Starting phenix.real_space_refine on Fri Jul 3 03:26:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tj9_25920/07_2026/7tj9_25920.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tj9_25920/07_2026/7tj9_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tj9_25920/07_2026/7tj9_25920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tj9_25920/07_2026/7tj9_25920.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tj9_25920/07_2026/7tj9_25920.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tj9_25920/07_2026/7tj9_25920.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tj9_25920/07_2026/7tj9_25920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tj9_25920/07_2026/7tj9_25920.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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: 62 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-2': 2, 'POV:plan-3': 1, 'PLM:plan-1': 1, 'POV: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 chiralities: 4 Time building chain proxies: 2.42, per 1000 atoms: 0.22 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: 1.06 Conformation dependent library (CDL) restraints added in 412.7 milliseconds 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: 0.20 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: 1.80 Time building geometry restraints manager: 1.38 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 - 26.33: 6254 26.33 - 52.66: 360 52.66 - 78.99: 51 78.99 - 105.32: 31 105.32 - 131.66: 23 Dihedral angle restraints: 6719 sinusoidal: 2991 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=" C2C Q7G A2418 " pdb=" C1C Q7G A2418 " pdb=" O5C Q7G A2418 " pdb=" C5C Q7G A2418 " ideal model delta sinusoidal sigma weight residual -60.67 70.99 -131.66 1 3.00e+01 1.11e-03 1.78e+01 ... (remaining 6716 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.620 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:8.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 19.114 131.656 4288 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.30 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.000 ARG A 602 TYR 0.021 0.002 TYR A 354 PHE 0.031 0.002 PHE A1031 TRP 0.068 0.002 TRP A1144 HIS 0.005 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.01563 / 0.77 (11252) covalent geometry : angle 1.01410 / 0.44 (15175) SS BOND : bond 0.00579 / 0.31 ( 7) SS BOND : angle 1.99316 / 1.20 ( 14) hydrogen bonds : bond 0.14257 / 9.47 ( 651) hydrogen bonds : angle 5.48523 / 4.15 ( 1854) link_BETA1-4 : bond 0.00408 / 0.21 ( 1) link_BETA1-4 : angle 2.28844 / 1.12 ( 3) link_NAG-ASN : bond 0.01214 / 0.61 ( 6) link_NAG-ASN : angle 3.58645 / 2.42 ( 18) *********************** 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 : 0.400 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: 0.4222 time to fit residues: 123.5521 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 : 0.375 ------------------------------------------------------------------------------- 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 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3845 r_free = 0.3845 target = 0.160853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.131615 restraints weight = 13941.798| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.76 r_work: 0.3372 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11266 Z= 0.158 Angle : 0.659 14.230 15210 Z= 0.318 Chirality : 0.045 0.414 1727 Planarity : 0.005 0.072 1791 Dihedral : 16.175 114.145 1848 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.99 % Allowed : 11.97 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.24), residues: 1263 helix: 1.68 (0.18), residues: 779 sheet: -1.09 (0.62), residues: 76 loop : -1.04 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 209 TYR 0.012 0.001 TYR A 354 PHE 0.020 0.002 PHE A1031 TRP 0.028 0.001 TRP A1144 HIS 0.004 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (11252) covalent geometry : angle 0.64766 / 0.32 (15175) SS BOND : bond 0.00457 / 0.24 ( 7) SS BOND : angle 1.84493 / 1.12 ( 14) hydrogen bonds : bond 0.04916 / 3.24 ( 651) hydrogen bonds : angle 4.31375 / 3.19 ( 1854) link_BETA1-4 : bond 