Starting phenix.real_space_refine on Fri Sep 11 14:45:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xi2_66894/09_2026/9xi2_66894.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xi2_66894/09_2026/9xi2_66894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xi2_66894/09_2026/9xi2_66894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xi2_66894/09_2026/9xi2_66894.map" model { file = "/net/cci-nas-00/data/ceres_data/9xi2_66894/09_2026/9xi2_66894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xi2_66894/09_2026/9xi2_66894.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 47 5.16 5 C 6153 2.51 5 N 1603 2.21 5 O 1865 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9669 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4864 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1540 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 11, 'TRANS': 181} Chain: "H" Number of atoms: 1650 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 222, 1646 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 210} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 222, 1646 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 210} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1678 Chain: "L" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1558 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.29, per 1000 atoms: 0.24 Number of scatterers: 9669 At special positions: 0 Unit cell: (79.788, 142.74, 126.636, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 47 16.00 O 1865 8.00 N 1603 7.00 C 6153 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 207 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 198 " distance=2.03 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 Links applied NAG-ASN " NAG A 902 " - " ASN A 53 " " NAG A 903 " - " ASN A 90 " " NAG A 904 " - " ASN A 322 " " NAG A 905 " - " ASN A 546 " Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 413.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2276 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 18 sheets defined 37.0% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 Processing helix chain 'A' and resid 55 through 82 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.675A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 149 through 154 removed outlier: 3.547A pdb=" N ASN A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 170 Processing helix chain 'A' and resid 176 through 194 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.640A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.673A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.606A pdb=" N PHE A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.839A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 412 removed outlier: 3.745A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.810A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.056A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.559A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.903A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 4.371A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.928A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 369 removed outlier: 3.624A pdb=" N VAL E 367 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR E 369 " --> pdb=" O SER E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 410 Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.601A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.005A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 169 No H-bonds generated for 'chain 'H' and resid 167 through 169' Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'L' and resid 129 through 133 removed outlier: 3.800A pdb=" N ASN L 133 " --> pdb=" O LEU L 130 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.915A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.125A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.050A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS E 378 " --> pdb=" O VAL E 433 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 466 through 467 Processing sheet with id=AA7, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB1, first strand: chain 'H' and resid 57 through 60 removed outlier: 3.679A pdb=" N THR H 57 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR H 113 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 57 through 60 removed outlier: 3.679A pdb=" N THR H 57 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 131 through 135 removed outlier: 3.510A pdb=" N PHE H 133 " --> pdb=" O LEU H 152 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU H 152 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY H 150 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL H 195 " --> pdb=" O ALA H 147 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU H 149 " --> pdb=" O VAL H 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 163 through 165 removed outlier: 3.933A pdb=" N SER H 164 " --> pdb=" O ASN H 208 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN H 208 " --> pdb=" O SER H 164 