Starting phenix.real_space_refine on Thu Jul 2 21:22:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bpa_16147/07_2026/8bpa_16147.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bpa_16147/07_2026/8bpa_16147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8bpa_16147/07_2026/8bpa_16147.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bpa_16147/07_2026/8bpa_16147.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bpa_16147/07_2026/8bpa_16147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bpa_16147/07_2026/8bpa_16147.map" model { file = "/net/cci-nas-00/data/ceres_data/8bpa_16147/07_2026/8bpa_16147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bpa_16147/07_2026/8bpa_16147.cif" } resolution = 3.7 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= 0.002 sd= 0.037 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 Ca 2 9.91 5 Zn 5 6.06 5 S 71 5.16 5 C 6618 2.51 5 N 1791 2.21 5 O 1906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 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: 10393 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4403 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 518} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2956 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 368, 2956 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 351} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1692 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 191} Chain breaks: 3 Chain: "D" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 153} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8431 SG CYS C 289 39.856 57.677 45.495 1.00125.91 S ATOM 8457 SG CYS C 292 37.187 56.181 43.096 1.00124.81 S ATOM 8640 SG CYS C 315 40.824 55.364 42.492 1.00117.18 S ATOM 8315 SG CYS C 274 39.422 44.839 47.811 1.00110.14 S ATOM 8339 SG CYS C 277 40.602 41.173 47.436 1.00113.17 S ATOM 8523 SG CYS C 300 42.904 43.509 48.758 1.00 86.93 S ATOM 7590 SG CYS C 71 48.790 94.141 75.277 1.00204.68 S ATOM 7614 SG CYS C 74 45.627 93.112 73.314 1.00205.36 S ATOM 7806 SG CYS C 99 47.990 95.411 71.662 1.00187.58 S ATOM 7833 SG CYS C 102 46.167 96.786 74.406 1.00184.08 S ATOM 7508 SG CYS C 59 50.564 85.329 66.806 1.00204.38 S ATOM 7528 SG CYS C 62 51.157 83.018 63.861 1.00188.96 S ATOM 7675 SG CYS C 82 53.191 86.280 64.136 1.00181.00 S Time building chain proxies: 2.06, per 1000 atoms: 0.20 Number of scatterers: 10393 At special positions: 0 Unit cell: (122.094, 124.146, 112.86, 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) Zn 5 29.99 Ca 2 19.99 S 71 16.00 O 1906 8.00 N 1791 7.00 C 6618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 249.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 179 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 318 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 292 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 315 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 289 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" ND1 HIS C 297 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 300 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 277 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 274 " pdb=" ZN C1103 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 99 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 102 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 74 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 71 " pdb=" ZN C1104 " pdb="ZN ZN C1104 " - pdb=" ND1 HIS C 79 " pdb="ZN ZN C1104 " - pdb=" SG CYS C 62 " pdb="ZN ZN C1104 " - pdb=" SG CYS C 59 " pdb="ZN ZN C1104 " - pdb=" SG CYS C 82 " Number of angles added : 15 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2434 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 5 sheets defined 59.2% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 304 through 319 Processing helix chain 'A' and resid 320 through 336 removed outlier: 3.583A pdb=" N TYR A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 417 through 424 removed outlier: 3.594A pdb=" N LEU A 424 " --> pdb=" O CYS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 484 removed outlier: 3.760A pdb=" N GLU A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN A 451 " --> pdb=" O PRO A 447 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 486 No H-bonds generated for 'chain 'A' and resid 485 through 486' Processing helix chain 'A' and resid 487 through 494 removed outlier: 5.005A pdb=" N GLU A 492 " --> pdb=" O GLU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 517 Processing helix chain 'A' and resid 519 through 530 removed outlier: 3.880A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 561 removed outlier: 3.560A pdb=" N ALA A 534 " --> pdb=" O ASN A 530 " (cutoff:3.500A) Proline residue: A 536 - end of helix Processing helix chain 'A' and resid 567 through 573 removed outlier: 3.630A pdb=" N ASP A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 587 removed outlier: 4.126A pdb=" N GLN A 581 " --> pdb=" O VAL A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 610 removed outlier: 3.909A pdb=" N ILE A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 642 Processing helix chain 'A' and resid 648 through 667 removed outlier: 4.171A pdb=" N VAL A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Proline residue: A 664 - end of helix Processing helix chain 'A' and resid 746 through 786 removed outlier: 3.918A pdb=" N LEU A 786 " --> pdb=" O GLU A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 792 removed outlier: 3.548A pdb=" N ARG A 792 " --> pdb=" O GLU A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 829 removed outlier: 4.797A pdb=" N TYR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Proline residue: A 817 - end of helix Processing helix chain 'A' and resid 832 through 845 Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.889A pdb=" N TYR A 849 " --> pdb=" O ILE A 846 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL A 850 " --> pdb=" O HIS A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 871 Processing helix chain 'A' and resid 871 through 887 removed outlier: 3.671A pdb=" N LEU A 875 " --> pdb=" O ASP A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 916 removed outlier: 5.379A pdb=" N ALA A 902 " --> pdb=" O CYS A 898 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ARG A 903 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 46 Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 70 through 80 Processing helix chain 'B' and resid 81 through 87 removed outlier: 3.721A pdb=" N MET B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N SER B 86 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 87 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 95 Processing helix chain 'B' and resid 106 through 127 removed outlier: 3.734A pdb=" N SER B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.740A pdb=" N LEU B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 188 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 234 through 253 Proline residue: B 244 - end of helix Processing helix chain 'B' and resid 263 through 267 removed outlier: 3.922A pdb=" N SER B 266 " --> pdb=" O GLY B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 291 removed outlier: 3.982A pdb=" N CYS B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL B 286 " --> pdb=" O HIS B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 321 Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.903A pdb=" N GLY B 339 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 373 removed outlier: 3.787A pdb=" N MET B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 28 Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 206 through 220 Processing helix chain 'C' and resid 228 through 233 Processing helix chain 'C' and resid 320 through 325 Processing helix chain 'C' and resid 330 through 342 removed outlier: 3.509A pdb=" N ARG C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE C 341 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 360 removed outlier: 3.583A pdb=" N LYS C 360 " --> pdb=" O ASN C 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 216 removed outlier: 3.975A pdb=" N VAL D 208 " --> pdb=" O LYS D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 242 removed outlier: 3.914A pdb=" N SER D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 267 removed outlier: 3.995A pdb=" N GLU D 255 " --> pdb=" O TYR D 251 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 276 No H-bonds generated for 'chain 'D' and resid 274 through 276' Processing helix chain 'D' and resid 277 through 288 Processing helix chain 'D' and resid 299 through 313 removed outlier: 3.859A pdb=" N LEU D 303 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG D 304 " --> pdb=" O PRO D 300 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 305 " --> pdb=" O HIS D 301 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA D 311 " --> pdb=" O VAL