Starting phenix.real_space_refine on Tue Jun 10 21:21:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yot_33986/06_2025/7yot_33986.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yot_33986/06_2025/7yot_33986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yot_33986/06_2025/7yot_33986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yot_33986/06_2025/7yot_33986.map" model { file = "/net/cci-nas-00/data/ceres_data/7yot_33986/06_2025/7yot_33986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yot_33986/06_2025/7yot_33986.cif" } resolution = 3.0 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= 0.008 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 76 5.16 5 C 7714 2.51 5 N 2126 2.21 5 O 2266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 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: 12182 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 376 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 51, 371 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Conformer: "B" Number of residues, atoms: 51, 371 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} bond proxies already assigned to first conformer: 367 Chain: "C" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 303 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "B" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 244 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "E" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 849 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 11, 'TRANS': 103} Chain breaks: 2 Chain: "A" Number of atoms: 10410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1309, 10410 Classifications: {'peptide': 1309} Link IDs: {'PCIS': 1, 'PTRANS': 56, 'TRANS': 1251} Chain breaks: 7 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA D 301 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA D 301 " occ=0.50 Time building chain proxies: 7.80, per 1000 atoms: 0.64 Number of scatterers: 12182 At special positions: 0 Unit cell: (102.96, 112.32, 111.28, 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 76 16.00 O 2266 8.00 N 2126 7.00 C 7714 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A1112 " - pdb=" SG CYS A1350 " distance=2.03 Simple disulfide: pdb=" SG CYS A1157 " - pdb=" SG CYS A1160 " 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: 3.14 Conformation dependent library (CDL) restraints added in 1.8 seconds 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2962 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 7 sheets defined 54.4% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'D' and resid 262 through 281 removed outlier: 3.535A pdb=" N ALA D 278 " --> pdb=" O ALA D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 303 removed outlier: 3.667A pdb=" N ARG D 300 " --> pdb=" O LEU D 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 286 removed outlier: 3.713A pdb=" N THR C 271 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL C 275 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU C 277 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 291 Processing helix chain 'C' and resid 298 through 305 Processing helix chain 'B' and resid 269 through 280 removed outlier: 3.842A pdb=" N VAL B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.898A pdb=" N ALA E 278 " --> pdb=" O VAL E 275 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN E 279 " --> pdb=" O MET E 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 275 through 279' Processing helix chain 'E' and resid 296 through 302 Processing helix chain 'E' and resid 337 through 342 Processing helix chain 'E' and resid 352 through 366 removed outlier: 3.586A pdb=" N VAL E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 Processing helix chain 'E' and resid 389 through 397 Processing helix chain 'A' and resid 9 through 13 removed outlier: 3.514A pdb=" N GLN A 12 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 13 " --> pdb=" O GLU A 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 9 through 13' Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.934A pdb=" N LEU A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 4.067A pdb=" N ASP A 45 " --> pdb=" O ASP A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 63 through 80 removed outlier: 4.001A pdb=" N MET A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.540A pdb=" N GLY A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 141 removed outlier: 3.509A pdb=" N ASN A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE A 113 " --> pdb=" O LYS A 109 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLU A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) Proline residue: A 127 - end of helix Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 169 through 192 removed outlier: 3.970A pdb=" N THR A 192 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 254 removed outlier: 3.540A pdb=" N VAL A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 235 " --> pdb=" O GLN A 231 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 279 removed outlier: 3.646A pdb=" N ALA A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS A 263 " --> pdb=" O CYS A 259 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 296 removed outlier: 4.023A pdb=" N LEU A 288 " --> pdb=" O ASP A 284 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU A 290 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 296 " --> pdb=" O PHE A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 323 Processing helix chain 'A' and resid 327 through 342 Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.732A pdb=" N ALA A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 356 removed outlier: 3.642A pdb=" N LEU A 356 " --> pdb=" O MET A 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 356' Processing helix chain 'A' and resid 366 through 379 removed outlier: 4.153A pdb=" N GLN A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 408 Processing helix chain 'A' and resid 416 through 420 removed outlier: 4.053A pdb=" N ILE A 420 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 432 removed outlier: 3.753A pdb=" N ALA A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 443 Processing helix chain 'A' and resid 443 through 448 Processing helix chain 'A' and resid 479 through 