Starting phenix.real_space_refine on Tue Jul 29 14:15:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yi3_33850/07_2025/7yi3_33850.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yi3_33850/07_2025/7yi3_33850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yi3_33850/07_2025/7yi3_33850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yi3_33850/07_2025/7yi3_33850.map" model { file = "/net/cci-nas-00/data/ceres_data/7yi3_33850/07_2025/7yi3_33850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yi3_33850/07_2025/7yi3_33850.cif" } resolution = 3.3 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 5 6.06 5 S 66 5.16 5 C 7300 2.51 5 N 1919 2.21 5 O 2135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11425 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4258 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 7, 'TRANS': 498} Chain breaks: 5 Chain: "B" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2923 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain: "C" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1473 Classifications: {'peptide': 182} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 174} Chain: "D" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2588 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 298} Chain breaks: 5 Chain: "E" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 178 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10169 SG CYS D 417 69.984 60.745 32.968 1.00 40.15 S ATOM 10196 SG CYS D 420 71.715 57.465 33.828 1.00 55.87 S ATOM 10452 SG CYS D 451 71.468 60.228 36.443 1.00 62.19 S ATOM 9108 SG CYS D 263 35.162 94.931 38.011 1.00 93.60 S ATOM 9125 SG CYS D 266 38.264 92.690 37.687 1.00 76.39 S ATOM 9278 SG CYS D 286 38.493 95.811 39.869 1.00 74.17 S ATOM 9413 SG CYS D 303 27.320 102.172 35.913 1.00108.66 S ATOM 9436 SG CYS D 306 23.561 104.664 35.015 1.00110.05 S ATOM 10357 SG CYS D 440 64.800 70.261 28.800 1.00 45.36 S ATOM 10383 SG CYS D 443 67.690 69.873 26.226 1.00 52.08 S ATOM 10572 SG CYS D 466 68.566 70.907 29.657 1.00 62.77 S Time building chain proxies: 6.98, per 1000 atoms: 0.61 Number of scatterers: 11425 At special positions: 0 Unit cell: (120.157, 139.643, 107.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 5 29.99 S 66 16.00 O 2135 8.00 N 1919 7.00 C 7300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 188 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" ND1 HIS D 448 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 420 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 417 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 451 " pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" ND1 HIS D 283 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 266 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 286 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 263 " pdb=" ZN D 703 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 303 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 306 " pdb=" ZN D 704 " pdb="ZN ZN D 704 " - pdb=" NE2 HIS D 469 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 466 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 443 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 440 " Number of angles added : 9 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2652 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 7 sheets defined 54.5% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 665 through 677 Processing helix chain 'A' and resid 678 through 694 removed outlier: 3.724A pdb=" N GLU A 684 " --> pdb=" O HIS A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 711 removed outlier: 3.506A pdb=" N LEU A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 722 Processing helix chain 'A' and resid 759 through 763 Processing helix chain 'A' and resid 771 through 777 Processing helix chain 'A' and resid 785 through 790 removed outlier: 3.866A pdb=" N ALA A 789 " --> pdb=" O HIS A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 838 Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 875 through 885 Processing helix chain 'A' and resid 891 through 922 removed outlier: 4.094A pdb=" N LYS A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 928 removed outlier: 3.884A pdb=" N LEU A 928 " --> pdb=" O PHE A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 934 removed outlier: 4.142A pdb=" N THR A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 943 Processing helix chain 'A' and resid 944 through 961 Processing helix chain 