0.00746 / 0.39 ( 1) link_BETA1-4 : angle 2.04892 / 1.01 ( 3) link_NAG-ASN : bond 0.00501 / 0.22 ( 6) link_NAG-ASN : angle 3.22406 / 2.11 ( 18) *********************** 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 278 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 232 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 596 ARG cc_start: 0.7527 (tmt170) cc_final: 0.7167 (tmt170) REVERT: A 974 ILE cc_start: 0.8218 (mm) cc_final: 0.7963 (mt) REVERT: A 1078 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7730 (m-30) REVERT: A 1437 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8194 (p0) REVERT: A 1490 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8626 (mtp) REVERT: B 37 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8147 (tm-30) REVERT: B 83 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.6928 (pp20) REVERT: B 97 SER cc_start: 0.9335 (m) cc_final: 0.9064 (m) outliers start: 46 outliers final: 21 residues processed: 249 average time/residue: 0.4066 time to fit residues: 112.0833 Evaluate side-chains 241 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 543 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 1157 VAL Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1288 SER Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain A residue 1470 SER Chi-restraints excluded: chain A residue 1490 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 83 GLU 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 56 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 93 optimal weight: 10.0000 chunk 35 optimal weight: 0.0070 chunk 36 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 GLN A 518 ASN A 614 GLN A1166 ASN A1275 GLN A1367 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.164918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.135736 restraints weight = 14081.463| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.79 r_work: 0.3426 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11266 Z= 0.112 Angle : 0.552 10.052 15210 Z= 0.271 Chirality : 0.041 0.335 1727 Planarity : 0.004 0.056 1791 Dihedral : 12.309 113.131 1846 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.04 % Allowed : 15.44 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.24), residues: 1263 helix: 2.16 (0.18), residues: 780 sheet: -0.72 (0.63), residues: 76 loop : -0.84 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 209 TYR 0.010 0.001 TYR A1475 PHE 0.019 0.001 PHE A 578 TRP 0.013 0.001 TRP A1144 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (11252) covalent geometry : angle 0.54555 / 0.27 (15175) SS BOND : bond 0.00343 / 0.18 ( 7) SS BOND : angle 1.19809 / 0.71 ( 14) hydrogen bonds : bond 0.03759 / 2.45 ( 651) hydrogen bonds : angle 3.94830 / 2.90 ( 1854) link_BETA1-4 : bond 0.00385 / 0.20 ( 1) link_BETA1-4 : angle 1.32915 / 0.64 ( 3) link_NAG-ASN : bond 0.00603 / 0.31 ( 6) link_NAG-ASN : angle 2.27482 / 1.52 ( 18) *********************** 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 268 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8263 (tp) REVERT: A 200 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6867 (t0) REVERT: A 596 ARG cc_start: 0.7372 (tmt170) cc_final: 0.7076 (tmt170) REVERT: A 625 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8267 (p) REVERT: A 955 ASP cc_start: 0.8707 (p0) cc_final: 0.8425 (p0) REVERT: A 974 ILE cc_start: 0.8199 (mm) cc_final: 0.7911 (OUTLIER) REVERT: A 1020 ARG cc_start: 0.5983 (mmt-90) cc_final: 0.5476 (ttm170) REVERT: A 1086 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7782 (pt0) REVERT: A 1279 MET cc_start: 0.8389 (tpp) cc_final: 0.7969 (mmm) REVERT: B 37 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8103 (tt0) REVERT: B 53 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7720 (mp0) REVERT: B 83 GLU cc_start: 0.7660 (pp20) cc_final: 0.6855 (pp20) REVERT: B 112 LEU cc_start: 0.8220 (pt) cc_final: 0.7994 (pp) outliers start: 35 outliers final: 12 residues processed: 248 average time/residue: 0.4030 time to fit residues: 110.3851 Evaluate side-chains 229 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 213 