Starting phenix.real_space_refine on Fri Aug 22 23:31:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubt_42102/08_2025/8ubt_42102.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubt_42102/08_2025/8ubt_42102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ubt_42102/08_2025/8ubt_42102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubt_42102/08_2025/8ubt_42102.map" model { file = "/net/cci-nas-00/data/ceres_data/8ubt_42102/08_2025/8ubt_42102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubt_42102/08_2025/8ubt_42102.cif" } resolution = 3.1 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= 0.035 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5494 2.51 5 N 1444 2.21 5 O 1646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8642 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3651 Classifications: {'peptide': 448} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 442} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1163 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 8, 'TRANS': 137} Chain breaks: 2 Chain: "C" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2937 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 6, 'TRANS': 368} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ARG:plan': 14} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 891 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 1.66, per 1000 atoms: 0.19 Number of scatterers: 8642 At special positions: 0 Unit cell: (76.529, 125.567, 150.829, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1646 8.00 N 1444 7.00 C 5494 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 396 " - pdb=" SG CYS C 422 " 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 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 511.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 3 sheets defined 58.2% alpha, 3.2% 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 23 through 26 Processing helix chain 'A' and resid 27 through 32 removed outlier: 3.844A pdb=" N TYR A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 54 removed outlier: 3.646A pdb=" N TYR A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 104 Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.581A pdb=" N THR A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 128 removed outlier: 3.729A pdb=" N GLU A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP A 125 " --> pdb=" O GLN A 121 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TYR A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 133 removed outlier: 3.764A pdb=" N VAL A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 128 through 133' Processing helix chain 'A' and resid 138 through 143 removed outlier: 3.797A pdb=" N HIS A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 179 through 188 Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.824A pdb=" N ILE A 201 " --> pdb=" O ASN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.698A pdb=" N ALA A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP A 239 " --> pdb=" O GLN A 235 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 248 " --> pdb=" O TYR A 244 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 274 removed outlier: 3.637A pdb=" N GLU A 265 " --> pdb=" O MET A 261 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 289 through 292 removed outlier: 3.523A pdb=" N GLU A 292 " --> pdb=" O ARG A 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 289 through 292' Processing helix chain 'A' and resid 303 through 313 Processing helix chain 'A' and resid 316 through 328 removed outlier: 3.709A pdb=" N ARG A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 356 removed outlier: 3.690A pdb=" N ILE A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY A 356 " --> pdb=" O ILE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 removed outlier: 3.541A pdb=" N LEU A 360 " --> pdb=" O GLU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 384 removed outlier: 3.583A pdb=" N VAL A 370 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR A 377 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 400 removed outlier: 3.584A pdb=" N ALA A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 430 Processing helix chain 'A' and resid 440 through 454 removed outlier: 4.448A pdb=" N LEU A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 452 " --> pdb=" O GLN A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 476 removed outlier: 3.693A pdb=" N LYS A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 495 removed outlier: 3.862A pdb=" N GLU A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 24 through 33 Processing helix chain 'B' and resid 51 through 65 Processing helix chain 'B' and resid 86 through 93 Processing helix chain 'B' and resid 96 through 111 Processing helix chain 'B' and resid 112 through 128 Processing helix chain 'B' and resid 131 through 140 Processing helix chain 'B' and resid 146 through 157 Processing helix