D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 316 No H-bonds generated for 'chain 'D' and resid 314 through 316' Processing helix chain 'D' and resid 319 through 340 Processing helix chain 'D' and resid 340 through 345 Processing helix chain 'D' and resid 354 through 362 Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 397 removed outlier: 3.706A pdb=" N TYR A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 620 through 624 removed outlier: 3.639A pdb=" N LEU A 926 " --> pdb=" O ILE A 933 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N CYS A 920 " --> pdb=" O LEU A 939 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL A 739 " --> pdb=" O GLN A 927 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 55 removed outlier: 6.576A pdb=" N TYR B 14 " --> pdb=" O TYR B 55 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N CYS B 13 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA B 133 " --> pdb=" O MET B 298 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B 172 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N GLN B 261 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE B 174 " --> pdb=" O GLN B 261 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET B 195 " --> pdb=" O VAL B 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 68 through 70 Processing sheet with id=AA5, first strand: chain 'C' and resid 287 through 288 532 hydrogen bonds defined for protein. 1548 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2411 1.33 - 1.45: 2238 1.45 - 1.57: 5872 1.57 - 1.69: 2 1.69 - 1.81: 104 Bond restraints: 10627 Sorted by residual: bond pdb=" CB PRO A 521 " pdb=" CG PRO A 521 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.03e+00 bond pdb=" CG PRO B 102 " pdb=" CD PRO B 102 " ideal model delta sigma weight residual 1.503 1.562 -0.059 3.40e-02 8.65e+02 3.03e+00 bond pdb=" CB PRO B 102 " pdb=" CG PRO B 102 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.94e+00 bond pdb=" CG PRO A 521 " pdb=" CD PRO A 521 " ideal model delta sigma weight residual 1.503 1.448 0.055 3.40e-02 8.65e+02 2.61e+00 bond pdb=" CB PRO C 316 " pdb=" CG PRO C 316 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.40e+00 ... (remaining 10622 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 14012 2.34 - 4.67: 269 4.67 - 7.01: 51 7.01 - 9.35: 13 9.35 - 11.69: 7 Bond angle restraints: 14352 Sorted by residual: angle pdb=" CA PRO A 521 " pdb=" N PRO A 521 " pdb=" CD PRO A 521 " ideal model delta sigma weight residual 112.00 102.42 9.58 1.40e+00 5.10e-01 4.68e+01 angle pdb=" CA GLU A 562 " pdb=" CB GLU A 562 " pdb=" CG GLU A 562 " ideal model delta sigma weight residual 114.10 124.56 -10.46 2.00e+00 2.50e-01 2.73e+01 angle pdb=" C LYS C 32 " pdb=" CA LYS C 32 " pdb=" CB LYS C 32 " ideal model delta sigma weight residual 115.79 110.05 5.74 1.19e+00 7.06e-01 2.33e+01 angle pdb=" CA LYS A 885 " pdb=" CB LYS A 885 " pdb=" CG LYS A 885 " ideal model delta sigma weight residual 114.10 122.28 -8.18 2.00e+00 2.50e-01 1.67e+01 angle pdb=" CA GLU A 879 " pdb=" CB GLU A 879 " pdb=" CG GLU A 879 " ideal model delta sigma weight residual 114.10 121.86 -7.76 2.00e+00 2.50e-01 1.50e+01 ... (remaining 14347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5369 17.86 - 35.72: 779 35.72 - 53.58: 245 53.58 - 71.44: 40 71.44 - 89.29: 16 Dihedral angle restraints: 6449 sinusoidal: 2681 harmonic: 3768 Sorted by residual: dihedral pdb=" CA THR B 305 " pdb=" C THR B 305 " pdb=" N ILE B 306 " pdb=" CA ILE B 306 " ideal model delta harmonic sigma weight residual -180.00 -151.39 -28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ARG A 402 " pdb=" C ARG A 402 " pdb=" N ALA A 403 " pdb=" CA ALA A 403 " ideal model delta harmonic sigma weight residual -180.00 -157.45 -22.55 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA MET A 934 " pdb=" C MET A 934 " pdb=" N THR A 935 " pdb=" CA THR A 935 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 6446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1009 0.041 - 0.081: 398 0.081 - 0.122: 108 0.122 - 0.163: 16 0.163 - 0.203: 3 Chirality restraints: 1534 Sorted by residual: chirality pdb=" CB VAL A 923 " pdb=" CA VAL A 923 " pdb=" CG1 VAL A 923 " pdb=" CG2 VAL A 923 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA PRO A 521 " pdb=" N PRO A 521 " pdb=" C PRO A 521 " pdb=" CB PRO A 521 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" CG LEU B 212 " pdb=" CB LEU B 212 " pdb=" CD1 LEU B 212 " pdb=" CD2 LEU B 212 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.72e-01 ... (remaining 1531 not shown) Planarity restraints: 1862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.067 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO A 521 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 315 " -0.047 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO C 316 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 316 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 316 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 562 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.95e+00 pdb=" C GLU A 562 " 0.046 2.00e-02 2.50e+03 pdb=" O GLU A 562 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN A 563 " -0.015 2.00e-02 2.50e+03 ... (remaining 1859 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 282 2.68 - 3.24: 10701 3.24 - 3.79: 17009 3.79 - 4.35: 21650 4.35 - 4.90: 34359 Nonbonded interactions: 84001 Sorted by model distance: nonbonded pdb=" O HIS B 179 " pdb="CA CA B 502 " model vdw 2.127 2.510 nonbonded pdb=" OD2 ASP B 265 " pdb="ZN ZN B 501 " model vdw 2.141 2.230 nonbonded pdb=" OG1 THR C 330 " pdb=" OD1 ASN C 333 " model vdw 2.154 3.040 nonbonded pdb=" OD1 ASP B 175 " pdb="CA CA B 502 " model vdw 2.172 2.510 nonbonded pdb=" N GLN A 835 " pdb=" OE1 GLN A 835 " model vdw 2.194 3.120 ... (remaining 83996 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.750 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 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 : 0.005 0.087 10644 Z= 0.216 Angle : 0.863 12.165 14367 Z= 0.447 Chirality : 0.046 0.203 1534 Planarity : 0.006 0.095 1862 Dihedral : 18.501 89.294 4015 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.97 % Allowed : 33.75 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.00 (0.24), residues: 1260 helix: 0.74 (0.20), residues: 672 sheet: -0.57 (0.60), residues: 77 loop : -0.81 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 903 TYR 0.030 0.002 TYR B 16 PHE 0.027 0.002 PHE B 335 TRP 0.025 0.003 TRP A 434 HIS 0.006 0.001 HIS A 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.22 (10627) covalent geometry : angle 0.85040 / 0.45 (14352) hydrogen bonds : bond 0.13988 / 8.71 ( 532) hydrogen bonds : angle 5.67936 / 4.03 ( 1548) metal coordination : bond 0.01205 / 0.55 ( 17) metal coordination : angle 4.58591 / 2.56 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 349 time to evaluate : 0.382 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: A 308 PHE cc_start: 0.6464 (t80) cc_final: 0.6263 (t80) REVERT: A 315 ARG cc_start: 0.6055 (mmm160) cc_final: 0.5842 (tpm170) REVERT: A 327 PHE cc_start: 0.7344 (t80) cc_final: 0.7120 (t80) REVERT: A 449 GLU cc_start: 0.7502 (tt0) cc_final: 0.7238 (tp30) REVERT: A 462 LEU cc_start: 0.8402 (tp) cc_final: 0.8027 (mp) REVERT: A 469 ASN cc_start: 0.8342 (t0) cc_final: 0.8027 (t0) REVERT: A 539 LEU cc_start: 0.8167 (mp) cc_final: 0.7900 (tp) REVERT: A 563 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7887 (tp40) REVERT: A 566 LYS cc_start: 0.7793 (mtpm) cc_final: 0.7590 (mtpm) REVERT: A 595 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7297 (tm-30) REVERT: A 636 LEU cc_start: 0.8653 (mm) cc_final: 0.8287 (mm) REVERT: A 772 LYS cc_start: 0.7938 (ttmm) cc_final: 0.7538 (tmmt) REVERT: A 835 GLN cc_start: 0.8066 (pm20) cc_final: 0.7782 (pm20) REVERT: A 859 GLN cc_start: 0.7272 (pt0) cc_final: 0.6918 (mt0) REVERT: A 863 ARG cc_start: 0.7605 (mmp-170) cc_final: 0.7216 (mmp-170) REVERT: A 922 LYS cc_start: 0.8411 (ttmm) cc_final: 0.7881 (ttmm) REVERT: B 41 ASN cc_start: 0.8234 (t0) cc_final: 0.7857 (t0) REVERT: B 56 ARG cc_start: 0.7682 (mtp180) cc_final: 0.7298 (mmm-85) REVERT: B 91 GLN cc_start: 0.8126 (mt0) cc_final: 0.7771 (mm-40) REVERT: B 156 ASP cc_start: 0.7474 (t0) cc_final: 0.7213 (t0) REVERT: B 308 ASN cc_start: 0.8400 (m-40) cc_final: 0.8182 (m110) REVERT: D 312 MET cc_start: 0.6319 (mmm) cc_final: 0.6054 (mmm) REVERT: D 335 LYS cc_start: 0.8830 (pptt) cc_final: 0.8333 (pttt) REVERT: D 336 TYR cc_start: 0.7208 (t80) cc_final: 0.6641 (t80) outliers start: 11 outliers final: 5 residues processed: 352 average time/residue: 0.1107 time to fit residues: 52.6392 Evaluate side-chains 339 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 333 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 332 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 ASN A 469 ASN A 563 GLN A 606 GLN A 607 HIS A 660 HIS A 883 ASN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 GLN A ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.166921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.139587 restraints weight = 20616.