'A' and resid 983 through 999 Processing helix chain 'A' and resid 1003 through 1023 Processing helix chain 'A' and resid 1141 through 1164 removed outlier: 4.157A pdb=" N MET A1164 " --> pdb=" O GLU A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1174 Processing helix chain 'A' and resid 1189 through 1194 removed outlier: 4.162A pdb=" N MET A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1217 Processing helix chain 'A' and resid 1220 through 1233 Processing helix chain 'A' and resid 1236 through 1240 removed outlier: 3.682A pdb=" N LEU A1239 " --> pdb=" O ALA A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1259 Processing helix chain 'A' and resid 1259 through 1276 Processing helix chain 'A' and resid 1280 through 1294 removed outlier: 4.373A pdb=" N ILE A1284 " --> pdb=" O ALA A1280 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS A1293 " --> pdb=" O GLN A1289 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.794A pdb=" N TYR B 32 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 54 removed outlier: 3.858A pdb=" N ARG B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 79 through 87 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 98 through 105 Processing helix chain 'B' and resid 115 through 137 Processing helix chain 'B' and resid 164 through 177 removed outlier: 3.594A pdb=" N ARG B 175 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 243 through 262 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 287 through 300 removed outlier: 4.592A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 330 Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.520A pdb=" N TYR B 346 " --> pdb=" O TYR B 343 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY B 348 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 381 Processing helix chain 'C' and resid 225 through 241 Processing helix chain 'C' and resid 253 through 267 removed outlier: 3.936A pdb=" N GLN C 267 " --> pdb=" O HIS C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 297 removed outlier: 3.798A pdb=" N LEU C 278 " --> pdb=" O SER C 274 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER C 279 " --> pdb=" O GLN C 275 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLY C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASN C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 316 removed outlier: 3.607A pdb=" N ASP C 316 " --> pdb=" O LYS C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 325 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.501A pdb=" N SER C 343 " --> pdb=" O PRO C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 369 removed outlier: 3.522A pdb=" N GLN C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU C 354 " --> pdb=" O GLN C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 401 removed outlier: 3.599A pdb=" N MET C 401 " --> pdb=" O VAL C 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 182 through 187 removed outlier: 4.419A pdb=" N GLY D 186 " --> pdb=" O SER D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 312 Processing helix chain 'D' and resid 317 through 331 removed outlier: 3.758A pdb=" N LYS D 321 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASN D 331 " --> pdb=" O ILE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 344 removed outlier: 4.374A pdb=" N ASP D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 407 Processing helix chain 'D' and resid 430 through 434 Processing helix chain 'D' and resid 544 through 562 removed outlier: 3.668A pdb=" N LYS D 548 " --> pdb=" O GLU D 544 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR D 549 " --> pdb=" O ASN D 545 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE D 552 " --> pdb=" O LYS D 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 563 Processing sheet with id=AA1, first strand: chain 'A' and resid 756 through 757 removed outlier: 3.566A pdb=" N VAL A 783 " --> pdb=" O LYS A 756 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 975 through 978 Processing sheet with id=AA3, first strand: chain 'B' and resid 62 through 64 removed outlier: 6.866A pdb=" N VAL B 21 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N TYR B 64 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TYR B 23 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA B 142 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL B 267 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL B 308 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU B 269 