Starting phenix.real_space_refine on Sat Jun 7 07:31:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubt_42102/06_2025/8ubt_42102.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubt_42102/06_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_42102/06_2025/8ubt_42102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubt_42102/06_2025/8ubt_42102.map" model { file = "/net/cci-nas-00/data/ceres_data/8ubt_42102/06_2025/8ubt_42102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubt_42102/06_2025/8ubt_42102.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.74, per 1000 atoms: 0.66 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: 2.30 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.85 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: 2.15 Time building geometry restraints manager: 2.75 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: 1.550 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: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.570 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.750 ------------------------------------------------------------------------------- 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 : 9.21 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP B 88 HIS 0.007 0.001 HIS A 345 PHE 0.019 0.001 PHE A 251 TYR 0.011 0.001 TYR A 260 ARG 0.004 0.000 ARG A 242 Details of bonding type rmsd hydrogen bonds : bond 0.18834 ( 359) hydrogen bonds : angle 5.99429 ( 1032) SS BOND : bond 0.00092 ( 1) SS BOND : angle 0.31163 ( 2) covalent geometry : bond 0.00244 ( 8777) covalent geometry : angle 0.70557 (11819) *********************** 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 : 1.091 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: 0.2331 time to fit residues: 47.6548 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 : 0.983 ------------------------------------------------------------------------------- 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 89 optimal weight: 20.0000 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 0.4980 chunk 96 optimal weight: 9.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 447 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.273576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.226490 restraints weight = 9678.993| |-----------------------------------------------------------------------------| r_work (start): 0.4480 rms_B_bonded: 1.86 r_work: 0.4038 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8778 Z= 0.173 Angle : 0.692 9.184 11821 Z= 0.375 Chirality : 0.043 0.189 1359 Planarity : 0.004 0.053 1498 Dihedral : 7.502 56.944 1184 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.31 % Favored : 87.22 % Rotamer: Outliers : 4.60 % Allowed : 25.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.26), residues: 1064 helix: -0.37 (0.22), residues: 611 sheet: -1.91 (0.79), residues: 52 loop : -2.47 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 362 HIS 0.007 0.001 HIS A 345 PHE 0.022 0.002 PHE A 402 TYR 0.027 0.002 TYR A 260 ARG 0.005 0.001 ARG A 401 Details of bonding type rmsd hydrogen bonds : bond 0.04580 ( 359) hydrogen bonds : angle 4.36784 ( 1032) SS BOND : bond 0.00290 ( 1) SS BOND : angle 1.17466 ( 2) covalent geometry : bond 0.00392 ( 8777) covalent geometry : angle 0.69143 (11819) *********************** 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 140 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 95 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8328 (tt0) cc_final: 0.7885 (tp-100) REVERT: A 43 MET cc_start: 0.8212 (mmp) cc_final: 0.7985 (mmt) REVERT: A 172 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.7209 (t80) REVERT: A 190 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.5929 (mt-10) REVERT: A 241 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6941 (mt-10) REVERT: A 246 ARG cc_start: 0.7876 (tmm-80) cc_final: 0.7561 (ttp-110) REVERT: A 278 TYR cc_start: 0.6323 (OUTLIER) cc_final: 0.5180 (m-80) REVERT: A 289 ARG cc_start: 0.8157 (mmp80) cc_final: 0.7812 (ttp80) REVERT: A 293 GLN cc_start: 0.8194 (pp30) cc_final: 0.7833 (pt0) REVERT: A 353 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.6671 (mp0) REVERT: B 94 LYS cc_start: 0.7674 (mmtt) cc_final: 0.7435 (mmtm) REVERT: C 559 MET cc_start: 0.3688 (mmt) cc_final: 0.2826 (mpp) REVERT: C 595 LYS cc_start: 0.6681 (mtpt) cc_final: 0.6437 (ttpt) outliers start: 45 outliers final: 25 residues processed: 130 average time/residue: 0.2164 time to fit residues: 39.4904 Evaluate side-chains 111 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 190 GLU 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 282 SER 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 431 LYS 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 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 46 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 80 optimal weight: 8.9990 chunk 103 optimal weight: 50.0000 chunk 67 optimal weight: 0.5980 chunk 73 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.275033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.227837 restraints weight = 