chain 'C' and resid 320 through 324 Processing helix chain 'C' and resid 325 through 334 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 344 through 348 removed outlier: 3.541A pdb=" N VAL C 348 " --> pdb=" O ALA C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 357 Processing helix chain 'C' and resid 377 through 385 Processing helix chain 'C' and resid 400 through 404 removed outlier: 3.608A pdb=" N GLY C 403 " --> pdb=" O SER C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 426 through 437 removed outlier: 4.129A pdb=" N ILE C 430 " --> pdb=" O SER C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 463 removed outlier: 3.671A pdb=" N LEU C 456 " --> pdb=" O THR C 452 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN C 458 " --> pdb=" O GLU C 454 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS C 463 " --> pdb=" O LEU C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 488 removed outlier: 3.653A pdb=" N GLY C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 512 removed outlier: 3.759A pdb=" N VAL C 508 " --> pdb=" O THR C 504 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA C 510 " --> pdb=" O GLN C 506 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA C 512 " --> pdb=" O VAL C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 555 through 563 removed outlier: 3.716A pdb=" N MET C 559 " --> pdb=" O ASN C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 591 removed outlier: 3.902A pdb=" N VAL C 584 " --> pdb=" O ASN C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 616 removed outlier: 3.672A pdb=" N SER C 616 " --> pdb=" O ILE C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 642 removed outlier: 3.521A pdb=" N ALA C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN C 640 " --> pdb=" O THR C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 668 removed outlier: 3.844A pdb=" N GLN C 663 " --> pdb=" O VAL C 659 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N VAL C 665 " --> pdb=" O VAL C 661 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN C 666 " --> pdb=" O GLU C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 688 removed outlier: 5.446A pdb=" N ARG C 686 " --> pdb=" O THR C 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 30 removed outlier: 3.716A pdb=" N LEU D 24 " --> pdb=" O VAL D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 56 Processing helix chain 'D' and resid 56 through 65 removed outlier: 3.623A pdb=" N ARG D 62 " --> pdb=" O TYR D 58 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 85 Processing helix chain 'D' and resid 88 through 93 Processing helix chain 'D' and resid 103 through 114 Processing sheet with id=AA1, first strand: chain 'B' and resid 13 through 16 removed outlier: 7.020A pdb=" N LYS B 5 " --> pdb=" O VAL B 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 417 through 418 removed outlier: 7.247A pdb=" N TYR C 417 " --> pdb=" O HIS C 444 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR C 496 " --> pdb=" O ILE C 469 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE C 523 " --> pdb=" O ASP C 546 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 597 " --> pdb=" O THR C 621 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 43 through 47 removed outlier: 6.293A pdb=" N THR D 37 " --> pdb=" O ILE D 73 " (cutoff:3.500A) 359 hydrogen bonds defined for protein. 1032 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: 1.38 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2836 1.35 - 1.46: 1846 1.46 - 1.58: 4016 1.58 - 1.70: 0 1.70 - 1.82: 79 Bond restraints: 8777 Sorted by residual: bond pdb=" CD2 TRP C 626 " pdb=" CE2 TRP C 626 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.73e+00 bond pdb=" CD2 TRP C 577 " pdb=" CE2 TRP C 577 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.67e+00 bond pdb=" CD2 TRP C 577 " pdb=" CE3 TRP C 577 " ideal model delta sigma weight residual 1.398 1.427 -0.029 1.60e-02 3.91e+03 3.31e+00 bond pdb=" CD2 TRP C 626 " pdb=" CE3 TRP C 626 " ideal model delta sigma weight residual 1.398 1.427 -0.029 1.60e-02 3.91e+03 3.23e+00 bond pdb=" C ARG A 173 " pdb=" N PRO A 174 " ideal model delta sigma weight residual 1.334 1.366 -0.033 2.34e-02 1.83e+03 1.93e+00 ... (remaining 8772 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 11620 2.31 - 4.63: 169 4.63 - 6.94: 20 6.94 - 9.26: 8 9.26 - 11.57: 2 Bond angle restraints: 11819 Sorted by residual: angle pdb=" C ASP C 449 " pdb=" N LYS C 450 " pdb=" CA LYS C 450 " ideal model delta sigma weight residual 121.54 132.63 -11.09 1.91e+00 2.74e-01 3.37e+01 angle pdb=" N GLU C 662 " pdb=" CA GLU C 662 " pdb=" C GLU C 662 " ideal model delta sigma weight residual 113.18 105.49 7.69 1.33e+00 5.65e-01 3.34e+01 angle pdb=" N GLN A 178 " pdb=" CA GLN A 178 " pdb=" C GLN A 178 " ideal model delta sigma weight residual 114.75 108.40 6.35 1.26e+00 6.30e-01 2.54e+01 angle pdb=" C TRP A 144 " pdb=" N VAL A 145 " pdb=" CA VAL A 145 " ideal model delta sigma