Starting phenix.real_space_refine on Tue Jun 10 17:12:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tj9_25920/06_2025/7tj9_25920.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tj9_25920/06_2025/7tj9_25920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tj9_25920/06_2025/7tj9_25920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tj9_25920/06_2025/7tj9_25920.map" model { file = "/net/cci-nas-00/data/ceres_data/7tj9_25920/06_2025/7tj9_25920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tj9_25920/06_2025/7tj9_25920.cif" } resolution = 2.9 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= 0.036 sd= 0.047 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 P 4 5.49 5 S 92 5.16 5 C 7379 2.51 5 N 1642 2.21 5 O 1858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 10975 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 9054 Classifications: {'peptide': 1111} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 1072} Chain breaks: 3 Chain: "B" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1322 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 6, 'TRANS': 155} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 515 Unusual residues: {'CLR': 2, 'NAG': 1, 'PEV': 3, 'PLM': 8, 'POV': 3, 'Q7G': 1} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 2, 'POV:plan-1': 1, 'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 7.13, per 1000 atoms: 0.65 Number of scatterers: 10975 At special positions: 0 Unit cell: (126.963, 114.15, 114.15, 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) S 92 16.00 P 4 15.00 O 1858 8.00 N 1642 7.00 C 7379 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 267 " - pdb=" SG CYS A 307 " distance=2.05 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 664 " distance=2.03 Simple disulfide: pdb=" SG CYS A 696 " - pdb=" SG CYS A 705 " distance=2.03 Simple disulfide: pdb=" SG CYS A1087 " - pdb=" SG CYS A1107 " distance=2.03 Simple disulfide: pdb=" SG CYS A1451 " - pdb=" SG CYS A1466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 48 " distance=2.03 Simple disulfide: pdb=" SG CYS B 45 " - pdb=" SG CYS B 120 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A2412 " - " ASN A1103 " " NAG B 301 " - " ASN B 121 " " NAG B 302 " - " ASN B 95 " " NAG B 303 " - " ASN B 113 " " NAG B 304 " - " ASN B 109 " " NAG C 1 " - " ASN A 309 " Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.3 seconds 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2410 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 68.6% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 117 through 136 removed outlier: 3.842A pdb=" N GLN A 121 " --> pdb=" O HIS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 167 Processing helix chain 'A' and resid 178 through 196 removed outlier: 3.722A pdb=" N TRP A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 183 " --> pdb=" O PRO A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 211 removed outlier: 3.518A pdb=" N THR A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU A 211 " --> pdb=" O THR A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 220 through 237 Processing helix chain 'A' and resid 237 through 260 Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 329 through 333 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 354 through 366 removed outlier: 4.243A pdb=" N LEU A 358 " --> pdb=" O TYR A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 382 removed outlier: 3.953A pdb=" N PHE A 374 " --> pdb=" O TYR A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 404 Processing helix chain 'A' and resid 507 through 524 removed outlier: 3.934A pdb=" N LEU A 511 " --> pdb=" O THR A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 559 removed outlier: 3.749A pdb=" N LEU A 537 " --> pdb=" O THR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 565 removed outlier: 3.706A pdb=" N PHE A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 585 removed outlier: 3.891A pdb=" N ILE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 609 removed outlier: 4.282A pdb=" N MET A 600 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR A 609 " --> pdb=" O LEU A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 656 removed outlier: 4.732A pdb=" N VAL A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ALA A 626 " --> pdb=" O ASN A 622 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP A 629 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LYS A 651 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ASN A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 660 Processing helix chain 'A' and resid 673 through 686 Processing helix chain 'A' and resid 690 through 700 removed outlier: 3.597A pdb=" N ASP A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 733 Proline residue: A 707 - end of helix removed outlier: 3.714A pdb=" N SER A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 933 Processing helix chain 'A' and resid 933 through 950 Processing helix chain 'A' and resid 951 through 954 Processing helix chain 'A' and resid 961 through 991 removed outlier: 3.646A