9862.748| |-----------------------------------------------------------------------------| r_work (start): 0.4573 rms_B_bonded: 1.75 r_work: 0.4266 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4052 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8778 Z= 0.123 Angle : 0.605 9.152 11821 Z= 0.333 Chirality : 0.041 0.187 1359 Planarity : 0.003 0.034 1498 Dihedral : 6.345 55.437 1142 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.03 % Favored : 87.50 % Rotamer: Outliers : 4.60 % Allowed : 24.34 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.27), residues: 1064 helix: -0.08 (0.22), residues: 607 sheet: -1.86 (0.78), residues: 52 loop : -2.47 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 362 HIS 0.006 0.001 HIS B 64 PHE 0.016 0.001 PHE A 402 TYR 0.015 0.001 TYR A 260 ARG 0.003 0.000 ARG A 401 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 359) hydrogen bonds : angle 4.13697 ( 1032) SS BOND : bond 0.00123 ( 1) SS BOND : angle 1.22123 ( 2) covalent geometry : bond 0.00254 ( 8777) covalent geometry : angle 0.60497 (11819) *********************** 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 133 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 88 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8402 (tt0) cc_final: 0.7947 (tp-100) REVERT: A 172 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.7247 (t80) REVERT: A 241 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6788 (mt-10) REVERT: A 246 ARG cc_start: 0.7994 (tmm-80) cc_final: 0.7615 (ttp-110) REVERT: A 278 TYR cc_start: 0.6269 (OUTLIER) cc_final: 0.4622 (m-80) REVERT: A 293 GLN cc_start: 0.8217 (pp30) cc_final: 0.7877 (pt0) REVERT: A 353 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.6514 (mp0) REVERT: B 94 LYS cc_start: 0.7652 (mmtt) cc_final: 0.7418 (mmtm) REVERT: C 497 MET cc_start: 0.4968 (tpt) cc_final: 0.2715 (mmt) REVERT: D 98 LEU cc_start: 0.1613 (OUTLIER) cc_final: 0.1373 (mm) REVERT: D 113 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6921 (mp) outliers start: 45 outliers final: 22 residues processed: 123 average time/residue: 0.1913 time to fit residues: 33.8420 Evaluate side-chains 110 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 84 VAL 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 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 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 397 ARG Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 636 THR 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 86 optimal weight: 50.0000 chunk 30 optimal weight: 0.9990 chunk 87 optimal weight: 30.0000 chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 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 = 0.4884 r_free = 0.4884 target = 0.270412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.228261 restraints weight = 9724.171| |-----------------------------------------------------------------------------| r_work (start): 0.4501 rms_B_bonded: 1.67 r_work: 0.4075 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 8778 Z= 0.249 Angle : 0.732 8.878 11821 Z= 0.398 Chirality : 0.046 0.191 1359 Planarity : 0.004 0.051 1498 Dihedral : 6.627 58.650 1138 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.72 % Favored : 85.81 % Rotamer: Outliers : 5.62 % Allowed : 23.82 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.26), residues: 1064 helix: -0.55 (0.21), residues: 619 sheet: -1.11 (0.94), residues: 39 loop : -2.56 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 362 HIS 0.006 0.001 HIS D 60 PHE 0.026 0.002 PHE A 402 TYR 0.030 0.002 TYR A 208 ARG 0.004 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.05262 ( 359) hydrogen bonds : angle 4.42615 ( 1032) SS BOND : bond 0.00068 ( 1) SS BOND : angle 1.16958 ( 2) covalent geometry : bond 0.00598 ( 8777) covalent geometry : angle 0.73168 (11819) *********************** 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 143 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 88 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8320 (tt0) cc_final: 0.7918 (tp-100) REVERT: A 172 PHE cc_start: 0.7530 (OUTLIER) cc_final: 0.7085 (t80) REVERT: A 241 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6801 (mt-10) REVERT: A 246 ARG cc_start: 0.7977 (tmm-80) cc_final: 0.7713 (ttp-110) REVERT: A 278 TYR cc_start: 0.6947 (OUTLIER) cc_final: 0.5102 (m-80) REVERT: A 293 GLN cc_start: 0.8352 (pp30) cc_final: 0.7959 (pt0) REVERT: A 353 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6328 (mp0) REVERT: B 94 LYS cc_start: 0.7754 (mmtt) cc_final: 0.7511 (mmtm) REVERT: C 399 MET cc_start: 0.6600 (ptt) cc_final: 0.6208 (ptt) REVERT: C 492 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7957 (tt) REVERT: C 497 MET cc_start: 0.6058 (tpt) cc_final: 0.4902 (mmm) REVERT: D 113 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.7053 (mp) outliers start: 55 outliers final: 35 residues processed: 131 average time/residue: 0.2113 time to fit residues: 40.2126 Evaluate side-chains 121 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 80 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 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 59 