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 183 LEU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 84 VAL 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 37 optimal weight: 8.9990 chunk 35 optimal weight: 0.0980 chunk 66 optimal weight: 0.0670 chunk 27 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 123 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.2324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 GLN A 352 GLN B 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.164731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.135471 restraints weight = 14134.634| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.78 r_work: 0.3422 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11266 Z= 0.114 Angle : 0.530 8.432 15210 Z= 0.263 Chirality : 0.041 0.346 1727 Planarity : 0.004 0.047 1791 Dihedral : 11.196 113.124 1846 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.38 % Allowed : 16.74 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.24), residues: 1263 helix: 2.34 (0.18), residues: 779 sheet: -0.56 (0.63), residues: 76 loop : -0.74 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 144 TYR 0.009 0.001 TYR A1475 PHE 0.017 0.001 PHE A 578 TRP 0.010 0.001 TRP A1144 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (11252) covalent geometry : angle 0.52399 / 0.26 (15175) SS BOND : bond 0.00339 / 0.18 ( 7) SS BOND : angle 1.19823 / 0.71 ( 14) hydrogen bonds : bond 0.03656 / 2.38 ( 651) hydrogen bonds : angle 3.80448 / 2.79 ( 1854) link_BETA1-4 : bond 0.00305 / 0.16 ( 1) link_BETA1-4 : angle 1.36668 / 0.64 ( 3) link_NAG-ASN : bond 0.00472 / 0.24 ( 6) link_NAG-ASN : angle 2.13575 / 1.45 ( 18) *********************** 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 270 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 231 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7110 (t80) REVERT: A 201 PHE cc_start: 0.8150 (m-80) cc_final: 0.7927 (m-80) REVERT: A 400 GLU cc_start: 0.8508 (tp30) cc_final: 0.8139 (tp30) REVERT: A 562 TYR cc_start: 0.6875 (t80) cc_final: 0.6408 (t80) REVERT: A 597 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8346 (tp) REVERT: A 955 ASP cc_start: 0.8606 (p0) cc_final: 0.8285 (p0) REVERT: A 974 ILE cc_start: 0.8237 (mm) cc_final: 0.7979 (OUTLIER) REVERT: A 1020 ARG cc_start: 0.6098 (mmt-90) cc_final: 0.5544 (mtt-85) REVERT: A 1038 LEU cc_start: 0.8687 (mt) cc_final: 0.8468 (tp) REVERT: A 1086 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7766 (pt0) REVERT: A 1165 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8736 (m) REVERT: B 32 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: B 37 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8114 (tt0) REVERT: B 83 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7071 (pp20) REVERT: B 112 LEU cc_start: 0.8178 (pt) cc_final: 0.7921 (pp) outliers start: 39 outliers final: 13 residues processed: 252 average time/residue: 0.3974 time to fit residues: 110.8026 Evaluate side-chains 235 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 217 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 509 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 1009 ILE Chi-restraints excluded: chain A residue 1010 VAL 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 B residue 28 GLU 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 186 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 6 optimal weight: 10.0000 chunk 116 optimal weight: 0.0040 chunk 94 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1199 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.167076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.137840 restraints weight = 13988.772| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.78 r_work: 0.3455 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11266 Z= 0.100 Angle : 0.505 7.972 15210 Z= 0.250 Chirality : 0.040 0.319 1727 Planarity : 0.004 0.046 1791 Dihedral : 10.743 112.852 1846 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.38 % Allowed : 18.