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.144091 restraints weight = 11198.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.147155 restraints weight = 7159.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.149159 restraints weight = 5028.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.150613 restraints weight = 3893.857| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4099 r_free = 0.4099 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4100 r_free = 0.4100 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.4100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10644 Z= 0.145 Angle : 0.689 12.228 14367 Z= 0.344 Chirality : 0.042 0.171 1534 Planarity : 0.005 0.049 1862 Dihedral : 5.434 52.581 1421 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.06 % Allowed : 27.21 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.30 (0.24), residues: 1260 helix: 1.08 (0.20), residues: 676 sheet: -0.50 (0.58), residues: 74 loop : -0.85 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 454 TYR 0.024 0.002 TYR A 513 PHE 0.017 0.001 PHE A 921 TRP 0.013 0.002 TRP A 428 HIS 0.006 0.001 HIS A 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (10627) covalent geometry : angle 0.67669 / 0.34 (14352) hydrogen bonds : bond 0.04757 / 3.11 ( 532) hydrogen bonds : angle 4.81988 / 3.43 ( 1548) metal coordination : bond 0.01015 / 0.40 ( 17) metal coordination : angle 4.10463 / 2.22 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 342 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 PHE cc_start: 0.6809 (t80) cc_final: 0.6556 (t80) REVERT: A 325 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7649 (mm-30) REVERT: A 327 PHE cc_start: 0.7334 (t80) cc_final: 0.7026 (t80) REVERT: A 428 TRP cc_start: 0.7981 (m100) cc_final: 0.7713 (m100) REVERT: A 449 GLU cc_start: 0.7406 (tt0) cc_final: 0.6981 (tp30) REVERT: A 454 ARG cc_start: 0.7202 (tpp80) cc_final: 0.6596 (tpp80) REVERT: A 462 LEU cc_start: 0.8119 (tp) cc_final: 0.7787 (mp) REVERT: A 469 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.8081 (t0) REVERT: A 473 ILE cc_start: 0.7981 (mt) cc_final: 0.7652 (mm) REVERT: A 477 GLU cc_start: 0.7273 (tp30) cc_final: 0.6780 (mm-30) REVERT: A 480 GLN cc_start: 0.8272 (tp-100) cc_final: 0.8055 (tp-100) REVERT: A 505 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7197 (mm-30) REVERT: A 539 LEU cc_start: 0.8267 (mp) cc_final: 0.7739 (tp) REVERT: A 595 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7266 (tm-30) REVERT: A 742 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7861 (tt) REVERT: A 772 LYS cc_start: 0.7751 (ttmm) cc_final: 0.7342 (ttmm) REVERT: A 776 GLU cc_start: 0.7340 (mt-10) cc_final: 0.7075 (mt-10) REVERT: A 852 PHE cc_start: 0.7288 (m-80) cc_final: 0.6938 (m-80) REVERT: A 859 GLN cc_start: 0.7210 (pt0) cc_final: 0.6966 (pt0) REVERT: A 863 ARG cc_start: 0.7649 (mmp-170) cc_final: 0.7256 (mmp-170) REVERT: A 884 GLU cc_start: 0.6649 (tt0) cc_final: 0.6420 (tt0) REVERT: A 903 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7468 (ptp90) REVERT: A 922 LYS cc_start: 0.8118 (ttmm) cc_final: 0.7560 (ttmm) REVERT: A 934 MET cc_start: 0.7385 (tpt) cc_final: 0.7143 (tpt) REVERT: B 41 ASN cc_start: 0.8182 (t0) cc_final: 0.7843 (t0) REVERT: B 56 ARG cc_start: 0.7746 (mtp180) cc_final: 0.7373 (mmm-85) REVERT: B 68 TYR cc_start: 0.7672 (t80) cc_final: 0.7327 (t80) REVERT: B 69 HIS cc_start: 0.7741 (m170) cc_final: 0.7467 (m-70) REVERT: B 114 SER cc_start: 0.7775 (t) cc_final: 0.7436 (p) REVERT: B 156 ASP cc_start: 0.7393 (t0) cc_final: 0.7122 (t0) REVERT: B 166 LYS cc_start: 0.8547 (mmpt) cc_final: 0.8186 (mmpt) REVERT: B 195 MET cc_start: 0.6953 (mtp) cc_final: 0.6737 (mtp) REVERT: B 225 VAL cc_start: 0.7544 (p) cc_final: 0.7194 (m) REVERT: B 229 MET cc_start: 0.7847 (mtm) cc_final: 0.7492 (mtm) REVERT: B 248 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7683 (tptm) REVERT: B 253 TYR cc_start: 0.6551 (t80) cc_final: 0.6158 (t80) REVERT: B 290 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7591 (ptmm) REVERT: B 308 ASN cc_start: 0.8326 (m-40) cc_final: 0.8067 (m110) REVERT: D 240 LYS cc_start: 0.4229 (OUTLIER) cc_final: 0.3762 (ttpp) REVERT: D 281 TYR cc_start: 0.6567 (t80) cc_final: 0.6261 (t80) REVERT: D 335 LYS cc_start: 0.8878 (pptt) cc_final: 0.8348 (pttt) REVERT: D 336 TYR cc_start: 0.7040 (t80) cc_final: 0.6478 (t80) outliers start: 46 outliers final: 23 residues processed: 369 average time/residue: 0.1034 time to fit residues: 52.0754 Evaluate side-chains 362 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 333 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 469 ASN Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 607 HIS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 866 HIS Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 903 ARG Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 298 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 272 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 111 optimal weight: 0.0060 chunk 86 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 119 optimal weight: 20.0000 chunk 117 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 660 HIS ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 GLN A B 282 HIS ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.167438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.140026 restraints weight = 20775.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.144507 restraints weight = 11232.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.147488 restraints weight = 7186.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.149499 restraints weight = 5110.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.150817 restraints weight = 3939.320| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4091 r_free = 0.4091 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4091 r_free = 0.4091 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10644 Z= 0.135 Angle : 0.669 11.439 14367 Z= 0.329 Chirality : 0.043 0.444 1534 Planarity : 0.004 0.053 1862 Dihedral : 4.949 55.943 1412 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.24 % Allowed : 27.83 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.37 (0.24), residues: 1260 helix: 1.18 (0.20), residues: 675 sheet: -0.46 (0.58), residues: 75 loop : -0.87 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 78 TYR 0.021 0.002 TYR A 513 PHE 0.009 0.001 PHE A 460 TRP 0.023 0.002 TRP A 909 HIS 0.008 0.001 HIS A 607 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (10627) covalent geometry : angle 0.65876 / 0.33 (14352) hydrogen bonds : bond 0.04444 / 2.94 ( 532) hydrogen bonds : angle 4.63489 / 3.30 ( 1548) metal coordination : bond 0.00902 / 0.35 ( 17) metal coordination : angle 3.60118 / 1.96 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 337 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 PHE cc_start: 0.6729 (t80) cc_final: 0.6419 (t80) REVERT: A 325 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7666 (mm-30) REVERT: A 327 PHE cc_start: 0.7400 (t80) cc_final: 0.7092 (t80) REVERT: A 404 LEU cc_start: 0.5105 (mt) cc_final: 0.4631 (mp) REVERT: A 449 GLU cc_start: 0.7384 (tt0) cc_final: 0.6880 (tp30) REVERT: A 462 LEU cc_start: 0.8080 (tp) cc_final: 0.7712 (mp) REVERT: A 473 ILE cc_start: 0.8011 (mt) cc_final: 0.7700 (mm) REVERT: A 477 GLU cc_start: 0.7259 (tp30) cc_final: 0.6998 (mm-30) REVERT: A 480 GLN cc_start: 0.8255 (tp-100) cc_final: 0.8054 (tm-30) REVERT: A 505 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7313 (mm-30) REVERT: A 509 ARG cc_start: 0.8037 (ttm110) cc_final: 0.7588 (mtt180) REVERT: A 510 ARG cc_start: 0.7820 (tpp-160) cc_final: 0.7459 (tpp-160) REVERT: A 529 LYS cc_start: 0.7001 (mmtp) cc_final: 0.6733 (mmtt) REVERT: A 539 LEU cc_start: 0.8179 (mp) cc_final: 0.7875 (tp) REVERT: A 595 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7245 (tm-30) REVERT: A 597 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6998 (mt-10) REVERT: A 622 PHE cc_start: 0.6261 (m-80) cc_final: 0.4901 (m-10) REVERT: A 742 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7893 (tt) REVERT: A 772 LYS cc_start: 0.7774 (ttmm) cc_final: 0.7302 (ttmm) REVERT: A 776 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7087 (mt-10) REVERT: A 859 GLN cc_start: 0.7416 (pt0) cc_final: 0.7167 (pt0) REVERT: A 863 ARG cc_start: 0.7636 (mmp-170) cc_final: 0.7207 (mmp-170) REVERT: A 871 ASP cc_start: 0.4024 (OUTLIER) cc_final: 0.3808 (t0) REVERT: A 884 GLU cc_start: 0.6891 (tt0) cc_final: 0.6645 (tt0) REVERT: A 903 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7042 (ptp90) REVERT: A 922 LYS cc_start: 0.8262 (ttmm) cc_final: 0.7732 (ttmm) REVERT: A 934 MET cc_start: 0.7500 (tpt) cc_final: 0.7288 (tpp) REVERT: B 23 TYR cc_start: 0.8344 (m-80) cc_final: 0.7382 (m-80) REVERT: B 56 ARG cc_start: 0.7728 (mtp180) cc_final: 0.7318 (mmm-85) REVERT: B 68 TYR cc_start: 0.7689 (t80) cc_final: 0.7245 (t80) REVERT: B 156 ASP cc_start: 0.7412 (t0) cc_final: 0.7180 (t0) REVERT: B 166 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8104 (mmpt) REVERT: B 229 MET cc_start: 0.7847 (mtm) cc_final: 0.7500 (mtp) REVERT: B 253 TYR cc_start: 0.6725 (t80) cc_final: 0.6265 (t80) REVERT: B 308 ASN cc_start: 0.8201 (m-40) cc_final: 0.7923 (m110) REVERT: B 354 GLN cc_start: 0.8268 (mp10) cc_final: 0.7934 (mp10) REVERT: C 208 ARG cc_start: 0.4638 (OUTLIER) cc_final: 0.4102 (ptm160) REVERT: D 206 TRP cc_start: 0.6119 (t-100) cc_final: 0.5686 (t-100) REVERT: D 281 TYR cc_start: 0.6569 (t80) cc_final: 0.6226 (t80) REVERT: D 335 LYS cc_start: 0.8884 (pptt) cc_final: 0.8663 (pptt) outliers start: 48 outliers final: 28 residues processed: 363 average time/residue: 0.1147 time to fit residues: 55.8604 Evaluate side-chains 364 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 331 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 866 HIS Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 871 ASP Chi-restraints excluded: chain A residue 903 ARG Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 298 MET Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 272 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 100 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 0.0770 chunk 69 optimal weight: 3.9990 overall best weight: 1.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 908 GLN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 GLN A ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 HIS D 358 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.162800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.135694 restraints weight = 20653.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.140145 restraints weight = 11308.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.143238 restraints weight = 7184.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.145243 restraints weight = 5039.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.146612 restraints weight = 3911.052| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4030 r_free = 0.4030 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4030 r_free = 0.4030 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.4030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 10644 Z= 0.228 Angle : 0.735 11.732 14367 Z= 0.372 Chirality : 0.045 0.225 1534 Planarity : 0.005 0.061 1862 Dihedral : 5.232 51.201 1412 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 5.65 % Allowed : 27.74 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.13 (0.24), residues: 1260 helix: 0.96 (0.20), residues: 673 sheet: -0.48 (0.56), residues: 74 loop : -0.96 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 778 TYR 0.026 0.002 TYR A 513 PHE 0.019 0.002 PHE B 338 TRP 0.022 0.002 TRP A 909 HIS 0.006 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.23 (10627) covalent geometry : angle 0.71979 / 0.37 (14352) hydrogen bonds : bond 0.05346 / 3.50 ( 532) hydrogen bonds : angle 4.93146 / 3.50 ( 1548) metal coordination : bond 0.01253 / 0.76 ( 17) metal coordination : angle 4.65338 / 2.44 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 371 time to evaluate : 0.390 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: A 323 VAL cc_start: 0.8598 (OUTLIER) cc_final: 0.8325 (m) REVERT: A 327 PHE cc_start: 0.7475 (t80) cc_final: 0.7117 (t80) REVERT: A 354 LYS cc_start: 0.3921 (OUTLIER) cc_final: 0.2857 (ptpp) REVERT: A 450 GLU cc_start: 0.7213 (pp20) cc_final: 0.6634 (tm-30) REVERT: A 462 LEU cc_start: 0.8108 (tp) cc_final: 0.7602 (mp) REVERT: A 477 GLU cc_start: 0.7379 (tp30) cc_final: 0.6875 (mm-30) REVERT: A 480 GLN cc_start: 0.8254 (tp-100) cc_final: 0.7987 (tm-30) REVERT: A 505 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7209 (mm-30) REVERT: A 509 ARG cc_start: 0.8020 (ttm110) cc_final: 0.7787 (ttm110) REVERT: A 510 ARG cc_start: 0.8027 (tpp-160) cc_final: 0.7780 (tpp-160) REVERT: A 513 TYR cc_start: 0.7247 (m-10) cc_final: 0.7006 (m-80) REVERT: A 529 LYS cc_start: 0.6929 (mmtp) cc_final: 0.6641 (mmtt) REVERT: A 539 LEU cc_start: 0.8142 (mp) cc_final: 0.7533 (tp) REVERT: A 545 LYS cc_start: 0.7514 (tptt) cc_final: 0.7208 (mptt) REVERT: A 570 LYS cc_start: 0.7842 (mtpt) cc_final: 0.7166 (ttmm) REVERT: A 595 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7280 (tm-30) REVERT: A 597 GLU cc_start: 0.7426 (mt-10) cc_final: 0.6945 (mt-10) REVERT: A 622 PHE cc_start: 0.6652 (m-80) cc_final: 0.5522 (m-10) REVERT: A 742 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7680 (tt) REVERT: A 748 ASN cc_start: 0.7291 (m-40) cc_final: 0.7036 (m-40) REVERT: A 771 GLN cc_start: 0.8226 (tp-100) cc_final: 0.7939 (tp40) REVERT: A 772 LYS cc_start: 0.7839 (ttmm) cc_final: 0.7393 (tmmt) REVERT: A 776 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6687 (mt-10) REVERT: A 778 ARG cc_start: 0.7907 (ttm110) cc_final: 0.7523 (ptp-110) REVERT: A 837 GLU cc_start: 0.7920 (pt0) cc_final: 0.7628 (pt0) REVERT: A 884 GLU cc_start: 0.7105 (tt0) cc_final: 0.6761 (tt0) REVERT: A 903 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7057 (ptp90) REVERT: A 915 MET cc_start: 0.7791 (ppp) cc_final: 0.7550 (tmm) REVERT: A 922 LYS cc_start: 0.8421 (ttmm) cc_final: 0.7891 (ttmm) REVERT: A 933 ILE cc_start: 0.8193 (mt) cc_final: 0.7958 (mp) REVERT: B 22 ASN cc_start: 0.7809 (t0) cc_final: 0.7584 (t0) REVERT: B 42 LEU cc_start: 0.8328 (mt) cc_final: 0.8054 (tt) REVERT: B 56 ARG cc_start: 0.7755 (mtp180) cc_final: 0.7287 (mtp180) REVERT: B 68 TYR cc_start: 0.7736 (t80) cc_final: 0.7455 (t80) REVERT: B 157 ILE cc_start: 0.8142 (mt) cc_final: 0.7852 (mp) REVERT: B 166 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8189 (mmpt) REVERT: B 195 MET cc_start: 0.7208 (mtp) cc_final: 0.6504 (mtp) REVERT: B 206 PHE cc_start: 0.7933 (t80) cc_final: 0.7705 (t80) REVERT: B 225 VAL cc_start: 0.7678 (p) cc_final: 0.7390 (m) REVERT: B 229 MET cc_start: 0.7830 (mtm) cc_final: 0.7613 (mtp) REVERT: B 253 TYR cc_start: 0.6987 (t80) cc_final: 0.6420 (t80) REVERT: B 315 TYR cc_start: 0.8198 (t80) cc_final: 0.7398 (t80) REVERT: B 354 GLN cc_start: 0.8343 (mp10) cc_final: 0.7913 (mp10) REVERT: C 23 GLN cc_start: 0.8691 (tt0) cc_final: 0.8148 (tt0) REVERT: C 208 ARG cc_start: 0.4442 (OUTLIER) cc_final: 0.3988 (ptm160) REVERT: C 320 GLU cc_start: 0.7001 (mp0) cc_final: 0.6493 (mp0) REVERT: D 281 TYR cc_start: 0.6528 (t80) cc_final: 0.6079 (t80) REVERT: D 335 LYS cc_start: 0.8905 (pptt) cc_final: 0.8578 (pptt) outliers start: 64 outliers final: 30 residues processed: 408 average time/residue: 0.1042 time to fit residues: 58.2092 Evaluate side-chains 389 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 353 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 660 HIS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 866 HIS Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 903 ARG Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 298 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 359 HIS Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 272 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 49 optimal weight: 0.0980 chunk 15 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 859 GLN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 GLN A ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.163987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.136776 restraints weight = 20561.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.141408 restraints weight = 11071.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.144446 restraints weight = 7009.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.146394 restraints weight = 4968.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.147822 restraints weight = 3856.128| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.4055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10644 Z= 0.147 Angle : 0.703 11.915 14367 Z= 0.344 Chirality : 0.043 0.343 1534 Planarity : 0.005 0.064 1862 Dihedral : 5.050 58.812 1412 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.62 % Allowed : 30.21 % Favored : 66.