Starting phenix.real_space_refine on Wed Jun 3 18:39:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30je_57830/06_2026/30je_57830.cif Found real_map, /net/cci-nas-00/data/ceres_data/30je_57830/06_2026/30je_57830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/30je_57830/06_2026/30je_57830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30je_57830/06_2026/30je_57830.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/30je_57830/06_2026/30je_57830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30je_57830/06_2026/30je_57830.map" } resolution = 3.5 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= 0.004 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 5049 2.51 5 N 1342 2.21 5 O 1469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7888 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1276 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 13, 'TRANS': 149} Chain breaks: 4 Chain: "B" Number of atoms: 4210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4210 Classifications: {'peptide': 536} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 504} Chain breaks: 18 Chain: "C" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2402 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 8 Time building chain proxies: 1.86, per 1000 atoms: 0.24 Number of scatterers: 7888 At special positions: 0 Unit cell: (83.62, 88.8, 143.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1469 8.00 N 1342 7.00 C 5049 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 112 " distance=2.16 Simple disulfide: pdb=" SG CYS B 559 " - pdb=" SG CYS C 816 " distance=2.04 Simple disulfide: pdb=" SG CYS C1358 " - pdb=" SG CYS C1489 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 383.0 milliseconds 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1876 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 30 sheets defined 7.2% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.892A pdb=" N GLY A 180 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'B' and resid 285 through 288 Processing helix chain 'B' and resid 303 through 310 Processing helix chain 'B' and resid 432 through 436 Processing helix chain 'B' and resid 522 through 526 Processing helix chain 'B' and resid 600 through 606 removed outlier: 3.776A pdb=" N VAL B 604 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 605 " --> pdb=" O GLY B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 624 removed outlier: 3.506A pdb=" N ILE B 616 " --> pdb=" O THR B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.623A pdb=" N ALA B 642 " --> pdb=" O VAL B 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 1416 through 1424 removed outlier: 4.097A pdb=" N GLY C1424 " --> pdb=" O GLN C1420 " (cutoff:3.500A) Processing helix chain 'C' and resid 1497 through 1501 Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 110 Processing sheet with id=AA2, first strand: chain 'A' and resid 238 through 240 removed outlier: 3.552A pdb=" N THR A 238 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A 294 " --> pdb=" O GLN A 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 274 through 275 removed outlier: 3.929A pdb=" N ARG A 329 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA5, first strand: chain 'B' and resid 43 through 44 removed outlier: 3.596A pdb=" N THR B 647 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR B 30 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 71 through 73 Processing sheet with id=AA7, first strand: chain 'B' and resid 129 through 134 removed outlier: 3.565A pdb=" N ARG B 148 " --> pdb=" O GLN B 133 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.749A pdb=" N VAL B 224 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY B 202 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL B 165 " --> pdb=" O GLN B 177 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN B 177 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE B 167 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.749A pdb=" N VAL B 224 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY B 202 " --> pdb=" O VAL B 224 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 144 through 145 Processing sheet with id=AB2, first strand: chain 'B' and resid 232 through 238 removed outlier: 3.585A pdb=" N LYS B 263 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 232 through 238 removed outlier: 3.721A pdb=" N LEU B 251 " --> pdb=" O LEU B 302 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 243 through 244 removed outlier: 3.716A pdb=" N VAL B 349 " --> pdb=" O TYR B 243 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N MET B 338 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU B 332 " --> pdb=" O MET B 338 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN B 340 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL B 330 " --> pdb=" O GLN B 340 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLU B 342 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA B 328 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N SER B 344 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 326 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 243 through 244 removed outlier: 3.716A pdb=" N VAL B 349 " --> pdb=" O TYR B 243 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N MET B 338 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU B 332 " --> pdb=" O MET B 338 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN B 340 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL B 330 " --> pdb=" O GLN B 340 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLU B 342 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA B 328 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N SER B 344 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 326 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 354 through 356 Processing sheet with id=AB7, first strand: chain 'B' and resid 363 through 364 Processing sheet with id=AB8, first strand: chain 'B' and resid 399 through 400 removed outlier: 3.582A pdb=" N VAL B 424 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG B 439 " --> pdb=" O VAL B 424 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 455 through 459 Processing sheet with id=AC1, first strand: chain 'B' and resid 499 through 507 removed outlier: 6.836A pdb=" N ILE B 494 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA B 503 " --> pdb=" O TYR B 492 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR B 492 " --> pdb=" O ALA B 503 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARG B 505 " --> pdb=" O TYR B 490 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR B 490 " --> pdb=" O ARG B 505 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 564 through 567 Processing sheet with id=AC3, first strand: chain 'C' and resid 776 through 777 Processing sheet with id=AC4, first strand: chain 'C' and resid 770 through 771 removed outlier: 3.566A pdb=" N VAL B 598 " --> pdb=" O GLU C 803 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 829 through 834 removed outlier: 3.566A pdb=" N PHE C 830 " --> pdb=" O TYR C 852 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL C 850 " --> pdb=" O ASP C 832 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG C 848 " --> pdb=" O ARG C 834 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 829 through 834 removed outlier: 3.566A pdb=" N PHE C 830 " --> pdb=" O TYR C 852 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL C 850 " --> pdb=" O ASP C 832 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG C 848 " --> pdb=" O ARG C 834 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 838 through 840 removed outlier: 3.550A pdb=" N VAL C 932 " --> pdb=" O VAL C 839 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 882 through 888 removed outlier: 4.476A pdb=" N HIS C 882 " --> pdb=" O LEU C 866 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 866 " --> pdb=" O HIS C 882 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 888 " --> pdb=" O LEU C 860 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C 860 " --> pdb=" O ILE C 888 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1367 through 1369 removed outlier: 3.538A pdb=" N ALA C1412 " --> pdb=" O HIS C1464 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1401 through 1403 Processing sheet with id=AD2, first strand: chain 'C' and resid 1428 through 1429 Processing sheet with id=AD3, first strand: chain 'C' and resid 1475 through 1477 252 hydrogen bonds defined for protein. 