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.24), residues: 1263 helix: 2.48 (0.18), residues: 781 sheet: -0.33 (0.63), residues: 74 loop : -0.69 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 51 TYR 0.009 0.001 TYR A1475 PHE 0.016 0.001 PHE A1031 TRP 0.007 0.001 TRP A1118 HIS 0.002 0.001 HIS A 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (11252) covalent geometry : angle 0.49962 / 0.25 (15175) SS BOND : bond 0.00289 / 0.15 ( 7) SS BOND : angle 1.10564 / 0.67 ( 14) hydrogen bonds : bond 0.03279 / 2.13 ( 651) hydrogen bonds : angle 3.71844 / 2.74 ( 1854) link_BETA1-4 : bond 0.00289 / 0.15 ( 1) link_BETA1-4 : angle 1.22465 / 0.58 ( 3) link_NAG-ASN : bond 0.00502 / 0.26 ( 6) link_NAG-ASN : angle 1.94927 / 1.33 ( 18) *********************** 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 270 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 231 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7705 (t80) REVERT: A 183 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8044 (tp) REVERT: A 201 PHE cc_start: 0.8013 (m-80) cc_final: 0.7746 (m-80) REVERT: A 400 GLU cc_start: 0.8471 (tp30) cc_final: 0.8144 (tp30) REVERT: A 562 TYR cc_start: 0.6754 (t80) cc_final: 0.6170 (t80) REVERT: A 625 VAL cc_start: 0.8381 (t) cc_final: 0.8172 (p) REVERT: A 955 ASP cc_start: 0.8491 (p0) cc_final: 0.8193 (p0) REVERT: A 974 ILE cc_start: 0.8219 (mm) cc_final: 0.7968 (OUTLIER) REVERT: A 1020 ARG cc_start: 0.6013 (mmt-90) cc_final: 0.5481 (mtt-85) REVERT: A 1086 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7637 (pt0) REVERT: A 1100 GLU cc_start: 0.7526 (mp0) cc_final: 0.7026 (mp0) REVERT: A 1165 VAL cc_start: 0.9025 (OUTLIER) cc_final: 0.8691 (m) REVERT: A 1296 MET cc_start: 0.7988 (mtp) cc_final: 0.7581 (tpt) REVERT: A 1333 MET cc_start: 0.7278 (ptt) cc_final: 0.6594 (ppp) REVERT: B 32 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7547 (mm-30) REVERT: B 37 GLN cc_start: 0.8351 (tm-30) cc_final: 0.8038 (tt0) REVERT: B 50 LYS cc_start: 0.7749 (mtpt) cc_final: 0.7398 (mmtm) REVERT: B 83 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7086 (pp20) REVERT: B 112 LEU cc_start: 0.8195 (pt) cc_final: 0.7883 (pp) outliers start: 39 outliers final: 11 residues processed: 254 average time/residue: 0.3898 time to fit residues: 110.1161 Evaluate side-chains 236 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 220 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 183 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1010 VAL 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 B residue 28 GLU 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 145 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 38 optimal weight: 4.9990 chunk 121 optimal weight: 0.4980 chunk 96 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1199 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.164846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.135329 restraints weight = 13988.618| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.79 r_work: 0.3418 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2250 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= 0.126 Angle : 0.536 8.263 15210 Z= 0.264 Chirality : 0.041 0.342 1727 Planarity : 0.004 0.044 1791 Dihedral : 10.709 112.545 1846 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.38 % Allowed : 18.47 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.24), residues: 1263 helix: 2.44 (0.18), residues: 780 sheet: -0.34 (0.63), residues: 74 loop : -0.67 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 209 TYR 0.010 0.001 TYR A1475 PHE 0.015 0.001 PHE A 578 TRP 0.010 0.001 TRP A1144 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (11252) covalent geometry : angle 0.52925 / 0.26 (15175) SS BOND : bond 0.00398 / 0.26 ( 7) SS BOND : angle 1.48063 / 0.88 ( 14) hydrogen bonds : bond 0.03634 / 2.37 ( 651) hydrogen bonds : angle 3.74757 / 2.76 ( 1854) link_BETA1-4 : bond 0.00145 / 0.08 ( 1) link_BETA1-4 : angle 1.35336 / 0.63 ( 3) link_NAG-ASN : bond 0.00447 / 0.21 ( 6) link_NAG-ASN : angle 2.06517 / 1.42 ( 18) *********************** 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 257 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 218 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7782 (t80) REVERT: A 183 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7950 (tp) REVERT: A 201 PHE cc_start: 0.8002 (m-80) cc_final: 0.7723 (m-80) REVERT: A 400 GLU cc_start: 0.8488 (tp30) cc_final: 0.8123 (tp30) REVERT: A 562 TYR cc_start: 0.6759 (t80) cc_final: 0.6171 (t80) REVERT: A 625 VAL cc_start: 0.8418 (t) cc_final: 0.8193 (p) REVERT: A 955 ASP cc_start: 0.8572 (p0) cc_final: 0.8243 (p0) REVERT: A 974 ILE cc_start: 0.8225 (mm) cc_final: 0.7976 (OUTLIER) REVERT: A 1020 ARG cc_start: 0.6074 (mmt-90) cc_final: 0.5530 (mtt-85) REVERT: A 1086 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7601 (pt0) REVERT: A 1100 GLU cc_start: 0.7531 (mp0) cc_final: 0.7016 (mp0) REVERT: A 1165 VAL cc_start: 0.9051 (OUTLIER) cc_final: 0.8626 (m) REVERT: A 1371 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8373 (mt) REVERT: B 32 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7725 (mm-30) REVERT: B 37 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7989 (tt0) REVERT: B 50 LYS cc_start: 0.7785 (mtpt) cc_final: 0.7416 (mmtm) REVERT: B 83 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6932 (pp20) REVERT: B 112 LEU cc_start: 0.8221 (pt) cc_final: 0.7963 (pp) outliers start: 39 outliers final: 21 residues processed: 240 average time/residue: 0.3680 time to fit residues: 98.7020 Evaluate side-chains 240 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 213 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 174 SER Chi-restraints excluded: chain A residue 183 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 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 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 1293 LEU Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain B residue 28 GLU 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 138 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 93 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 94 optimal weight: 0.0050 chunk 50 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1199 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.163385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.133827 restraints weight = 13893.983| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.78 r_work: 0.3395 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11266 Z= 0.146 Angle : 0.559 8.440 15210 Z= 0.275 Chirality : 0.041 0.361 1727 Planarity : 0.004 0.043 1791 Dihedral : 10.809 112.454 1846 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.73 % Allowed : 18.39 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.24), residues: 1263 helix: 2.33 (0.18), residues: 780 sheet: -0.42 (0.62), residues: 72 loop : -0.66 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 124 TYR 0.011 0.001 TYR A 977 PHE 0.022 0.001 PHE A1031 TRP 0.013 0.001 TRP A1144 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (11252) covalent geometry : angle 0.55244 / 0.27 (15175) SS BOND : bond 0.00394 / 0.23 ( 7) SS BOND : angle 1.40425 / 0.85 ( 14) hydrogen bonds : bond 0.03970 / 2.59 ( 651) hydrogen bonds : angle 3.82272 / 2.80 ( 1854) link_BETA1-4 : bond 0.00063 / 0.03 ( 1) link_BETA1-4 : angle 1.45844 / 0.67 ( 3) link_NAG-ASN : bond 0.00430 / 0.19 ( 6) link_NAG-ASN : angle 2.13655 / 1.48 ( 18) *********************** 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 263 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 220 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7269 (t80) REVERT: A 183 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7924 (tp) REVERT: A 201 PHE cc_start: 0.8084 (m-80) cc_final: 0.7830 (m-80) REVERT: A 400 GLU cc_start: 0.8457 (tp30) cc_final: 0.8069 (tp30) REVERT: A 562 TYR cc_start: 0.6747 (t80) cc_final: 0.6126 (t80) REVERT: A 974 ILE cc_start: 0.8259 (mm) cc_final: 0.8010 (mt) REVERT: A 1086 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7784 (pt0) REVERT: A 1371 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8484 (mt) REVERT: B 32 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7675 (mm-30) REVERT: B 37 GLN cc_start: 0.8430 (tm-30) cc_final: 0.8078 (tt0) REVERT: B 83 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.6933 (pp20) REVERT: B 112 LEU cc_start: 0.8213 (pt) cc_final: 0.7955 (pp) outliers start: 43 outliers final: 25 residues processed: 242 average time/residue: 0.3862 time to fit residues: 104.0643 Evaluate side-chains 244 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 174 SER Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 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 543 VAL 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 1009 ILE Chi-restraints excluded: chain A residue 1010 VAL 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 1293 LEU Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1451 CYS Chi-restraints excluded: chain A residue 1490 MET Chi-restraints excluded: chain B residue 28 GLU 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 138 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 17 optimal weight: 0.0870 chunk 22 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 40 optimal weight: 0.2980 chunk 74 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 87 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1199 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.165130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.135739 restraints weight = 13950.079| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.80 r_work: 0.3424 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11266 Z= 0.100 Angle : 0.512 7.306 15210 Z= 0.252 Chirality : 0.039 0.308 1727 Planarity : 0.003 0.042 1791 Dihedral : 10.429 112.778 1846 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.25 % Allowed : 19.86 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.24), residues: 1263 helix: 2.54 (0.18), residues: 779 sheet: -0.15 (0.62), residues: 70 loop : -0.65 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 44 TYR 0.011 0.001 TYR A1475 PHE 0.012 0.001 PHE A 578 TRP 0.009 0.001 TRP A1118 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (11252) covalent geometry : angle 0.50767 / 0.25 (15175) SS BOND : bond 0.00287 / 0.16 ( 7) SS BOND : angle 1.01636 / 0.60 ( 14) hydrogen bonds : bond 0.03329 / 2.16 ( 651) hydrogen bonds : angle 3.68637 / 2.71 ( 1854) link_BETA1-4 : bond 0.00366 / 0.19 ( 1) link_BETA1-4 : angle 1.27652 / 0.61 ( 3) link_NAG-ASN : bond 0.00467 / 0.23 ( 6) link_NAG-ASN : angle 1.86165 / 1.28 ( 18) *********************** 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 248 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 222 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7227 (t80) REVERT: A 183 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7817 (tp) REVERT: A 189 VAL cc_start: 0.8621 (t) cc_final: 0.8244 (m) REVERT: A 201 PHE cc_start: 0.7900 (m-80) cc_final: 0.7684 (m-80) REVERT: A 400 GLU cc_start: 0.8423 (tp30) cc_final: 0.8066 (tp30) REVERT: A 562 TYR cc_start: 0.6650 (t80) cc_final: 0.6062 (t80) REVERT: A 625 VAL cc_start: 0.8427 (t) cc_final: 0.8178 (p) REVERT: A 955 ASP cc_start: 0.8503 (p0) cc_final: 0.8248 (p0) REVERT: A 974 ILE cc_start: 0.8175 (mm) cc_final: 0.7925 (mt) REVERT: A 1020 ARG cc_start: 0.6111 (mmt-90) cc_final: 0.5549 (mtt-85) REVERT: A 1086 GLU cc_start: 0.8031 (pt0) cc_final: 0.7610 (pt0) REVERT: A 1100 GLU cc_start: 0.7512 (mp0) cc_final: 0.7026 (mp0) REVERT: A 1165 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8526 (m) REVERT: A 1296 MET cc_start: 0.7983 (mtp) cc_final: 0.7541 (tpt) REVERT: A 1371 LEU cc_start: 0.8669 (mm) cc_final: 0.8303 (mt) REVERT: A 1439 MET cc_start: 0.8695 (mtt) cc_final: 0.8269 (mtt) REVERT: B 32 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7584 (mm-30) REVERT: B 37 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8047 (tt0) REVERT: B 50 LYS cc_start: 0.7676 (mtpt) cc_final: 0.7384 (mmtm) REVERT: B 83 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7065 (pp20) REVERT: B 112 LEU cc_start: 0.8142 (pt) cc_final: 0.7768 (pp) outliers start: 26 outliers final: 15 residues processed: 237 average time/residue: 0.4182 time to fit residues: 109.7429 Evaluate side-chains 236 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 183 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 509 