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS H 220 " --> pdb=" O CYS H 207 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL H 209 " --> pdb=" O VAL H 218 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL H 218 " --> pdb=" O VAL H 209 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR H 216 " --> pdb=" O HIS H 211 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.736A pdb=" N VAL L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.736A pdb=" N VAL L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AB8, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.567A pdb=" N SER L 119 " --> pdb=" O SER L 142 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE L 123 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER L 181 " --> pdb=" O CYS L 139 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE L 141 " --> pdb=" O ALA L 179 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA L 179 " --> pdb=" O ILE L 141 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP L 143 " --> pdb=" O TYR L 177 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N TYR L 177 " --> pdb=" O ASP L 143 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 151 through 154 removed outlier: 3.971A pdb=" N LYS L 154 " --> pdb=" O SER L 197 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR L 196 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL L 211 " --> pdb=" O TYR L 196 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS L 209 " --> pdb=" O CYS L 198 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL L 200 " --> pdb=" O VAL L 207 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL L 207 " --> pdb=" O VAL L 200 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1106 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: 1.64 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1941 1.33 - 1.45: 2638 1.45 - 1.58: 5282 1.58 - 1.70: 0 1.70 - 1.83: 72 Bond restraints: 9933 Sorted by residual: bond pdb=" C PHE H 157 " pdb=" N PRO H 158 " ideal model delta sigma weight residual 1.332 1.368 -0.036 1.12e-02 7.97e+03 1.03e+01 bond pdb=" N GLY E 431 " pdb=" CA GLY E 431 " ideal model delta sigma weight residual 1.448 1.477 -0.030 9.20e-03 1.18e+04 1.03e+01 bond pdb=" N CYS E 432 " pdb=" CA CYS E 432 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.18e-02 7.18e+03 8.71e+00 bond pdb=" N VAL A 172 " pdb=" CA VAL A 172 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.30e-02 5.92e+03 8.43e+00 bond pdb=" N ILE E 434 " pdb=" CA ILE E 434 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.27e-02 6.20e+03 8.07e+00 ... (remaining 9928 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 13249 2.09 - 4.18: 236 4.18 - 6.27: 22 6.27 - 8.36: 12 8.36 - 10.45: 2 Bond angle restraints: 13521 Sorted by residual: angle pdb=" CA GLY E 431 " pdb=" C GLY E 431 " pdb=" O GLY E 431 " ideal model delta sigma weight residual 121.83 118.01 3.82 1.02e+00 9.61e-01 1.41e+01 angle pdb=" C GLY H 27 " pdb=" N THR H 28 " pdb=" CA THR H 28 " ideal model delta sigma weight residual 121.54 128.65 -7.11 1.91e+00 2.74e-01 1.38e+01 angle pdb=" N VAL A 172 " pdb=" CA VAL A 172 " pdb=" C VAL A 172 " ideal model delta sigma weight residual 111.81 108.70 3.11 8.60e-01 1.35e+00 1.31e+01 angle pdb=" CB GLN A 60 " pdb=" CG GLN A 60 " pdb=" CD GLN A 60 " ideal model delta sigma weight residual 112.60 118.71 -6.11 1.70e+00 3.46e-01 1.29e+01 angle pdb=" CA GLU A 182 " pdb=" CB GLU A 182 " pdb=" CG GLU A 182 " ideal model delta sigma weight residual 114.10 121.13 -7.03 2.00e+00 2.50e-01 1.23e+01 ... (remaining 13516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 5080 16.97 - 33.95: 615 33.95 - 50.92: 182 50.92 - 67.89: 35 67.89 - 84.86: 18 Dihedral angle restraints: 5930 sinusoidal: 2364 harmonic: 3566 Sorted by residual: dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual -86.00 -158.88 72.88 1 1.00e+01 1.00e-02 6.77e+01 dihedral pdb=" CB CYS L 139 " pdb=" SG CYS L 139 " pdb=" SG CYS L 198 " pdb=" CB CYS L 198 " ideal model delta sinusoidal sigma weight residual 93.00 141.02 -48.02 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" CB CYS E 391 " pdb=" SG CYS E 391 " pdb=" SG CYS E 525 " pdb=" CB CYS E 525 " ideal model delta sinusoidal sigma weight residual 93.00 45.83 47.17 1 1.00e+01 1.00e-02 3.07e+01 ... (remaining 5927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 892 0.035 - 0.069: 359 0.069 - 0.104: 139 0.104 - 0.139: 59 0.139 - 0.173: 12 Chirality restraints: 1461 Sorted by residual: chirality pdb=" CA MET A 480 " pdb=" N MET A 480 " pdb=" C MET A 480 " pdb=" CB MET A 480 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" CB ILE H 52 " pdb=" CA ILE H 52 " pdb=" CG1 ILE H 52 " pdb=" CG2 ILE H 52 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.42e-01 chirality pdb=" CA VAL E 433 " pdb=" N VAL E 433 " pdb=" C VAL E 433 " pdb=" CB VAL E 433 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.17e-01 ... (remaining 1458 not shown) Planarity restraints: 1748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY L 112 " -0.033 2.00e-02 2.50e+03 6.53e-02 