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU B 181 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N GLN B 270 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE B 183 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N VAL B 234 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL B 236 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N SER B 207 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU B 238 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N HIS B 209 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 244 through 246 Processing sheet with id=AA5, first strand: chain 'D' and resid 364 through 366 Processing sheet with id=AA6, first strand: chain 'D' and resid 473 through 476 Processing sheet with id=AA7, first strand: chain 'D' and resid 505 through 506 removed outlier: 3.778A pdb=" N TYR D 506 " --> pdb=" O ILE D 539 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1521 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: 3.96 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3658 1.34 - 1.46: 2696 1.46 - 1.58: 5218 1.58 - 1.70: 0 1.70 - 1.81: 100 Bond restraints: 11672 Sorted by residual: bond pdb=" CG PRO A 786 " pdb=" CD PRO A 786 " ideal model delta sigma weight residual 1.503 1.380 0.123 3.40e-02 8.65e+02 1.31e+01 bond pdb=" CA GLU D 104 " pdb=" C GLU D 104 " ideal model delta sigma weight residual 1.523 1.538 -0.015 1.41e-02 5.03e+03 1.17e+00 bond pdb=" CG PRO D 119 " pdb=" CD PRO D 119 " ideal model delta sigma weight residual 1.503 1.538 -0.035 3.40e-02 8.65e+02 1.05e+00 bond pdb=" CG1 ILE A1018 " pdb=" CD1 ILE A1018 " ideal model delta sigma weight residual 1.513 1.477 0.036 3.90e-02 6.57e+02 8.75e-01 bond pdb=" C ARG A 907 " pdb=" O ARG A 907 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.15e-02 7.56e+03 8.49e-01 ... (remaining 11667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 15593 2.19 - 4.38: 111 4.38 - 6.57: 21 6.57 - 8.77: 3 8.77 - 10.96: 2 Bond angle restraints: 15730 Sorted by residual: angle pdb=" N PRO A 786 " pdb=" CD PRO A 786 " pdb=" CG PRO A 786 " ideal model delta sigma weight residual 103.20 92.52 10.68 1.50e+00 4.44e-01 5.07e+01 angle pdb=" CA PRO A 786 " pdb=" N PRO A 786 " pdb=" CD PRO A 786 " ideal model delta sigma weight residual 112.00 103.45 8.55 1.40e+00 5.10e-01 3.73e+01 angle pdb=" CA PRO A 786 " pdb=" CB PRO A 786 " pdb=" CG PRO A 786 " ideal model delta sigma weight residual 104.50 96.77 7.73 1.90e+00 2.77e-01 1.65e+01 angle pdb=" CB PRO A 786 " pdb=" CG PRO A 786 " pdb=" CD PRO A 786 " ideal model delta sigma weight residual 106.10 95.14 10.96 3.20e+00 9.77e-02 1.17e+01 angle pdb=" C VAL B 106 " pdb=" CA VAL B 106 " pdb=" CB VAL B 106 " ideal model delta sigma weight residual 111.29 116.84 -5.55 1.64e+00 3.72e-01 1.15e+01 ... (remaining 15725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 6009 17.16 - 34.31: 779 34.31 - 51.47: 190 51.47 - 68.63: 36 68.63 - 85.78: 14 Dihedral angle restraints: 7028 sinusoidal: 2926 harmonic: 4102 Sorted by residual: dihedral pdb=" CA TYR B 347 " pdb=" C TYR B 347 " pdb=" N GLY B 348 " pdb=" CA GLY B 348 " ideal model delta harmonic sigma weight residual 180.00 157.43 22.57 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ILE C 335 " pdb=" C ILE C 335 " pdb=" N SER C 336 " pdb=" CA SER C 336 " ideal model delta harmonic sigma weight residual 180.00 158.82 21.18 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA LYS B 153 " pdb=" C LYS B 153 " pdb=" N LYS B 154 " pdb=" CA LYS B 154 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 7025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1127 0.035 - 0.069: 417 0.069 - 0.104: 108 0.104 - 0.139: 35 0.139 - 0.173: 1 Chirality restraints: 1688 Sorted by residual: chirality pdb=" CB ILE D 312 " pdb=" CA ILE D 312 " pdb=" CG1 ILE D 312 " pdb=" CG2 ILE D 312 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CG LEU A 689 " pdb=" CB LEU A 689 " pdb=" CD1 LEU A 689 " pdb=" CD2 LEU A 689 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CB VAL B 106 " pdb=" CA VAL B 106 " pdb=" CG1 VAL B 106 " pdb=" CG2 VAL B 106 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 1685 not shown) Planarity restraints: 2005 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 118 " 0.079 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO D 119 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 785 " -0.073 5.00e-02 4.00e+02 1.06e-01 1.78e+01 pdb=" N PRO A 786 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO A 786 