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 1117 LEU Chi-restraints excluded: chain A residue 1165 VAL 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 83 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 VAL 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 41 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 106 optimal weight: 0.2980 chunk 68 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1162 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.165282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.135795 restraints weight = 13917.901| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.81 r_work: 0.3424 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2507 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= 0.106 Angle : 0.535 10.389 15210 Z= 0.260 Chirality : 0.040 0.314 1727 Planarity : 0.003 0.042 1791 Dihedral : 10.279 112.248 1846 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.25 % Allowed : 20.47 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.24), residues: 1263 helix: 2.62 (0.18), residues: 773 sheet: -0.04 (0.63), residues: 69 loop : -0.61 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 44 TYR 0.011 0.001 TYR A1218 PHE 0.018 0.001 PHE A1031 TRP 0.008 0.001 TRP A 935 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (11252) covalent geometry : angle 0.52759 / 0.26 (15175) SS BOND : bond 0.00304 / 0.17 ( 7) SS BOND : angle 1.06445 / 0.63 ( 14) hydrogen bonds : bond 0.03353 / 2.18 ( 651) hydrogen bonds : angle 3.65842 / 2.69 ( 1854) link_BETA1-4 : bond 0.00260 / 0.14 ( 1) link_BETA1-4 : angle 1.28015 / 0.60 ( 3) link_NAG-ASN : bond 0.00451 / 0.20 ( 6) link_NAG-ASN : angle 2.46637 / 1.77 ( 18) *********************** 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 247 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7270 (t80) REVERT: A 183 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7802 (tp) REVERT: A 189 VAL cc_start: 0.8622 (t) cc_final: 0.8235 (m) REVERT: A 400 GLU cc_start: 0.8435 (tp30) cc_final: 0.8083 (tp30) REVERT: A 562 TYR cc_start: 0.6728 (t80) cc_final: 0.6093 (t80) REVERT: A 625 VAL cc_start: 0.8379 (t) cc_final: 0.8170 (p) REVERT: A 955 ASP cc_start: 0.8447 (p0) cc_final: 0.8185 (p0) REVERT: A 974 ILE cc_start: 0.8179 (mm) cc_final: 0.7939 (mt) REVERT: A 988 MET cc_start: 0.8464 (tpp) cc_final: 0.8208 (tpt) REVERT: A 1020 ARG cc_start: 0.6106 (mmt-90) cc_final: 0.5543 (mtt-85) REVERT: A 1086 GLU cc_start: 0.8032 (pt0) cc_final: 0.7613 (pt0) REVERT: A 1100 GLU cc_start: 0.7503 (mp0) cc_final: 0.7222 (pt0) REVERT: A 1165 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8474 (m) REVERT: A 1296 MET cc_start: 0.7990 (mtp) cc_final: 0.7547 (tpt) REVERT: A 1371 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8373 (mt) REVERT: A 1439 MET cc_start: 0.8660 (mtt) cc_final: 0.8182 (mtt) REVERT: B 32 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7568 (mm-30) REVERT: B 37 GLN cc_start: 0.8393 (tm-30) cc_final: 0.8034 (tt0) REVERT: B 83 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6810 (pp20) REVERT: B 112 LEU cc_start: 0.8148 (pt) cc_final: 0.7769 (pp) outliers start: 26 outliers final: 15 residues processed: 239 average time/residue: 0.3848 time to fit residues: 102.4637 Evaluate side-chains 239 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 218 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 183 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 597 LEU 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 1165 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1451 CYS Chi-restraints excluded: chain B residue 28 GLU 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 138 THR 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 37 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 24 optimal weight: 0.0020 chunk 28 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.166358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.137013 restraints weight = 13958.989| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.80 r_work: 0.3440 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11266 Z= 0.100 Angle : 0.535 9.737 15210 Z= 0.259 Chirality : 0.039 0.301 1727 Planarity : 0.004 0.051 1791 Dihedral : 10.073 111.931 1846 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.91 % Allowed : 21.