484 removed outlier: 3.752A pdb=" N PHE A 484 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 489 removed outlier: 3.526A pdb=" N LEU A 489 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 removed outlier: 3.533A pdb=" N ASN A 496 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 497 " --> pdb=" O LYS A 494 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 493 through 497' Processing helix chain 'A' and resid 505 through 512 Processing helix chain 'A' and resid 517 through 522 Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 558 through 576 Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 599 through 603 removed outlier: 3.561A pdb=" N LEU A 602 " --> pdb=" O MET A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 649 removed outlier: 3.951A pdb=" N TRP A 649 " --> pdb=" O CYS A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 666 removed outlier: 5.485A pdb=" N LEU A 656 " --> pdb=" O GLN A 652 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE A 657 " --> pdb=" O THR A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 681 removed outlier: 3.908A pdb=" N LEU A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 721 through 739 removed outlier: 3.568A pdb=" N TRP A 725 " --> pdb=" O CYS A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 791 Processing helix chain 'A' and resid 823 through 829 removed outlier: 3.643A pdb=" N ASN A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 859 removed outlier: 3.681A pdb=" N SER A 845 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 881 Processing helix chain 'A' and resid 901 through 911 Processing helix chain 'A' and resid 922 through 926 Processing helix chain 'A' and resid 933 through 948 Processing helix chain 'A' and resid 952 through 961 removed outlier: 4.394A pdb=" N MET A 956 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR A 957 " --> pdb=" O PRO A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 975 Processing helix chain 'A' and resid 986 through 1000 removed outlier: 3.580A pdb=" N PHE A1000 " --> pdb=" O GLN A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1029 Processing helix chain 'A' and resid 1034 through 1045 Processing helix chain 'A' and resid 1045 through 1055 Processing helix chain 'A' and resid 1060 through 1071 Processing helix chain 'A' and resid 1075 through 1083 Processing helix chain 'A' and resid 1083 through 1096 Processing helix chain 'A' and resid 1112 through 1125 Processing helix chain 'A' and resid 1125 through 1130 Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.513A pdb=" N VAL A1146 " --> pdb=" O THR A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1212 through 1230 removed outlier: 3.585A pdb=" N TYR A1229 " --> pdb=" O LEU A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1244 Processing helix chain 'A' and resid 1251 through 1256 removed outlier: 3.809A pdb=" N ARG A1255 " --> pdb=" O SER A1251 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A1256 " --> pdb=" O GLU A1252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1251 through 1256' Processing helix chain 'A' and resid 1287 through 1291 removed outlier: 3.647A pdb=" N VAL A1291 " --> pdb=" O SER A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1327 removed outlier: 3.506A pdb=" N LEU A1327 " --> pdb=" O LEU A1323 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 308 through 310 removed outlier: 6.493A pdb=" N LYS B 284 " --> pdb=" O LEU E 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 204 removed outlier: 3.623A pdb=" N GLY A 207 " --> pdb=" O HIS A 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 555 through 556 removed outlier: 4.825A pdb=" N VAL A 538 " --> pdb=" O THR A 682 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 684 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 743 through 748 removed outlier: 4.338A pdb=" N ARG A 743 " --> pdb=" O THR A 758 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASN A 795 " --> pdb=" O GLN A 643 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 743 through 748 removed outlier: 4.338A pdb=" N ARG A 743 " --> pdb=" O THR A 758 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 807 through 810 Processing sheet with id=AA7, first strand: chain 'A' and resid 1292 through 1294 removed outlier: 3.541A pdb=" N THR A1168 " --> pdb=" O LEU A1343 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A1339 " --> pdb=" O LEU A1172 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1621 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: 4.10 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3015 1.33 - 1.45: 2500 1.45 - 1.58: 6782 1.58 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 12420 Sorted by residual: bond pdb=" CG1 ILE A 117 " pdb=" CD1 ILE A 117 " ideal model delta sigma weight residual 1.513 1.394 0.119 3.90e-02 6.57e+02 9.32e+00 bond pdb=" CG LEU A 647 " pdb=" CD1 LEU A 647 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.18e+00 bond pdb=" CB VAL A 748 " pdb=" CG1 VAL A 748 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.62e+00 bond pdb=" CG1 ILE A 267 " pdb=" CD1 ILE A 267 " ideal model delta sigma weight residual 1.513 1.422 0.091 3.90e-02 6.57e+02 5.41e+00 bond pdb=" CB PRO A 92 " pdb=" CG PRO A 92 " ideal model delta sigma weight residual 1.506 1.419 0.087 3.90e-02 6.57e+02 4.97e+00 ... (remaining 12415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 16548 3.30 - 6.61: 235 6.61 - 9.91: 28 9.91 - 13.21: 4 13.21 - 16.52: 3 Bond angle restraints: 16818 Sorted by residual: angle pdb=" C ASP A 706 " pdb=" N ASP A 707 " pdb=" CA ASP A 707 " ideal model delta sigma weight residual 121.54 131.27 -9.73 1.91e+00 2.74e-01 2.60e+01 angle pdb=" CA LEU A1008 " pdb=" CB LEU A1008 " pdb=" CG LEU A1008 " ideal model delta sigma weight residual 116.30 132.82 -16.52 3.50e+00 8.16e-02 2.23e+01 angle pdb=" CA LEU E 286 " pdb=" CB LEU E 286 " pdb=" CG LEU E 286 " ideal model delta sigma weight residual 116.30 132.35 -16.05 3.50e+00 8.16e-02 2.10e+01 angle pdb=" C ASN A 463 " pdb=" N LEU A 464 " pdb=" CA LEU A 464 " ideal model delta sigma weight residual 121.54 129.74 -8.20 1.91e+00 2.74e-01 1.84e+01 angle pdb=" N ILE A 792 " pdb=" CA ILE A 792 " pdb=" C ILE A 792 " ideal model delta sigma weight residual 112.29 108.60 3.69 9.40e-01 1.13e+00 1.54e+01 ... (remaining 16813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.58: 7151 15.58 - 31.16: 329 31.16 - 46.74: 93 46.74 - 62.32: 6 62.32 - 77.90: 11 Dihedral angle restraints: 7590 sinusoidal: 3048 harmonic: 4542 Sorted by residual: dihedral pdb=" CB CYS A1157 " pdb=" SG CYS A1157 " pdb=" SG CYS A1160 " pdb=" CB CYS A1160 " ideal model delta sinusoidal sigma weight residual 93.00 170.90 -77.90 1 1.00e+01 1.00e-02 7.59e+01 dihedral pdb=" CA ASN A 705 " pdb=" C ASN A 705 " pdb=" N ASP A 706 " pdb=" CA ASP A 706 " ideal model delta harmonic sigma weight residual -180.00 -154.26 -25.74 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA THR A 526 " pdb=" C THR A 526 " pdb=" N THR A 527 " pdb=" CA THR A 527 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 7587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1322 0.056 - 0.112: 503 0.112 - 0.168: 103 0.168 - 0.223: 6 0.223 - 0.279: 5 Chirality restraints: 1939 Sorted by residual: chirality pdb=" CB VAL A1037 " pdb=" CA VAL A1037 " pdb=" CG1 VAL A1037 " pdb=" CG2 VAL A1037 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CB VAL E 335 " pdb=" CA VAL E 335 " pdb=" CG1 VAL E 335 " pdb=" CG2 VAL E 335 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CG LEU A 489 " pdb=" CB LEU A 489 " pdb=" CD1 LEU A 489 " pdb=" CD2 LEU A 489 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 1936 not shown) Planarity restraints: 2144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 33 " -0.021 2.00e-02 2.50e+03 2.46e-02 1.51e+01 pdb=" CG TRP A 33 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP A 33 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP A 33 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 33 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 33 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 33 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 33 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 33 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 33 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 395 " -0.021 2.00e-02 2.50e+03 2.87e-02 1.45e+01 pdb=" CG PHE A 395 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE A 395 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE A 395 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 395 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 395 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 395 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 265 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.12e+00 pdb=" C ASP A 265 " 0.052 2.00e-02 2.50e+03 pdb=" O ASP A 265 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP A 266 " -0.018 2.00e-02 2.50e+03 ... (remaining 2141 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3199 2.80 - 3.33: 10898 3.33 - 3.85: 20215 3.85 - 4.38: 24316 4.38 - 4.90: 41786 Nonbonded interactions: 100414 Sorted by model distance: nonbonded pdb=" OG SER A1108 " pdb=" OD1 ASP A1110 " model vdw 2.279 3.040 nonbonded pdb=" OG SER A 167 " pdb=" OD1 ASP A 245 " model vdw 2.281 3.040 nonbonded pdb=" NH1 ARG A 319 " pdb=" OD1 ASP A 332 " model vdw 2.324 3.120 nonbonded pdb=" OG SER E 385 " pdb=" O GLU E 387 " model vdw 2.337 3.040 nonbonded pdb=" O LEU A1145 " pdb=" OG SER A1348 " model vdw 2.342 3.040 ... (remaining 100409 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.590 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.340 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.060 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:16.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 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 : 0.009 0.119 12422 Z= 0.344 Angle : 1.031 16.518 16822 Z= 0.530 Chirality : 0.059 0.279 1939 Planarity : 0.008 0.065 2144 Dihedral : 10.474 76.529 4622 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.66 % Allowed : 2.93 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -3.64 (0.17), residues: 1526 helix: -2.58 (0.13), residues: 762 sheet: -0.81 (0.57), residues: 85 loop : -2.29 (0.20), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.004 TRP A 33 HIS 0.013 0.003 HIS A 178 PHE 0.061 0.004 PHE A 395 TYR 0.035 0.003 TYR A 868 ARG 0.013 0.002 ARG A 150 Details of bonding type rmsd hydrogen bonds : bond 0.15583 ( 553) hydrogen bonds : angle 6.57375 ( 1621) SS BOND : bond 0.00156 ( 2) SS BOND : angle 2.99483 ( 4) covalent geometry : bond 0.00882 (12420) covalent geometry : angle 1.02998 (16818) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 292 time to evaluate : 1.408 Fit side-chains REVERT: D 304 LYS cc_start: 0.7974 (mttt) cc_final: 0.7302 (mmtt) REVERT: B 287 ASP cc_start: 0.8159 (t70) cc_final: 0.7806 (t70) REVERT: E 325 GLU cc_start: 0.7978 (pt0) cc_final: 0.7560 (pt0) REVERT: E 378 SER cc_start: 0.8341 (m) cc_final: 0.8133 (m) REVERT: A 96 GLU cc_start: 0.7669 (tt0) cc_final: 0.7425 (tt0) REVERT: A 137 LYS cc_start: 0.8114 (tttt) cc_final: 0.7753 (ttmm) REVERT: A 769 SER cc_start: 0.8767 (m) cc_final: 0.8404 (p) REVERT: A 956 MET cc_start: 0.8831 (tpt) cc_final: 0.8541 (tpp) REVERT: A 989 ILE cc_start: 0.8716 (mt) cc_final: 0.8489 (mp) REVERT: A 997 ARG cc_start: 0.7423 (mtp180) cc_final: 0.7125 (mtm110) REVERT: A 1087 MET cc_start: 0.8719 (mtp) cc_final: 0.8472 (mtm) REVERT: A 1174 SER cc_start: 0.8638 (t) cc_final: 0.8201 (t) REVERT: A 1222 SER cc_start: 0.8583 (m) cc_final: 0.8367 (p) REVERT: A 1340 THR cc_start: 0.7360 (p) cc_final: 0.6961 (m) outliers start: 9 outliers final: 3 residues processed: 299 average time/residue: 1.3678 time to fit residues: 441.9795 Evaluate side-chains 195 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 192 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 1037 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 64 optimal weight: 0.0570 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 119 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 138 optimal weight: 9.