pdb=" N ILE A 966 " --> pdb=" O LYS A 962 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 997 Processing helix chain 'A' and resid 998 through 1017 Processing helix chain 'A' and resid 1023 through 1034 removed outlier: 3.602A pdb=" N SER A1028 " --> pdb=" O PRO A1025 " (cutoff:3.500A) Proline residue: A1034 - end of helix Processing helix chain 'A' and resid 1035 through 1041 removed outlier: 3.764A pdb=" N SER A1039 " --> pdb=" O LEU A1035 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE A1041 " --> pdb=" O VAL A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1056 Processing helix chain 'A' and resid 1058 through 1081 Processing helix chain 'A' and resid 1103 through 1109 removed outlier: 3.548A pdb=" N CYS A1107 " --> pdb=" O ASN A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1140 Processing helix chain 'A' and resid 1143 through 1152 removed outlier: 3.501A pdb=" N ILE A1147 " --> pdb=" O GLY A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1168 No H-bonds generated for 'chain 'A' and resid 1166 through 1168' Processing helix chain 'A' and resid 1169 through 1180 removed outlier: 3.730A pdb=" N PHE A1173 " --> pdb=" O MET A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1204 Processing helix chain 'A' and resid 1211 through 1225 removed outlier: 4.313A pdb=" N LYS A1216 " --> pdb=" O VAL A1212 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN A1217 " --> pdb=" O LYS A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1245 through 1250 removed outlier: 3.588A pdb=" N THR A1249 " --> pdb=" O PHE A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1269 removed outlier: 3.530A pdb=" N MET A1268 " --> pdb=" O GLN A1264 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET A1269 " --> pdb=" O ALA A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1305 removed outlier: 3.524A pdb=" N ILE A1281 " --> pdb=" O LEU A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1335 Proline residue: A1332 - end of helix Processing helix chain 'A' and resid 1343 through 1351 removed outlier: 3.574A pdb=" N SER A1351 " --> pdb=" O LEU A1347 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1358 Processing helix chain 'A' and resid 1363 through 1403 removed outlier: 3.944A pdb=" N HIS A1367 " --> pdb=" O PRO A1363 " (cutoff:3.500A) Proline residue: A1372 - end of helix Proline residue: A1378 - end of helix removed outlier: 3.784A pdb=" N ALA A1403 " --> pdb=" O MET A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1419 through 1432 Processing helix chain 'A' and resid 1435 through 1444 removed outlier: 4.008A pdb=" N MET A1439 " --> pdb=" O GLY A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1445 through 1447 No H-bonds generated for 'chain 'A' and resid 1445 through 1447' Processing helix chain 'A' and resid 1468 through 1503 Processing helix chain 'B' and resid 152 through 186 Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 269 Processing sheet with id=AA2, first strand: chain 'A' and resid 1086 through 1088 Processing sheet with id=AA3, first strand: chain 'B' and resid 41 through 43 Processing sheet with id=AA4, first strand: chain 'B' and resid 72 through 77 removed outlier: 3.520A pdb=" N PHE B 72 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP B 62 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU B 76 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL B 60 " --> pdb=" O GLU B 76 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 122 " --> pdb=" O THR B 137 " (cutoff:3.500A) 651 hydrogen bonds defined for protein. 1854 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: 3.29 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3070 1.34 - 1.46: 2878 1.46 - 1.59: 4970 1.59 - 1.71: 177 1.71 - 1.84: 157 Bond restraints: 11252 Sorted by residual: bond pdb=" C29 POV A2403 " pdb="C210 POV A2403 " ideal model delta sigma weight residual 1.333 1.638 -0.305 2.00e-02 2.50e+03 2.33e+02 bond pdb=" O14 POV A2408 " pdb=" P POV A2408 " ideal model delta sigma weight residual 1.496 1.748 -0.252 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C09 Q7G A2418 " pdb=" C10 Q7G A2418 " ideal model delta sigma weight residual 1.533 1.716 -0.183 2.00e-02 2.50e+03 8.34e+01 bond pdb=" C31 POV A2402 " pdb=" O31 POV A2402 " ideal model delta sigma weight residual 1.327 1.506 -0.179 2.00e-02 2.50e+03 7.98e+01 bond pdb=" C31 POV A2408 " pdb=" O31 POV A2408 " ideal model delta sigma weight residual 1.327 1.504 -0.177 2.00e-02 2.50e+03 7.87e+01 ... (remaining 11247 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.64: 15075 4.64 - 9.28: 77 9.28 - 13.91: 14 13.91 - 18.55: 8 18.55 - 23.19: 1 Bond angle restraints: 15175 Sorted by residual: angle pdb=" C51 Q7G A2418 " pdb=" C61 Q7G A2418 " pdb=" O61 Q7G A2418 " ideal model delta sigma weight residual 107.71 130.90 -23.19 3.00e+00 1.11e-01 5.98e+01 angle pdb=" O3P PEV A2411 " pdb=" P PEV A2411 " pdb=" O4P PEV A2411 " ideal model delta sigma weight residual 93.57 110.99 -17.42 3.00e+00 1.11e-01 3.37e+01 angle pdb=" C74 Q7G A2418 " pdb=" C73 Q7G A2418 " pdb=" O80 Q7G A2418 " ideal model delta sigma