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 786 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR D 439 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C THR D 439 " -0.038 2.00e-02 2.50e+03 pdb=" O THR D 439 " 0.015 2.00e-02 2.50e+03 pdb=" N CYS D 440 " 0.013 2.00e-02 2.50e+03 ... (remaining 2002 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 99 2.59 - 3.17: 9437 3.17 - 3.75: 17650 3.75 - 4.32: 24863 4.32 - 4.90: 40761 Nonbonded interactions: 92810 Sorted by model distance: nonbonded pdb=" OD2 ASP B 186 " pdb="ZN ZN B 501 " model vdw 2.014 2.230 nonbonded pdb=" OG SER C 313 " pdb=" O LYS C 318 " model vdw 2.090 3.040 nonbonded pdb=" OG SER B 123 " pdb=" OD2 ASP B 165 " model vdw 2.106 3.040 nonbonded pdb=" OD2 ASP B 244 " pdb=" OG SER B 287 " model vdw 2.167 3.040 nonbonded pdb=" O ILE C 342 " pdb=" OG1 THR C 345 " model vdw 2.184 3.040 ... (remaining 92805 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.030 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 : 0.003 0.123 11687 Z= 0.124 Angle : 0.527 10.958 15739 Z= 0.286 Chirality : 0.040 0.173 1688 Planarity : 0.005 0.120 2005 Dihedral : 16.299 85.785 4376 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.16 % Allowed : 21.13 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.23), residues: 1362 helix: 0.85 (0.20), residues: 712 sheet: -0.58 (0.60), residues: 85 loop : -1.50 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 261 HIS 0.003 0.001 HIS A1252 PHE 0.018 0.001 PHE A1305 TYR 0.015 0.001 TYR B 347 ARG 0.003 0.000 ARG D 369 Details of bonding type rmsd hydrogen bonds : bond 0.14657 ( 531) hydrogen bonds : angle 6.03494 ( 1521) metal coordination : bond 0.00570 ( 15) metal coordination : angle 2.76105 ( 9) covalent geometry : bond 0.00278 (11672) covalent geometry : angle 0.52315 (15730) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 1.295 Fit side-chains revert: symmetry clash REVERT: A 1164 MET cc_start: 0.8311 (ptt) cc_final: 0.8083 (ptt) REVERT: D 548 LYS cc_start: 0.7389 (mtmt) cc_final: 0.6844 (mtmt) outliers start: 2 outliers final: 0 residues processed: 111 average time/residue: 0.2852 time to fit residues: 44.9156 Evaluate side-chains 105 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN C 275 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.130010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.107051 restraints weight = 19133.904| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.94 r_work: 0.3337 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.0599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11687 Z= 0.141 Angle : 0.525 6.587 15739 Z= 0.280 Chirality : 0.040 0.137 1688 Planarity : 0.004 0.073 2005 Dihedral : 4.575 23.094 1511 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.36 % Allowed : 19.25 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.04 (0.23), residues: 1362 helix: 1.08 (0.19), residues: 705 sheet: -0.41 (0.62), residues: 84 loop : -1.39 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1223 HIS 0.004 0.001 HIS B 49 PHE 0.013 0.001 PHE D 308 TYR 0.018 0.001 TYR B 347 ARG 0.003 0.000 ARG B 44 Details of bonding type rmsd hydrogen bonds : bond 0.04937 ( 531) hydrogen bonds : angle 4.64735 ( 1521) metal coordination : bond 0.00559 ( 15) metal coordination : angle 2.82584 ( 9) covalent geometry : bond 0.00312 (11672) covalent geometry : angle 0.52113 (15730) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 1.427 Fit side-chains REVERT: A 1164 MET cc_start: 0.8427 (ptt) cc_final: 0.8226 (ptt) REVERT: A 1288 LEU cc_start: 0.6468 (OUTLIER) cc_final: 0.6178 (mm) REVERT: D 116 ASN cc_start: 0.6837 (OUTLIER) cc_final: 0.6295 (t0) REVERT: D 312 ILE cc_start: 0.5998 (OUTLIER) cc_final: 0.5672 (mt) REVERT: D 552 PHE cc_start: 0.7407 (m-80) cc_final: 0.7046 (m-10) outliers start: 30 outliers final: 15 residues processed: 138 average time/residue: 0.2369 time to fit residues: 48.0031 Evaluate side-chains 120 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 774 CYS Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 26 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 0.3980 chunk 32 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 119 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN D 116 ASN D 342 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.130516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.107675 restraints weight = 19275.928| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.94 r_work: 0.3345 