4.26e+01 pdb=" C GLY L 112 " 0.113 2.00e-02 2.50e+03 pdb=" O GLY L 112 " -0.042 2.00e-02 2.50e+03 pdb=" N GLN L 113 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 429 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.80e+00 pdb=" C PHE E 429 " -0.042 2.00e-02 2.50e+03 pdb=" O PHE E 429 " 0.016 2.00e-02 2.50e+03 pdb=" N THR E 430 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 202 " 0.010 2.00e-02 2.50e+03 1.46e-02 4.24e+00 pdb=" CG TYR A 202 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 202 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 202 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 202 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 202 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 202 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 202 " -0.001 2.00e-02 2.50e+03 ... (remaining 1745 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 181 2.68 - 3.23: 8421 3.23 - 3.79: 15500 3.79 - 4.34: 21239 4.34 - 4.90: 35060 Nonbonded interactions: 80401 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.119 2.230 nonbonded pdb=" O THR E 393 " pdb=" OG1 THR E 523 " model vdw 2.282 3.040 nonbonded pdb=" OD2 ASP E 398 " pdb=" OH TYR E 423 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR H 102 " pdb=" OD2 ASP L 34 " model vdw 2.299 3.040 nonbonded pdb=" OD1 ASP E 467 " pdb=" OG SER E 469 " model vdw 2.303 3.040 ... (remaining 80396 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=0.31 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.480 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.150 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 9950 Z= 0.211 Angle : 0.671 10.454 13557 Z= 0.363 Chirality : 0.048 0.173 1461 Planarity : 0.005 0.065 1744 Dihedral : 16.501 84.864 3618 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.96 % Allowed : 23.78 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.23), residues: 1218 helix: -0.12 (0.24), residues: 389 sheet: 0.19 (0.35), residues: 222 loop : -0.75 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 460 TYR 0.035 0.002 TYR A 202 PHE 0.016 0.002 PHE H 157 TRP 0.012 0.001 TRP A 477 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.21 ( 9933) covalent geometry : angle 0.66918 / 0.36 (13521) SS BOND : bond 0.00392 / 0.23 ( 11) SS BOND : angle 1.17860 / 0.68 ( 24) hydrogen bonds : bond 0.18384 / 12.10 ( 391) hydrogen bonds : angle 6.96799 / 5.16 ( 1106) metal coordination : bond 0.00227 / 0.11 ( 2) link_NAG-ASN : bond 0.00121 / 0.06 ( 4) link_NAG-ASN : angle 1.30426 / 0.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 305 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: L 106 THR cc_start: 0.7758 (p) cc_final: 0.7325 (t) outliers start: 10 outliers final: 6 residues processed: 103 average time/residue: 0.5198 time to fit residues: 58.0830 Evaluate side-chains 92 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain H residue 112 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 30.0000 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS A 175 GLN E 334 ASN E 360 ASN H 210 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.221446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.190336 restraints weight = 8972.204| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 1.14 r_work: 0.3590 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 9950 Z= 0.219 Angle : 0.623 11.507 13557 Z= 0.317 Chirality : 0.046 0.172 1461 Planarity : 0.005 0.038 1744 Dihedral : 6.311 68.550 1430 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.01 % Allowed : 21.11 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.24), residues: 1218 helix: 0.33 (0.25), residues: 403 sheet: 0.60 (0.32), residues: 256 loop : -0.54 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 393 TYR 0.018 0.002 TYR A 41 PHE 0.017 0.002 PHE A 32 TRP 0.014 0.002 TRP A 477 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.22 ( 9933) covalent geometry : angle 0.61798 / 0.32 (13521) SS BOND : bond 0.00494 / 0.32 ( 11) SS BOND : angle 1.64285 / 0.91 ( 24) hydrogen bonds : bond 0.05944 / 3.90 ( 391) hydrogen bonds : angle 5.37170 / 3.97 ( 1106) metal coordination : bond 0.00417 / 0.20 ( 2) link_NAG-ASN : bond 0.00097 / 0.04 ( 4) link_NAG-ASN : angle 1.63042 / 0.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: E 358 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8353 (mm) REVERT: E 424 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8224 (tttp) REVERT: E 440 LYS cc_start: 0.8418 (mttp) cc_final: 0.7565 (mptt) outliers start: 42 outliers final: 20 residues processed: 119 average time/residue: 0.4929 time to fit residues: 63.8145 Evaluate side-chains 111 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 357 ARG Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 418 ILE Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 76 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 29 optimal weight: 0.0870 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.0270 chunk 0 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 105 optimal weight: 