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 268 GLN E 306 HIS E 369 HIS A 54 GLN A 78 GLN ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN A 336 HIS A 348 ASN A 463 ASN A 487 ASN A 565 GLN A 575 GLN A 648 ASN A 652 GLN A 662 ASN A 669 HIS A 827 ASN A 906 HIS A 922 GLN A 974 ASN A1088 HIS A1235 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.135188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.101693 restraints weight = 29585.678| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.89 r_work: 0.2818 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12422 Z= 0.101 Angle : 0.536 9.440 16822 Z= 0.273 Chirality : 0.041 0.156 1939 Planarity : 0.005 0.043 2144 Dihedral : 4.959 47.479 1669 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.86 % Allowed : 9.89 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.38 (0.20), residues: 1526 helix: -0.35 (0.18), residues: 741 sheet: -0.60 (0.58), residues: 81 loop : -1.51 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 33 HIS 0.004 0.001 HIS A 27 PHE 0.017 0.001 PHE A 395 TYR 0.013 0.001 TYR A 524 ARG 0.005 0.000 ARG A 319 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 553) hydrogen bonds : angle 4.14723 ( 1621) SS BOND : bond 0.00249 ( 2) SS BOND : angle 2.08408 ( 4) covalent geometry : bond 0.00231 (12420) covalent geometry : angle 0.53525 (16818) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 1.412 Fit side-chains REVERT: D 282 MET cc_start: 0.8320 (mtm) cc_final: 0.8089 (mtp) REVERT: D 304 LYS cc_start: 0.7565 (mttt) cc_final: 0.6794 (mmtt) REVERT: C 282 MET cc_start: 0.8854 (mtt) cc_final: 0.8528 (mtt) REVERT: B 276 MET cc_start: 0.7348 (mmm) cc_final: 0.7147 (mmm) REVERT: B 282 MET cc_start: 0.7119 (mmt) cc_final: 0.6778 (mmt) REVERT: B 287 ASP cc_start: 0.8176 (t70) cc_final: 0.7836 (t70) REVERT: B 300 ARG cc_start: 0.8663 (mtt180) cc_final: 0.8433 (mtm-85) REVERT: E 284 LYS cc_start: 0.8306 (tppp) cc_final: 0.8045 (tppp) REVERT: E 325 GLU cc_start: 0.8118 (pt0) cc_final: 0.7779 (pt0) REVERT: A 137 LYS cc_start: 0.7907 (tttt) cc_final: 0.7578 (ttmm) REVERT: A 277 ASP cc_start: 0.8314 (p0) cc_final: 0.8103 (p0) REVERT: A 520 LYS cc_start: 0.8686 (ttmm) cc_final: 0.8009 (ttpp) REVERT: A 702 LYS cc_start: 0.8826 (mttt) cc_final: 0.8572 (mttm) REVERT: A 760 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6709 (mt-10) REVERT: A 776 GLU cc_start: 0.8085 (tt0) cc_final: 0.7539 (mm-30) REVERT: A 896 GLN cc_start: 0.7289 (mp10) cc_final: 0.6561 (mm110) REVERT: A 914 GLN cc_start: 0.8738 (mp10) cc_final: 0.7894 (mm-40) REVERT: A 956 MET cc_start: 0.8815 (tpt) cc_final: 0.8537 (tpp) REVERT: A 961 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8602 (p) REVERT: A 989 ILE cc_start: 0.8576 (mt) cc_final: 0.8326 (mp) REVERT: A 997 ARG cc_start: 0.7976 (mtp180) cc_final: 0.7216 (mtm110) REVERT: A 1019 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8314 (mt-10) REVERT: A 1052 GLN cc_start: 0.8525 (tt0) cc_final: 0.8123 (mt0) REVERT: A 1090 MET cc_start: 0.8648 (mmm) cc_final: 0.8371 (tpt) REVERT: A 1111 MET cc_start: 0.8158 (mtt) cc_final: 0.7753 (mtp) REVERT: A 1334 LYS cc_start: 0.7528 (mttt) cc_final: 0.6756 (mptt) REVERT: A 1340 THR cc_start: 0.7487 (p) cc_final: 0.7191 (m) REVERT: A 1370 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7525 (ptt-90) outliers start: 39 outliers final: 18 residues processed: 243 average time/residue: 1.2017 time to fit residues: 318.4497 Evaluate side-chains 201 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1086 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1183 SER Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1370 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 35 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 152 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 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 54 GLN A 78 GLN A 120 HIS A 183 GLN A 463 ASN A 478 ASN A 487 ASN A1171 HIS A1314 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.127600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.092086 restraints weight = 22371.217| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.33 r_work: 0.2730 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12422 Z= 0.208 Angle : 0.622 11.752 16822 Z= 0.310 Chirality : 0.045 0.168 1939 Planarity : 0.005 0.045 2144 Dihedral : 5.109 56.696 1669 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.54 % Allowed : 12.23 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -0.78 (0.21), residues: 1526 helix: 0.12 (0.19), residues: 749 sheet: -0.30 (0.60), residues: 83 loop : -1.20 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 33 HIS 0.009 0.002 HIS A 178 PHE 0.027 0.002 PHE A 395 TYR 0.020 0.002 TYR A 977 ARG 0.005 0.001 ARG A1123 Details of bonding type rmsd hydrogen bonds : bond 0.04242 ( 553) hydrogen bonds : angle 4.07532 ( 1621) SS BOND : bond 0.00175 ( 2) SS BOND : angle 2.08983 ( 4) covalent geometry : bond 0.00520 (12420) covalent geometry : angle 0.62103 (16818) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 185 time to evaluate : 1.293 Fit side-chains REVERT: D 282 MET cc_start: 0.8416 (mtm) cc_final: 0.8193 (mtp) REVERT: D 304 LYS cc_start: 0.7476 (mttt) cc_final: 0.6842 (mptt) REVERT: B 282 MET cc_start: 0.7311 (mmt) cc_final: 0.6491 (mmt) REVERT: B 300 ARG cc_start: 0.8792 (mtt180) cc_final: 0.8568 (mtm-85) REVERT: E 325 GLU cc_start: 0.8205 (pt0) cc_final: 0.7824 (pt0) REVERT: A 137 LYS cc_start: 0.7827 (tttt) cc_final: 0.7427 (ttmm) REVERT: A 173 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8850 (ttpt) REVERT: A 377 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.7515 (mp10) REVERT: A 520 LYS cc_start: 0.8764 (ttmm) cc_final: 0.7983 (ttpp) REVERT: A 702 LYS cc_start: 0.8821 (mttt) cc_final: 0.8602 (mttm) REVERT: A 776 GLU cc_start: 0.8352 (tt0) cc_final: 0.7828 (mm-30) REVERT: A 896 GLN cc_start: 0.7396 (mp10) cc_final: 0.6641 (mm110) REVERT: A 956 MET cc_start: 0.8836 (tpt) cc_final: 0.8500 (tpp) REVERT: A 961 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8567 (p) REVERT: A 989 ILE cc_start: 0.8531 (mt) cc_final: 0.8280 (mp) REVERT: A 997 ARG cc_start: 0.8106 (mtp180) cc_final: 0.7285 (mtm110) REVERT: A 1025 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7186 (tm-30) REVERT: A 1090 MET cc_start: 0.8728 (mmm) cc_final: 0.8462 (tpt) REVERT: A 1111 MET cc_start: 0.8248 (mtt) cc_final: 0.7798 (mtm) REVERT: A 1133 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8275 (mmtp) REVERT: A 1340 THR cc_start: 0.7535 (p) cc_final: 0.7219 (m) outliers start: 62 outliers final: 30 residues processed: 222 average time/residue: 1.2274 time to fit residues: 296.4549 Evaluate side-chains 207 