621 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: 1.42 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1282 1.31 - 1.44: 2083 1.44 - 1.57: 4626 1.57 - 1.69: 0 1.69 - 1.82: 45 Bond restraints: 8036 Sorted by residual: bond pdb=" C CYS A 95 " pdb=" N ASN A 96 " ideal model delta sigma weight residual 1.335 1.380 -0.045 1.36e-02 5.41e+03 1.08e+01 bond pdb=" C CYS A 95 " pdb=" O CYS A 95 " ideal model delta sigma weight residual 1.231 1.186 0.045 2.00e-02 2.50e+03 5.06e+00 bond pdb=" CA SER C1406 " pdb=" CB SER C1406 " ideal model delta sigma weight residual 1.527 1.487 0.040 2.48e-02 1.63e+03 2.66e+00 bond pdb=" CB CYS A 112 " pdb=" SG CYS A 112 " ideal model delta sigma weight residual 1.808 1.761 0.047 3.30e-02 9.18e+02 2.01e+00 bond pdb=" CA CYS C1489 " pdb=" C CYS C1489 " ideal model delta sigma weight residual 1.530 1.518 0.013 1.08e-02 8.57e+03 1.41e+00 ... (remaining 8031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 10242 1.15 - 2.30: 507 2.30 - 3.45: 93 3.45 - 4.60: 27 4.60 - 5.74: 10 Bond angle restraints: 10879 Sorted by residual: angle pdb=" N LEU C1485 " pdb=" CA LEU C1485 " pdb=" C LEU C1485 " ideal model delta sigma weight residual 113.18 108.27 4.91 1.21e+00 6.83e-01 1.64e+01 angle pdb=" CA CYS A 95 " pdb=" C CYS A 95 " pdb=" O CYS A 95 " ideal model delta sigma weight residual 120.80 126.54 -5.74 1.70e+00 3.46e-01 1.14e+01 angle pdb=" N ARG A 111 " pdb=" CA ARG A 111 " pdb=" C ARG A 111 " ideal model delta sigma weight residual 107.49 112.94 -5.45 1.74e+00 3.30e-01 9.81e+00 angle pdb=" C ARG A 111 " pdb=" N CYS A 112 " pdb=" CA CYS A 112 " ideal model delta sigma weight residual 122.59 127.34 -4.75 1.57e+00 4.06e-01 9.17e+00 angle pdb=" N TYR A 259 " pdb=" CA TYR A 259 " pdb=" CB TYR A 259 " ideal model delta sigma weight residual 111.65 107.58 4.07 1.40e+00 5.10e-01 8.45e+00 ... (remaining 10874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 4166 17.58 - 35.17: 499 35.17 - 52.75: 141 52.75 - 70.34: 30 70.34 - 87.92: 16 Dihedral angle restraints: 4852 sinusoidal: 1972 harmonic: 2880 Sorted by residual: dihedral pdb=" CB CYS A 95 " pdb=" SG CYS A 95 " pdb=" SG CYS A 112 " pdb=" CB CYS A 112 " ideal model delta sinusoidal sigma weight residual 93.00 17.49 75.51 1 1.00e+01 1.00e-02 7.20e+01 dihedral pdb=" CA TYR A 260 " pdb=" C TYR A 260 " pdb=" N PRO A 261 " pdb=" CA PRO A 261 " ideal model delta harmonic sigma weight residual 180.00 -157.65 -22.35 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA SER B 219 " pdb=" C SER B 219 " pdb=" N THR B 220 " pdb=" CA THR B 220 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 4849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 892 0.039 - 0.078: 218 0.078 - 0.117: 118 0.117 - 0.156: 36 0.156 - 0.195: 1 Chirality restraints: 1265 Sorted by residual: chirality pdb=" CA CYS A 112 " pdb=" N CYS A 112 " pdb=" C CYS A 112 " pdb=" CB CYS A 112 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CA ILE B 206 " pdb=" N ILE B 206 " pdb=" C ILE B 206 " pdb=" CB ILE B 206 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE B 346 " pdb=" N ILE B 346 " pdb=" C ILE B 346 " pdb=" CB ILE B 346 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 1262 not shown) Planarity restraints: 1371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 309 " 0.050 5.00e-02 4.00e+02 7.55e-02 9.13e+00 pdb=" N PRO A 310 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 310 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 310 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 173 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO B 174 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 174 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 174 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 240 " -0.019 5.00e-02 4.00e+02 2.94e-02 1.38e+00 pdb=" N PRO A 241 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 241 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 241 " -0.016 5.00e-02 4.00e+02 ... (remaining 1368 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 71 2.53 - 3.13: 5897 3.13 - 3.72: 10895 3.72 - 4.31: 15168 4.31 - 4.90: 26242 Nonbonded interactions: 58273 Sorted by model distance: nonbonded pdb=" OD1 ASP B 135 " pdb=" OH TYR B 139 " model vdw 1.942 3.040 nonbonded pdb=" OD1 ASP B 371 " pdb=" OG SER B 410 " model vdw 2.096 3.040 nonbonded pdb=" O LEU B 34 " pdb=" N SER B 124 " model vdw 2.114 3.120 nonbonded pdb=" ND2 ASN B 496 " pdb=" O ASP B 524 " model vdw 2.128 3.120 nonbonded pdb=" OE1 GLU B 168 " pdb=" NE ARG B 207 " model vdw 2.133 3.120 ... (remaining 58268 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 group one per residue 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: 1.780 