0.0770 chunk 44 optimal weight: 0.5980 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.215558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.167274 restraints weight = 9179.025| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.18 r_work: 0.3410 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.3410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9950 Z= 0.103 Angle : 0.497 8.426 13557 Z= 0.251 Chirality : 0.042 0.159 1461 Planarity : 0.003 0.033 1744 Dihedral : 5.229 66.961 1423 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.58 % Allowed : 23.50 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.24), residues: 1218 helix: 1.07 (0.26), residues: 389 sheet: 0.75 (0.33), residues: 241 loop : -0.48 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 56 TYR 0.021 0.001 TYR H 102 PHE 0.013 0.001 PHE H 157 TRP 0.010 0.001 TRP H 36 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 9933) covalent geometry : angle 0.49410 / 0.25 (13521) SS BOND : bond 0.00265 / 0.15 ( 11) SS BOND : angle 0.96790 / 0.57 ( 24) hydrogen bonds : bond 0.04467 / 2.96 ( 391) hydrogen bonds : angle 4.92829 / 3.62 ( 1106) metal coordination : bond 0.00046 / 0.02 ( 2) link_NAG-ASN : bond 0.00130 / 0.06 ( 4) link_NAG-ASN : angle 1.46623 / 0.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.393 Fit side-chains REVERT: A 295 ASP cc_start: 0.7975 (m-30) cc_final: 0.7621 (m-30) REVERT: A 332 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7830 (ptt) REVERT: A 441 LYS cc_start: 0.8000 (ttpp) cc_final: 0.7604 (pttp) REVERT: E 357 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8273 (ttt180) REVERT: E 503 VAL cc_start: 0.8876 (t) cc_final: 0.8623 (p) outliers start: 27 outliers final: 13 residues processed: 108 average time/residue: 0.5064 time to fit residues: 59.3516 Evaluate side-chains 103 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 355 ARG Chi-restraints excluded: chain E residue 357 ARG Chi-restraints excluded: chain E residue 418 ILE Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 120 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.0870 chunk 106 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 334 ASN E 450 ASN ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.212849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.159085 restraints weight = 9232.735| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 3.63 r_work: 0.3358 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9950 Z= 0.146 Angle : 0.548 9.454 13557 Z= 0.275 Chirality : 0.044 0.156 1461 Planarity : 0.004 0.032 1744 Dihedral : 4.453 48.722 1414 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.34 % Allowed : 22.54 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.24), residues: 1218 helix: 1.14 (0.26), residues: 390 sheet: 0.65 (0.32), residues: 253 loop : -0.43 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 56 TYR 0.017 0.002 TYR H 102 PHE 0.013 0.001 PHE H 157 TRP 0.011 0.001 TRP A 477 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 9933) covalent geometry : angle 0.54412 / 0.27 (13521) SS BOND : bond 0.00388 / 0.24 ( 11) SS BOND : angle 1.22445 / 0.73 ( 24) hydrogen bonds : bond 0.04961 / 3.27 ( 391) hydrogen bonds : angle 4.86501 / 3.59 ( 1106) metal coordination : bond 0.00207 / 0.10 ( 2) link_NAG-ASN : bond 0.00137 / 0.05 ( 4) link_NAG-ASN : angle 1.73312 / 0.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 85 time to evaluate : 0.366 Fit side-chains REVERT: A 295 ASP cc_start: 0.7921 (m-30) cc_final: 0.7548 (m-30) REVERT: A 441 LYS cc_start: 0.8002 (ttpp) cc_final: 0.7605 (pttp) REVERT: E 357 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8295 (ttt180) REVERT: E 358 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8217 (mm) REVERT: E 424 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8240 (tttp) outliers start: 35 outliers final: 20 residues processed: 109 average time/residue: 0.5678 time to fit residues: 66.6812 Evaluate side-chains 106 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 357 ARG Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 418 ILE Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain E residue 480 CYS Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain L residue 28 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 120 optimal weight: 6.9990 chunk 116 optimal weight: 30.0000 chunk 78 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 74 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 35 optimal weight: 0.4980 chunk 98 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 ASN A 89 GLN A 508 ASN E 334 ASN H 175 HIS ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.210385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.161735 restraints weight = 9174.852| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.31 r_work: 0.3416 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 9950 Z= 0.190 Angle : 0.596 10.129 13557 Z= 0.299 Chirality : 0.045 0.161 1461 Planarity : 0.004 0.032 1744 Dihedral : 4.664 47.811 1414 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.92 % Allowed : 21.97 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.24), residues: 1218 helix: 0.85 (0.26), residues: 403 sheet: 0.69 (0.32), residues: 255 loop : -0.41 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 56 TYR 0.014 0.002 TYR H 102 PHE 0.014 0.002 PHE H 157 TRP 0.011 0.001 TRP A 477 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 ( 9933) covalent geometry : angle 0.59128 / 0.30 (13521) SS BOND : bond 0.00461 / 0.29 ( 11) SS BOND : angle 1.49094 / 0.88 ( 24) hydrogen bonds : bond 0.05470 / 3.58 ( 391) hydrogen bonds : angle 4.92634 / 3.64 ( 1106) metal coordination : bond 0.00344 / 0.17 ( 2) link_NAG-ASN : bond 0.00150 / 0.07 ( 4) link_NAG-ASN : angle 1.76276 / 1.