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11687 Z= 0.122 Angle : 0.496 6.045 15739 Z= 0.265 Chirality : 0.040 0.152 1688 Planarity : 0.004 0.056 2005 Dihedral : 4.459 22.949 1511 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.44 % Allowed : 20.35 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.09 (0.23), residues: 1362 helix: 1.20 (0.19), residues: 703 sheet: -0.27 (0.62), residues: 84 loop : -1.34 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1223 HIS 0.004 0.001 HIS B 49 PHE 0.013 0.001 PHE A1305 TYR 0.016 0.001 TYR B 347 ARG 0.003 0.000 ARG D 369 Details of bonding type rmsd hydrogen bonds : bond 0.04568 ( 531) hydrogen bonds : angle 4.43702 ( 1521) metal coordination : bond 0.00483 ( 15) metal coordination : angle 2.60290 ( 9) covalent geometry : bond 0.00262 (11672) covalent geometry : angle 0.49267 (15730) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 1.447 Fit side-chains REVERT: A 818 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7978 (m-30) REVERT: A 989 LEU cc_start: 0.8222 (mt) cc_final: 0.7887 (mm) REVERT: A 1164 MET cc_start: 0.8414 (ptt) cc_final: 0.8200 (ptt) REVERT: A 1288 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.6003 (mm) REVERT: D 310 ILE cc_start: 0.6014 (OUTLIER) cc_final: 0.5497 (mm) REVERT: D 312 ILE cc_start: 0.6183 (OUTLIER) cc_final: 0.5730 (mt) REVERT: D 552 PHE cc_start: 0.7448 (m-10) cc_final: 0.7063 (m-10) outliers start: 31 outliers final: 16 residues processed: 139 average time/residue: 0.2244 time to fit residues: 46.4983 Evaluate side-chains 123 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 774 CYS Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 470 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 118 optimal weight: 0.3980 chunk 133 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 79 optimal weight: 0.0270 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.132034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.108912 restraints weight = 19113.220| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.93 r_work: 0.3375 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11687 Z= 0.100 Angle : 0.469 5.478 15739 Z= 0.251 Chirality : 0.039 0.151 1688 Planarity : 0.004 0.060 2005 Dihedral : 4.261 22.802 1511 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.12 % Allowed : 21.52 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.25 (0.23), residues: 1362 helix: 1.32 (0.19), residues: 710 sheet: -0.19 (0.63), residues: 84 loop : -1.29 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1223 HIS 0.004 0.001 HIS B 49 PHE 0.011 0.001 PHE A 995 TYR 0.014 0.001 TYR B 347 ARG 0.003 0.000 ARG D 369 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 531) hydrogen bonds : angle 4.26109 ( 1521) metal coordination : bond 0.00408 ( 15) metal coordination : angle 2.31274 ( 9) covalent geometry : bond 0.00204 (11672) covalent geometry : angle 0.46625 (15730) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 1.442 Fit side-chains REVERT: A 719 TRP cc_start: 0.6544 (t60) cc_final: 0.6134 (t60) REVERT: A 818 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7969 (m-30) REVERT: C 360 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7811 (mt-10) REVERT: D 310 ILE cc_start: 0.6013 (OUTLIER) cc_final: 0.5501 (mm) REVERT: D 312 ILE cc_start: 0.6133 (OUTLIER) cc_final: 0.5692 (mt) REVERT: D 495 GLN cc_start: 0.7315 (mt0) cc_final: 0.7089 (mt0) REVERT: D 552 PHE cc_start: 0.7434 (m-10) cc_final: 0.7028 (m-10) outliers start: 27 outliers final: 17 residues processed: 137 average time/residue: 0.2272 time to fit residues: 46.6377 Evaluate side-chains 131 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 774 CYS Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 516 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 99 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 37 optimal weight: 7.9990 chunk 127 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN D 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.129428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.106394 restraints weight = 19003.837| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.86 r_work: 0.3340 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11687 Z= 0.151 Angle : 0.525 6.992 15739 Z= 0.278 Chirality : 0.041 0.153 1688 Planarity : 0.004 0.068 2005 Dihedral : 4.517 23.387 1511 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.83 % Allowed : 21.37 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.07 (0.23), residues: 1362 helix: 