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: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.390 Find NCS groups from input model: 0.030 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 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 : 0.004 0.127 8039 Z= 0.198 Angle : 0.680 28.770 10885 Z= 0.369 Chirality : 0.047 0.195 1265 Planarity : 0.004 0.076 1371 Dihedral : 17.244 87.923 2967 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.45 % Allowed : 26.74 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.75 (0.28), residues: 931 helix: 0.99 (0.87), residues: 32 sheet: -0.39 (0.26), residues: 411 loop : -0.59 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 148 TYR 0.017 0.001 TYR A 259 PHE 0.017 0.001 PHE A 326 TRP 0.010 0.001 TRP A 319 HIS 0.004 0.001 HIS C 882 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 ( 8036) covalent geometry : angle 0.61461 / 0.34 (10879) SS BOND : bond 0.07328 / 3.86 ( 3) SS BOND : angle 12.37111 / 6.58 ( 6) hydrogen bonds : bond 0.17819 / 12.83 ( 231) hydrogen bonds : angle 7.74922 / 5.18 ( 621) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.285 Fit side-chains REVERT: B 225 LYS cc_start: 0.7602 (ttpt) cc_final: 0.7108 (mmtt) REVERT: B 461 LEU cc_start: 0.7921 (mt) cc_final: 0.7445 (tp) REVERT: B 635 TYR cc_start: 0.8148 (p90) cc_final: 0.7756 (p90) REVERT: C 1396 GLN cc_start: 0.8395 (pm20) cc_final: 0.8139 (pm20) REVERT: C 1473 GLN cc_start: 0.8726 (mt0) cc_final: 0.8287 (tt0) outliers start: 4 outliers final: 3 residues processed: 127 average time/residue: 0.0795 time to fit residues: 14.1374 Evaluate side-chains 123 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 120 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 1472 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.164346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.113989 restraints weight = 11023.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.117916 restraints weight = 6023.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.120402 restraints weight = 4167.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.121904 restraints weight = 3326.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.122908 restraints weight = 2898.283| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8039 Z= 0.225 Angle : 0.642 10.422 10885 Z= 0.329 Chirality : 0.048 0.201 1265 Planarity : 0.005 0.053 1371 Dihedral : 4.803 43.500 1064 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.04 % Allowed : 24.49 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.89 (0.28), residues: 931 helix: 1.04 (0.90), residues: 33 sheet: -0.40 (0.26), residues: 395 loop : -0.79 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 148 TYR 0.032 0.002 TYR A 259 PHE 0.021 0.002 PHE A 326 TRP 0.018 0.002 TRP C 773 HIS 0.007 0.001 HIS C 882 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.22 ( 8036) covalent geometry : angle 0.64188 / 0.33 (10879) SS BOND : bond 0.00379 / 0.19 ( 3) SS BOND : angle 1.06383 / 0.57 ( 6) hydrogen bonds : bond 0.04021 / 2.74 ( 231) hydrogen bonds : angle 5.90026 / 3.98 ( 621) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8087 (tm-30) REVERT: B 137 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8586 (m) REVERT: B 167 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8213 (mp) REVERT: B 180 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8472 (mm) REVERT: B 225 LYS cc_start: 0.7921 (ttpt) cc_final: 0.7474 (mmtt) REVERT: B 461 LEU cc_start: 0.7946 (mt) cc_final: 0.7501 (tp) REVERT: B 552 TRP cc_start: 0.8509 (t60) cc_final: 0.8034 (t60) REVERT: C 904 LYS cc_start: 0.7870 (mttt) cc_final: 0.7519 (mtmm) REVERT: C 1387 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6626 (tm-30) REVERT: C 1393 ARG cc_start: 0.7345 (ttm110) cc_final: 0.7094 (ttm110) REVERT: C 1396 GLN cc_start: 0.8502 (pm20) cc_final: 0.8168 (pm20) outliers start: 36 outliers final: 21 residues processed: 151 average time/residue: 0.0782 time to fit residues: 16.2700 Evaluate side-chains 142 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 457 HIS Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 815 ILE Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 845 VAL Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 932 VAL Chi-restraints excluded: chain C residue 1387 GLU Chi-restraints excluded: chain C residue 1390 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 16 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 0.3980 chunk 69 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 882 HIS C 884 GLN C1473 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.167644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.118479 restraints weight = 10649.