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 88 time to evaluate : 0.381 Fit side-chains REVERT: A 295 ASP cc_start: 0.7974 (m-30) cc_final: 0.7618 (m-30) REVERT: A 305 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: A 441 LYS cc_start: 0.8057 (ttpp) cc_final: 0.7722 (pttp) REVERT: E 357 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8347 (ttt180) REVERT: E 358 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8262 (mm) REVERT: E 424 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8234 (tttp) REVERT: E 440 LYS cc_start: 0.8410 (mttp) cc_final: 0.7577 (mptt) REVERT: H 13 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.6603 (tptt) outliers start: 41 outliers final: 24 residues processed: 116 average time/residue: 0.5082 time to fit residues: 64.0445 Evaluate side-chains 114 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 355 ARG Chi-restraints excluded: chain E residue 357 ARG Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 418 ILE Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 480 CYS Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 96 optimal weight: 0.0970 chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 114 optimal weight: 0.2980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN H 175 HIS ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.213639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.160987 restraints weight = 9200.805| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 3.23 r_work: 0.3400 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9950 Z= 0.110 Angle : 0.513 9.794 13557 Z= 0.258 Chirality : 0.042 0.155 1461 Planarity : 0.003 0.031 1744 Dihedral : 4.271 46.470 1414 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.87 % Allowed : 23.30 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.24), residues: 1218 helix: 1.34 (0.26), residues: 389 sheet: 0.66 (0.32), residues: 253 loop : -0.43 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 56 TYR 0.020 0.001 TYR H 102 PHE 0.013 0.001 PHE H 157 TRP 0.010 0.001 TRP H 36 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 9933) covalent geometry : angle 0.50966 / 0.26 (13521) SS BOND : bond 0.00270 / 0.15 ( 11) SS BOND : angle 0.99827 / 0.60 ( 24) hydrogen bonds : bond 0.04430 / 2.94 ( 391) hydrogen bonds : angle 4.71653 / 3.48 ( 1106) metal coordination : bond 0.00140 / 0.07 ( 2) link_NAG-ASN : bond 0.00078 / 0.04 ( 4) link_NAG-ASN : angle 1.59887 / 0.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 295 ASP cc_start: 0.7934 (m-30) cc_final: 0.7548 (m-30) REVERT: A 323 MET cc_start: 0.9056 (mmp) cc_final: 0.8696 (mmp) REVERT: A 332 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7837 (ptt) REVERT: E 357 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8303 (ttt180) REVERT: E 418 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.6748 (pp) REVERT: H 13 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6457 (tptt) outliers start: 30 outliers final: 14 residues processed: 111 average time/residue: 0.4910 time to fit residues: 59.6993 Evaluate side-chains 106 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 357 ARG Chi-restraints excluded: chain E residue 418 ILE Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 55 optimal weight: 0.9990 chunk 113 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 63 optimal weight: 0.0980 chunk 18 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 25 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.212756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.159534 restraints weight = 9219.025| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.34 r_work: 0.3398 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9950 Z= 0.130 Angle : 0.535 10.254 13557 Z= 0.267 Chirality : 0.043 0.155 1461 Planarity : 0.003 0.031 1744 Dihedral : 4.268 46.435 1414 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.77 % Allowed : 23.59 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.24), residues: 1218 helix: 1.20 (0.26), residues: 396 sheet: 0.64 (0.32), residues: 253 loop : -0.38 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 56 TYR 0.018 0.001 TYR H 102 PHE 0.013 0.001 PHE H 157 TRP 0.010 0.001 TRP H 36 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 9933) covalent geometry : angle 0.53073 / 0.27 (13521) SS BOND : bond 0.00336 / 0.21 ( 11) SS BOND : angle 1.27386 / 0.73 ( 24) hydrogen bonds : bond 0.04661 / 3.09 ( 391) hydrogen bonds : angle 4.68803 / 3.47 ( 1106) metal coordination : bond 0.00202 / 0.10 ( 2) link_NAG-ASN : bond 0.00088 / 0.04 ( 4) link_NAG-ASN : angle 1.56232 / 0.