96 ASP Chi-restraints excluded: chain f residue 188 PHE Chi-restraints excluded: chain f residue 385 VAL Chi-restraints excluded: chain f residue 520 ILE Chi-restraints excluded: chain f residue 651 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain d residue 102 ILE Chi-restraints excluded: chain d residue 152 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 62 optimal weight: 0.9990 chunk 109 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 176 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.200840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.126959 restraints weight = 54123.088| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 3.03 r_work: 0.3622 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15916 Z= 0.144 Angle : 0.539 8.792 21751 Z= 0.300 Chirality : 0.038 0.159 2471 Planarity : 0.004 0.054 2602 Dihedral : 16.295 59.640 2589 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.95 % Allowed : 10.80 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.64 (0.21), residues: 1775 helix: 1.82 (0.16), residues: 1034 sheet: -1.47 (0.43), residues: 128 loop : -1.64 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 604 TYR 0.015 0.001 TYR f 66 PHE 0.017 0.001 PHE f 554 TRP 0.009 0.001 TRP f 645 HIS 0.005 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (15916) covalent geometry : angle 0.53863 / 0.30 (21751) hydrogen bonds : bond 0.04447 / 2.98 ( 903) hydrogen bonds : angle 4.10773 / 2.95 ( 2569) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 68 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 394 GLN cc_start: 0.8053 (tp40) cc_final: 0.7690 (tp40) REVERT: B 408 ARG cc_start: 0.7705 (ttp80) cc_final: 0.7324 (ttp80) REVERT: B 426 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8394 (tm-30) REVERT: B 472 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7911 (tp30) REVERT: f 1 MET cc_start: 0.3877 (mtt) cc_final: 0.1396 (ppp) REVERT: f 275 LYS cc_start: 0.8241 (mtpt) cc_final: 0.7932 (mtpp) REVERT: f 334 LYS cc_start: 0.8629 (mttm) cc_final: 0.7844 (pttm) REVERT: f 364 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7653 (mm-40) REVERT: f 369 ARG cc_start: 0.6691 (mtt180) cc_final: 0.6390 (mtt180) REVERT: f 561 ASN cc_start: 0.7502 (m110) cc_final: 0.7170 (m-40) REVERT: A 195 GLU cc_start: 0.6238 (mm-30) cc_final: 0.5097 (mt-10) REVERT: A 243 TRP cc_start: 0.8038 (m-10) cc_final: 0.7477 (m-10) REVERT: A 348 ASP cc_start: 0.8113 (m-30) cc_final: 0.7750 (m-30) REVERT: A 365 GLN cc_start: 0.7811 (tp40) cc_final: 0.7225 (pt0) REVERT: d 58 LYS cc_start: 0.8120 (tttt) cc_final: 0.7882 (ttmt) outliers start: 15 outliers final: 13 residues processed: 165 average time/residue: 0.3121 time to fit residues: 73.1152 Evaluate side-chains 165 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain B residue 561 ASN Chi-restraints excluded: chain f residue 80 GLU Chi-restraints excluded: chain f residue 96 ASP Chi-restraints excluded: chain f residue 188 PHE Chi-restraints excluded: chain f residue 385 VAL Chi-restraints excluded: chain f residue 520 ILE Chi-restraints excluded: chain f residue 651 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain d residue 102 ILE Chi-restraints excluded: chain d residue 152 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 28 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 153 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.201514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.128879 restraints weight = 53507.221| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 3.43 r_work: 0.3559 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15916 Z= 0.202 Angle : 0.570 8.019 21751 Z= 0.318 Chirality : 0.039 0.156 2471 Planarity : 0.005 0.053 2602 Dihedral : 16.379 59.783 2589 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.88 % Allowed : 10.87 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.47 (0.20), residues: 1775 helix: 1.68 (0.16), residues: 1034 sheet: -1.53 (0.43), residues: 128 loop : -1.71 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG f 425 TYR 0.014 0.002 TYR A 288 PHE 0.022 0.001 PHE B 3 TRP 0.014 0.001 TRP A 308 HIS 0.008 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (15916) covalent geometry : angle 0.56974 / 0.32 (21751) hydrogen bonds : bond 0.04623 / 3.09 ( 903) hydrogen bonds : angle 4.20670 / 3.02 ( 2569) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 68 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 394 GLN cc_start: 0.8140 (tp40) cc_final: 0.7744 (tp40) REVERT: B 408 ARG cc_start: 0.7670 (ttp80) cc_final: 0.7272 (ttp80) REVERT: B 426 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8385 (tm-30) REVERT: B 442 GLU cc_start: 0.8064 (tt0) cc_final: 0.7607 (tp30) REVERT: B 472 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7924 (tp30) REVERT: f 1 MET cc_start: 0.3914 (mtt) cc_final: 0.1442 (ppp) REVERT: f 275 LYS cc_start: 0.8274 (mtpt) cc_final: 0.7965 (mtpp) REVERT: f 334 LYS cc_start: 0.8613 (mttm) cc_final: 0.7821 (pttm) REVERT: f 364 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7644 (mm-40) REVERT: f 369 ARG cc_start: 0.6729 (mtt180) cc_final: 0.6428 (mtt180) REVERT: f 561 ASN cc_start: 0.7507 (m110) cc_final: 0.7164 (m-40) REVERT: A 195 GLU cc_start: 0.6223 (mm-30) cc_final: 0.5070 (mt-10) REVERT: A 243 TRP cc_start: 0.8031 (m-10) cc_final: 0.7685 (m-10) REVERT: A 348 ASP cc_start: 0.8143 (m-30) cc_final: 0.7820 (m-30) REVERT: d 58 LYS cc_start: 0.8125 (tttt) cc_final: 0.7880 (ttmt) outliers start: 14 outliers final: 13 residues processed: 160 average time/residue: 0.3137 time to fit residues: 72.1117 Evaluate side-chains 164 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain B residue 561 ASN Chi-restraints excluded: chain f residue 80 GLU Chi-restraints excluded: chain f residue 96 ASP Chi-restraints excluded: chain f residue 188 PHE Chi-restraints excluded: chain f residue 385 VAL Chi-restraints excluded: chain f residue 505 GLU Chi-restraints excluded: chain f residue 520 ILE Chi-restraints excluded: chain f residue 651 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain d residue 102 ILE Chi-restraints excluded: chain d residue 152 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 180 optimal weight: 40.0000 chunk 146 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.202175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.127107 restraints weight = 53549.914| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 3.03 r_work: 0.3599 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15916 Z= 0.169 Angle : 0.552 8.244 21751 Z= 0.307 Chirality : 0.039 0.155 2471 Planarity : 0.004 0.054 2602 Dihedral : 16.423 59.773 2589 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.88 % Allowed : 11.24 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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 (0.20), residues: 1775 helix: 1.72 (0.16), residues: 1034 sheet: -1.47 (0.43), residues: 126 loop : -1.68 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 604 TYR 0.016 0.001 TYR f 66 PHE 0.017 0.001 PHE B 3 TRP 0.009 0.001 TRP f 645 HIS 0.007 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (15916) covalent geometry : angle 0.55153 / 0.31 (21751) hydrogen bonds : bond 0.04506 / 3.01 ( 903) hydrogen bonds : angle 4.15540 / 2.99 ( 2569) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8007.40 seconds wall clock time: 136 minutes 14.91 seconds (8174.91 seconds total)