1.12 (0.19), residues: 721 sheet: -0.28 (0.61), residues: 85 loop : -1.34 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1223 HIS 0.004 0.001 HIS A 815 PHE 0.012 0.001 PHE D 308 TYR 0.019 0.002 TYR B 347 ARG 0.002 0.000 ARG D 369 Details of bonding type rmsd hydrogen bonds : bond 0.04759 ( 531) hydrogen bonds : angle 4.36247 ( 1521) metal coordination : bond 0.00595 ( 15) metal coordination : angle 2.98773 ( 9) covalent geometry : bond 0.00339 (11672) covalent geometry : angle 0.51990 (15730) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 1.737 Fit side-chains REVERT: A 1288 LEU cc_start: 0.6249 (OUTLIER) cc_final: 0.5945 (mm) REVERT: B 238 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7982 (mt) REVERT: D 312 ILE cc_start: 0.5997 (OUTLIER) cc_final: 0.5632 (mt) REVERT: D 552 PHE cc_start: 0.7440 (m-10) cc_final: 0.7028 (m-10) outliers start: 36 outliers final: 22 residues processed: 141 average time/residue: 0.2469 time to fit residues: 51.7675 Evaluate side-chains 128 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 774 CYS Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 516 ASN Chi-restraints excluded: chain D residue 562 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 97 optimal weight: 0.5980 chunk 31 optimal weight: 0.0770 chunk 73 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 119 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 921 GLN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN D 342 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.131272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.108447 restraints weight = 19344.159| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.95 r_work: 0.3358 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11687 Z= 0.107 Angle : 0.480 6.175 15739 Z= 0.255 Chirality : 0.039 0.156 1688 Planarity : 0.004 0.066 2005 Dihedral : 4.325 22.831 1511 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.75 % Allowed : 21.37 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.31 (0.23), residues: 1362 helix: 1.35 (0.19), residues: 707 sheet: -0.24 (0.58), residues: 94 loop : -1.22 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 261 HIS 0.004 0.001 HIS B 49 PHE 0.011 0.001 PHE D 308 TYR 0.015 0.001 TYR B 347 ARG 0.002 0.000 ARG D 369 Details of bonding type rmsd hydrogen bonds : bond 0.04254 ( 531) hydrogen bonds : angle 4.22791 ( 1521) metal coordination : bond 0.00493 ( 15) metal coordination : angle 2.50073 ( 9) covalent geometry : bond 0.00223 (11672) covalent geometry : angle 0.47650 (15730) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 1.585 Fit side-chains REVERT: A 818 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7985 (m-30) REVERT: A 1288 LEU cc_start: 0.6228 (OUTLIER) cc_final: 0.5935 (mm) REVERT: B 213 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6695 (mp0) REVERT: B 238 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7937 (mt) REVERT: D 312 ILE cc_start: 0.6157 (OUTLIER) cc_final: 0.5698 (mt) REVERT: D 552 PHE cc_start: 0.7436 (m-10) cc_final: 0.7085 (m-10) outliers start: 35 outliers final: 24 residues processed: 139 average time/residue: 0.2615 time to fit residues: 54.7954 Evaluate side-chains 132 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 774 CYS Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 516 ASN Chi-restraints excluded: chain D residue 562 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 89 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 108 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN D 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.130128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.107211 restraints weight = 19510.958| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.94 r_work: 0.3341 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11687 Z= 0.133 Angle : 0.510 7.508 15739 Z= 0.269 Chirality : 0.040 0.155 1688 Planarity : 0.004 0.072 2005 Dihedral : 4.429 23.255 1511 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.67 % Allowed : 21.60 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.24 (0.23), residues: 1362 helix: 1.25 (0.19), residues: 715 sheet: -0.29 (0.57), residues: 95 loop : -1.21 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1151 HIS 0.003 0.001 HIS A 815 PHE 0.012 0.001 PHE D 308 TYR 0.018 0.001 TYR B 347 ARG 0.004 0.000 ARG D 369 Details of bonding type rmsd hydrogen bonds : bond 0.04537 ( 531) hydrogen bonds : angle 4.28197 ( 1521) metal coordination : bond 0.00538 ( 15) metal coordination : angle 2.82148 ( 9) covalent geometry : bond 0.00295 (11672) covalent geometry : angle 0.50538 (15730) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 2.359 Fit side-chains REVERT: A 1288 LEU cc_start: 0.6228 (OUTLIER) cc_final: 0.5923 (mm) REVERT: B 238 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7959 (mt) REVERT: D 312 ILE cc_start: 0.6209 (OUTLIER) cc_final: 0.5750 (mt) REVERT: D 552 PHE cc_start: 0.7444 (m-10) cc_final: 0.7068 (m-10) outliers start: 34 outliers final: 26 residues processed: 134 average time/residue: 0.2807 time to fit residues: 57.6963 Evaluate side-chains 130 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 774 CYS Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 516 ASN Chi-restraints excluded: chain D residue 560 MET Chi-restraints excluded: chain D residue 562 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 18 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 124 optimal weight: 0.0770 chunk 67 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN D 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.130788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.107667 restraints weight = 19266.185| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.90 r_work: 0.3355 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11687 Z= 0.117 Angle : 0.490 6.336 15739 Z= 0.259 Chirality : 0.040 0.156 1688 Planarity : 0.004 0.072 2005 Dihedral : 4.363 22.698 1511 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.22 % Allowed : 20.97 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.31 (0.23), residues: 1362 helix: 1.29 (0.19), residues: 715 sheet: -0.26 (0.57), residues: 95 loop : -1.16 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 261 HIS 0.002 0.001 HIS B 49 PHE 0.011 0.001 PHE D 308 TYR 0.016 0.001 TYR B 347 ARG 0.004 0.000 ARG D 369 Details of bonding type rmsd hydrogen bonds : bond 0.04347 ( 531) hydrogen bonds : angle 4.22505 ( 1521) metal coordination : bond 0.00478 ( 15) metal coordination : angle 2.63554 ( 9) covalent geometry : bond 0.00251 (11672) covalent geometry : angle 0.48562 (15730) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 108 time to evaluate : 2.168 Fit side-chains REVERT: A 818 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7981 (m-30) REVERT: A 1288 LEU cc_start: 0.6217 (OUTLIER) cc_final: 0.5937 (mm) REVERT: B 213 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6812 (mp0) REVERT: B 238 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7930 (mt) REVERT: D 312 ILE cc_start: 0.6156 (OUTLIER) cc_final: 0.5678 (mt) REVERT: D 552 PHE cc_start: 0.7412 (m-10) cc_final: 0.7044 (m-10) outliers start: 41 outliers final: 29 residues processed: 144 average time/residue: 0.2866 time to fit residues: 62.6256 Evaluate side-chains 139 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 774 CYS Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 516 ASN Chi-restraints excluded: chain D residue 560 MET Chi-restraints excluded: chain D residue 562 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 73 optimal weight: 0.0570 chunk 65 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 89 optimal weight: 0.1980 chunk 62 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 121 optimal weight: 5.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN D 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.131985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.109033 restraints weight = 19273.085| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.87 r_work: 0.3385 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11687 Z= 0.102 Angle : 0.473 5.978 15739 Z= 0.251 Chirality : 0.039 0.156 1688 Planarity : 0.004 0.071 2005 Dihedral : 4.200 21.913 1511 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.75 % Allowed : 22.15 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.45 (0.23), residues: 1362 helix: 1.43 (0.19), residues: 708 sheet: -0.19 (0.57), residues: 95 loop : -1.10 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 719 HIS 0.003 0.001 HIS B 49 PHE 0.011 0.001 PHE A 995 TYR 0.014 0.001 TYR B 347 ARG 0.003 0.000 ARG D 369 Details of bonding type rmsd hydrogen bonds : bond 0.04056 ( 531) hydrogen bonds : angle 4.13490 ( 1521) metal coordination : bond 0.00430 ( 15) metal coordination : angle 2.40333 ( 9) covalent geometry : bond 0.00211 (11672) covalent geometry : angle 0.46935 (15730) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 1.492 Fit side-chains REVERT: A 