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 295 ASP cc_start: 0.8020 (m-30) cc_final: 0.7612 (m-30) REVERT: A 305 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7580 (tm-30) REVERT: A 323 MET cc_start: 0.9167 (mmp) cc_final: 0.8811 (mmp) REVERT: A 350 ASP cc_start: 0.8484 (t0) cc_final: 0.8183 (t70) REVERT: E 357 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8495 (ttt180) REVERT: E 358 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8048 (mp) REVERT: E 424 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8218 (tttp) REVERT: E 440 LYS cc_start: 0.8505 (mttp) cc_final: 0.7502 (mptt) REVERT: H 13 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6441 (tptt) outliers start: 29 outliers final: 19 residues processed: 108 average time/residue: 0.4867 time to fit residues: 56.9538 Evaluate side-chains 111 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 357 ARG Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 418 ILE Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 51 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 112 optimal weight: 0.0970 chunk 42 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN H 175 HIS ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.212532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.158269 restraints weight = 9147.623| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 3.49 r_work: 0.3347 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9950 Z= 0.133 Angle : 0.539 10.627 13557 Z= 0.269 Chirality : 0.043 0.158 1461 Planarity : 0.003 0.031 1744 Dihedral : 4.277 46.205 1414 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.96 % Allowed : 23.50 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.24), residues: 1218 helix: 1.19 (0.26), residues: 396 sheet: 0.68 (0.32), residues: 255 loop : -0.37 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.017 0.001 TYR H 102 PHE 0.013 0.001 PHE H 157 TRP 0.010 0.001 TRP H 36 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 9933) covalent geometry : angle 0.53504 / 0.27 (13521) SS BOND : bond 0.00332 / 0.20 ( 11) SS BOND : angle 1.23813 / 0.72 ( 24) hydrogen bonds : bond 0.04694 / 3.11 ( 391) hydrogen bonds : angle 4.67767 / 3.46 ( 1106) metal coordination : bond 0.00208 / 0.10 ( 2) link_NAG-ASN : bond 0.00106 / 0.04 ( 4) link_NAG-ASN : angle 1.53622 / 0.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 85 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 295 ASP cc_start: 0.7936 (m-30) cc_final: 0.7532 (m-30) REVERT: A 305 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7488 (tm-30) REVERT: A 323 MET cc_start: 0.9077 (mmp) cc_final: 0.8697 (mmp) REVERT: A 350 ASP cc_start: 0.8327 (t0) cc_final: 0.8005 (t70) REVERT: E 357 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8361 (ttt180) REVERT: E 358 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8039 (mp) REVERT: E 424 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7736 (tttp) REVERT: E 440 LYS cc_start: 0.8456 (mttp) cc_final: 0.7507 (mptt) REVERT: H 13 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6440 (tptt) REVERT: L 106 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7841 (p) outliers start: 31 outliers final: 20 residues processed: 110 average time/residue: 0.4815 time to fit residues: 57.7479 Evaluate side-chains 110 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 357 ARG Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 418 ILE Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 95 optimal weight: 5.9990 chunk 59 optimal weight: 0.0020 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 103 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.213239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.165347 restraints weight = 9114.362| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.15 r_work: 0.3369 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9950 Z= 0.128 Angle : 0.538 10.884 13557 Z= 0.269 Chirality : 0.043 0.157 1461 Planarity : 0.003 0.031 1744 Dihedral : 4.244 45.862 1414 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.67 % Allowed : 23.97 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.24), residues: 1218 helix: 1.29 (0.26), residues: 395 sheet: 0.71 (0.32), residues: 255 loop : -0.38 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 56 TYR 0.018 0.001 TYR H 102 PHE 0.013 0.001 PHE H 157 TRP 0.010 0.001 TRP H 36 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 9933) covalent geometry : angle 0.53473 / 0.27 (13521) SS BOND : bond 0.00322 / 0.19 ( 11) SS BOND : angle 1.17491 / 0.69 ( 24) hydrogen bonds : bond 0.04593 / 3.04 ( 391) hydrogen bonds : angle 4.65173 / 3.44 ( 1106) metal coordination : bond 0.00197 / 0.10 ( 2) link_NAG-ASN : bond 0.00086 / 0.04 ( 4) link_NAG-ASN : angle 1.51947 / 0.