weight residual 107.49 90.40 17.09 3.00e+00 1.11e-01 3.24e+01 angle pdb=" O3P PEV A2401 " pdb=" P PEV A2401 " pdb=" O4P PEV A2401 " ideal model delta sigma weight residual 93.57 110.49 -16.92 3.00e+00 1.11e-01 3.18e+01 angle pdb=" O3P PEV A2405 " pdb=" P PEV A2405 " pdb=" O4P PEV A2405 " ideal model delta sigma weight residual 93.57 110.44 -16.87 3.00e+00 1.11e-01 3.16e+01 ... (remaining 15170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.09: 6512 27.09 - 54.18: 375 54.18 - 81.27: 67 81.27 - 108.36: 33 108.36 - 135.45: 32 Dihedral angle restraints: 7019 sinusoidal: 3291 harmonic: 3728 Sorted by residual: dihedral pdb=" CB CYS A 267 " pdb=" SG CYS A 267 " pdb=" SG CYS A 307 " pdb=" CB CYS A 307 " ideal model delta sinusoidal sigma weight residual -86.00 -155.57 69.57 1 1.00e+01 1.00e-02 6.25e+01 dihedral pdb=" CA HIS A 560 " pdb=" C HIS A 560 " pdb=" N PRO A 561 " pdb=" CA PRO A 561 " ideal model delta harmonic sigma weight residual 180.00 -151.62 -28.38 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" C3 PEV A2401 " pdb=" C1 PEV A2401 " pdb=" C2 PEV A2401 " pdb=" O3P PEV A2401 " ideal model delta sinusoidal sigma weight residual -67.20 68.25 -135.45 1 3.00e+01 1.11e-03 1.83e+01 ... (remaining 7016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 1712 0.180 - 0.360: 12 0.360 - 0.540: 2 0.540 - 0.720: 0 0.720 - 0.900: 1 Chirality restraints: 1727 Sorted by residual: chirality pdb=" C1 NAG B 301 " pdb=" ND2 ASN B 121 " pdb=" C2 NAG B 301 " pdb=" O5 NAG B 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.03e+01 chirality pdb=" C2 POV A2402 " pdb=" C1 POV A2402 " pdb=" C3 POV A2402 " pdb=" O21 POV A2402 " both_signs ideal model delta sigma weight residual False 2.43 2.92 -0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" C17 CLR A2417 " pdb=" C13 CLR A2417 " pdb=" C16 CLR A2417 " pdb=" C20 CLR A2417 " both_signs ideal model delta sigma weight residual False 2.55 2.93 -0.38 2.00e-01 2.50e+01 3.57e+00 ... (remaining 1724 not shown) Planarity restraints: 1797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 303 " -0.331 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG B 303 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG B 303 " -0.140 2.00e-02 2.50e+03 pdb=" N2 NAG B 303 " 0.511 2.00e-02 2.50e+03 pdb=" O7 NAG B 303 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 301 " 0.289 2.00e-02 2.50e+03 2.42e-01 7.32e+02 pdb=" C7 NAG B 301 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG B 301 " 0.185 2.00e-02 2.50e+03 pdb=" N2 NAG B 301 " -0.412 2.00e-02 2.50e+03 pdb=" O7 NAG B 301 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2412 " 0.239 2.00e-02 2.50e+03 2.00e-01 5.00e+02 pdb=" C7 NAG A2412 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG A2412 " 0.163 2.00e-02 2.50e+03 pdb=" N2 NAG A2412 " -0.336 2.00e-02 2.50e+03 pdb=" O7 NAG A2412 " -0.006 2.00e-02 2.50e+03 ... (remaining 1794 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 433 2.71 - 3.26: 11129 3.26 - 3.81: 17183 3.81 - 4.35: 21530 4.35 - 4.90: 36731 Nonbonded interactions: 87006 Sorted by model distance: nonbonded pdb=" O THR A 207 " pdb=" OG1 THR A 210 " model vdw 2.167 3.040 nonbonded pdb=" OD1 ASN A 149 " pdb=" OH TYR A 196 " model vdw 2.210 3.040 nonbonded pdb=" O ALA A 642 " pdb=" OG SER A 677 " model vdw 2.238 3.040 nonbonded pdb=" O THR B 111 " pdb=" OD1 ASP B 114 " model vdw 2.253 3.040 nonbonded pdb=" O PHE A1072 " pdb=" OH TYR A1172 " model vdw 2.297 3.040 ... (remaining 87001 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.370 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 : 0.016 0.305 11266 Z= 0.770 Angle : 1.023 23.190 15210 Z= 0.443 Chirality : 0.054 0.900 1727 Planarity : 0.013 0.287 1791 Dihedral : 20.667 135.454 4588 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.09 % Allowed : 0.78 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.12 (0.24), residues: 1263 helix: 1.16 (0.18), residues: 770 sheet: -1.47 (0.61), residues: 74 loop : -1.64 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP A1144 HIS 0.005 0.001 HIS B 131 PHE 0.031 0.002 PHE A1031 TYR 0.021 0.002 TYR A 354 ARG 0.004 0.000 ARG A 602 Details of bonding type rmsd link_NAG-ASN : bond 0.01214 ( 6) link_NAG-ASN : angle 3.58645 ( 18) link_BETA1-4 : bond 0.00408 ( 1) link_BETA1-4 : angle 2.28844 ( 3) hydrogen bonds : bond 0.14257 ( 651) hydrogen bonds : angle 5.48523 ( 1854) SS BOND : bond 0.00579 ( 7) SS BOND : angle 1.99316 ( 14) covalent geometry : bond 0.01563 (11252) covalent geometry : angle 1.01410 (15175) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.8162 (tp30) cc_final: 0.7845 (tp30) REVERT: B 37 GLN cc_start: 0.8270 (tm-30) cc_final: 0.8063 (tm-30) REVERT: B 97 SER cc_start: 0.9245 (m) cc_final: 0.9030 (m) outliers start: 1 outliers final: 1 residues processed: 265 average time/residue: 1.0432 time to fit residues: 304.8539 Evaluate side-chains 213 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 113 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 ASN A 676 HIS ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1195 ASN A1287 