Starting phenix.real_space_refine on Sat Dec 28 13:25:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubt_42102/12_2024/8ubt_42102.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubt_42102/12_2024/8ubt_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_42102/12_2024/8ubt_42102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubt_42102/12_2024/8ubt_42102.map" model { file = "/net/cci-nas-00/data/ceres_data/8ubt_42102/12_2024/8ubt_42102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubt_42102/12_2024/8ubt_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-5532/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: 5.70, 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: 2.38 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: 0.87 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: 2.19 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2836 1.35 - 1.46: 1846 1.46 - 1.58: 4016 1.58 - 1.70: 0 1.70 - 1.82: 79 Bond restraints: 8777 Sorted by residual: bond pdb=" CD2 TRP C 626 " pdb=" CE2 TRP C 626 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.73e+00 bond pdb=" CD2 TRP C 577 " pdb=" CE2 TRP C 577 " ideal model delta sigma weight residual 1.409 1.446 -0.037 1.70e-02 3.46e+03 4.67e+00 bond pdb=" CD2 TRP C 577 " pdb=" CE3 TRP C 577 " ideal model delta sigma weight residual 1.398 1.427 -0.029 1.60e-02 3.91e+03 3.31e+00 bond pdb=" CD2 TRP C 626 " pdb=" CE3 TRP C 626 " ideal model delta sigma weight residual 1.398 1.427 -0.029 1.60e-02 3.91e+03 3.23e+00 bond pdb=" C ARG A 173 " pdb=" N PRO A 174 " ideal model delta sigma weight residual 1.334 1.366 -0.033 2.34e-02 1.83e+03 1.93e+00 ... (remaining 8772 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 11620 2.31 - 4.63: 169 4.63 - 6.94: 20 6.94 - 9.26: 8 9.26 - 11.57: 2 Bond angle restraints: 11819 Sorted by residual: angle pdb=" C ASP C 449 " pdb=" N LYS C 450 " pdb=" CA LYS C 450 " ideal model delta sigma weight residual 121.54 132.63 -11.09 1.91e+00 2.74e-01 3.37e+01 angle pdb=" N GLU C 662 " pdb=" CA GLU C 662 " pdb=" C GLU C 662 " ideal model delta sigma weight residual 113.18 105.49 7.69 1.33e+00 5.65e-01 3.34e+01 angle pdb=" N GLN A 178 " pdb=" CA GLN A 178 " pdb=" C GLN A 178 " ideal model delta sigma weight residual 114.75 108.40 6.35 1.26e+00 6.30e-01 2.54e+01 angle pdb=" C TRP A 144 " pdb=" N VAL A 145 " pdb=" CA VAL A 145 " ideal model delta sigma weight residual 121.97 130.55 -8.58 1.80e+00 3.09e-01 2.27e+01 angle pdb=" CD2 TRP C 577 " pdb=" CE3 TRP C 577 " pdb=" CZ3 TRP C 577 " ideal model delta sigma weight residual 118.60 123.99 -5.39 1.30e+00 5.92e-01 1.72e+01 ... (remaining 11814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4491 17.94 - 35.89: 643 35.89 - 53.83: 195 53.83 - 71.77: 29 71.77 - 89.71: 20 Dihedral angle restraints: 5378 sinusoidal: 2205 harmonic: 3173 Sorted by residual: dihedral pdb=" CB CYS C 396 " pdb=" SG CYS C 396 " pdb=" SG CYS C 422 " pdb=" CB CYS C 422 " ideal model delta sinusoidal sigma weight residual 93.00 162.05 -69.05 1 1.00e+01 1.00e-02 6.17e+01 dihedral pdb=" CA GLY A 135 " pdb=" C GLY A 135 " pdb=" N ILE A 136 " pdb=" CA ILE A 136 " ideal model delta harmonic sigma weight residual 180.00 152.37 27.63 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA ILE A 296 " pdb=" C ILE A 296 " pdb=" N GLU A 297 " pdb=" CA GLU A 297 " ideal model delta harmonic sigma weight residual 180.00 152.51 27.49 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 5375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 928 0.037 - 0.075: 335 0.075 - 0.112: 80 0.112 - 0.149: 13 0.149 - 0.186: 3 Chirality restraints: 1359 Sorted by residual: chirality pdb=" CG LEU A 279 " pdb=" CB LEU A 279 " pdb=" CD1 LEU A 279 " pdb=" CD2 LEU A 279 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" CB ILE B 85 " pdb=" CA ILE B 85 " pdb=" CG1 ILE B 85 " pdb=" CG2 ILE B 85 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" CA LYS C 363 " pdb=" N LYS C 363 " pdb=" C LYS C 363 " pdb=" CB LYS C 363 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.06e-01 ... (remaining 1356 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 173 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO A 174 