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 295 ASP cc_start: 0.7999 (m-30) cc_final: 0.7606 (m-30) REVERT: A 305 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7522 (tm-30) REVERT: A 323 MET cc_start: 0.9099 (mmp) cc_final: 0.8719 (mmp) REVERT: A 332 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7906 (ptt) REVERT: A 350 ASP cc_start: 0.8341 (t0) cc_final: 0.8002 (t70) REVERT: E 357 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8386 (ttt180) REVERT: E 358 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8067 (mp) REVERT: E 424 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7767 (tttp) REVERT: H 13 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6502 (tptt) REVERT: L 106 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7822 (p) outliers start: 28 outliers final: 19 residues processed: 108 average time/residue: 0.4539 time to fit residues: 53.4394 Evaluate side-chains 113 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 357 ARG Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 418 ILE Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 12 optimal weight: 0.9990 chunk 44 optimal weight: 0.0060 chunk 36 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 117 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 105 optimal weight: 0.4980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.212840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.159349 restraints weight = 9166.963| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 3.08 r_work: 0.3399 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9950 Z= 0.126 Angle : 0.538 11.098 13557 Z= 0.268 Chirality : 0.043 0.158 1461 Planarity : 0.003 0.031 1744 Dihedral : 4.229 45.724 1414 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.48 % Allowed : 23.97 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.24), residues: 1218 helix: 1.29 (0.26), residues: 396 sheet: 0.72 (0.32), residues: 255 loop : -0.36 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 56 TYR 0.018 0.001 TYR H 102 PHE 0.012 0.001 PHE H 157 TRP 0.010 0.001 TRP H 36 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 9933) covalent geometry : angle 0.53504 / 0.27 (13521) SS BOND : bond 0.00317 / 0.19 ( 11) SS BOND : angle 1.15624 / 0.68 ( 24) hydrogen bonds : bond 0.04580 / 3.03 ( 391) hydrogen bonds : angle 4.64632 / 3.44 ( 1106) metal coordination : bond 0.00182 / 0.09 ( 2) link_NAG-ASN : bond 0.00107 / 0.04 ( 4) link_NAG-ASN : angle 1.48986 / 0.85 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.365 Fit side-chains REVERT: A 295 ASP cc_start: 0.8045 (m-30) cc_final: 0.7637 (m-30) REVERT: A 305 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7582 (tm-30) REVERT: A 323 MET cc_start: 0.9169 (mmp) cc_final: 0.8800 (mmp) REVERT: A 332 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7948 (ptt) REVERT: A 350 ASP cc_start: 0.8487 (t0) cc_final: 0.8164 (t70) REVERT: E 357 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8504 (ttt180) REVERT: E 358 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8052 (mp) REVERT: E 424 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7788 (tttp) REVERT: H 13 LYS cc_start: 0.7187 (OUTLIER) cc_final: 0.6472 (tptt) REVERT: L 106 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.7930 (p) outliers start: 26 outliers final: 19 residues processed: 107 average time/residue: 0.4468 time to fit residues: 52.3228 Evaluate side-chains 111 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 357 ARG Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 418 ILE Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 480 CYS Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 15 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 44 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 74 optimal weight: 0.0070 chunk 108 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.212228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.158414 restraints weight = 9197.640| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.45 r_work: 0.3382 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9950 Z= 0.137 Angle : 0.551 11.205 13557 Z= 0.275 Chirality : 0.043 0.161 1461 Planarity : 0.003 0.031 1744 Dihedral : 4.272 45.635 1414 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.67 % Allowed : 23.88 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.24), residues: 1218 helix: 1.27 (0.26), residues: 396 sheet: 0.72 (0.32), residues: 255 loop : -0.38 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 56 TYR 0.017 0.001 TYR H 102 PHE 0.012 0.001 PHE H 157 TRP 0.010 0.001 TRP H 36 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 9933) covalent geometry : angle 0.54777 / 0.27 (13521) SS BOND : bond 0.00341 / 0.20 ( 11) SS BOND : angle 1.21331 / 0.72 ( 24) hydrogen bonds : bond 0.04731 / 3.13 ( 391) hydrogen bonds : angle 4.65526 / 3.45 ( 1106) metal coordination : bond 0.00220 / 0.11 ( 2) link_NAG-ASN : bond 0.00118 / 0.05 ( 4) link_NAG-ASN : angle 1.49020 / 0.85 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3700.33 seconds wall clock time: 63 minutes 54.36 seconds (3834.36 seconds total)