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.24), residues: 1260 helix: 1.20 (0.20), residues: 670 sheet: -0.46 (0.54), residues: 80 loop : -0.97 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 78 TYR 0.031 0.002 TYR A 777 PHE 0.012 0.001 PHE A 460 TRP 0.012 0.001 TRP A 428 HIS 0.005 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (10627) covalent geometry : angle 0.68794 / 0.34 (14352) hydrogen bonds : bond 0.04548 / 2.99 ( 532) hydrogen bonds : angle 4.63987 / 3.29 ( 1548) metal coordination : bond 0.00889 / 0.42 ( 17) metal coordination : angle 4.46497 / 2.28 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 358 time to evaluate : 0.365 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: A 327 PHE cc_start: 0.7353 (t80) cc_final: 0.6993 (t80) REVERT: A 346 GLN cc_start: 0.7242 (OUTLIER) cc_final: 0.6897 (pp30) REVERT: A 347 LEU cc_start: 0.8207 (mp) cc_final: 0.7743 (mp) REVERT: A 354 LYS cc_start: 0.3988 (OUTLIER) cc_final: 0.2930 (ptpp) REVERT: A 428 TRP cc_start: 0.7911 (m100) cc_final: 0.7529 (m100) REVERT: A 450 GLU cc_start: 0.7158 (pp20) cc_final: 0.6592 (tm-30) REVERT: A 458 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7116 (mt-10) REVERT: A 462 LEU cc_start: 0.7985 (tp) cc_final: 0.7572 (mp) REVERT: A 477 GLU cc_start: 0.7340 (tp30) cc_final: 0.6838 (mm-30) REVERT: A 480 GLN cc_start: 0.8194 (tp-100) cc_final: 0.7911 (tm-30) REVERT: A 505 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7144 (mm-30) REVERT: A 509 ARG cc_start: 0.7983 (ttm110) cc_final: 0.7703 (ttm110) REVERT: A 513 TYR cc_start: 0.7279 (m-10) cc_final: 0.7029 (m-80) REVERT: A 539 LEU cc_start: 0.8105 (mp) cc_final: 0.7568 (tp) REVERT: A 545 LYS cc_start: 0.7450 (tptt) cc_final: 0.7164 (mptt) REVERT: A 570 LYS cc_start: 0.7768 (mtpt) cc_final: 0.7555 (mtpp) REVERT: A 595 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7228 (tm-30) REVERT: A 597 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6864 (mt-10) REVERT: A 742 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7788 (tt) REVERT: A 771 GLN cc_start: 0.8219 (tp-100) cc_final: 0.7992 (tp-100) REVERT: A 772 LYS cc_start: 0.7842 (ttmm) cc_final: 0.7419 (tmmt) REVERT: A 813 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7763 (tm-30) REVERT: A 837 GLU cc_start: 0.7842 (pt0) cc_final: 0.7588 (pt0) REVERT: A 849 TYR cc_start: 0.7138 (p90) cc_final: 0.6902 (p90) REVERT: A 863 ARG cc_start: 0.7405 (mmp-170) cc_final: 0.7129 (mmp80) REVERT: A 884 GLU cc_start: 0.7052 (tt0) cc_final: 0.6730 (tt0) REVERT: A 903 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7035 (ptp90) REVERT: A 922 LYS cc_start: 0.8432 (ttmm) cc_final: 0.7926 (ttmm) REVERT: A 933 ILE cc_start: 0.8178 (mt) cc_final: 0.7927 (mp) REVERT: B 22 ASN cc_start: 0.7763 (t0) cc_final: 0.7520 (t0) REVERT: B 23 TYR cc_start: 0.8329 (m-80) cc_final: 0.7450 (m-80) REVERT: B 42 LEU cc_start: 0.8306 (mt) cc_final: 0.7999 (tt) REVERT: B 56 ARG cc_start: 0.7697 (mtp180) cc_final: 0.7257 (mmm-85) REVERT: B 68 TYR cc_start: 0.7747 (t80) cc_final: 0.7199 (t80) REVERT: B 72 GLU cc_start: 0.7389 (tp30) cc_final: 0.6816 (tp30) REVERT: B 157 ILE cc_start: 0.8181 (mt) cc_final: 0.7901 (mp) REVERT: B 166 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8143 (mmpt) REVERT: B 195 MET cc_start: 0.7183 (mtp) cc_final: 0.6447 (mtp) REVERT: B 206 PHE cc_start: 0.7901 (t80) cc_final: 0.7669 (t80) REVERT: B 225 VAL cc_start: 0.7626 (p) cc_final: 0.7270 (m) REVERT: B 253 TYR cc_start: 0.6772 (t80) cc_final: 0.6129 (t80) REVERT: B 335 PHE cc_start: 0.8118 (t80) cc_final: 0.7904 (t80) REVERT: B 354 GLN cc_start: 0.8242 (mp10) cc_final: 0.7823 (mp10) REVERT: C 23 GLN cc_start: 0.8743 (tt0) cc_final: 0.8199 (tt0) REVERT: C 208 ARG cc_start: 0.4521 (OUTLIER) cc_final: 0.4052 (ptm160) REVERT: C 308 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6854 (mmp) REVERT: C 320 GLU cc_start: 0.6981 (mp0) cc_final: 0.6485 (mp0) REVERT: D 281 TYR cc_start: 0.6516 (t80) cc_final: 0.6038 (t80) REVERT: D 335 LYS cc_start: 0.8904 (pptt) cc_final: 0.8586 (pptt) outliers start: 41 outliers final: 22 residues processed: 381 average time/residue: 0.1031 time to fit residues: 53.1573 Evaluate side-chains 374 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 345 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 866 HIS Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 903 ARG Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 276 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 GLN ** A 867 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.163322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.136031 restraints weight = 20721.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.140690 restraints weight = 11146.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.143752 restraints weight = 7046.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.145659 restraints weight = 4986.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.147058 restraints weight = 3908.795| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4047 r_free = 0.4047 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4047 r_free = 0.4047 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10644 Z= 0.155 Angle : 0.696 12.208 14367 Z= 0.345 Chirality : 0.043 0.375 1534 Planarity : 0.005 0.060 1862 Dihedral : 4.745 52.693 1409 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.15 % Allowed : 30.83 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.24), residues: 1260 helix: 1.17 (0.20), residues: 671 sheet: -0.45 (0.55), residues: 79 loop : -0.91 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 78 TYR 0.033 0.002 TYR A 777 PHE 0.039 0.002 PHE B 108 TRP 0.013 0.001 TRP D 206 HIS 0.004 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (10627) covalent geometry : angle 0.68272 / 0.34 (14352) hydrogen bonds : bond 0.04572 / 3.01 ( 532) hydrogen bonds : angle 4.60215 / 3.28 ( 1548) metal coordination : bond 0.01273 / 0.72 ( 17) metal coordination : angle 4.31790 / 2.38 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 341 time to evaluate : 0.367 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: A 327 PHE cc_start: 0.7336 (t80) cc_final: 0.6941 (t80) REVERT: A 346 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6938 (pp30) REVERT: A 347 LEU cc_start: 0.8258 (mp) cc_final: 0.7765 (mp) REVERT: A 354 LYS cc_start: 0.3938 (OUTLIER) cc_final: 0.2868 (ptpp) REVERT: A 428 TRP cc_start: 0.7879 (m100) cc_final: 0.7664 (m100) REVERT: A 450 GLU cc_start: 0.7078 (pp20) cc_final: 0.6628 (tm-30) REVERT: A 458 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7014 (mm-30) REVERT: A 462 LEU cc_start: 0.7991 (tp) cc_final: 0.7560 (mp) REVERT: A 477 GLU cc_start: 0.7336 (tp30) cc_final: 0.6818 (mm-30) REVERT: A 480 GLN cc_start: 0.8226 (tp-100) cc_final: 0.7931 (tm-30) REVERT: A 505 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7081 (mm-30) REVERT: A 509 ARG cc_start: 0.8001 (ttm110) cc_final: 0.7654 (ttm110) REVERT: A 513 TYR cc_start: 0.7251 (m-10) cc_final: 0.6940 (m-80) REVERT: A 539 LEU cc_start: 0.8106 (mp) cc_final: 0.7555 (tp) REVERT: A 545 LYS cc_start: 0.7535 (tptt) cc_final: 0.7212 (mptt) REVERT: A 570 LYS cc_start: 0.7856 (mtpt) cc_final: 0.7617 (mtpp) REVERT: A 595 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7206 (tm-30) REVERT: A 597 GLU cc_start: 0.7442 (mt-10) cc_final: 0.6839 (mt-10) REVERT: A 742 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7843 (tt) REVERT: A 771 GLN cc_start: 0.8219 (tp-100) cc_final: 0.7979 (tp-100) REVERT: A 772 LYS cc_start: 0.7908 (ttmm) cc_final: 0.7472 (tmmt) REVERT: A 778 ARG cc_start: 0.7860 (ttm110) cc_final: 0.7544 (ptp-110) REVERT: A 813 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7769 (tm-30) REVERT: A 828 GLU cc_start: 0.5641 (mm-30) cc_final: 0.5374 (mm-30) REVERT: A 863 ARG cc_start: 0.7500 (mmp-170) cc_final: 0.7108 (mmp80) REVERT: A 879 GLU cc_start: 0.7093 (pp20) cc_final: 0.6690 (pp20) REVERT: A 884 GLU cc_start: 0.7204 (tt0) cc_final: 0.6929 (tt0) REVERT: A 903 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7044 (ptp90) REVERT: A 922 LYS cc_start: 0.8414 (ttmm) cc_final: 0.7962 (ttmm) REVERT: A 933 ILE cc_start: 0.8184 (mt) cc_final: 0.7923 (mp) REVERT: B 22 ASN cc_start: 0.7705 (t0) cc_final: 0.7442 (t0) REVERT: B 42 LEU cc_start: 0.8273 (mt) cc_final: 0.8009 (tt) REVERT: B 56 ARG cc_start: 0.7660 (mtp180) cc_final: 0.7207 (mtp180) REVERT: B 68 TYR cc_start: 0.7746 (t80) cc_final: 0.7228 (t80) REVERT: B 72 GLU cc_start: 0.7170 (tp30) cc_final: 0.6815 (tp30) REVERT: B 157 ILE cc_start: 0.8072 (mt) cc_final: 0.7862 (mp) REVERT: B 166 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8130 (mmpt) REVERT: B 193 ARG cc_start: 0.7265 (mmm160) cc_final: 0.6989 (mmm160) REVERT: B 195 MET cc_start: 0.7296 (mtp) cc_final: 0.6960 (mtp) REVERT: B 206 PHE cc_start: 0.7938 (t80) cc_final: 0.7712 (t80) REVERT: B 225 VAL cc_start: 0.7667 (p) cc_final: 0.7386 (m) REVERT: B 308 ASN cc_start: 0.8209 (m-40) cc_final: 0.7935 (m110) REVERT: B 315 TYR cc_start: 0.8120 (t80) cc_final: 0.7263 (t80) REVERT: B 354 GLN cc_start: 0.8261 (mp10) cc_final: 0.7693 (mp10) REVERT: B 355 ASN cc_start: 0.7616 (m-40) cc_final: 0.7323 (m-40) REVERT: C 20 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7364 (mt) REVERT: C 23 GLN cc_start: 0.8724 (tt0) cc_final: 0.8206 (tt0) REVERT: C 208 ARG cc_start: 0.4553 (OUTLIER) cc_final: 0.4051 (ptm160) REVERT: C 298 MET cc_start: 0.8220 (mmm) cc_final: 0.7393 (mmm) REVERT: C 313 TRP cc_start: 0.7271 (t60) cc_final: 0.6971 (t60) REVERT: C 320 GLU cc_start: 0.7006 (mp0) cc_final: 0.6551 (mp0) REVERT: D 281 TYR cc_start: 0.6573 (t80) cc_final: 0.6069 (t80) REVERT: D 335 LYS cc_start: 0.8916 (pptt) cc_final: 0.8572 (pptt) outliers start: 47 outliers final: 32 residues processed: 364 average time/residue: 0.1076 time to fit residues: 53.0839 Evaluate side-chains 374 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 335 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 866 HIS Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 903 ARG Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 359 HIS Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 276 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN A 748 ASN A 769 GLN A 859 GLN A 867 HIS ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 HIS ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.159433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.132440 restraints weight = 20452.