weight residual 121.97 130.55 -8.58 1.80e+00 3.09e-01 2.27e+01 angle pdb=" CD2 TRP C 577 " pdb=" CE3 TRP C 577 " pdb=" CZ3 TRP C 577 " ideal model delta sigma weight residual 118.60 123.99 -5.39 1.30e+00 5.92e-01 1.72e+01 ... (remaining 11814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4491 17.94 - 35.89: 643 35.89 - 53.83: 195 53.83 - 71.77: 29 71.77 - 89.71: 20 Dihedral angle restraints: 5378 sinusoidal: 2205 harmonic: 3173 Sorted by residual: dihedral pdb=" CB CYS C 396 " pdb=" SG CYS C 396 " pdb=" SG CYS C 422 " pdb=" CB CYS C 422 " ideal model delta sinusoidal sigma weight residual 93.00 162.05 -69.05 1 1.00e+01 1.00e-02 6.17e+01 dihedral pdb=" CA GLY A 135 " pdb=" C GLY A 135 " pdb=" N ILE A 136 " pdb=" CA ILE A 136 " ideal model delta harmonic sigma weight residual 180.00 152.37 27.63 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA ILE A 296 " pdb=" C ILE A 296 " pdb=" N GLU A 297 " pdb=" CA GLU A 297 " ideal model delta harmonic sigma weight residual 180.00 152.51 27.49 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 5375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 928 0.037 - 0.075: 335 0.075 - 0.112: 80 0.112 - 0.149: 13 0.149 - 0.186: 3 Chirality restraints: 1359 Sorted by residual: chirality pdb=" CG LEU A 279 " pdb=" CB LEU A 279 " pdb=" CD1 LEU A 279 " pdb=" CD2 LEU A 279 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" CB ILE B 85 " pdb=" CA ILE B 85 " pdb=" CG1 ILE B 85 " pdb=" CG2 ILE B 85 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" CA LYS C 363 " pdb=" N LYS C 363 " pdb=" C LYS C 363 " pdb=" CB LYS C 363 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.06e-01 ... (remaining 1356 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 173 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO A 174 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 174 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 174 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 24 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C LEU A 24 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU A 24 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG A 25 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 449 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C ASP C 449 " 0.029 2.00e-02 2.50e+03 pdb=" O ASP C 449 " -0.011 2.00e-02 2.50e+03 pdb=" N LYS C 450 " -0.010 2.00e-02 2.50e+03 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 167 2.67 - 3.23: 8261 3.23 - 3.79: 12638 3.79 - 4.34: 17373 4.34 - 4.90: 28502 Nonbonded interactions: 66941 Sorted by model distance: nonbonded pdb=" OG SER C 337 " pdb=" OD1 ASP C 339 " model vdw 2.114 3.040 nonbonded pdb=" O ILE C 381 " pdb=" OG SER C 385 " model vdw 2.199 3.040 nonbonded pdb=" O PRO A 174 " pdb=" N ASN A 176 " model vdw 2.249 3.120 nonbonded pdb=" O SER A 36 " pdb=" OG SER A 36 " model vdw 2.253 3.040 nonbonded pdb=" O LYS A 229 " pdb=" OG SER A 234 " model vdw 2.253 3.040 ... (remaining 66936 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.080 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 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 : 0.002 0.037 8778 Z= 0.132 Angle : 0.706 11.572 11821 Z= 0.407 Chirality : 0.040 0.186 1359 Planarity : 0.003 0.044 1498 Dihedral : 18.971 89.715 3301 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.65 % Favored : 87.88 % Rotamer: Outliers : 1.94 % Allowed : 28.32 % Favored : 69.73 % 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 aren not related in a simple way. whole: -2.09 (0.26), residues: 1064 helix: -0.58 (0.21), residues: 617 sheet: -1.66 (0.84), residues: 52 loop : -2.57 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 242 TYR 0.011 0.001 TYR A 260 PHE 0.019 0.001 PHE A 251 TRP 0.010 0.001 TRP B 88 HIS 0.007 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 8777) covalent geometry : angle 0.70557 (11819) SS BOND : bond 0.00092 ( 1) SS BOND : angle 0.31163 ( 2) hydrogen bonds : bond 0.18834 ( 359) hydrogen bonds : angle 5.99429 ( 1032) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 269 LEU cc_start: 0.8233 (mt) cc_final: 0.7981 (mp) REVERT: A 293 GLN cc_start: 0.7833 (pp30) cc_final: 0.7561 (pt0) REVERT: B 94 LYS cc_start: 0.7645 (mmtt) cc_final: 0.7091 (mmtt) REVERT: B 144 ASP cc_start: 0.7325 (p0) cc_final: 0.7122 (p0) REVERT: C 497 MET cc_start: 0.6095 (tpt) cc_final: 0.3589 (mmt) outliers start: 19 outliers final: 14 residues processed: 152 average time/residue: 0.1040 time to fit residues: 21.4867 Evaluate side-chains 106 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain C residue 370 ARG Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 416 ARG Chi-restraints excluded: chain C residue 494 ARG Chi-restraints excluded: chain C residue 540 ARG Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 614 ARG Chi-restraints excluded: chain C residue 626 TRP Chi-restraints excluded: chain C residue 652 ARG Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 49 ARG