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 GLN Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1025 GLU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1086 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1337 ASP Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1365 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 78 GLN A 463 ASN A 475 HIS A 498 GLN A 974 ASN A1314 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.127677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.093430 restraints weight = 17891.917| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.95 r_work: 0.2749 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12422 Z= 0.168 Angle : 0.561 10.347 16822 Z= 0.283 Chirality : 0.043 0.152 1939 Planarity : 0.004 0.045 2144 Dihedral : 4.707 46.147 1668 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.59 % Allowed : 13.92 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -0.35 (0.22), residues: 1526 helix: 0.50 (0.19), residues: 744 sheet: 0.36 (0.63), residues: 72 loop : -1.05 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 33 HIS 0.006 0.001 HIS A 178 PHE 0.019 0.002 PHE A 395 TYR 0.015 0.001 TYR A 977 ARG 0.004 0.001 ARG A1123 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 553) hydrogen bonds : angle 3.88397 ( 1621) SS BOND : bond 0.00162 ( 2) SS BOND : angle 1.93048 ( 4) covalent geometry : bond 0.00416 (12420) covalent geometry : angle 0.55994 (16818) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 176 time to evaluate : 1.321 Fit side-chains REVERT: D 304 LYS cc_start: 0.7485 (mttt) cc_final: 0.6716 (mmtt) REVERT: B 282 MET cc_start: 0.7198 (mmt) cc_final: 0.6323 (mmt) REVERT: B 300 ARG cc_start: 0.8820 (mtt180) cc_final: 0.8583 (mtm-85) REVERT: E 325 GLU cc_start: 0.8209 (pt0) cc_final: 0.7885 (pt0) REVERT: A 137 LYS cc_start: 0.7851 (tttt) cc_final: 0.7451 (ttmm) REVERT: A 359 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8618 (mp) REVERT: A 414 ARG cc_start: 0.8663 (mtp85) cc_final: 0.8389 (mtp-110) REVERT: A 520 LYS cc_start: 0.8767 (ttmm) cc_final: 0.7981 (ttpp) REVERT: A 702 LYS cc_start: 0.8793 (mttt) cc_final: 0.8569 (mttm) REVERT: A 776 GLU cc_start: 0.8264 (tt0) cc_final: 0.7744 (mm-30) REVERT: A 896 GLN cc_start: 0.7409 (mp10) cc_final: 0.6612 (mm110) REVERT: A 956 MET cc_start: 0.8849 (tpt) cc_final: 0.8495 (tpp) REVERT: A 961 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8594 (p) REVERT: A 989 ILE cc_start: 0.8550 (mt) cc_final: 0.8293 (mp) REVERT: A 997 ARG cc_start: 0.8079 (mtp180) cc_final: 0.7281 (mtm110) REVERT: A 1090 MET cc_start: 0.8660 (mmm) cc_final: 0.8423 (tpt) REVERT: A 1111 MET cc_start: 0.8170 (mtt) cc_final: 0.7777 (mtp) REVERT: A 1123 ARG cc_start: 0.8913 (ttt-90) cc_final: 0.8707 (ttt-90) REVERT: A 1133 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8103 (mmtp) REVERT: A 1317 MET cc_start: 0.7868 (mtm) cc_final: 0.7610 (mtp) REVERT: A 1340 THR cc_start: 0.7503 (p) cc_final: 0.7188 (m) outliers start: 49 outliers final: 26 residues processed: 206 average time/residue: 1.2810 time to fit residues: 286.7584 Evaluate side-chains 202 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 GLN Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1043 GLU Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1086 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1337 ASP Chi-restraints excluded: chain A residue 1365 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 8 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 0.0970 chunk 46 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 463 ASN A 648 ASN A1314 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.128608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.094379 restraints weight = 17876.524| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.96 r_work: 0.2784 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12422 Z= 0.129 Angle : 0.523 9.714 16822 Z= 0.263 Chirality : 0.042 0.182 1939 Planarity : 0.004 0.041 2144 Dihedral : 4.524 45.285 1668 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.52 % Allowed : 14.36 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -0.06 (0.22), residues: 1526 helix: 0.78 (0.19), residues: 743 sheet: 0.36 (0.62), residues: 72 loop : -0.94 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 169 HIS 0.008 0.001 HIS A 475 PHE 0.014 0.001 PHE A 396 TYR 0.012 0.001 TYR A 977 ARG 0.003 0.000 ARG A1123 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 553) hydrogen bonds : angle 3.75758 ( 1621) SS BOND : bond 0.00145 ( 2) SS BOND : angle 1.75856 ( 4) covalent geometry : bond 0.00316 (12420) covalent geometry : angle 0.52266 (16818) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 174 time to evaluate : 1.355 Fit side-chains REVERT: D 283 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7686 (mtt) REVERT: D 304 LYS cc_start: 0.7503 (mttt) cc_final: 0.6885 (mptt) REVERT: B 300 ARG cc_start: 0.8836 (mtt180) cc_final: 0.8633 (mtm-85) REVERT: E 325 GLU cc_start: 0.8177 (pt0) cc_final: 0.7915 (pt0) REVERT: A 137 LYS cc_start: 0.7837 (tttt) cc_final: 0.7440 (ttmm) REVERT: A 377 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.7710 (mp10) REVERT: A 414 ARG cc_start: 0.8683 (mtp85) cc_final: 0.8413 (mtp-110) REVERT: A 492 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7717 (pm20) REVERT: A 680 ASP cc_start: 0.8959 (t0) cc_final: 0.8712 (t0) REVERT: A 702 LYS cc_start: 0.8793 (mttt) cc_final: 0.8565 (mttm) REVERT: A 776 GLU cc_start: 0.8268 (tt0) cc_final: 0.7753 (mm-30) REVERT: A 896 GLN cc_start: 0.7496 (mp10) cc_final: 0.6695 (mm110) REVERT: A 956 MET cc_start: 0.8855 (tpt) cc_final: 0.8533 (tpp) REVERT: A 961 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8578 (p) REVERT: A 989 ILE cc_start: 0.8511 (mt) cc_final: 0.8260 (mp) REVERT: A 997 ARG cc_start: 0.8059 (mtp180) cc_final: 0.7281 (mtm110) REVERT: A 1025 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: A 1042 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8270 (ttp) REVERT: A 1052 GLN cc_start: 0.8619 (tt0) cc_final: 0.8184 (mt0) REVERT: A 1090 MET cc_start: 0.8673 (mmm) cc_final: 0.8443 (tpt) REVERT: A 1111 MET cc_start: 0.8134 (mtt) cc_final: 0.7727 (mtp) REVERT: A 1123 ARG cc_start: 0.8855 (ttt-90) cc_final: 0.8608 (ttt-90) REVERT: A 1133 