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.24), residues: 1263 helix: 2.69 (0.18), residues: 773 sheet: 0.16 (0.62), residues: 71 loop : -0.62 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 209 TYR 0.009 0.001 TYR A1218 PHE 0.017 0.001 PHE A 201 TRP 0.009 0.001 TRP A 935 HIS 0.002 0.001 HIS A1162 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (11252) covalent geometry : angle 0.52510 / 0.26 (15175) SS BOND : bond 0.00282 / 0.16 ( 7) SS BOND : angle 0.99520 / 0.59 ( 14) hydrogen bonds : bond 0.03169 / 2.05 ( 651) hydrogen bonds : angle 3.61995 / 2.67 ( 1854) link_BETA1-4 : bond 0.00331 / 0.17 ( 1) link_BETA1-4 : angle 1.21908 / 0.58 ( 3) link_NAG-ASN : bond 0.00417 / 0.19 ( 6) link_NAG-ASN : angle 2.92337 / 2.14 ( 18) ********************** 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 240 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 218 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7269 (t80) REVERT: A 183 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7765 (tp) REVERT: A 189 VAL cc_start: 0.8626 (t) cc_final: 0.8243 (m) REVERT: A 400 GLU cc_start: 0.8425 (tp30) cc_final: 0.8103 (tp30) REVERT: A 562 TYR cc_start: 0.6634 (t80) cc_final: 0.6006 (t80) REVERT: A 974 ILE cc_start: 0.8143 (mm) cc_final: 0.7893 (mt) REVERT: A 988 MET cc_start: 0.8471 (tpp) cc_final: 0.8219 (tpt) REVERT: A 1020 ARG cc_start: 0.6069 (mmt-90) cc_final: 0.5509 (mtt-85) REVERT: A 1086 GLU cc_start: 0.8006 (pt0) cc_final: 0.7591 (pt0) REVERT: A 1100 GLU cc_start: 0.7508 (mp0) cc_final: 0.7242 (pt0) REVERT: A 1165 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8529 (m) REVERT: A 1296 MET cc_start: 0.8004 (mtp) cc_final: 0.7560 (tpt) REVERT: B 32 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7574 (mm-30) REVERT: B 37 GLN cc_start: 0.8355 (tm-30) cc_final: 0.8001 (tt0) REVERT: B 50 LYS cc_start: 0.7684 (mtpt) cc_final: 0.7380 (mmtm) REVERT: B 83 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.6850 (pp20) REVERT: B 112 LEU cc_start: 0.8091 (pt) cc_final: 0.7710 (pp) REVERT: B 186 LYS cc_start: 0.6861 (OUTLIER) cc_final: 0.6460 (mtpt) outliers start: 22 outliers final: 12 residues processed: 231 average time/residue: 0.3880 time to fit residues: 99.1147 Evaluate side-chains 232 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 183 LEU Chi-restraints excluded: chain A residue 346 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 1010 VAL Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1451 CYS 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 138 THR 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 61 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.166102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.136772 restraints weight = 13929.167| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.81 r_work: 0.3442 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11266 Z= 0.102 Angle : 0.533 9.518 15210 Z= 0.258 Chirality : 0.039 0.306 1727 Planarity : 0.004 0.044 1791 Dihedral : 9.983 111.641 1846 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.91 % Allowed : 21.60 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.24), residues: 1263 helix: 2.69 (0.18), residues: 774 sheet: 0.19 (0.65), residues: 64 loop : -0.62 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 209 TYR 0.009 0.001 TYR A1475 PHE 0.018 0.001 PHE A1031 TRP 0.010 0.001 TRP A 935 HIS 0.002 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (11252) covalent geometry : angle 0.52054 / 0.26 (15175) SS BOND : bond 0.00290 / 0.16 ( 7) SS BOND : angle 1.03110 / 0.61 ( 14) hydrogen bonds : bond 0.03227 / 2.09 ( 651) hydrogen bonds : angle 3.60811 / 2.66 ( 1854) link_BETA1-4 : bond 0.00269 / 0.14 ( 1) link_BETA1-4 : angle 1.24294 / 0.58 ( 3) link_NAG-ASN : bond 0.00461 / 0.20 ( 6) link_NAG-ASN : angle 3.23719 / 2.39 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3823.97 seconds wall clock time: 65 minutes 54.15 seconds (3954.15 seconds total)