ILE Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 116 LEU 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 427 ASP Chi-restraints excluded: chain C residue 489 CYS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 552 GLU 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 113 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 22 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 105 optimal weight: 0.0040 chunk 44 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- 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 458 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN D 72 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.274433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.225250 restraints weight = 9793.506| |-----------------------------------------------------------------------------| r_work (start): 0.4545 rms_B_bonded: 2.06 r_work: 0.4206 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8778 Z= 0.140 Angle : 0.633 8.967 11821 Z= 0.348 Chirality : 0.041 0.214 1359 Planarity : 0.003 0.032 1498 Dihedral : 6.344 55.758 1138 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.65 % Favored : 87.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.27), residues: 1064 helix: -0.19 (0.22), residues: 606 sheet: -1.65 (0.80), residues: 52 loop : -2.43 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 362 HIS 0.006 0.001 HIS B 64 PHE 0.017 0.001 PHE A 402 TYR 0.014 0.001 TYR A 260 ARG 0.002 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 359) hydrogen bonds : angle 4.07884 ( 1032) SS BOND : bond 0.00045 ( 1) SS BOND : angle 0.88356 ( 2) covalent geometry : bond 0.00305 ( 8777) covalent geometry : angle 0.63310 (11819) *********************** 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 137 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 87 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8157 (tt0) cc_final: 0.7774 (tp-100) REVERT: A 172 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.7006 (t80) REVERT: A 241 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6706 (mt-10) REVERT: A 246 ARG cc_start: 0.7840 (tmm-80) cc_final: 0.7605 (ttp-170) REVERT: A 278 TYR cc_start: 0.6629 (OUTLIER) cc_final: 0.4594 (m-80) REVERT: A 293 GLN cc_start: 0.8121 (pp30) cc_final: 0.7805 (pt0) REVERT: A 353 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6267 (mp0) REVERT: B 94 LYS cc_start: 0.7705 (mmtt) cc_final: 0.7456 (mmtm) REVERT: C 399 MET cc_start: 0.6390 (ptt) cc_final: 0.6089 (ptt) REVERT: C 492 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7525 (tt) REVERT: C 497 MET cc_start: 0.5394 (tpt) cc_final: 0.4364 (mmm) REVERT: D 113 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6918 (mp) outliers start: 50 outliers final: 32 residues processed: 124 average time/residue: 0.1972 time to fit residues: 35.0895 Evaluate side-chains 117 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 79 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 282 SER 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 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 397 ARG Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 552 GLU 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 C residue 690 MET Chi-restraints excluded: chain D residue 72 ASN 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 90 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 458 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN D 72 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.272510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.229136 restraints weight = 9734.944| |-----------------------------------------------------------------------------| r_work (start): 0.4573 rms_B_bonded: 1.79 r_work: 0.4237 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4010 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8778 Z= 0.161 Angle : 0.643 8.869 11821 Z= 0.352 Chirality : 0.042 0.186 1359 Planarity : 0.003 0.033 1498 Dihedral : 6.296 57.032 1138 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.31 % Favored : 87.31 % Rotamer: Outliers : 5.52 % Allowed : 24.64 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.26), residues: 1064 helix: -0.25 (0.21), residues: 620 sheet: -1.29 (0.93), residues: 39 loop : -2.50 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 362 HIS 0.005 0.001 HIS B 64 PHE 0.018 0.001 PHE A 402 TYR 0.016 0.002 TYR A 208 ARG 0.002 0.000 ARG A 401 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 359) hydrogen bonds : angle 4.06588 ( 1032) SS BOND : bond 0.00008 ( 1) SS BOND : angle 0.85652 ( 2) covalent geometry : bond 0.00369 ( 8777) covalent geometry : angle 0.64288 (11819) *********************** 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 135 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 81 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8450 (tt0) cc_final: 0.8033 (tp-100) REVERT: A 112 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7390 (m-30) REVERT: A 172 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.7198 (t80) REVERT: A 241 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6839 (mt-10) REVERT: A 246 ARG cc_start: 0.8103 (tmm-80) cc_final: 