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 174 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 174 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 24 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C LEU A 24 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU A 24 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG A 25 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 449 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C ASP C 449 " 0.029 2.00e-02 2.50e+03 pdb=" O ASP C 449 " -0.011 2.00e-02 2.50e+03 pdb=" N LYS C 450 " -0.010 2.00e-02 2.50e+03 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 167 2.67 - 3.23: 8261 3.23 - 3.79: 12638 3.79 - 4.34: 17373 4.34 - 4.90: 28502 Nonbonded interactions: 66941 Sorted by model distance: nonbonded pdb=" OG SER C 337 " pdb=" OD1 ASP C 339 " model vdw 2.114 3.040 nonbonded pdb=" O ILE C 381 " pdb=" OG SER C 385 " model vdw 2.199 3.040 nonbonded pdb=" O PRO A 174 " pdb=" N ASN A 176 " model vdw 2.249 3.120 nonbonded pdb=" O SER A 36 " pdb=" OG SER A 36 " model vdw 2.253 3.040 nonbonded pdb=" O LYS A 229 " pdb=" OG SER A 234 " model vdw 2.253 3.040 ... (remaining 66936 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 22.160 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.650 ------------------------------------------------------------------------------- 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 8777 Z= 0.157 Angle : 0.706 11.572 11819 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 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.960 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: 0.2266 time to fit residues: 46.7093 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 : 0.917 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 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 8777 Z= 0.255 Angle : 0.691 9.184 11819 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 *********************** 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 : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8320 (tt0) cc_final: 0.7753 (tp-100) REVERT: A 43 MET cc_start: 0.8378 (mmp) cc_final: 0.8072 (mmt) REVERT: A 172 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.7115 (t80) REVERT: A 241 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6952 (mt-10) REVERT: A 246 ARG cc_start: 0.7419 (tmm-80) cc_final: 0.7206 (ttp-110) REVERT: A 278 TYR cc_start: 0.6344 (OUTLIER) cc_final: 0.5162 (m-80) REVERT: A 289 ARG cc_start: 0.7922 (mmp80) cc_final: 0.7492 (ttp80) REVERT: A 293 GLN cc_start: 0.7987 (pp30) cc_final: 0.7675 (pt0) REVERT: A 353 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.6726 (mp0) REVERT: B 94 LYS cc_start: 0.7620 (mmtt) cc_final: 0.7330 (mmtm) REVERT: C 559 MET cc_start: 0.3944 (mmt) cc_final: 0.3122 (mpp) REVERT: C 655 LYS cc_start: 0.4725 (OUTLIER) cc_final: 0.4507 (pttm) outliers start: 45 outliers final: 25 residues processed: 130 average time/residue: 0.2086 time to fit residues: 37.8927 Evaluate side-chains 110 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 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 C residue 655 LYS 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 53 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 77 optimal weight: 9.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8777 Z= 0.201 Angle : 0.624 9.098 11819 Z= 0.343 Chirality : 0.041 0.189 1359 Planarity : 0.003 0.036 1498 Dihedral : 6.395 55.782 1142 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.41 % Favored : 87.12 % Rotamer: Outliers : 4.91 % Allowed : 24.23 % Favored : 70.86 % 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: -1.70 (0.27), residues: 1064 helix: -0.18 (0.22), residues: 610 sheet: -1.90 (0.77), residues: 52 loop : -2.46 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 362 HIS 0.006 0.001 HIS B 64 PHE 0.018 0.001 PHE A 402 TYR 0.019 0.002 TYR A 208 ARG 0.003 0.000 ARG A 401 *********************** 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 135 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 87 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8331 (tt0) cc_final: 0.7768 (tp-100) REVERT: A 172 