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.162971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.133749 restraints weight = 13821.689| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.76 r_work: 0.3402 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11266 Z= 0.132 Angle : 0.670 13.686 15210 Z= 0.314 Chirality : 0.044 0.310 1727 Planarity : 0.004 0.068 1791 Dihedral : 16.783 128.825 2148 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.47 % Allowed : 12.58 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.12 (0.24), residues: 1263 helix: 1.81 (0.18), residues: 780 sheet: -1.04 (0.62), residues: 76 loop : -1.00 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1144 HIS 0.004 0.001 HIS B 131 PHE 0.019 0.001 PHE A 578 TYR 0.011 0.001 TYR A 354 ARG 0.004 0.000 ARG A 209 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 6) link_NAG-ASN : angle 3.81114 ( 18) link_BETA1-4 : bond 0.00678 ( 1) link_BETA1-4 : angle 2.56764 ( 3) hydrogen bonds : bond 0.04421 ( 651) hydrogen bonds : angle 4.21596 ( 1854) SS BOND : bond 0.00483 ( 7) SS BOND : angle 1.61093 ( 14) covalent geometry : bond 0.00283 (11252) covalent geometry : angle 0.65449 (15175) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 235 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 596 ARG cc_start: 0.7431 (tmt170) cc_final: 0.7112 (tmt170) REVERT: A 974 ILE cc_start: 0.8221 (mm) cc_final: 0.7963 (OUTLIER) REVERT: A 1078 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7648 (m-30) REVERT: B 37 GLN cc_start: 0.8500 (tm-30) cc_final: 0.8153 (tt0) REVERT: B 53 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: B 83 GLU cc_start: 0.7800 (pp20) cc_final: 0.6966 (pp20) REVERT: B 97 SER cc_start: 0.9327 (m) cc_final: 0.9053 (m) outliers start: 40 outliers final: 19 residues processed: 251 average time/residue: 1.3317 time to fit residues: 367.1517 Evaluate side-chains 242 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 222 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1078 ASP Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1288 SER Chi-restraints excluded: chain A residue 1470 SER Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 171 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 87 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 75 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN A 518 ASN ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1275 GLN A1367 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.162417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.133031 restraints weight = 14070.581| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.77 r_work: 0.3389 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11266 Z= 0.145 Angle : 0.599 10.046 15210 Z= 0.290 Chirality : 0.042 0.250 1727 Planarity : 0.004 0.058 1791 Dihedral : 13.636 122.734 2146 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.38 % Allowed : 15.61 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.40 (0.24), residues: 1263 helix: 2.01 (0.18), residues: 780 sheet: -0.77 (0.61), residues: 76 loop : -0.88 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1144 HIS 0.003 0.001 HIS B 131 PHE 0.013 0.001 PHE A 246 TYR 0.010 0.001 TYR A 354 ARG 0.003 0.000 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 6) link_NAG-ASN : angle 3.65134 ( 18) link_BETA1-4 : bond 0.00030 ( 1) link_BETA1-4 : angle 1.88979 ( 3) hydrogen bonds : bond 0.04295 ( 651) hydrogen bonds : angle 4.03770 ( 1854) SS BOND : bond 0.00417 ( 7) SS BOND : angle 1.47072 ( 14) covalent geometry : bond 0.00338 (11252) covalent geometry : angle 0.58372 (15175) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 232 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8313 (tp) REVERT: A 400 GLU cc_start: 0.8481 (tp30) cc_final: 0.8127 (tp30) REVERT: A 596 ARG cc_start: 0.7548 (tmt170) cc_final: 0.7219 (tmt170) REVERT: A 625 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8333 (p) REVERT: A 974 ILE cc_start: 0.8243 (mm) cc_final: 0.7965 (mt) REVERT: A 1078 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7843 (m-30) REVERT: A 1086 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7879 (pt0) REVERT: B 37 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8146 (tt0) REVERT: B 83 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6909 (pp20) REVERT: B 112 LEU cc_start: 0.8269 (pt) cc_final: 0.8017 (pp) outliers start: 39 outliers final: 19 residues processed: 250 average time/residue: 1.2519 time to fit residues: 345.4257 Evaluate side-chains 236 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 212 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1078 ASP Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1221 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 186 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 50 optimal weight: 0.0670 chunk 120 optimal weight: 30.0000 chunk 44 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 overall best weight: 3.