Chi-restraints excluded: chain D residue 62 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.0270 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 447 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.262226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.223401 restraints weight = 9139.836| |-----------------------------------------------------------------------------| r_work (start): 0.4626 rms_B_bonded: 2.04 r_work: 0.4193 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4015 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8778 Z= 0.155 Angle : 0.664 9.483 11821 Z= 0.361 Chirality : 0.042 0.174 1359 Planarity : 0.004 0.051 1498 Dihedral : 7.454 55.736 1184 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.03 % Favored : 87.50 % Rotamer: Outliers : 4.19 % Allowed : 25.15 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 aren not related in a simple way. whole: -1.75 (0.27), residues: 1064 helix: -0.22 (0.22), residues: 606 sheet: -1.86 (0.80), residues: 52 loop : -2.48 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 401 TYR 0.022 0.002 TYR A 260 PHE 0.020 0.001 PHE A 402 TRP 0.013 0.001 TRP C 362 HIS 0.008 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8777) covalent geometry : angle 0.66332 (11819) SS BOND : bond 0.00557 ( 1) SS BOND : angle 1.55188 ( 2) hydrogen bonds : bond 0.04386 ( 359) hydrogen bonds : angle 4.35887 ( 1032) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 95 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8486 (tt0) cc_final: 0.8009 (tp-100) REVERT: A 43 MET cc_start: 0.8186 (mmp) cc_final: 0.7947 (mmt) REVERT: A 172 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.7176 (t80) REVERT: A 241 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6902 (mt-10) REVERT: A 246 ARG cc_start: 0.7953 (tmm-80) cc_final: 0.7547 (ttp-110) REVERT: A 278 TYR cc_start: 0.6172 (OUTLIER) cc_final: 0.4424 (m-80) REVERT: A 293 GLN cc_start: 0.8271 (pp30) cc_final: 0.7896 (pt0) REVERT: A 353 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.6612 (mp0) REVERT: B 94 LYS cc_start: 0.7639 (mmtt) cc_final: 0.7054 (mmtt) REVERT: C 559 MET cc_start: 0.3933 (mmt) cc_final: 0.3118 (mpp) outliers start: 41 outliers final: 23 residues processed: 127 average time/residue: 0.0953 time to fit residues: 16.8863 Evaluate side-chains 104 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 447 ASN Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain D residue 44 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 86 optimal weight: 30.0000 chunk 0 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 284 GLN C 387 ASN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.271825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.4529 r_free = 0.4529 target = 0.221314 restraints weight = 9737.597| |-----------------------------------------------------------------------------| r_work (start): 0.4458 rms_B_bonded: 1.45 r_work: 0.4118 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8778 Z= 0.232 Angle : 0.737 8.885 11821 Z= 0.401 Chirality : 0.046 0.194 1359 Planarity : 0.005 0.050 1498 Dihedral : 6.750 59.466 1142 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.91 % Favored : 85.62 % Rotamer: Outliers : 6.34 % Allowed : 23.31 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 aren not related in a simple way. whole: -2.10 (0.26), residues: 1064 helix: -0.58 (0.21), residues: 617 sheet: -2.02 (0.73), residues: 52 loop : -2.56 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 168 TYR 0.039 0.003 TYR A 208 PHE 0.025 0.002 PHE A 402 TRP 0.014 0.002 TRP C 362 HIS 0.007 0.002 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 8777) covalent geometry : angle 0.73722 (11819) SS BOND : bond 0.00518 ( 1) SS BOND : angle 1.65208 ( 2) hydrogen bonds : bond 0.05218 ( 359) hydrogen bonds : angle 4.44809 ( 1032) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 87 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8265 (tt0) cc_final: 0.7872 (tp-100) REVERT: A 172 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.7122 (t80) REVERT: A 241 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6725 (mt-10) REVERT: A 278 TYR cc_start: 0.6868 (OUTLIER) cc_final: 0.5178 (m-80) REVERT: A 293 GLN cc_start: 0.8288 (pp30) cc_final: 0.7894 (pt0) REVERT: A 353 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.6336 (mp0) REVERT: B 94 LYS cc_start: 0.7744 (mmtt) cc_final: 0.7469 (mmtm) REVERT: C 497 MET cc_start: 0.5971 (tpt) cc_final: 0.4763 (mmm) REVERT: D 98 LEU cc_start: 0.1328 (OUTLIER) cc_final: 0.1111 (mm) REVERT: D 113 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.7045 (mp) outliers start: 62 outliers final: 36 residues processed: 135 average time/residue: 0.0917 time to fit residues: 17.5297 Evaluate side-chains 120 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 78 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 489 CYS Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 626 