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.136986 restraints weight = 11107.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.140010 restraints weight = 7110.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.142017 restraints weight = 5005.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.143323 restraints weight = 3883.469| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3990 r_free = 0.3990 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3990 r_free = 0.3990 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 10644 Z= 0.282 Angle : 0.824 13.581 14367 Z= 0.418 Chirality : 0.049 0.333 1534 Planarity : 0.006 0.059 1862 Dihedral : 5.362 50.692 1409 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 5.74 % Allowed : 30.04 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: -0.35 (0.23), residues: 1260 helix: 0.60 (0.19), residues: 678 sheet: -0.75 (0.54), residues: 80 loop : -1.24 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 550 TYR 0.033 0.003 TYR A 777 PHE 0.028 0.002 PHE D 345 TRP 0.014 0.002 TRP A 428 HIS 0.007 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.28 (10627) covalent geometry : angle 0.79968 / 0.42 (14352) hydrogen bonds : bond 0.05875 / 3.85 ( 532) hydrogen bonds : angle 5.15342 / 3.66 ( 1548) metal coordination : bond 0.01942 / 1.29 ( 17) metal coordination : angle 6.14290 / 3.25 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 342 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.7468 (t80) cc_final: 0.7076 (t80) REVERT: A 347 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7885 (mp) REVERT: A 354 LYS cc_start: 0.4854 (OUTLIER) cc_final: 0.3806 (ptpp) REVERT: A 355 PHE cc_start: 0.5408 (m-80) cc_final: 0.5119 (m-10) REVERT: A 428 TRP cc_start: 0.7911 (m100) cc_final: 0.7599 (m100) REVERT: A 449 GLU cc_start: 0.7608 (tt0) cc_final: 0.6965 (tp30) REVERT: A 450 GLU cc_start: 0.7237 (pp20) cc_final: 0.6844 (tm-30) REVERT: A 458 GLU cc_start: 0.7492 (mm-30) cc_final: 0.6961 (mm-30) REVERT: A 477 GLU cc_start: 0.7331 (tp30) cc_final: 0.7038 (mm-30) REVERT: A 480 GLN cc_start: 0.8163 (tp-100) cc_final: 0.7863 (tm-30) REVERT: A 505 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7146 (mm-30) REVERT: A 509 ARG cc_start: 0.7974 (ttm110) cc_final: 0.7573 (ttm110) REVERT: A 513 TYR cc_start: 0.7368 (m-10) cc_final: 0.7010 (m-80) REVERT: A 539 LEU cc_start: 0.8140 (mp) cc_final: 0.7789 (mm) REVERT: A 545 LYS cc_start: 0.7608 (tptt) cc_final: 0.7211 (mptt) REVERT: A 570 LYS cc_start: 0.7984 (mtpt) cc_final: 0.7692 (mtpp) REVERT: A 595 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7218 (tm-30) REVERT: A 597 GLU cc_start: 0.7457 (mt-10) cc_final: 0.6836 (mt-10) REVERT: A 742 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7959 (tt) REVERT: A 771 GLN cc_start: 0.8260 (tp-100) cc_final: 0.7939 (tp-100) REVERT: A 772 LYS cc_start: 0.7990 (ttmm) cc_final: 0.7710 (mmmm) REVERT: A 778 ARG cc_start: 0.7826 (ttm110) cc_final: 0.7556 (ptp-110) REVERT: A 813 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7880 (tm-30) REVERT: A 828 GLU cc_start: 0.5701 (mm-30) cc_final: 0.5491 (mm-30) REVERT: A 843 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7035 (mpp) REVERT: A 863 ARG cc_start: 0.7427 (mmp-170) cc_final: 0.7063 (mmp80) REVERT: A 868 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6825 (tp) REVERT: A 879 GLU cc_start: 0.7314 (pp20) cc_final: 0.6967 (pp20) REVERT: A 884 GLU cc_start: 0.7136 (tt0) cc_final: 0.6905 (tt0) REVERT: A 903 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7317 (ptp90) REVERT: A 909 TRP cc_start: 0.7467 (t60) cc_final: 0.7178 (t60) REVERT: A 922 LYS cc_start: 0.8478 (ttmm) cc_final: 0.7941 (ttmm) REVERT: A 933 ILE cc_start: 0.8415 (mt) cc_final: 0.8074 (mp) REVERT: A 934 MET cc_start: 0.7795 (ttt) cc_final: 0.7463 (ttm) REVERT: B 19 ASP cc_start: 0.7599 (m-30) cc_final: 0.7382 (m-30) REVERT: B 22 ASN cc_start: 0.7858 (t0) cc_final: 0.7554 (t0) REVERT: B 31 MET cc_start: 0.7883 (tmm) cc_final: 0.7617 (tmm) REVERT: B 42 LEU cc_start: 0.8328 (mt) cc_final: 0.8013 (tt) REVERT: B 56 ARG cc_start: 0.7680 (mtp180) cc_final: 0.7161 (mtp180) REVERT: B 68 TYR cc_start: 0.7764 (t80) cc_final: 0.7553 (t80) REVERT: B 72 GLU cc_start: 0.7558 (tp30) cc_final: 0.7336 (tp30) REVERT: B 157 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7905 (mp) REVERT: B 193 ARG cc_start: 0.7302 (mmm160) cc_final: 0.6664 (mtp85) REVERT: B 195 MET cc_start: 0.7321 (mtp) cc_final: 0.6944 (mtp) REVERT: B 221 LYS cc_start: 0.7259 (ttpt) cc_final: 0.6664 (ttpp) REVERT: B 225 VAL cc_start: 0.7784 (p) cc_final: 0.7430 (m) REVERT: B 236 GLU cc_start: 0.7886 (pm20) cc_final: 0.7656 (pm20) REVERT: B 250 MET cc_start: 0.6753 (mtp) cc_final: 0.6531 (mtp) REVERT: B 354 GLN cc_start: 0.8323 (mp10) cc_final: 0.7839 (mp10) REVERT: C 21 MET cc_start: 0.6607 (tmm) cc_final: 0.6006 (tmm) REVERT: C 23 GLN cc_start: 0.8557 (tt0) cc_final: 0.7969 (tt0) REVERT: C 208 ARG cc_start: 0.4626 (OUTLIER) cc_final: 0.4078 (ptm160) REVERT: C 298 MET cc_start: 0.8182 (mmm) cc_final: 0.7285 (mmm) REVERT: C 320 GLU cc_start: 0.7121 (mp0) cc_final: 0.6690 (mp0) REVERT: D 335 LYS cc_start: 0.8916 (pptt) cc_final: 0.8573 (pptt) outliers start: 65 outliers final: 45 residues processed: 371 average time/residue: 0.1086 time to fit residues: 54.3811 Evaluate side-chains 398 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 345 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 469 ASN Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 866 HIS Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 903 ARG Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 359 HIS Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 276 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 100 optimal weight: 0.0060 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN B 69 HIS B 93 GLN ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN D 295 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.163801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.137104 restraints weight = 20283.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.141778 restraints weight = 10911.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.144805 restraints weight = 6867.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.146857 restraints weight = 4848.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.148136 restraints weight = 3724.932| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4050 r_free = 0.4050 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4050 r_free = 0.4050 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10644 Z= 0.142 Angle : 0.758 13.470 14367 Z= 0.372 Chirality : 0.045 0.407 1534 Planarity : 0.005 0.068 1862 Dihedral : 4.994 55.043 1409 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.71 % Allowed : 32.77 % Favored : 63.