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8128 (mmtp) REVERT: A 1249 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8445 (pp) REVERT: A 1317 MET cc_start: 0.7783 (mtm) cc_final: 0.7529 (mtp) REVERT: A 1331 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8420 (t) REVERT: A 1334 LYS cc_start: 0.7411 (mttt) cc_final: 0.6642 (mppt) REVERT: A 1340 THR cc_start: 0.7444 (p) cc_final: 0.7137 (m) outliers start: 48 outliers final: 22 residues processed: 202 average time/residue: 1.3756 time to fit residues: 301.5790 Evaluate side-chains 201 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 GLN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1025 GLU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1043 GLU Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1086 SER Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1365 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 70 optimal weight: 0.0870 chunk 149 optimal weight: 20.0000 chunk 25 optimal weight: 0.6980 chunk 134 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 5 optimal weight: 0.0070 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN A 475 HIS A1314 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.133646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.099912 restraints weight = 32492.454| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.25 r_work: 0.2754 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12422 Z= 0.087 Angle : 0.476 10.851 16822 Z= 0.240 Chirality : 0.040 0.153 1939 Planarity : 0.004 0.041 2144 Dihedral : 4.197 40.177 1668 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.42 % Allowed : 15.75 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 0.30 (0.22), residues: 1526 helix: 1.12 (0.19), residues: 745 sheet: 0.41 (0.62), residues: 72 loop : -0.80 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 169 HIS 0.004 0.001 HIS A 27 PHE 0.014 0.001 PHE A 396 TYR 0.011 0.001 TYR A 908 ARG 0.006 0.000 ARG A 276 Details of bonding type rmsd hydrogen bonds : bond 0.02848 ( 553) hydrogen bonds : angle 3.53894 ( 1621) SS BOND : bond 0.00199 ( 2) SS BOND : angle 1.62411 ( 4) covalent geometry : bond 0.00200 (12420) covalent geometry : angle 0.47589 (16818) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 1.271 Fit side-chains REVERT: D 282 MET cc_start: 0.8407 (mtm) cc_final: 0.8162 (mtp) REVERT: D 304 LYS cc_start: 0.7557 (mttt) cc_final: 0.6860 (mmtt) REVERT: C 276 MET cc_start: 0.8215 (mtt) cc_final: 0.7906 (mtt) REVERT: E 325 GLU cc_start: 0.8150 (pt0) cc_final: 0.7855 (pt0) REVERT: A 137 LYS cc_start: 0.7781 (tttt) cc_final: 0.7413 (ttmm) REVERT: A 414 ARG cc_start: 0.8556 (mtp85) cc_final: 0.8341 (mtp-110) REVERT: A 492 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7705 (pm20) REVERT: A 520 LYS cc_start: 0.8690 (ttmm) cc_final: 0.7955 (ttpp) REVERT: A 543 LYS cc_start: 0.7466 (ptpt) cc_final: 0.6727 (mttt) REVERT: A 680 ASP cc_start: 0.8828 (t0) cc_final: 0.8588 (t0) REVERT: A 702 LYS cc_start: 0.8771 (mttt) cc_final: 0.8564 (mttm) REVERT: A 776 GLU cc_start: 0.8186 (tt0) cc_final: 0.7677 (mm-30) REVERT: A 826 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8405 (tttt) REVERT: A 873 MET cc_start: 0.9227 (mmm) cc_final: 0.9023 (mmp) REVERT: A 896 GLN cc_start: 0.7429 (mp10) cc_final: 0.6717 (mm-40) REVERT: A 956 MET cc_start: 0.8829 (tpt) cc_final: 0.8526 (tpp) REVERT: A 961 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8619 (p) REVERT: A 997 ARG cc_start: 0.8012 (mtp180) cc_final: 0.7254 (mtm110) REVERT: A 1042 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8149 (ttp) REVERT: A 1052 GLN cc_start: 0.8490 (tt0) cc_final: 0.8140 (mt0) REVERT: A 1090 MET cc_start: 0.8587 (mmm) cc_final: 0.8348 (tpt) REVERT: A 1111 MET cc_start: 0.8087 (mtt) cc_final: 0.7714 (mtp) REVERT: A 1133 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8103 (mmtp) REVERT: A 1249 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8434 (pp) REVERT: A 1331 THR cc_start: 0.8736 (p) cc_final: 0.8530 (t) REVERT: A 1334 LYS cc_start: 0.7444 (mttt) cc_final: 0.6685 (mppt) REVERT: A 1340 THR cc_start: 0.7277 (p) cc_final: 0.7051 (m) outliers start: 33 outliers final: 18 residues processed: 201 average time/residue: 1.3265 time to fit residues: 288.2712 Evaluate side-chains 196 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1365 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 104 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 0.0070 chunk 100 optimal weight: 0.5980 chunk 112 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 146 optimal weight: 20.0000 chunk 4 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 ASN A 463 ASN A 475 HIS A 859 ASN A 974 ASN A1314 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.133410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.098154 restraints weight = 24915.246| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.47 r_work: 0.2787 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12422 Z= 0.087 Angle : 0.472 10.169 16822 Z= 0.237 Chirality : 0.039 0.146 1939 Planarity : 0.004 0.050 2144 Dihedral : 4.103 38.565 1668 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.27 % Allowed : 16.48 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 0.46 (0.22), residues: 1526 helix: 1.25 (0.19), residues: 749 sheet: 0.37 (0.60), residues: 72 loop : -0.72 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 169 HIS 0.005 0.001 HIS A 27 PHE 0.015 0.001 PHE A 396 TYR 0.010 0.001 TYR A 908 ARG 0.008 0.000 ARG A1189 Details of bonding type rmsd hydrogen bonds : bond 0.02825 ( 553) hydrogen bonds : angle 3.48190 ( 1621) SS BOND : bond 0.00198 ( 2) SS BOND : angle 1.53494 ( 4) covalent geometry : bond 0.00201 (12420) covalent geometry : angle 0.47144 (16818) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 1.587 Fit side-chains REVERT: D 282 MET cc_start: 0.8503 (mtm) cc_final: 0.8255 (mtp) REVERT: D 304 LYS cc_start: 0.7483 (mttt) cc_final: 0.6744 (mmtt) REVERT: E 325 GLU cc_start: 0.8150 (pt0) cc_final: 0.7850 (pt0) REVERT: A 137 LYS cc_start: 0.7810 (tttt) cc_final: 0.7460 (ttmm) REVERT: A 329 ARG cc_start: 0.7993 (ttp80) cc_final: 0.7523 (pmm-80) REVERT: A 414 ARG cc_start: 0.8696 (mtp85) cc_final: 0.8452 (mtp-110) REVERT: A 492 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7720 (pm20) REVERT: A 520 