TRP Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 113 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 81 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 284 GLN B 23 GLN C 387 ASN C 447 ASN ** C 500 ASN ** 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 = 0.4916 r_free = 0.4916 target = 0.275169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.231091 restraints weight = 9935.325| |-----------------------------------------------------------------------------| r_work (start): 0.4593 rms_B_bonded: 1.92 r_work: 0.4254 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4009 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8778 Z= 0.137 Angle : 0.635 8.886 11821 Z= 0.349 Chirality : 0.041 0.214 1359 Planarity : 0.003 0.032 1498 Dihedral : 6.398 57.221 1138 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.12 % Favored : 87.41 % Rotamer: Outliers : 5.01 % Allowed : 24.85 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 aren not related in a simple way. whole: -1.76 (0.26), residues: 1064 helix: -0.22 (0.22), residues: 605 sheet: -1.31 (0.92), residues: 39 loop : -2.57 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 401 TYR 0.015 0.001 TYR A 260 PHE 0.016 0.001 PHE A 402 TRP 0.012 0.001 TRP C 362 HIS 0.007 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8777) covalent geometry : angle 0.63452 (11819) SS BOND : bond 0.00076 ( 1) SS BOND : angle 0.94161 ( 2) hydrogen bonds : bond 0.03843 ( 359) hydrogen bonds : angle 4.13566 ( 1032) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 84 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8530 (tt0) cc_final: 0.8109 (tp-100) REVERT: A 172 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.7236 (t80) REVERT: A 241 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6814 (mt-10) REVERT: A 278 TYR cc_start: 0.6664 (OUTLIER) cc_final: 0.4681 (m-80) REVERT: A 293 GLN cc_start: 0.8436 (pp30) cc_final: 0.8041 (pt0) REVERT: A 353 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: B 94 LYS cc_start: 0.7647 (mmtt) cc_final: 0.7414 (mmtm) REVERT: C 497 MET cc_start: 0.5074 (tpt) cc_final: 0.3797 (mmm) REVERT: D 98 LEU cc_start: 0.1800 (OUTLIER) cc_final: 0.1556 (mm) outliers start: 49 outliers final: 31 residues processed: 123 average time/residue: 0.0882 time to fit residues: 15.4864 Evaluate side-chains 114 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 78 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 447 ASN Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 552 GLU Chi-restraints excluded: chain C residue 595 LYS Chi-restraints excluded: chain C residue 626 TRP Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 90 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 60 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 284 GLN B 90 GLN C 387 ASN C 458 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.272174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.229209 restraints weight = 9853.452| |-----------------------------------------------------------------------------| r_work (start): 0.4500 rms_B_bonded: 1.72 r_work: 0.4087 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8778 Z= 0.173 Angle : 0.660 9.071 11821 Z= 0.361 Chirality : 0.044 0.387 1359 Planarity : 0.004 0.035 1498 Dihedral : 6.362 56.700 1138 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.59 % Favored : 86.94 % Rotamer: Outliers : 5.62 % Allowed : 24.13 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 aren not related in a simple way. whole: -1.77 (0.26), residues: 1064 helix: -0.31 (0.22), residues: 612 sheet: -1.31 (0.90), residues: 39 loop : -2.47 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 401 TYR 0.018 0.002 TYR A 208 PHE 0.019 0.001 PHE A 402 TRP 0.011 0.001 TRP C 362 HIS 0.005 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 8777) covalent geometry : angle 0.65983 (11819) SS BOND : bond 0.00125 ( 1) SS BOND : angle 0.97284 ( 2) hydrogen bonds : bond 0.04200 ( 359) hydrogen bonds : angle 4.15092 ( 1032) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 81 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8266 (tt0) cc_final: 0.7876 (tp-100) REVERT: A 112 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7384 (m-30) REVERT: A 172 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.7102 (t80) REVERT: A 241 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6820 (mt-10) REVERT: A 278 TYR cc_start: 0.6785 (OUTLIER) cc_final: 0.4382 (m-80) REVERT: A 293 GLN cc_start: 0.8271 (pp30) cc_final: 0.7924 (pt0) REVERT: A 353 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6456 (mp0) REVERT: B 94 LYS cc_start: 0.7721 (mmtt) cc_final: 0.7461 (mmtm) REVERT: C 399 MET cc_start: 0.6589 (ptt) cc_final: 0.6227 (ptt) REVERT: C 497 MET cc_start: 0.5982 (tpt) cc_final: 0.5077 (mmm) REVERT: D 113 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6984 (mp) outliers start: 55 outliers final: 36 residues processed: 124 average time/residue: 0.0800 time to fit