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.24), residues: 1260 helix: 1.10 (0.20), residues: 666 sheet: -0.58 (0.55), residues: 79 loop : -1.04 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 94 TYR 0.033 0.002 TYR A 777 PHE 0.026 0.002 PHE A 310 TRP 0.011 0.001 TRP D 206 HIS 0.005 0.001 HIS C 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10627) covalent geometry : angle 0.74550 / 0.37 (14352) hydrogen bonds : bond 0.04483 / 2.96 ( 532) hydrogen bonds : angle 4.60705 / 3.29 ( 1548) metal coordination : bond 0.01162 / 0.46 ( 17) metal coordination : angle 4.37285 / 2.39 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 339 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.7422 (t80) cc_final: 0.7005 (t80) REVERT: A 352 LEU cc_start: 0.7998 (mm) cc_final: 0.7606 (tp) REVERT: A 354 LYS cc_start: 0.4473 (OUTLIER) cc_final: 0.3252 (ptpp) REVERT: A 450 GLU cc_start: 0.7030 (pp20) cc_final: 0.6450 (tm-30) REVERT: A 462 LEU cc_start: 0.7908 (tp) cc_final: 0.7432 (mp) REVERT: A 473 ILE cc_start: 0.7961 (mt) cc_final: 0.7641 (mm) REVERT: A 474 ARG cc_start: 0.7705 (ttm110) cc_final: 0.7480 (ttm110) REVERT: A 477 GLU cc_start: 0.7291 (tp30) cc_final: 0.6782 (mm-30) REVERT: A 480 GLN cc_start: 0.8221 (tp-100) cc_final: 0.7928 (tm-30) REVERT: A 486 MET cc_start: 0.4181 (pmm) cc_final: 0.3800 (pmm) REVERT: A 505 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7012 (mm-30) REVERT: A 509 ARG cc_start: 0.8008 (ttm110) cc_final: 0.7365 (ttm110) REVERT: A 513 TYR cc_start: 0.7292 (m-10) cc_final: 0.6952 (m-80) REVERT: A 539 LEU cc_start: 0.8010 (mp) cc_final: 0.7502 (tp) REVERT: A 545 LYS cc_start: 0.7507 (tptt) cc_final: 0.7127 (mptt) REVERT: A 570 LYS cc_start: 0.7943 (mtpt) cc_final: 0.7667 (mtpp) REVERT: A 595 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7179 (tm-30) REVERT: A 597 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6739 (mt-10) REVERT: A 622 PHE cc_start: 0.6748 (m-80) cc_final: 0.5268 (m-10) REVERT: A 643 ARG cc_start: 0.7867 (mtt90) cc_final: 0.7621 (mtt90) REVERT: A 742 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7870 (tt) REVERT: A 771 GLN cc_start: 0.8265 (tp-100) cc_final: 0.7920 (tp-100) REVERT: A 772 LYS cc_start: 0.7935 (ttmm) cc_final: 0.7510 (mmmm) REVERT: A 813 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7821 (tm-30) REVERT: A 843 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.6854 (mpp) REVERT: A 863 ARG cc_start: 0.7442 (mmp-170) cc_final: 0.7116 (mmp80) REVERT: A 879 GLU cc_start: 0.7169 (pp20) cc_final: 0.6788 (pp20) REVERT: A 884 GLU cc_start: 0.7114 (tt0) cc_final: 0.6778 (tt0) REVERT: A 903 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.6739 (ptp90) REVERT: A 919 ASN cc_start: 0.6179 (t0) cc_final: 0.5886 (t0) REVERT: A 921 PHE cc_start: 0.7525 (m-80) cc_final: 0.7232 (m-80) REVERT: A 922 LYS cc_start: 0.8431 (ttmm) cc_final: 0.7955 (ttmm) REVERT: A 934 MET cc_start: 0.7782 (ttt) cc_final: 0.7450 (ttm) REVERT: B 19 ASP cc_start: 0.7441 (m-30) cc_final: 0.7194 (m-30) REVERT: B 22 ASN cc_start: 0.7774 (t0) cc_final: 0.7424 (t0) REVERT: B 31 MET cc_start: 0.7850 (tmm) cc_final: 0.7610 (tmm) REVERT: B 42 LEU cc_start: 0.8334 (mt) cc_final: 0.8028 (tt) REVERT: B 56 ARG cc_start: 0.7577 (mtp180) cc_final: 0.7064 (mtp180) REVERT: B 68 TYR cc_start: 0.7724 (t80) cc_final: 0.7291 (t80) REVERT: B 69 HIS cc_start: 0.8142 (OUTLIER) cc_final: 0.7871 (m-70) REVERT: B 72 GLU cc_start: 0.7358 (tp30) cc_final: 0.7130 (tp30) REVERT: B 78 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7576 (ptm160) REVERT: B 157 ILE cc_start: 0.8151 (mt) cc_final: 0.7933 (mp) REVERT: B 167 TYR cc_start: 0.7135 (m-80) cc_final: 0.6802 (m-80) REVERT: B 195 MET cc_start: 0.7272 (mtp) cc_final: 0.6951 (mtp) REVERT: B 225 VAL cc_start: 0.7664 (p) cc_final: 0.7327 (m) REVERT: B 250 MET cc_start: 0.6616 (mtp) cc_final: 0.6370 (mtp) REVERT: B 342 PHE cc_start: 0.7796 (m-10) cc_final: 0.7402 (m-80) REVERT: B 354 GLN cc_start: 0.8208 (mp10) cc_final: 0.7568 (mp10) REVERT: C 21 MET cc_start: 0.6559 (tmm) cc_final: 0.6172 (tmm) REVERT: C 23 GLN cc_start: 0.8644 (tt0) cc_final: 0.8084 (tm-30) REVERT: C 208 ARG cc_start: 0.4591 (OUTLIER) cc_final: 0.4057 (ptm160) REVERT: C 279 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6756 (mtm-85) REVERT: C 298 MET cc_start: 0.8151 (mmm) cc_final: 0.7870 (mmm) REVERT: C 320 GLU cc_start: 0.7110 (mp0) cc_final: 0.6654 (mp0) REVERT: D 335 LYS cc_start: 0.8924 (pptt) cc_final: 0.8550 (pptt) outliers start: 42 outliers final: 25 residues processed: 363 average time/residue: 0.1128 time to fit residues: 55.3769 Evaluate side-chains 366 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 333 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 469 ASN Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 866 HIS Chi-restraints excluded: chain A residue 903 ARG Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 359 HIS Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 276 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 100 optimal weight: 0.0000 chunk 62 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 114 optimal weight: 0.2980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN A 582 ASN ** A 867 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 HIS D 219 GLN D 228 ASN D 271 GLN D 280 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.164192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.137260 restraints weight = 20283.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.141884 restraints weight = 10943.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.144932 restraints weight = 6929.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.146970 restraints weight = 4888.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.148227 restraints weight = 3781.548| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10644 Z= 0.141 Angle : 0.758 14.452 14367 Z= 0.371 Chirality : 0.044 0.388 1534 Planarity : 0.005 0.069 1862 Dihedral : 4.923 56.633 1409 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.27 % Allowed : 33.66 % Favored : 63.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.30 (0.24), residues: 1260 helix: 1.21 (0.20), residues: 667 sheet: -0.50 (0.56), residues: 79 loop : -1.01 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 550 TYR 0.032 0.002 TYR A 777 PHE 0.025 0.002 PHE B 76 TRP 0.011 0.001 TRP A 909 HIS 0.005 0.001 HIS C 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10627) covalent geometry : angle 0.74690 / 0.37 (14352) hydrogen bonds : bond 0.04377 / 2.93 ( 532) hydrogen bonds : angle 4.59345 / 3.29 ( 1548) metal coordination : bond 0.01050 / 0.43 ( 17) metal coordination : angle 4.13589 / 2.26 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 341 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.7417 (t80) cc_final: 0.7001 (t80) REVERT: A 352 LEU cc_start: 0.7999 (mm) cc_final: 0.7562 (tp) REVERT: A 354 LYS cc_start: 0.4405 (OUTLIER) cc_final: 0.3193 (ptpp) REVERT: A 450 GLU cc_start: 0.6947 (pp20) cc_final: 0.6345 (tm-30) REVERT: A 458 GLU cc_start: 0.7504 (mm-30) cc_final: 0.5791 (mm-30) REVERT: A 473 ILE cc_start: 0.7961 (mt) cc_final: 0.7684 (mm) REVERT: A 474 ARG cc_start: 0.7695 (ttm110) cc_final: 0.7421 (ttm110) REVERT: A 477 GLU cc_start: 0.7323 (tp30) cc_final: 0.6820 (mm-30) REVERT: A 480 GLN cc_start: 0.8221 (tp-100) cc_final: 0.7918 (tm-30) REVERT: A 486 MET cc_start: 0.4130 (pmm) cc_final: 0.3767 (pmm) REVERT: A 505 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7036 (mm-30) REVERT: A 509 ARG cc_start: 0.7988 (ttm110) cc_final: 0.7308 (ttm110) REVERT: A 510 ARG cc_start: 0.7953 (tpp-160) cc_final: 0.7607 (tpp-160) REVERT: A 513 TYR cc_start: 0.7296 (m-10) cc_final: 0.6556 (m-80) REVERT: A 539 LEU cc_start: 0.7997 (mp) cc_final: 0.7506 (tp) REVERT: A 545 LYS cc_start: 0.7507 (tptt) cc_final: 0.7116 (mptt) REVERT: A 570 LYS cc_start: 0.7936 (mtpt) cc_final: 0.7632 (mtpp) REVERT: A 581 GLN cc_start: 0.7425 (mp-120) cc_final: 0.7091 (mp10) REVERT: A 595 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7204 (tm-30) REVERT: A 597 GLU cc_start: 0.7453 (mt-10) cc_final: 0.6724 (mt-10) REVERT: A 622 PHE cc_start: 0.6735 (m-80) cc_final: 0.6256 (m-10) REVERT: A 742 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7844 (tt) REVERT: A 771 GLN cc_start: 0.8273 (tp-100) cc_final: 0.7899 (tp-100) REVERT: A 772 LYS cc_start: 0.7940 (ttmm) cc_final: 0.7552 (tmmt) REVERT: A 778 ARG cc_start: 0.7823 (ttm110) cc_final: 0.7490 (ptp-110) REVERT: A 813 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7795 (tm-30) REVERT: A 843 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.6861 (mpp) REVERT: A 863 ARG cc_start: 0.7484 (mmp-170) cc_final: 0.7175 (mmp80) REVERT: A 879 GLU cc_start: 0.7154 (pp20) cc_final: 0.6771 (pp20) REVERT: A 884 GLU cc_start: 0.7139 (tt0) cc_final: 0.6770 (tt0) REVERT: A 903 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.6755 (ptp90) REVERT: A 919 ASN cc_start: 0.6085 (t0) cc_final: 0.5884 (t0) REVERT: A 921 PHE cc_start: 0.7536 (m-80) cc_final: 0.7268 (m-80) REVERT: A 922 LYS cc_start: 0.8411 (ttmm) cc_final: 0.7939 (ttmm) REVERT: B 19 ASP cc_start: 0.7422 (m-30) cc_final: 0.7179 (m-30) REVERT: B 22 ASN cc_start: 0.7727 (t0) cc_final: 0.7382 (t0) REVERT: B 31 MET cc_start: 0.7753 (mmm) cc_final: 0.7259 (tpt) REVERT: B 42 LEU cc_start: 0.8306 (mt) cc_final: 0.8011 (tt) REVERT: B 43 LEU cc_start: 0.8319 (mt) cc_final: 0.8055 (mt) REVERT: B 68 TYR cc_start: 0.7686 (t80) cc_final: 0.7378 (t80) REVERT: B 72 GLU cc_start: 0.7425 (tp30) cc_final: 0.7159 (tp30) REVERT: B 78 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7516 (ptm160) REVERT: B 157 ILE cc_start: 0.8138 (mt) cc_final: 0.7934 (mp) REVERT: B 162 LEU cc_start: 0.8295 (mt) cc_final: 0.8069 (mp) REVERT: B 167 TYR cc_start: 0.7114 (m-80) cc_final: 0.6775 (m-80) REVERT: B 195 MET cc_start: 0.7318 (mtp) cc_final: 0.6164 (mtp) REVERT: B 225 VAL cc_start: 0.7663 (p) cc_final: 0.7337 (m) REVERT: B 250 MET cc_start: 0.6625 (mtp) cc_final: 0.6373 (mtp) REVERT: B 253 TYR cc_start: 0.6789 (t80) cc_final: 0.6092 (t80) REVERT: B 354 GLN cc_start: 0.8203 (mp10) cc_final: 0.7498 (mp10) REVERT: C 21 MET cc_start: 0.6623 (tmm) cc_final: 0.6414 (mmm) REVERT: C 208 ARG cc_start: 0.4865 (OUTLIER) cc_final: 0.4295 (ptm160) REVERT: C 279 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6754 (mtm-85) REVERT: C 298 MET cc_start: 0.8140 (mmm) cc_final: 0.7829 (mmm) REVERT: C 320 GLU cc_start: 0.7181 (mp0) cc_final: 0.6701 (mp0) REVERT: D 335 LYS cc_start: 0.8894 (pptt) cc_final: 0.8499 (pptt) outliers start: 37 outliers final: 26 residues processed: 360 average time/residue: 0.1082 time to fit residues: 52.6750 Evaluate side-chains 369 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 336 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 469 ASN Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 866 HIS Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 903 ARG Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 276 PHE Chi-restraints excluded: chain D residue 280 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 89 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 0.0570 chunk 28 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 99 optimal weight: 0.0040 chunk 52 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 overall best weight: 0.4310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 GLN ** A 867 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN D 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.165225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.138309 restraints weight = 20305.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.142989 restraints weight = 10959.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.146079 restraints weight = 6902.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.148134 restraints weight = 4868.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.149447 restraints weight = 3757.498| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4065 r_free = 0.4065 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4065 r_free = 0.4065 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.4065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10644 Z= 0.141 Angle : 0.767 14.175 14367 Z= 0.375 Chirality : 0.044 0.397 1534 Planarity : 0.005 0.067 1862 Dihedral : 4.903 58.780 1409 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.00 % Allowed : 34.10 % Favored : 62.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.27 (0.24), residues: 1260 helix: 1.16 (0.20), residues: 673 sheet: -0.52 (0.56), residues: 79 loop : -1.01 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 193 TYR 0.031 0.001 TYR A 777 PHE 0.026 0.002 PHE B 335 TRP 0.055 0.003 TRP B 313 HIS 0.003 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10627) covalent geometry : angle 0.75628 / 0.37 (14352) hydrogen bonds : bond 0.04269 / 2.85 ( 532) hydrogen bonds : angle 4.55026 / 3.27 ( 1548) metal coordination : bond 0.01040 / 0.40 ( 17) metal coordination : angle 3.94439 / 2.16 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 344 time to evaluate : 0.342 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: A 327 PHE cc_start: 0.7449 (t80) cc_final: 0.7005 (t80) REVERT: A 352 LEU cc_start: 0.7981 (mm) cc_final: 0.7616 (tp) REVERT: A 354 LYS cc_start: 0.4336 (OUTLIER) cc_final: 0.3169 (ptpp) REVERT: A 450 GLU cc_start: 0.6908 (pp20) cc_final: 0.6329 (tm-30) REVERT: A 458 GLU cc_start: 0.7465 (mm-30) cc_final: 0.6362 (mm-30) REVERT: A 473 ILE cc_start: 0.7898 (mt) cc_final: 0.7574 (mm) REVERT: A 477 GLU cc_start: 0.7311 (tp30) cc_final: 0.6785 (mm-30) REVERT: A 480 GLN cc_start: 0.8215 (tp-100) cc_final: 0.7913 (tm-30) REVERT: A 486 MET cc_start: 0.4130 (pmm) cc_final: 0.3781 (pmm) REVERT: A 505 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7055 (mm-30) REVERT: A 509 ARG cc_start: 0.8027 (ttm110) cc_final: 0.7317 (ttm110) REVERT: A 510 ARG cc_start: 0.7941 (tpp-160) cc_final: 0.7589 (tpp-160) REVERT: A 513 TYR cc_start: 0.7304 (m-10) cc_final: 0.6508 (m-80) REVERT: A 539 LEU cc_start: 0.7995 (mp) cc_final: 0.7507 (tp) REVERT: A 545 LYS cc_start: 0.7511 (tptt) cc_final: 0.7127 (mptt) REVERT: A 570 LYS cc_start: 0.7932 (mtpt) cc_final: 0.7626 (mtpp) REVERT: A 581 GLN cc_start: 0.7430 (mp-120) cc_final: 0.7092 (mp10) REVERT: A 595 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7195 (tm-30) REVERT: A 597 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6717 (mt-10) REVERT: A 742 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7847 (tt) REVERT: A 771 GLN cc_start: 0.8254 (tp-100) cc_final: 0.7879 (tp-100) REVERT: A 772 LYS cc_start: 0.7903 (ttmm) cc_final: 0.7536 (tmmt) REVERT: A 778 ARG cc_start: 0.7843 (ttm110) cc_final: 0.7394 (ptp-110) REVERT: A 828 GLU cc_start: 0.5550 (mp0) cc_final: 0.5332 (mm-30) REVERT: A 840 LEU cc_start: 0.8189 (tp) cc_final: 0.7986 (tp) REVERT: A 843 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.6842 (mpp) REVERT: A 863 ARG cc_start: 0.7520 (mmp-170) cc_final: 0.7174 (mmp80) REVERT: A 879 GLU cc_start: 0.7129 (pp20) cc_final: 0.6769 (pp20) REVERT: A 884 GLU cc_start: 0.7229 (tt0) cc_final: 0.6950 (tt0) REVERT: A 903 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.6741 (ptp90) REVERT: A 922 LYS cc_start: 0.8384 (ttmm) cc_final: 0.7907 (ttmm) REVERT: B 22 ASN cc_start: 0.7677 (t0) cc_final: 0.7320 (t0) REVERT: B 31 MET cc_start: 0.7748 (mmm) cc_final: 0.7447 (tpt) REVERT: B 42 LEU cc_start: 0.8322 (mt) cc_final: 0.8076 (tt) REVERT: B 43 LEU cc_start: 0.8328 (mt) cc_final: 0.8072 (mt) REVERT: B 65 MET cc_start: 0.6887 (mtt) cc_final: 0.6500 (mtp) REVERT: B 68 TYR cc_start: 0.7674 (t80) cc_final: 0.7397 (t80) REVERT: B 72 GLU cc_start: 0.7371 (tp30) cc_final: 0.7115 (tp30) REVERT: B 118 SER cc_start: 0.7720 (m) cc_final: 0.7370 (p) REVERT: B 155 ASN cc_start: 0.7872 (OUTLIER) cc_final: 0.7124 (m-40) REVERT: B 162 LEU cc_start: 0.8290 (mt) cc_final: 0.8063 (mp) REVERT: B 167 TYR cc_start: 0.7049 (m-80) cc_final: 0.6725 (m-80) REVERT: B 195 MET cc_start: 0.7334 (mtp) cc_final: 0.7003 (mtp) REVERT: B 225 VAL cc_start: 0.7643 (p) cc_final: 0.7345 (m) REVERT: B 250 MET cc_start: 0.6630 (mtp) cc_final: 0.6362 (mtp) REVERT: B 315 TYR cc_start: 0.8078 (t80) cc_final: 0.7244 (t80) REVERT: B 332 ASN cc_start: 0.6102 (p0) cc_final: 0.5623 (p0) REVERT: B 337 TYR cc_start: 0.7456 (m-80) cc_final: 0.7137 (m-80) REVERT: B 354 GLN cc_start: 0.8170 (mp10) cc_final: 0.7458 (mp10) REVERT: C 208 ARG cc_start: 0.4752 (OUTLIER) cc_final: 0.4188 (ptm160) REVERT: C 274 CYS cc_start: 0.6566 (OUTLIER) cc_final: 0.6304 (p) REVERT: C 279 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6834 (mtm-85) REVERT: C 298 MET cc_start: 0.8132 (mmm) cc_final: 0.7772 (mmm) REVERT: C 320 GLU cc_start: 0.7169 (mp0) cc_final: 0.6699 (mp0) REVERT: D 335 LYS cc_start: 0.8898 (pptt) cc_final: 0.8511 (pptt) outliers start: 34 outliers final: 22 residues processed: 362 average time/residue: 0.0978 time to fit residues: 48.6385 Evaluate side-chains 366 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 336 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 866 HIS Chi-restraints excluded: chain A residue 903 ARG Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 276 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 89 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 469 ASN ** A 867 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.165060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.138203 restraints weight = 20511.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.142843 restraints weight = 11102.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.145902 restraints weight = 7030.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.147972 restraints weight = 4984.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.149231 restraints weight = 3818.105| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4065 r_free = 0.4065 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4065 r_free = 0.4065 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.232 10644 Z= 0.296 Angle : 1.142 59.200 14367 Z= 0.678 Chirality : 0.054 1.001 1534 Planarity : 0.008 0.219 1862 Dihedral : 4.955 58.711 1409 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.73 % Favored : 96.19 % Rotamer: Outliers : 3.09 % Allowed : 33.83 % Favored : 63.07 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 8.06 % 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 (0.24), residues: 1260 helix: 1.14 (0.20), residues: 673 sheet: -0.51 (0.56), residues: 79 loop : -1.03 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 94 TYR 0.029 0.001 TYR A 777 PHE 0.018 0.002 PHE B 108 TRP 0.048 0.003 TRP B 313 HIS 0.004 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.30 (10627) covalent geometry : angle 1.13576 / 0.68 (14352) hydrogen bonds : bond 0.04348 / 2.88 ( 532) hydrogen bonds : angle 4.56682 / 3.29 ( 1548) metal coordination : bond 0.01067 / 0.42 ( 17) metal coordination : angle 3.92220 / 2.15 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1972.41 seconds wall clock time: 34 minutes 41.28 seconds (2081.28 seconds total)