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 352 GLN A 614 GLN ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.161014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.131542 restraints weight = 13944.007| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.76 r_work: 0.3366 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11266 Z= 0.173 Angle : 0.600 9.036 15210 Z= 0.296 Chirality : 0.042 0.342 1727 Planarity : 0.004 0.052 1791 Dihedral : 12.973 121.497 2146 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.68 % Allowed : 16.13 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.39 (0.24), residues: 1263 helix: 1.98 (0.18), residues: 779 sheet: -0.57 (0.62), residues: 76 loop : -0.87 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1144 HIS 0.004 0.001 HIS B 131 PHE 0.025 0.002 PHE A1031 TYR 0.011 0.001 TYR A1168 ARG 0.003 0.000 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 6) link_NAG-ASN : angle 3.20276 ( 18) link_BETA1-4 : bond 0.00104 ( 1) link_BETA1-4 : angle 2.03700 ( 3) hydrogen bonds : bond 0.04477 ( 651) hydrogen bonds : angle 4.02201 ( 1854) SS BOND : bond 0.00409 ( 7) SS BOND : angle 1.57171 ( 14) covalent geometry : bond 0.00414 (11252) covalent geometry : angle 0.58789 (15175) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 219 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7304 (t0) REVERT: A 201 PHE cc_start: 0.8185 (m-80) cc_final: 0.7981 (m-80) REVERT: A 400 GLU cc_start: 0.8440 (tp30) cc_final: 0.8083 (tp30) REVERT: A 596 ARG cc_start: 0.7633 (tmt170) cc_final: 0.7369 (tmt170) REVERT: A 974 ILE cc_start: 0.8280 (mm) cc_final: 0.8016 (mt) REVERT: A 1078 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7873 (m-30) REVERT: A 1086 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7831 (pt0) REVERT: A 1243 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7864 (m-10) REVERT: B 37 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8126 (tt0) REVERT: B 44 ARG cc_start: 0.8460 (ttm170) cc_final: 0.7434 (ttm-80) REVERT: B 83 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6897 (pp20) REVERT: B 112 LEU cc_start: 0.8249 (pt) cc_final: 0.7977 (pp) outliers start: 54 outliers final: 28 residues processed: 245 average time/residue: 1.0685 time to fit residues: 289.3527 Evaluate side-chains 246 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1078 ASP Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1199 HIS Chi-restraints excluded: chain A residue 1211 THR Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1354 ILE Chi-restraints excluded: chain A residue 1470 SER Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 186 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 69 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1199 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.163161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.133808 restraints weight = 13933.816| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.76 r_work: 0.3396 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11266 Z= 0.125 Angle : 0.547 8.273 15210 Z= 0.271 Chirality : 0.040 0.248 1727 Planarity : 0.004 0.047 1791 Dihedral : 12.563 116.926 2146 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.25 % Allowed : 17.35 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.60 (0.24), residues: 1263 helix: 2.16 (0.18), residues: 779 sheet: -0.49 (0.61), residues: 76 loop : -0.81 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1144 HIS 0.002 0.001 HIS B 131 PHE 0.017 0.001 PHE A1031 TYR 0.010 0.001 TYR A1475 ARG 0.002 0.000 ARG A 209 Details of bonding type rmsd link_NAG-ASN : bond 0.00416 ( 6) link_NAG-ASN : angle 3.07062 ( 18) link_BETA1-4 : bond 0.00275 ( 1) link_BETA1-4 : angle 1.87365 ( 3) hydrogen bonds : bond 0.03901 ( 651) hydrogen bonds : angle 3.87775 ( 1854) SS BOND : bond 0.00363 ( 7) SS BOND : angle 1.37546 ( 14) covalent geometry : bond 0.00287 (11252) covalent geometry : angle 0.53498 (15175) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 224 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.7229 (t80) REVERT: A 183 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8266 (tp) REVERT: A 200 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7242 (t0) REVERT: A 201 PHE cc_start: 0.8130 (m-80) cc_final: 0.7886 (m-80) REVERT: A 400 GLU cc_start: 0.8471 (tp30) cc_final: 0.8135 (tp30) REVERT: A 596 ARG cc_start: 0.7500 (tmt170) cc_final: 0.7257 (tmt170) REVERT: A 974 ILE cc_start: 0.8239 (mm) cc_final: 0.7980 (mt) REVERT: A 1031 PHE cc_start: 0.8489 (m-10) cc_final: 0.8272 (m-10) REVERT: A 1078 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7766 (m-30) REVERT: A 1086 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7818 (pt0) REVERT: A 1165 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8588 (m) REVERT: A 1243 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7916 (m-10) REVERT: B 37 GLN cc_start: 0.8388 (tm-30) cc_final: 0.8017 (tt0) REVERT: B 83 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6956 (pp20) REVERT: B 112 LEU cc_start: 0.8234 (pt) cc_final: 0.7959 (pp) outliers start: 49 outliers final: 16 residues processed: 248 average time/residue: 0.9355 time to fit residues: 256.8347 Evaluate side-chains 