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.7090 (t80) REVERT: A 241 GLU cc_start: 0.7383 (mp0) cc_final: 0.6847 (mt-10) REVERT: A 278 TYR cc_start: 0.6364 (OUTLIER) cc_final: 0.4865 (m-80) REVERT: A 293 GLN cc_start: 0.7987 (pp30) cc_final: 0.7695 (pt0) REVERT: A 353 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6533 (mp0) REVERT: B 94 LYS cc_start: 0.7650 (mmtt) cc_final: 0.7348 (mmtm) REVERT: C 497 MET cc_start: 0.5020 (tpt) cc_final: 0.3950 (mmm) REVERT: D 98 LEU cc_start: 0.1296 (OUTLIER) cc_final: 0.1075 (mm) REVERT: D 113 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.7000 (mp) outliers start: 48 outliers final: 22 residues processed: 123 average time/residue: 0.2038 time to fit residues: 35.7114 Evaluate side-chains 108 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 111 MET 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 291 CYS Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain 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 95 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 8777 Z= 0.416 Angle : 0.752 8.838 11819 Z= 0.409 Chirality : 0.047 0.194 1359 Planarity : 0.005 0.055 1498 Dihedral : 6.747 59.150 1138 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.91 % Favored : 85.62 % Rotamer: Outliers : 5.83 % Allowed : 24.23 % 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: -2.06 (0.26), residues: 1064 helix: -0.59 (0.21), residues: 619 sheet: -1.18 (0.92), residues: 39 loop : -2.56 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 362 HIS 0.006 0.001 HIS B 64 PHE 0.024 0.002 PHE A 402 TYR 0.030 0.003 TYR A 208 ARG 0.004 0.000 ARG A 168 *********************** 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: 57 poor density : 86 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8388 (tt0) cc_final: 0.7851 (tp-100) REVERT: A 43 MET cc_start: 0.8339 (mmp) cc_final: 0.7933 (mmt) REVERT: A 172 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.7081 (t80) REVERT: A 241 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6802 (mt-10) REVERT: A 278 TYR cc_start: 0.6957 (OUTLIER) cc_final: 0.5024 (m-80) REVERT: A 293 GLN cc_start: 0.8126 (pp30) cc_final: 0.7762 (pt0) REVERT: A 353 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6364 (mp0) REVERT: B 94 LYS cc_start: 0.7650 (mmtt) cc_final: 0.7321 (mmtm) REVERT: C 492 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7372 (tt) REVERT: C 497 MET cc_start: 0.4977 (tpt) cc_final: 0.3873 (mmm) outliers start: 57 outliers final: 37 residues processed: 132 average time/residue: 0.2040 time to fit residues: 38.3761 Evaluate side-chains 121 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 79 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 18 VAL 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 595 LYS Chi-restraints excluded: chain C residue 626 TRP Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 87 optimal weight: 30.0000 chunk 70 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 25 optimal weight: 0.2980 chunk 34 optimal weight: 0.0970 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8777 Z= 0.171 Angle : 0.621 8.909 11819 Z= 0.340 Chirality : 0.041 0.226 1359 Planarity : 0.003 0.031 1498 Dihedral : 6.330 55.564 1138 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.75 % Favored : 87.78 % Rotamer: Outliers : 4.50 % Allowed : 25.56 % 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: -1.69 (0.26), residues: 1064 helix: -0.17 (0.22), residues: 610 sheet: -1.11 (0.97), residues: 39 loop : -2.57 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 167 HIS 0.007 0.001 HIS B 64 PHE 0.014 0.001 PHE A 402 TYR 0.012 0.001 TYR A 42 ARG 0.002 0.000 ARG A 401 *********************** 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 130 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 86 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8340 (tt0) cc_final: 0.7811 (tp-100) REVERT: A 172 PHE cc_start: 0.7522 (OUTLIER) cc_final: 0.7097 (t80) REVERT: A 241 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6848 (mt-10) REVERT: A 278 TYR cc_start: 0.6550 (OUTLIER) cc_final: 0.4858 (m-80) REVERT: A 293 GLN cc_start: 0.7986 (pp30) cc_final: 0.7699 (pt0) REVERT: A 353 