0.7732 (ttp-110) REVERT: A 278 TYR cc_start: 0.6772 (OUTLIER) cc_final: 0.4527 (m-80) REVERT: A 293 GLN cc_start: 0.8346 (pp30) cc_final: 0.7989 (pt0) REVERT: A 353 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6170 (mp0) REVERT: B 94 LYS cc_start: 0.7688 (mmtt) cc_final: 0.7427 (mmtm) REVERT: C 447 ASN cc_start: 0.7604 (m-40) cc_final: 0.7335 (m-40) REVERT: C 492 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7119 (tt) REVERT: C 497 MET cc_start: 0.5099 (tpt) cc_final: 0.4160 (mmm) REVERT: D 113 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6918 (mp) outliers start: 54 outliers final: 36 residues processed: 122 average time/residue: 0.2125 time to fit residues: 36.4839 Evaluate side-chains 120 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 77 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 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 59 ILE 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 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 492 LEU Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 552 GLU 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 C residue 690 MET Chi-restraints excluded: chain D residue 72 ASN 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 8 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 84 optimal weight: 9.9990 chunk 83 optimal weight: 40.0000 chunk 74 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.274038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.225272 restraints weight = 9823.432| |-----------------------------------------------------------------------------| r_work (start): 0.4547 rms_B_bonded: 1.93 r_work: 0.4222 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4009 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8778 Z= 0.139 Angle : 0.613 8.882 11821 Z= 0.337 Chirality : 0.041 0.186 1359 Planarity : 0.003 0.032 1498 Dihedral : 6.213 59.026 1138 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.84 % Favored : 87.88 % Rotamer: Outliers : 4.81 % Allowed : 25.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.27), residues: 1064 helix: 0.01 (0.22), residues: 601 sheet: -1.44 (0.93), residues: 39 loop : -2.45 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 362 HIS 0.005 0.001 HIS D 60 PHE 0.017 0.001 PHE A 402 TYR 0.013 0.001 TYR A 260 ARG 0.002 0.000 ARG A 401 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 359) hydrogen bonds : angle 3.96499 ( 1032) SS BOND : bond 0.00046 ( 1) SS BOND : angle 0.80115 ( 2) covalent geometry : bond 0.00308 ( 8777) covalent geometry : angle 0.61285 (11819) *********************** 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 130 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 83 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8484 (tt0) cc_final: 0.8071 (tp-100) REVERT: A 112 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7368 (m-30) REVERT: A 172 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.7135 (t80) REVERT: A 241 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6897 (mt-10) REVERT: A 246 ARG cc_start: 0.8144 (tmm-80) cc_final: 0.7766 (ttp-110) REVERT: A 278 TYR cc_start: 0.6714 (OUTLIER) cc_final: 0.4633 (m-80) REVERT: A 293 GLN cc_start: 0.8345 (pp30) cc_final: 0.7993 (pt0) REVERT: A 353 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6265 (mp0) REVERT: B 19 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7472 (mm-30) REVERT: B 94 LYS cc_start: 0.7665 (mmtt) cc_final: 0.7074 (mmtt) REVERT: C 447 ASN cc_start: 0.7530 (m-40) cc_final: 0.7214 (m110) REVERT: C 492 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7053 (tt) REVERT: C 497 MET cc_start: 0.4925 (tpt) cc_final: 0.4152 (mmm) outliers start: 47 outliers final: 34 residues processed: 118 average time/residue: 0.2069 time to fit residues: 34.4645 Evaluate side-chains 116 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 76 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 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 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 340 GLU Chi-restraints excluded: chain C residue 377 LEU 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 492 LEU Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 552 GLU 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 C residue 690 MET Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 81 VAL 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 68 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 82 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 92 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.274028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.231110 restraints weight = 9946.410| |-----------------------------------------------------------------------------| r_work (start): 0.4519 rms_B_bonded: 1.77 r_work: 0.4088 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3006 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= 0.130 Angle : 0.612 8.881 11821 Z= 0.335 Chirality : 0.041 0.186 1359 Planarity : 0.003 0.030 1498 Dihedral : 6.117 58.618 1138 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.84 % Favored : 87.88 % Rotamer: Outliers : 4.70 % Allowed : 25.46 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.27), residues: 1064 helix: 0.13 (0.22), residues: 601 sheet: -1.45 (0.93), residues: 39 loop : -2.42 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 362 HIS 0.005 0.001 HIS B 64 PHE 0.015 0.001 PHE A 402 TYR 0.012 0.001 TYR A 260 ARG 0.002 0.000 ARG A 401 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 359) hydrogen bonds : angle 3.89260 ( 1032) SS BOND : bond 0.00020 ( 1) SS BOND : angle 0.83367 ( 2) covalent geometry : bond 0.00280 ( 8777) covalent geometry : angle 0.61204 (11819) *********************** 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: 46 poor density : 76 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8289 (tt0) cc_final: 0.7899 (tp-100) REVERT: A 172 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.7078 (t80) REVERT: A 246 ARG cc_start: 0.8024 (tmm-80) cc_final: 0.7704 (ttp-110) REVERT: A 278 TYR cc_start: 0.6699 (OUTLIER) cc_final: 0.4616 (m-80) REVERT: A 293 GLN cc_start: 0.8221 (pp30) cc_final: 0.7913 (pt0) REVERT: B 19 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7325 (mm-30) REVERT: B 94 LYS cc_start: 0.7753 (mmtt) cc_final: 0.7237 (mmtt) REVERT: C 399 MET cc_start: 0.6770 (ptt) cc_final: 0.6445 (ptt) REVERT: C 492 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7866 (tt) REVERT: C 497 MET cc_start: 0.5889 (tpt) cc_final: 0.5296 (mmm) outliers start: 46 outliers final: 33 residues processed: 111 average time/residue: 0.2362 time to fit residues: 37.2581 Evaluate side-chains 110 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 74 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL 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 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 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 397 ARG Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 492 LEU 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 636 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 690 MET Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 81 VAL 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 56 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 52 optimal weight: 0.0870 chunk 68 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 0.0270 chunk 4 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 overall best weight: 0.4816 ------------------------------------------------------------------------------- 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 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.276698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.228528 restraints weight = 9913.058| |-----------------------------------------------------------------------------| r_work (start): 0.4559 rms_B_bonded: 1.84 r_work: 0.4247 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.4059 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8778 Z= 0.118 Angle : 0.599 8.859 11821 Z= 0.327 Chirality : 0.040 0.182 1359 Planarity : 0.003 0.030 1498 Dihedral : 5.975 57.893 1138 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.09 % Favored : 88.63 % Rotamer: Outliers : 3.58 % Allowed : 26.18 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.27), residues: 1064 helix: 0.28 (0.22), residues: 607 sheet: -1.53 (0.94), residues: 39 loop : -2.39 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 362 HIS 0.005 0.001 HIS B 64 PHE 0.013 0.001 PHE A 402 TYR 0.010 0.001 TYR A 52 ARG 0.001 0.000 ARG A 401 Details of bonding type rmsd hydrogen bonds : bond 0.03239 ( 359) hydrogen bonds : angle 3.81044 ( 1032) SS BOND : bond 0.00055 ( 1) SS BOND : angle 0.73871 ( 2) covalent geometry : bond 0.00242 ( 8777) covalent geometry : angle 0.59865 (11819) *********************** 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 115 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 80 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8373 (tt0) cc_final: 0.7965 (tp-100) REVERT: A 112 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7292 (m-30) REVERT: A 172 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.7110 (t80) REVERT: A 246 ARG cc_start: 0.8081 (tmm-80) cc_final: 0.7705 (ttp-110) REVERT: A 278 TYR cc_start: 0.6601 (OUTLIER) cc_final: 0.4641 (m-80) REVERT: A 293 GLN cc_start: 0.8290 (pp30) cc_final: 0.7934 (pt0) REVERT: A 353 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6252 (mp0) REVERT: B 19 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7334 (mm-30) REVERT: B 94 LYS cc_start: 0.7692 (mmtt) cc_final: 0.7173 (mmtp) REVERT: C 399 MET cc_start: 0.6587 (ptt) cc_final: 0.6324 (ptt) REVERT: C 492 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7127 (tt) REVERT: C 497 MET cc_start: 0.4982 (tpt) cc_final: 0.4380 (mmm) outliers start: 35 outliers final: 25 residues processed: 108 average time/residue: 0.2033 time to fit residues: 30.9863 Evaluate side-chains 105 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 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 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 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 463 GLN Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 