residues: 14.1608 Evaluate side-chains 118 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 76 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 552 GLU Chi-restraints excluded: chain C residue 555 ASN Chi-restraints excluded: chain C residue 595 LYS Chi-restraints excluded: chain C residue 626 TRP Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 32 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 284 GLN C 387 ASN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.273652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.231183 restraints weight = 9795.900| |-----------------------------------------------------------------------------| r_work (start): 0.4598 rms_B_bonded: 1.77 r_work: 0.4260 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.4032 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8778 Z= 0.135 Angle : 0.616 8.847 11821 Z= 0.338 Chirality : 0.041 0.188 1359 Planarity : 0.003 0.030 1498 Dihedral : 6.224 55.203 1138 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.31 % Favored : 87.41 % Rotamer: Outliers : 5.21 % Allowed : 24.74 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 aren not related in a simple way. whole: -1.56 (0.27), residues: 1064 helix: -0.09 (0.22), residues: 605 sheet: -1.71 (0.77), residues: 52 loop : -2.37 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 401 TYR 0.013 0.001 TYR A 260 PHE 0.016 0.001 PHE A 402 TRP 0.011 0.001 TRP C 362 HIS 0.005 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8777) covalent geometry : angle 0.61629 (11819) SS BOND : bond 0.00029 ( 1) SS BOND : angle 0.77417 ( 2) hydrogen bonds : bond 0.03690 ( 359) hydrogen bonds : angle 4.01585 ( 1032) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 82 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8450 (tt0) cc_final: 0.8038 (tp-100) REVERT: A 172 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.7154 (t80) REVERT: A 241 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6824 (mt-10) REVERT: A 278 TYR cc_start: 0.6689 (OUTLIER) cc_final: 0.4481 (m-80) REVERT: A 293 GLN cc_start: 0.8340 (pp30) cc_final: 0.7974 (pt0) REVERT: A 353 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6367 (mp0) REVERT: B 94 LYS cc_start: 0.7652 (mmtt) cc_final: 0.7400 (mmtm) REVERT: C 387 ASN cc_start: 0.6934 (OUTLIER) cc_final: 0.5866 (t0) REVERT: C 399 MET cc_start: 0.6562 (ptt) cc_final: 0.5973 (ptt) REVERT: D 113 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6894 (mp) outliers start: 51 outliers final: 35 residues processed: 121 average time/residue: 0.0821 time to fit residues: 14.1253 Evaluate side-chains 117 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 76 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 552 GLU Chi-restraints excluded: chain C residue 595 LYS Chi-restraints excluded: chain C residue 626 TRP Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 77 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 284 GLN B 23 GLN C 387 ASN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN C 572 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.272668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.228279 restraints weight = 9811.924| |-----------------------------------------------------------------------------| r_work (start): 0.4485 rms_B_bonded: 1.85 r_work: 0.4078 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8778 Z= 0.162 Angle : 0.644 8.959 11821 Z= 0.352 Chirality : 0.042 0.184 1359 Planarity : 0.003 0.030 1498 Dihedral : 6.240 57.118 1138 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.69 % Favored : 87.03 % Rotamer: Outliers : 5.11 % Allowed : 24.95 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 aren not related in a simple way. whole: -1.60 (0.27), residues: 1064 helix: -0.19 (0.22), residues: 616 sheet: -1.09 (0.94), residues: 39 loop : -2.39 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 401 TYR 0.015 0.002 TYR A 208 PHE 0.019 0.001 PHE A 402 TRP 0.010 0.001 TRP C 362 HIS 0.005 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8777) covalent geometry : angle 0.64359 (11819) SS BOND : bond 0.00004 ( 1) SS BOND : angle 0.82793 ( 2) hydrogen bonds : bond 0.04008 ( 359) hydrogen bonds : angle 4.06197 ( 1032) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 79 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8283 (tt0) cc_final: 0.7909 (tp-100) REVERT: A 112 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7425 (m-30) REVERT: A 172 PHE cc_start: 0.7499 (OUTLIER) cc_final: 0.7104 (t80) REVERT: A 241 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6842 (mt-10) REVERT: A 278 TYR cc_start: 0.6807 (OUTLIER) cc_final: 0.4391 (m-80) REVERT: A 293 GLN cc_start: 0.8366 (pp30) cc_final: 0.8011 (pt0) REVERT: A 353 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6181 (mp0) REVERT: B 94 LYS cc_start: 0.7764 (mmtt) cc_final: 0.7502 (mmtm) REVERT: C 387 ASN cc_start: 0.7177 (OUTLIER) cc_final: 0.6199 (t0) REVERT: C 399 MET cc_start: 0.6941 (ptt) cc_final: 0.6728 (ptt) REVERT: C 497 MET cc_start: 0.6020 (tpt) cc_final: 0.4883 (mmm) REVERT: D 113 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6865 (mp) outliers start: 50 outliers final: 36 residues processed: 117 average time/residue: 0.0937 time to fit residues: 15.6126 Evaluate side-chains 117 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 74 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 595 LYS Chi-restraints excluded: chain C residue 626 TRP Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 103 optimal weight: 20.0000 chunk 30 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 284 GLN C 387 ASN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.274030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.231580 restraints weight = 9783.503| |-----------------------------------------------------------------------------| r_work (start): 0.4594 rms_B_bonded: 1.90 r_work: 0.4249 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4000 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8778 Z= 0.127 Angle : 0.609 8.855 11821 Z= 0.335 Chirality : 0.040 0.184 1359 Planarity : 0.003 0.031 1498 Dihedral : 6.104 58.381 1138 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.65 % Favored : 88.06 % Rotamer: Outliers : 4.19 % Allowed : 25.87 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 aren not related in a simple way. whole: -1.35 (0.27), residues: 1064 helix: 0.09 (0.22), residues: 601 sheet: -1.05 (0.96), residues: 39 loop : -2.34 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 401 TYR 0.012 0.001 TYR A 260 PHE 0.015 0.001 PHE A 402 TRP 0.010 0.001 TRP C 362 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8777) covalent geometry : angle 0.60917 (11819) SS BOND : bond 0.00067 ( 1) SS BOND : angle 0.74843 ( 2) hydrogen bonds : bond 0.03499 ( 359) hydrogen bonds : angle 3.92372 ( 1032) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 81 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8545 (tt0) cc_final: 0.8122 (tp-100) REVERT: A 172 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.7161 (t80) REVERT: A 241 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6871 (mt-10) REVERT: A 278 TYR cc_start: 0.6658 (OUTLIER) cc_final: 0.4561 (m-80) REVERT: A 293 GLN cc_start: 0.8423 (pp30) cc_final: 0.8052 (pt0) REVERT: A 353 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6276 (mp0) REVERT: B 94 LYS cc_start: 0.7649 (mmtt) cc_final: 0.7038 (mmtt) REVERT: C 387 ASN cc_start: 0.6883 (OUTLIER) cc_final: 0.5937 (t0) REVERT: C 497 MET cc_start: 0.5012 (tpt) cc_final: 0.3790 (mmm) REVERT: D 113 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6920 (mp) outliers start: 41 outliers final: 31 residues processed: 111 average time/residue: 0.0936 time to fit residues: 14.6996 Evaluate side-chains 114 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 77 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 595 LYS Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 80 optimal weight: 20.0000 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 37 optimal weight: 0.0270 chunk 69 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 87 optimal weight: 30.0000 chunk 28 optimal weight: 0.0970 chunk 76 optimal weight: 7.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 284 GLN C 387 ASN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.273685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.232089 restraints weight = 9792.321| |-----------------------------------------------------------------------------| r_work (start): 0.4606 rms_B_bonded: 1.67 r_work: 0.4290 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.4079 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8778 Z= 0.123 Angle : 0.600 8.876 11821 Z= 0.329 Chirality : 0.040 0.181 1359 Planarity : 0.003 0.030 1498 Dihedral : 6.023 59.800 1138 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.75 % Favored : 87.97 % Rotamer: Outliers : 4.50 % Allowed : 25.97 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 aren not related in a simple way. whole: -1.22 (0.27), residues: 1064 helix: 0.21 (0.22), residues: 601 sheet: -1.00 (0.97), residues: 39 loop : -2.30 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 401 TYR 0.011 0.001 TYR A 260 PHE 0.014 0.001 PHE A 402 TRP 0.010 0.001 TRP C 362 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8777) covalent geometry : angle 0.60009 (11819) SS BOND : bond 0.00066 ( 1) SS BOND : angle 0.79379 ( 2) hydrogen bonds : bond 0.03364 ( 359) hydrogen bonds : angle 3.86168 ( 1032) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 81 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8371 (tt0) cc_final: 0.7975 (tp-100) REVERT: A 112 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7289 (m-30) REVERT: A 172 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.7182 (t80) REVERT: A 241 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6820 (mt-10) REVERT: A 278 TYR cc_start: 0.6560 (OUTLIER) cc_final: 