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6304 (mp0) REVERT: B 94 LYS cc_start: 0.7672 (mmtt) cc_final: 0.7077 (mmtt) REVERT: C 447 ASN cc_start: 0.7276 (m-40) cc_final: 0.7067 (m110) REVERT: C 497 MET cc_start: 0.4811 (tpt) cc_final: 0.3956 (mmm) outliers start: 44 outliers final: 23 residues processed: 121 average time/residue: 0.2057 time to fit residues: 35.5787 Evaluate side-chains 105 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 179 VAL Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 225 LEU 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 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 548 ARG Chi-restraints excluded: chain C residue 552 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 102 optimal weight: 0.0870 chunk 85 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN D 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8777 Z= 0.193 Angle : 0.616 8.882 11819 Z= 0.337 Chirality : 0.041 0.181 1359 Planarity : 0.003 0.030 1498 Dihedral : 6.179 57.033 1138 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.31 % Favored : 87.31 % Rotamer: Outliers : 4.60 % Allowed : 25.66 % Favored : 69.73 % 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: -1.53 (0.27), residues: 1064 helix: -0.01 (0.22), residues: 605 sheet: -1.16 (0.94), residues: 39 loop : -2.52 (0.30), residues: 420 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 0.016 0.001 PHE A 402 TYR 0.016 0.001 TYR A 377 ARG 0.002 0.000 ARG A 401 *********************** 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 129 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 84 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8348 (tt0) cc_final: 0.7821 (tp-100) REVERT: A 172 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.7068 (t80) REVERT: A 241 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6839 (mt-10) REVERT: A 278 TYR cc_start: 0.6627 (OUTLIER) cc_final: 0.4752 (m-80) REVERT: A 293 GLN cc_start: 0.7959 (pp30) cc_final: 0.7690 (pt0) REVERT: A 353 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6259 (mp0) REVERT: B 94 LYS cc_start: 0.7660 (mmtt) cc_final: 0.7324 (mmtm) REVERT: C 399 MET cc_start: 0.5675 (ptt) cc_final: 0.5299 (ptt) REVERT: C 447 ASN cc_start: 0.7223 (m-40) cc_final: 0.6898 (m110) REVERT: C 492 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7256 (tt) REVERT: C 497 MET cc_start: 0.4813 (tpt) cc_final: 0.4026 (mmm) REVERT: C 556 GLU cc_start: 0.6682 (tm-30) cc_final: 0.6352 (tt0) outliers start: 45 outliers final: 32 residues processed: 118 average time/residue: 0.2020 time to fit residues: 33.7147 Evaluate side-chains 117 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 80 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 196 ILE Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 225 LEU 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 336 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 0.2980 chunk 74 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN D 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8777 Z= 0.168 Angle : 0.602 8.912 11819 Z= 0.330 Chirality : 0.040 0.183 1359 Planarity : 0.003 0.030 1498 Dihedral : 6.071 58.888 1138 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.22 % Favored : 87.50 % Rotamer: Outliers : 4.09 % Allowed : 26.18 % Favored : 69.73 % 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: -1.36 (0.27), residues: 1064 helix: 0.14 (0.22), residues: 604 sheet: -1.26 (0.95), residues: 39 loop : -2.44 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 362 HIS 0.005 0.001 HIS B 64 PHE 0.014 0.001 PHE A 402 TYR 0.020 0.001 TYR A 377 ARG 0.001 0.000 ARG A 401 *********************** 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 124 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 84 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8337 (tt0) cc_final: 0.7817 (tp-100) REVERT: A 172 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.7043 (t80) REVERT: A 241 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6866 (mt-10) REVERT: A 278 TYR cc_start: 0.6486 (OUTLIER) cc_final: 0.4729 (m-80) REVERT: A 293 GLN cc_start: 0.7924 (pp30) cc_final: 0.7667 (pt0) REVERT: A 353 