377 LEU 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 492 LEU 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 636 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain D residue 72 ASN 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 41 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 64 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 51 optimal weight: 0.0570 chunk 102 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 86 optimal weight: 0.0050 overall best weight: 0.3512 ------------------------------------------------------------------------------- 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 444 HIS ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.276840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.234455 restraints weight = 9844.887| |-----------------------------------------------------------------------------| r_work (start): 0.4555 rms_B_bonded: 1.63 r_work: 0.4149 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8778 Z= 0.113 Angle : 0.587 8.876 11821 Z= 0.321 Chirality : 0.040 0.179 1359 Planarity : 0.003 0.030 1498 Dihedral : 5.847 57.315 1138 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.81 % Favored : 88.91 % Rotamer: Outliers : 3.37 % Allowed : 26.28 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.27), residues: 1064 helix: 0.40 (0.22), residues: 608 sheet: -1.50 (0.96), residues: 39 loop : -2.34 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 362 HIS 0.004 0.001 HIS B 64 PHE 0.012 0.001 PHE A 402 TYR 0.010 0.001 TYR A 52 ARG 0.001 0.000 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.03065 ( 359) hydrogen bonds : angle 3.71163 ( 1032) SS BOND : bond 0.00067 ( 1) SS BOND : angle 0.73274 ( 2) covalent geometry : bond 0.00229 ( 8777) covalent geometry : angle 0.58709 (11819) ********************** 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 110 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8198 (tt0) cc_final: 0.7820 (tp-100) REVERT: A 112 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7270 (m-30) REVERT: A 172 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.7082 (t80) REVERT: A 246 ARG cc_start: 0.7959 (tmm-80) cc_final: 0.7657 (ttp-110) REVERT: A 278 TYR cc_start: 0.6448 (OUTLIER) cc_final: 0.4427 (m-80) REVERT: A 293 GLN cc_start: 0.8153 (pp30) cc_final: 0.7817 (pt0) REVERT: A 353 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6277 (mp0) REVERT: B 19 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7273 (mm-30) REVERT: B 94 LYS cc_start: 0.7739 (mmtt) cc_final: 0.7261 (mmtp) REVERT: C 399 MET cc_start: 0.6571 (ptt) cc_final: 0.6311 (ptt) REVERT: C 482 MET cc_start: 0.5456 (mmt) cc_final: 0.5256 (mmt) REVERT: C 492 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7843 (tt) REVERT: C 497 MET cc_start: 0.5750 (tpt) cc_final: 0.5289 (mmm) outliers start: 33 outliers final: 25 residues processed: 104 average time/residue: 0.2126 time to fit residues: 31.1659 Evaluate side-chains 105 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 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 268 LEU Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 279 LEU 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 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 404 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 492 LEU 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 636 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 81 VAL 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 56 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 17 optimal weight: 0.0980 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 0.0030 chunk 80 optimal weight: 10.0000 overall best weight: 0.3390 ------------------------------------------------------------------------------- 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 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4943 r_free = 0.4943 target = 0.277597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.236393 restraints weight = 9857.390| |-----------------------------------------------------------------------------| r_work (start): 0.4570 rms_B_bonded: 1.64 r_work: 0.4161 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8778 Z= 0.111 Angle : 0.580 8.887 11821 Z= 0.317 Chirality : 0.040 0.179 1359 Planarity : 0.003 0.029 1498 Dihedral : 5.494 56.778 1134 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.09 % Favored : 88.63 % Rotamer: Outliers : 3.58 % Allowed : 26.07 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.27), residues: 1064 helix: 0.52 (0.22), residues: 609 sheet: -1.57 (0.97), residues: 39 loop : -2.29 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 362 HIS 0.004 0.001 HIS B 64 PHE 0.012 0.001 PHE A 402 TYR 0.010 0.001 TYR A 52 ARG 0.001 0.000 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.02989 ( 359) hydrogen bonds : angle 3.65802 ( 1032) SS BOND : bond 0.00061 ( 1) SS BOND : angle 0.72482 ( 2) covalent geometry : bond 0.00223 ( 8777) covalent geometry : angle 0.58043 (11819) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4854.90 seconds wall clock time: 84 minutes 25.02 seconds (5065.02 seconds total)