LYS cc_start: 0.8657 (ttmm) cc_final: 0.7902 (ttpp) REVERT: A 540 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.7642 (m-80) REVERT: A 543 LYS cc_start: 0.7504 (ptpt) cc_final: 0.6694 (mttt) REVERT: A 776 GLU cc_start: 0.8373 (tt0) cc_final: 0.7855 (mm-30) REVERT: A 873 MET cc_start: 0.9253 (mmm) cc_final: 0.9049 (mmp) REVERT: A 896 GLN cc_start: 0.7443 (mp10) cc_final: 0.6699 (mm-40) REVERT: A 956 MET cc_start: 0.8838 (tpt) cc_final: 0.8539 (tpp) REVERT: A 961 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8524 (p) REVERT: A 1042 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8380 (ttp) REVERT: A 1052 GLN cc_start: 0.8610 (tt0) cc_final: 0.8285 (mt0) REVERT: A 1090 MET cc_start: 0.8689 (mmm) cc_final: 0.8486 (tpt) REVERT: A 1111 MET cc_start: 0.8081 (mtt) cc_final: 0.7672 (mtp) REVERT: A 1123 ARG cc_start: 0.8863 (ttt-90) cc_final: 0.8512 (ttt-90) REVERT: A 1133 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8132 (mmtp) REVERT: A 1249 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8458 (pp) REVERT: A 1340 THR cc_start: 0.7301 (p) cc_final: 0.7090 (m) REVERT: A 1370 ARG cc_start: 0.8078 (ptp90) cc_final: 0.7544 (ptt-90) outliers start: 31 outliers final: 17 residues processed: 190 average time/residue: 1.6325 time to fit residues: 336.0985 Evaluate side-chains 190 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1365 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 106 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 143 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 ASN E 306 HIS A 78 GLN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN A 475 HIS A 974 ASN A1314 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.130325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.095176 restraints weight = 22701.645| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.31 r_work: 0.2755 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12422 Z= 0.141 Angle : 0.523 10.215 16822 Z= 0.262 Chirality : 0.042 0.153 1939 Planarity : 0.004 0.041 2144 Dihedral : 4.315 44.152 1668 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.49 % Allowed : 16.48 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 0.40 (0.22), residues: 1526 helix: 1.11 (0.19), residues: 755 sheet: 0.42 (0.59), residues: 72 loop : -0.65 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 169 HIS 0.006 0.001 HIS A 27 PHE 0.015 0.001 PHE A 396 TYR 0.019 0.001 TYR A 134 ARG 0.009 0.000 ARG A1189 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 553) hydrogen bonds : angle 3.61671 ( 1621) SS BOND : bond 0.00155 ( 2) SS BOND : angle 1.56003 ( 4) covalent geometry : bond 0.00349 (12420) covalent geometry : angle 0.52226 (16818) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 1.409 Fit side-chains REVERT: D 304 LYS cc_start: 0.7495 (mttt) cc_final: 0.6869 (mptt) REVERT: C 305 SER cc_start: 0.7870 (t) cc_final: 0.7592 (m) REVERT: E 325 GLU cc_start: 0.8189 (pt0) cc_final: 0.7859 (pt0) REVERT: A 137 LYS cc_start: 0.7769 (tttt) cc_final: 0.7395 (ttmm) REVERT: A 329 ARG cc_start: 0.7980 (ttp80) cc_final: 0.7466 (pmm-80) REVERT: A 457 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8521 (mm-30) REVERT: A 492 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7674 (pm20) REVERT: A 520 LYS cc_start: 0.8638 (ttmm) cc_final: 0.7848 (ttpp) REVERT: A 776 GLU cc_start: 0.8304 (tt0) cc_final: 0.7787 (mm-30) REVERT: A 896 GLN cc_start: 0.7451 (mp10) cc_final: 0.6687 (mm-40) REVERT: A 956 MET cc_start: 0.8815 (tpt) cc_final: 0.8528 (tpp) REVERT: A 961 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8511 (p) REVERT: A 1042 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8319 (ttp) REVERT: A 1052 GLN cc_start: 0.8598 (tt0) cc_final: 0.8232 (mt0) REVERT: A 1090 MET cc_start: 0.8683 (mmm) cc_final: 0.8441 (tpt) REVERT: A 1111 MET cc_start: 0.8133 (mtt) cc_final: 0.7725 (mtp) REVERT: A 1123 ARG cc_start: 0.8824 (ttt-90) cc_final: 0.8466 (ttt-90) REVERT: A 1133 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8132 (mmtp) REVERT: A 1249 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8347 (pp) REVERT: A 1340 THR cc_start: 0.7410 (p) cc_final: 0.7175 (m) outliers start: 34 outliers final: 20 residues processed: 189 average time/residue: 1.4871 time to fit residues: 306.1444 Evaluate side-chains 195 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 GLN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1086 SER Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1365 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 143 optimal weight: 0.0170 chunk 28 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 109 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 75 optimal weight: 0.0270 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 333 GLN A 78 GLN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN A 475 HIS A 749 GLN A 974 ASN A1314 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.135508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.100639 restraints weight = 23355.274| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.39 r_work: 0.2821 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12422 Z= 0.080 Angle : 0.464 9.497 16822 Z= 0.234 Chirality : 0.039 0.141 1939 Planarity : 0.004 0.041 2144 Dihedral : 4.053 39.229 1668 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.98 % Allowed : 17.07 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 0.67 (0.22), residues: 1526 helix: 1.41 (0.20), residues: 751 sheet: 0.46 (0.58), residues: 72 loop : -0.59 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1227 HIS 0.008 0.001 HIS A 475 PHE 0.014 0.001 PHE A 396 TYR 0.020 0.001 TYR A 134 ARG 0.008 0.000 ARG A1189 Details of bonding type rmsd hydrogen bonds : bond 0.02678 ( 553) hydrogen bonds : angle 3.42681 ( 1621) SS BOND : bond 0.00204 ( 2) SS BOND : angle 1.49190 ( 4) covalent geometry : bond 0.00177 (12420) covalent geometry : angle 0.46318 (16818) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 1.320 Fit side-chains REVERT: D 304 LYS cc_start: 0.7419 (mttt) cc_final: 0.6671 (mmtt) REVERT: C 305 SER cc_start: 0.7740 (t) cc_final: 0.7538 (m) REVERT: B 282 MET cc_start: 0.7281 (mmt) cc_final: 0.6901 (mmt) REVERT: E 325 GLU cc_start: 0.8126 (pt0) cc_final: 0.7819 (pt0) REVERT: A 137 LYS cc_start: 0.7734 (tttt) cc_final: 0.7366 (ttmm) REVERT: A 329 ARG cc_start: 0.7970 (ttp80) cc_final: 0.7553 (pmm-80) REVERT: A 414 ARG cc_start: 0.8709 (mtp85) cc_final: 0.8469 (mtp-110) REVERT: A 475 HIS cc_start: 0.7935 (OUTLIER) cc_final: 0.7724 (p90) REVERT: A 492 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7652 (pm20) REVERT: A 520 LYS cc_start: 0.8632 (ttmm) cc_final: 0.7862 (ttpp) REVERT: A 540 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.7667 (m-80) REVERT: A 743 ARG cc_start: 0.7599 (mtp85) cc_final: 0.7391 (mtp-110) REVERT: A 776 GLU cc_start: 0.8284 (tt0) cc_final: 0.7759 (mm-30) REVERT: A 873 MET cc_start: 0.9204 (mmm) cc_final: 0.8995 (mmp) REVERT: A 896 GLN cc_start: 0.7380 (mp10) cc_final: 0.6613 (mm-40) REVERT: A 956 MET cc_start: 0.8852 (tpt) cc_final: 0.8475 (tpp) REVERT: A 961 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8433 (p) REVERT: A 1025 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7112 (tm-30) REVERT: A 1042 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8241 (ttp) REVERT: A 1052 GLN cc_start: 0.8613 (tt0) cc_final: 0.8267 (mt0) REVERT: A 1111 MET cc_start: 0.8029 (mtt) cc_final: 0.7567 (mtp) REVERT: A 1123 ARG cc_start: 0.8823 (ttt-90) cc_final: 0.8463 (ttt-90) REVERT: A 1249 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8338 (pp) REVERT: A 1334 LYS cc_start: 0.7363 (tppt) cc_final: 0.6823 (tppt) REVERT: A 1340 THR cc_start: 0.7209 (p) cc_final: 0.7004 (m) outliers start: 27 outliers final: 14 residues processed: 186 average time/residue: 1.3745 time to fit residues: 277.9608 Evaluate side-chains 189 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 GLN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1025 GLU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1365 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 56 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 105 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 148 optimal weight: 0.2980 chunk 12 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 333 GLN A 78 GLN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN A 475 HIS A 749 GLN A 974 ASN A1034 HIS A1314 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.130962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.096089 restraints weight = 25219.708| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.46 r_work: 0.2755 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12422 Z= 0.125 Angle : 0.511 9.591 16822 Z= 0.256 Chirality : 0.041 0.151 1939 Planarity : 0.004 0.040 2144 Dihedral : 4.201 41.564 1668 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.47 % Allowed : 18.10 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 0.60 (0.22), residues: 1526 helix: 1.31 (0.19), residues: 756 sheet: 0.50 (0.58), residues: 72 loop : -0.59 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 169 HIS 0.006 0.001 HIS A 27 PHE 0.015 0.001 PHE A 396 TYR 0.018 0.001 TYR A 134 ARG 0.008 0.000 ARG A1189 Details of bonding type rmsd hydrogen bonds : bond 0.03175 ( 553) hydrogen bonds : angle 3.56108 ( 1621) SS BOND : bond 0.00167 ( 2) SS BOND : angle 1.51978 ( 4) covalent geometry : bond 0.00307 (12420) covalent geometry : angle 0.51049 (16818) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 1.415 Fit side-chains REVERT: D 304 LYS cc_start: 0.7433 (mttt) cc_final: 0.6702 (mmtt) REVERT: C 276 MET cc_start: 0.8226 (mtt) cc_final: 0.8004 (mtt) REVERT: C 304 LYS cc_start: 0.8344 (mptp) cc_final: 0.8138 (mptp) REVERT: C 305 SER cc_start: 0.7870 (t) cc_final: 0.7617 (m) REVERT: E 325 GLU cc_start: 0.8155 (pt0) cc_final: 0.7815 (pt0) REVERT: A 137 LYS cc_start: 0.7731 (tttt) cc_final: 0.7362 (ttmm) REVERT: A 329 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7423 (pmm-80) REVERT: A 492 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7620 (pm20) REVERT: A 520 LYS cc_start: 0.8633 (ttmm) cc_final: 0.7852 (ttpp) REVERT: A 540 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.7682 (m-80) REVERT: A 776 GLU cc_start: 0.8292 (tt0) cc_final: 0.7767 (mm-30) REVERT: A 896 GLN cc_start: 0.7418 (mp10) cc_final: 0.6635 (mm-40) REVERT: A 956 MET cc_start: 0.8857 (tpt) cc_final: 0.8490 (tpp) REVERT: A 1042 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8321 (ttp) REVERT: A 1052 GLN cc_start: 0.8533 (tt0) cc_final: 0.8279 (mt0) REVERT: A 1111 MET cc_start: 0.8072 (mtt) cc_final: 0.7640 (mtp) REVERT: A 1123 ARG cc_start: 0.8839 (ttt-90) cc_final: 0.8584 (ttp80) REVERT: A 1249 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8412 (pp) REVERT: A 1334 LYS cc_start: 0.7321 (tppt) cc_final: 0.6865 (tppt) REVERT: A 1340 THR cc_start: 0.7339 (p) cc_final: 0.7111 (m) outliers start: 20 outliers final: 14 residues processed: 180 average time/residue: 1.3800 time to fit residues: 269.6206 Evaluate side-chains 184 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 540 TYR Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1365 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 78 optimal weight: 0.7980 chunk 58 optimal weight: 0.3980 chunk 38 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN A 475 HIS A 974 ASN A1314 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.132716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.098931 restraints weight = 28183.992| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.71 r_work: 0.2778 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12422 Z= 0.104 Angle : 0.496 9.598 16822 Z= 0.248 Chirality : 0.041 0.170 1939 Planarity : 0.004 0.039 2144 Dihedral : 4.167 42.119 1668 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.61 % Allowed : 17.80 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 0.69 (0.22), residues: 1526 helix: 1.38 (0.19), residues: 755 sheet: 0.53 (0.57), residues: 72 loop : -0.54 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1227 HIS 0.005 0.001 HIS A 27 PHE 0.014 0.001 PHE A 396 TYR 0.018 0.001 TYR A 134 ARG 0.008 0.000 ARG A1189 Details of bonding type rmsd hydrogen bonds : bond 0.03023 ( 553) hydrogen bonds : angle 3.51021 ( 1621) SS BOND : bond 0.00168 ( 2) SS BOND : angle 1.52093 ( 4) covalent geometry : bond 0.00251 (12420) covalent geometry : angle 0.49524 (16818) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10216.52 seconds wall clock time: 177 minutes 14.97 seconds (10634.97 seconds total)