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6244 (mp0) REVERT: B 94 LYS cc_start: 0.7647 (mmtt) cc_final: 0.7050 (mmtt) REVERT: C 492 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7250 (tt) REVERT: C 497 MET cc_start: 0.4717 (tpt) cc_final: 0.4112 (mmm) REVERT: C 556 GLU cc_start: 0.6649 (tm-30) cc_final: 0.6301 (tt0) outliers start: 40 outliers final: 30 residues processed: 116 average time/residue: 0.2004 time to fit residues: 33.0412 Evaluate side-chains 111 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 76 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 225 LEU 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 336 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 429 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 64 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 80 optimal weight: 30.0000 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN D 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8777 Z= 0.273 Angle : 0.653 9.104 11819 Z= 0.356 Chirality : 0.042 0.180 1359 Planarity : 0.004 0.031 1498 Dihedral : 6.176 58.063 1138 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.69 % Favored : 87.03 % 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: -1.58 (0.26), residues: 1064 helix: -0.06 (0.22), residues: 609 sheet: -1.44 (0.91), residues: 39 loop : -2.51 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 362 HIS 0.004 0.001 HIS D 60 PHE 0.020 0.001 PHE A 402 TYR 0.021 0.002 TYR A 377 ARG 0.002 0.000 ARG A 153 *********************** 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 123 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 76 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8373 (tt0) cc_final: 0.7843 (tp-100) REVERT: A 172 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.7094 (t80) REVERT: A 241 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6863 (mt-10) REVERT: A 278 TYR cc_start: 0.6818 (OUTLIER) cc_final: 0.4806 (m-80) REVERT: A 293 GLN cc_start: 0.7998 (pp30) cc_final: 0.7730 (pt0) REVERT: B 94 LYS cc_start: 0.7660 (mmtt) cc_final: 0.7322 (mmtm) REVERT: C 492 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7317 (tt) REVERT: C 497 MET cc_start: 0.4864 (tpt) cc_final: 0.4279 (mmm) REVERT: C 556 GLU cc_start: 0.6550 (tm-30) cc_final: 0.6196 (tt0) outliers start: 47 outliers final: 37 residues processed: 113 average time/residue: 0.2113 time to fit residues: 33.8578 Evaluate side-chains 115 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 74 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 214 ASN 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 383 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 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 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 Chi-restraints excluded: chain D residue 125 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.0070 chunk 90 optimal weight: 30.0000 chunk 94 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN D 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8777 Z= 0.217 Angle : 0.629 9.003 11819 Z= 0.343 Chirality : 0.041 0.184 1359 Planarity : 0.003 0.029 1498 Dihedral : 6.122 56.148 1138 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.31 % Favored : 87.41 % Rotamer: Outliers : 4.60 % Allowed : 25.77 % Favored : 69.63 % 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: -1.47 (0.27), residues: 1064 helix: 0.05 (0.22), residues: 607 sheet: -1.43 (0.92), residues: 39 loop : -2.50 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 362 HIS 0.004 0.001 HIS D 60 PHE 0.018 0.001 PHE A 402 TYR 0.019 0.002 TYR A 377 ARG 0.002 0.000 ARG A 401 *********************** 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 124 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 79 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8363 (tt0) cc_final: 0.7841 (tp-100) REVERT: A 172 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7183 (t80) REVERT: A 241 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6850 (mt-10) REVERT: A 278 TYR cc_start: 0.6755 (OUTLIER) cc_final: 0.4911 (m-80) REVERT: A 293 GLN cc_start: 0.7965 (pp30) cc_final: 0.7699 (pt0) REVERT: A 353 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6223 (mp0) REVERT: B 94 LYS cc_start: 0.7654 (mmtt) cc_final: 0.7108 (mmtp) REVERT: C 447 ASN cc_start: 0.7093 (m-40) cc_final: 0.6847 (m110) REVERT: C 492 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7304 (tt) REVERT: C 497 MET cc_start: 0.4803 (tpt) cc_final: 0.4273 (mmm) REVERT: C 556 GLU cc_start: 0.6523 (tm-30) cc_final: 0.6172 (tt0) outliers start: 45 outliers final: 35 residues processed: 115 average time/residue: 0.2019 time to fit residues: 33.0532 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 : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 214 ASN 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 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 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 61 optimal weight: 0.1980 chunk 47 optimal weight: 0.3980 chunk 69 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 20.0000 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 284 GLN C 444 HIS ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8777 Z= 0.174 Angle : 0.606 8.938 11819 Z= 0.331 Chirality : 0.041 0.181 1359 Planarity : 0.003 0.030 1498 Dihedral : 5.992 54.280 1138 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.75 % Favored : 87.97 % Rotamer: Outliers : 4.29 % Allowed : 26.07 % Favored : 69.63 % 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: -1.28 (0.27), residues: 1064 helix: 0.21 (0.22), residues: 610 sheet: -1.57 (0.93), residues: 39 loop : -2.41 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 362 HIS 0.004 0.001 HIS A 345 PHE 0.015 0.001 PHE A 402 TYR 0.020 0.001 TYR A 377 ARG 0.002 0.000 ARG A 401 ********************** 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 121 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 79 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8336 (tt0) cc_final: 0.7814 (tp-100) REVERT: A 172 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.7366 (t80) REVERT: A 241 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6817 (mt-10) REVERT: A 278 TYR cc_start: 0.6541 (OUTLIER) cc_final: 0.4832 (m-80) REVERT: A 293 GLN cc_start: 0.7919 (pp30) cc_final: 0.7669 (pt0) REVERT: A 353 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6205 (mp0) REVERT: B 94 LYS cc_start: 0.7656 (mmtt) cc_final: 0.7116 (mmtp) REVERT: C 492 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7294 (tt) REVERT: C 497 MET cc_start: 0.4639 (tpt) cc_final: 0.4201 (mmm) REVERT: C 556 GLU cc_start: 0.6498 (tm-30) cc_final: 0.6141 (tt0) outliers start: 42 outliers final: 35 residues processed: 111 average time/residue: 0.2132 time to fit residues: 33.5118 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 : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 214 ASN 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 353 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 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 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 Chi-restraints excluded: chain D residue 125 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 12 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 73 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.274387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.233832 restraints weight = 9714.465| |-----------------------------------------------------------------------------| r_work (start): 0.4553 rms_B_bonded: 1.68 r_work: 0.4299 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8777 Z= 0.168 Angle : 0.600 8.968 11819 Z= 0.328 Chirality : 0.040 0.181 1359 Planarity : 0.003 0.029 1498 Dihedral : 5.914 53.538 1138 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.37 % Favored : 88.35 % Rotamer: Outliers : 3.99 % Allowed : 26.58 % Favored : 69.43 % 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: -1.19 (0.27), residues: 1064 helix: 0.28 (0.22), residues: 611 sheet: -1.53 (0.94), residues: 39 loop : -2.37 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 362 HIS 0.005 0.001 HIS D 60 PHE 0.014 0.001 PHE A 402 TYR 0.020 0.001 TYR A 377 ARG 0.001 0.000 ARG A 401 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1899.56 seconds wall clock time: 35 minutes 35.53 seconds (2135.53 seconds total)