0.4453 (m-80) REVERT: A 293 GLN cc_start: 0.8288 (pp30) cc_final: 0.7943 (pt0) REVERT: B 94 LYS cc_start: 0.7724 (mmtt) cc_final: 0.7120 (mmtt) REVERT: C 387 ASN cc_start: 0.6895 (OUTLIER) cc_final: 0.6070 (t0) REVERT: C 497 MET cc_start: 0.5168 (tpt) cc_final: 0.4910 (mmm) REVERT: D 113 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6909 (mp) outliers start: 44 outliers final: 31 residues processed: 116 average time/residue: 0.1004 time to fit residues: 16.3286 Evaluate side-chains 115 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 78 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 595 LYS Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 17 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 24 optimal weight: 0.2980 chunk 83 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 284 GLN C 387 ASN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.272418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.230987 restraints weight = 9710.656| |-----------------------------------------------------------------------------| r_work (start): 0.4603 rms_B_bonded: 1.67 r_work: 0.4285 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.4039 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8778 Z= 0.140 Angle : 0.618 8.984 11821 Z= 0.337 Chirality : 0.041 0.181 1359 Planarity : 0.003 0.030 1498 Dihedral : 6.023 58.458 1138 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.31 % Favored : 87.41 % Rotamer: Outliers : 4.50 % Allowed : 25.97 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 aren not related in a simple way. whole: -1.24 (0.27), residues: 1064 helix: 0.19 (0.22), residues: 603 sheet: -1.01 (0.97), residues: 39 loop : -2.32 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 191 TYR 0.013 0.001 TYR A 260 PHE 0.017 0.001 PHE A 402 TRP 0.009 0.001 TRP C 362 HIS 0.005 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8777) covalent geometry : angle 0.61810 (11819) SS BOND : bond 0.00137 ( 1) SS BOND : angle 0.90332 ( 2) hydrogen bonds : bond 0.03610 ( 359) hydrogen bonds : angle 3.89300 ( 1032) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 75 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8461 (tt0) cc_final: 0.8063 (tp-100) REVERT: A 112 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7308 (m-30) REVERT: A 172 PHE cc_start: 0.7621 (OUTLIER) cc_final: 0.7258 (t80) REVERT: A 241 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6853 (mt-10) REVERT: A 278 TYR cc_start: 0.6658 (OUTLIER) cc_final: 0.4367 (m-80) REVERT: A 293 GLN cc_start: 0.8386 (pp30) cc_final: 0.8019 (pt0) REVERT: A 353 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6249 (mp0) REVERT: B 94 LYS cc_start: 0.7707 (mmtt) cc_final: 0.7438 (mmtm) REVERT: C 387 ASN cc_start: 0.6989 (OUTLIER) cc_final: 0.6284 (t0) REVERT: C 497 MET cc_start: 0.5351 (tpt) cc_final: 0.5098 (mmm) outliers start: 44 outliers final: 33 residues processed: 110 average time/residue: 0.0963 time to fit residues: 15.0343 Evaluate side-chains 114 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 75 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 595 LYS Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 125 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 50 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 6 optimal weight: 0.0010 chunk 88 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 0.0670 chunk 87 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 24 optimal weight: 0.0570 chunk 44 optimal weight: 5.9990 overall best weight: 0.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 284 GLN C 387 ASN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4932 r_free = 0.4932 target = 0.276230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.233959 restraints weight = 9793.907| |-----------------------------------------------------------------------------| r_work (start): 0.4618 rms_B_bonded: 1.72 r_work: 0.4299 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4066 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 8778 Z= 0.115 Angle : 0.589 8.883 11821 Z= 0.322 Chirality : 0.040 0.180 1359 Planarity : 0.003 0.031 1498 Dihedral : 5.882 58.299 1138 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.47 % Favored : 88.25 % Rotamer: Outliers : 3.27 % Allowed : 27.10 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -0.99 (0.27), residues: 1064 helix: 0.42 (0.22), residues: 597 sheet: -0.92 (0.99), residues: 39 loop : -2.22 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 401 TYR 0.010 0.001 TYR A 52 PHE 0.012 0.001 PHE A 402 TRP 0.012 0.001 TRP A 167 HIS 0.005 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8777) covalent geometry : angle 0.58927 (11819) SS BOND : bond 0.00135 ( 1) SS BOND : angle 0.93485 ( 2) hydrogen bonds : bond 0.03083 ( 359) hydrogen bonds : angle 3.75934 ( 1032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2549.22 seconds wall clock time: 44 minutes 24.52 seconds (2664.52 seconds total)