241 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 217 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1078 ASP Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 186 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 116 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 55 optimal weight: 0.0970 chunk 80 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1199 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.161299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.132019 restraints weight = 14014.254| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.76 r_work: 0.3369 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11266 Z= 0.181 Angle : 0.598 8.801 15210 Z= 0.296 Chirality : 0.042 0.256 1727 Planarity : 0.004 0.046 1791 Dihedral : 12.624 117.567 2146 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.60 % Allowed : 17.69 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.45 (0.24), residues: 1263 helix: 2.03 (0.18), residues: 780 sheet: -0.38 (0.61), residues: 72 loop : -0.88 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1144 HIS 0.004 0.001 HIS B 131 PHE 0.020 0.002 PHE A1031 TYR 0.010 0.001 TYR A1168 ARG 0.003 0.000 ARG A 209 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 6) link_NAG-ASN : angle 3.13296 ( 18) link_BETA1-4 : bond 0.00196 ( 1) link_BETA1-4 : angle 2.00483 ( 3) hydrogen bonds : bond 0.04386 ( 651) hydrogen bonds : angle 3.96803 ( 1854) SS BOND : bond 0.00410 ( 7) SS BOND : angle 1.63053 ( 14) covalent geometry : bond 0.00434 (11252) covalent geometry : angle 0.58655 (15175) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 217 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7253 (t80) REVERT: A 201 PHE cc_start: 0.8182 (m-80) cc_final: 0.7954 (m-80) REVERT: A 400 GLU cc_start: 0.8466 (tp30) cc_final: 0.8096 (tp30) REVERT: A 578 PHE cc_start: 0.6920 (OUTLIER) cc_final: 0.6403 (t80) REVERT: A 596 ARG cc_start: 0.7612 (tmt170) cc_final: 0.7324 (tmt170) REVERT: A 974 ILE cc_start: 0.8315 (mm) cc_final: 0.8064 (mt) REVERT: A 1031 PHE cc_start: 0.8521 (m-10) cc_final: 0.8239 (m-10) REVERT: A 1078 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7877 (m-30) REVERT: A 1086 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7828 (pt0) REVERT: A 1333 MET cc_start: 0.7412 (ptt) cc_final: 0.6567 (ppp) REVERT: B 32 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: B 37 GLN cc_start: 0.8402 (tm-30) cc_final: 0.8067 (tt0) REVERT: B 83 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.6995 (pp20) REVERT: B 112 LEU cc_start: 0.8244 (pt) cc_final: 0.7983 (pp) REVERT: B 124 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7408 (ptm160) outliers start: 53 outliers final: 35 residues processed: 244 average time/residue: 0.9113 time to fit residues: 245.8801 Evaluate side-chains 257 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 215 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1078 ASP Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1221 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1470 SER Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 186 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 29 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1199 HIS A1275 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.162910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.133773 restraints weight = 14017.571| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.77 r_work: 0.3395 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11266 Z= 0.132 Angle : 0.557 8.201 15210 Z= 0.275 Chirality : 0.040 0.239 1727 Planarity : 0.004 0.044 1791 Dihedral : 12.476 115.036 2146 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.34 % Allowed : 17.95 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.58 (0.24), residues: 1263 helix: 2.14 (0.18), residues: 780 sheet: -0.33 (0.61), residues: 72 loop : -0.85 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1144 HIS 0.003 0.001 HIS B 131 PHE 0.018 0.001 PHE A1243 TYR 0.010 0.001 TYR A1475 ARG 0.002 0.000 ARG A 209 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 6) link_NAG-ASN : angle 3.05493 ( 18) link_BETA1-4 : bond 0.00242 ( 1) link_BETA1-4 : angle 1.92662 ( 3) hydrogen bonds : bond 0.03976 ( 651) hydrogen bonds : angle 3.88530 ( 1854) SS BOND : bond 0.00354 ( 7) SS BOND : angle 1.39520 ( 14) covalent geometry : bond 0.00309 (11252) covalent geometry : angle 0.54568 (15175) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 224 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7271 (t80) REVERT: A 201 PHE cc_start: 0.8021 (m-80) cc_final: 0.7780 (m-80) REVERT: A 400 GLU cc_start: 0.8457 (tp30) cc_final: 0.8088 (tp30) REVERT: A 562 TYR cc_start: 0.6777 (t80) cc_final: 0.6234 (t80) REVERT: A 596 ARG cc_start: 0.7522 (tmt170) cc_final: 0.7242 (tmt170) REVERT: A 974 ILE cc_start: 0.8278 (mm) cc_final: 0.8030 (mt) REVERT: A 1078 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7819 (m-30) REVERT: A 1086 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7806 (pt0) REVERT: A 1243 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.8171 (t80) REVERT: A 1333 MET cc_start: 0.7346 (ptt) cc_final: 0.6462 (ppp) REVERT: B 32 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: B 37 GLN cc_start: 0.8368 (tm-30) cc_final: 0.8040 (tt0) REVERT: B 83 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.6986 (pp20) REVERT: B 112 LEU cc_start: 0.8226 (pt) cc_final: 0.7960 (pp) REVERT: B 124 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7382 (ptm160) outliers start: 50 outliers final: 27 residues processed: 248 average time/residue: 0.9322 time to fit residues: 255.1863 Evaluate side-chains 246 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1078 ASP Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 171 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 78 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1275 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.163089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.133959 restraints weight = 14011.358| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.78 r_work: 0.3396 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11266 Z= 0.133 Angle : 0.560 8.039 15210 Z= 0.276 Chirality : 0.040 0.237 1727 Planarity : 0.004 0.042 1791 Dihedral : 12.296 112.880 2146 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.38 % Allowed : 18.91 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.64 (0.24), residues: 1263 helix: 2.19 (0.18), residues: 779 sheet: -0.29 (0.61), residues: 72 loop : -0.82 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 935 HIS 0.003 0.001 HIS B 131 PHE 0.025 0.001 PHE A1031 TYR 0.010 0.001 TYR A1475 ARG 0.003 0.000 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 6) link_NAG-ASN : angle 3.02946 ( 18) link_BETA1-4 : bond 0.00294 ( 1) link_BETA1-4 : angle 1.90797 ( 3) hydrogen bonds : bond 0.03937 ( 651) hydrogen bonds : angle 3.86081 ( 1854) SS BOND : bond 0.00357 ( 7) SS BOND : angle 1.36925 ( 14) covalent geometry : bond 0.00313 (11252) covalent geometry : angle 0.54861 (15175) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 220 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.7283 (t80) REVERT: A 201 PHE cc_start: 0.8096 (m-80) cc_final: 0.7885 (m-80) REVERT: A 400 GLU cc_start: 0.8433 (tp30) cc_final: 0.8065 (tp30) REVERT: A 562 TYR cc_start: 0.6746 (t80) cc_final: 0.6131 (t80) REVERT: A 596 ARG cc_start: 0.7476 (tmt170) cc_final: 0.7210 (tmt170) REVERT: A 974 ILE cc_start: 0.8272 (mm) cc_final: 0.8025 (mt) REVERT: A 1078 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7808 (m-30) REVERT: A 1086 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7828 (pt0) REVERT: A 1243 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.8051 (t80) REVERT: A 1371 LEU cc_start: 0.8729 (mm) cc_final: 0.8325 (mt) REVERT: B 32 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: B 37 GLN cc_start: 0.8389 (tm-30) cc_final: 0.8033 (tt0) REVERT: B 83 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7030 (pp20) outliers start: 39 outliers final: 26 residues processed: 242 average time/residue: 0.9244 time to fit residues: 247.2819 Evaluate side-chains 250 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 218 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1078 ASP Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1199 HIS Chi-restraints excluded: chain A residue 1211 THR Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 186 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 14 optimal weight: 0.0000 chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1199 HIS A1275 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.163687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.134523 restraints weight = 14069.511| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.78 r_work: 0.3405 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11266 Z= 0.124 Angle : 0.559 7.950 15210 Z= 0.275 Chirality : 0.040 0.232 1727 Planarity : 0.004 0.042 1791 Dihedral : 12.153 111.151 2146 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.38 % Allowed : 19.77 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.73 (0.24), residues: 1263 helix: 2.26 (0.18), residues: 778 sheet: -0.27 (0.61), residues: 72 loop : -0.80 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 935 HIS 0.002 0.001 HIS B 131 PHE 0.022 0.001 PHE A1031 TYR 0.010 0.001 TYR A1475 ARG 0.002 0.000 ARG A 209 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 6) link_NAG-ASN : angle 3.00175 ( 18) link_BETA1-4 : bond 0.00269 ( 1) link_BETA1-4 : angle 1.85897 ( 3) hydrogen bonds : bond 0.03798 ( 651) hydrogen bonds : angle 3.82583 ( 1854) SS BOND : bond 0.00413 ( 7) SS BOND : angle 1.55436 ( 14) covalent geometry : bond 0.00286 (11252) covalent geometry : angle 0.54716 (15175) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 221 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7282 (t80) REVERT: A 200 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.7136 (t0) REVERT: A 400 GLU cc_start: 0.8431 (tp30) cc_final: 0.8060 (tp30) REVERT: A 562 TYR cc_start: 0.6674 (t80) cc_final: 0.6084 (t80) REVERT: A 974 ILE cc_start: 0.8257 (mm) cc_final: 0.8012 (mt) REVERT: A 1078 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7866 (m-30) REVERT: A 1086 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7820 (pt0) REVERT: A 1243 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.8024 (t80) REVERT: A 1371 LEU cc_start: 0.8702 (mm) cc_final: 0.8291 (mt) REVERT: B 32 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: B 37 GLN cc_start: 0.8368 (tm-30) cc_final: 0.8017 (tt0) REVERT: B 83 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7016 (pp20) REVERT: B 112 LEU cc_start: 0.8173 (pt) cc_final: 0.7909 (pp) outliers start: 39 outliers final: 23 residues processed: 245 average time/residue: 0.9014 time to fit residues: 244.5201 Evaluate side-chains 247 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1078 ASP Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 186 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 7 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 0.0770 chunk 113 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 54 optimal weight: 0.0770 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1199 HIS A1275 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.166274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.136978 restraints weight = 14037.340| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.79 r_work: 0.3434 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11266 Z= 0.104 Angle : 0.533 7.694 15210 Z= 0.263 Chirality : 0.039 0.216 1727 Planarity : 0.004 0.042 1791 Dihedral : 11.673 107.218 2146 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.34 % Allowed : 20.73 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.24), residues: 1263 helix: 2.51 (0.18), residues: 773 sheet: -0.05 (0.61), residues: 70 loop : -0.65 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 689 HIS 0.002 0.001 HIS A 117 PHE 0.022 0.001 PHE A1031 TYR 0.009 0.001 TYR A1475 ARG 0.002 0.000 ARG A 209 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 6) link_NAG-ASN : angle 2.88691 ( 18) link_BETA1-4 : bond 0.00511 ( 1) link_BETA1-4 : angle 1.76126 ( 3) hydrogen bonds : bond 0.03359 ( 651) hydrogen bonds : angle 3.73704 ( 1854) SS BOND : bond 0.00286 ( 7) SS BOND : angle 1.21808 ( 14) covalent geometry : bond 0.00230 (11252) covalent geometry : angle 0.52212 (15175) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 225 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7269 (t80) REVERT: A 189 VAL cc_start: 0.8640 (t) cc_final: 0.8293 (m) REVERT: A 400 GLU cc_start: 0.8401 (tp30) cc_final: 0.8064 (tp30) REVERT: A 562 TYR cc_start: 0.6767 (t80) cc_final: 0.6125 (t80) REVERT: A 955 ASP cc_start: 0.8433 (p0) cc_final: 0.8185 (p0) REVERT: A 974 ILE cc_start: 0.8242 (mm) cc_final: 0.8006 (OUTLIER) REVERT: A 1086 GLU cc_start: 0.8073 (pt0) cc_final: 0.7667 (pt0) REVERT: A 1243 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7852 (t80) REVERT: A 1296 MET cc_start: 0.8071 (mtp) cc_final: 0.7593 (tpt) REVERT: A 1371 LEU cc_start: 0.8685 (mm) cc_final: 0.8304 (mt) REVERT: B 32 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7113 (mp0) REVERT: B 37 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7931 (tt0) REVERT: B 50 LYS cc_start: 0.7764 (mtpt) cc_final: 0.7366 (mmtm) REVERT: B 83 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7018 (pp20) REVERT: B 112 LEU cc_start: 0.8141 (pt) cc_final: 0.7903 (pp) outliers start: 27 outliers final: 15 residues processed: 241 average time/residue: 0.9141 time to fit residues: 244.8842 Evaluate side-chains 233 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 215 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 186 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 84 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1199 HIS A1275 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.164191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.134702 restraints weight = 13916.277| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.79 r_work: 0.3412 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11266 Z= 0.110 Angle : 0.542 8.318 15210 Z= 0.266 Chirality : 0.039 0.219 1727 Planarity : 0.004 0.042 1791 Dihedral : 11.536 107.040 2146 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.25 % Allowed : 21.51 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.24), residues: 1263 helix: 2.52 (0.18), residues: 773 sheet: -0.01 (0.61), residues: 70 loop : -0.63 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 935 HIS 0.002 0.001 HIS A 117 PHE 0.017 0.001 PHE A 201 TYR 0.009 0.001 TYR A1475 ARG 0.002 0.000 ARG A 209 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 6) link_NAG-ASN : angle 2.87576 ( 18) link_BETA1-4 : bond 0.00278 ( 1) link_BETA1-4 : angle 1.70709 ( 3) hydrogen bonds : bond 0.03409 ( 651) hydrogen bonds : angle 3.73231 ( 1854) SS BOND : bond 0.00297 ( 7) SS BOND : angle 1.22818 ( 14) covalent geometry : bond 0.00251 (11252) covalent geometry : angle 0.53187 (15175) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8947.42 seconds wall clock time: 157 minutes 32.36 seconds (9452.36 seconds total)