719 TRP cc_start: 0.6779 (t60) cc_final: 0.6229 (t60) REVERT: A 818 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7990 (m-30) REVERT: A 1288 LEU cc_start: 0.6264 (OUTLIER) cc_final: 0.5982 (mm) REVERT: B 213 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6766 (mp0) REVERT: C 360 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7770 (mt-10) REVERT: D 312 ILE cc_start: 0.6150 (OUTLIER) cc_final: 0.5705 (mp) REVERT: D 495 GLN cc_start: 0.7139 (mt0) cc_final: 0.6925 (mt0) REVERT: D 552 PHE cc_start: 0.7367 (m-10) cc_final: 0.7003 (m-10) outliers start: 35 outliers final: 27 residues processed: 145 average time/residue: 0.3040 time to fit residues: 67.5622 Evaluate side-chains 139 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 516 ASN Chi-restraints excluded: chain D residue 560 MET Chi-restraints excluded: chain D residue 562 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 85 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 108 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 0.4980 chunk 36 optimal weight: 10.0000 chunk 32 optimal weight: 0.0970 chunk 135 optimal weight: 0.9980 chunk 107 optimal weight: 0.0040 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.0770 overall best weight: 0.2348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN D 342 ASN D 519 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.133821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.110957 restraints weight = 19080.515| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.90 r_work: 0.3401 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11687 Z= 0.091 Angle : 0.455 6.306 15739 Z= 0.242 Chirality : 0.039 0.156 1688 Planarity : 0.004 0.069 2005 Dihedral : 4.019 21.240 1511 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.28 % Allowed : 23.10 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.63 (0.24), residues: 1362 helix: 1.56 (0.20), residues: 708 sheet: 0.20 (0.59), residues: 90 loop : -1.05 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 261 HIS 0.004 0.000 HIS B 49 PHE 0.013 0.001 PHE D 170 TYR 0.012 0.001 TYR B 347 ARG 0.003 0.000 ARG D 369 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 531) hydrogen bonds : angle 4.02724 ( 1521) metal coordination : bond 0.00401 ( 15) metal coordination : angle 2.00198 ( 9) covalent geometry : bond 0.00177 (11672) covalent geometry : angle 0.45244 (15730) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 1.358 Fit side-chains REVERT: A 719 TRP cc_start: 0.6755 (t60) cc_final: 0.6253 (t60) REVERT: A 818 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.8010 (m-30) REVERT: D 312 ILE cc_start: 0.6081 (OUTLIER) cc_final: 0.5646 (mp) REVERT: D 552 PHE cc_start: 0.7280 (m-10) cc_final: 0.6928 (m-10) outliers start: 29 outliers final: 21 residues processed: 145 average time/residue: 0.2202 time to fit residues: 47.4743 Evaluate side-chains 135 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 516 ASN Chi-restraints excluded: chain D residue 560 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 79 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 105 optimal weight: 0.0370 chunk 77 optimal weight: 3.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1274 ASN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN C 350 GLN D 342 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.131461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.108871 restraints weight = 19128.867| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.93 r_work: 0.3365 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11687 Z= 0.116 Angle : 0.494 6.770 15739 Z= 0.261 Chirality : 0.040 0.156 1688 Planarity : 0.004 0.068 2005 Dihedral : 4.173 21.679 1511 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.20 % Allowed : 23.02 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.56 (0.23), residues: 1362 helix: 1.50 (0.20), residues: 709 sheet: 0.17 (0.59), residues: 90 loop : -1.08 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 719 HIS 0.003 0.001 HIS B 49 PHE 0.021 0.001 PHE A 720 TYR 0.016 0.001 TYR B 347 ARG 0.008 0.000 ARG A1273 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 531) hydrogen bonds : angle 4.12144 ( 1521) metal coordination : bond 0.00542 ( 15) metal coordination : angle 2.74112 ( 9) covalent geometry : bond 0.00250 (11672) covalent geometry : angle 0.48953 (15730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6892.25 seconds wall clock time: 126 minutes 22.40 seconds (7582.40 seconds total)