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.122469 restraints weight = 5664.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.124989 restraints weight = 3853.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.126620 restraints weight = 3043.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.127459 restraints weight = 2632.105| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8039 Z= 0.111 Angle : 0.550 6.938 10885 Z= 0.279 Chirality : 0.045 0.154 1265 Planarity : 0.004 0.043 1371 Dihedral : 4.143 24.046 1059 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.60 % Allowed : 25.73 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.51 (0.28), residues: 931 helix: 0.60 (0.83), residues: 39 sheet: -0.02 (0.26), residues: 398 loop : -0.61 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 111 TYR 0.021 0.001 TYR A 259 PHE 0.009 0.001 PHE A 326 TRP 0.009 0.001 TRP C 773 HIS 0.005 0.001 HIS C 882 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 8036) covalent geometry : angle 0.55016 / 0.28 (10879) SS BOND : bond 0.00351 / 0.18 ( 3) SS BOND : angle 0.48620 / 0.23 ( 6) hydrogen bonds : bond 0.03203 / 2.15 ( 231) hydrogen bonds : angle 5.43072 / 3.67 ( 621) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.308 Fit side-chains REVERT: A 277 PHE cc_start: 0.7230 (m-10) cc_final: 0.7014 (m-80) REVERT: B 225 LYS cc_start: 0.7743 (ttpt) cc_final: 0.7249 (mmtt) REVERT: B 261 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.8484 (p90) REVERT: B 461 LEU cc_start: 0.7946 (mt) cc_final: 0.7512 (tp) REVERT: B 495 MET cc_start: 0.7148 (mtp) cc_final: 0.6829 (ttt) REVERT: B 581 MET cc_start: 0.7704 (ttp) cc_final: 0.7214 (ttt) REVERT: B 635 TYR cc_start: 0.8214 (p90) cc_final: 0.7821 (p90) REVERT: C 1385 ILE cc_start: 0.7375 (OUTLIER) cc_final: 0.6996 (mm) REVERT: C 1387 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6530 (tm-30) REVERT: C 1393 ARG cc_start: 0.7288 (ttm110) cc_final: 0.7023 (ttm110) REVERT: C 1396 GLN cc_start: 0.8510 (pm20) cc_final: 0.8147 (pm20) outliers start: 32 outliers final: 20 residues processed: 147 average time/residue: 0.0757 time to fit residues: 15.7050 Evaluate side-chains 139 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 333 HIS Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 457 HIS Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 815 ILE Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 845 VAL Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 882 HIS Chi-restraints excluded: chain C residue 1385 ILE Chi-restraints excluded: chain C residue 1387 GLU Chi-restraints excluded: chain C residue 1390 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 17 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 26 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 82 optimal weight: 0.0370 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 882 HIS C1473 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.168000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.125065 restraints weight = 10786.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.123329 restraints weight = 7213.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.125385 restraints weight = 5446.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.126198 restraints weight = 4023.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.126676 restraints weight = 3656.418| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8039 Z= 0.109 Angle : 0.535 6.008 10885 Z= 0.269 Chirality : 0.045 0.172 1265 Planarity : 0.004 0.039 1371 Dihedral : 3.973 22.937 1059 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.71 % Allowed : 24.94 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.37 (0.28), residues: 931 helix: 0.81 (0.84), residues: 39 sheet: 0.18 (0.26), residues: 393 loop : -0.63 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 148 TYR 0.021 0.001 TYR A 259 PHE 0.010 0.001 PHE A 326 TRP 0.012 0.001 TRP B 552 HIS 0.004 0.001 HIS C 882 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 8036) covalent geometry : angle 0.53458 / 0.27 (10879) SS BOND : bond 0.00192 / 0.10 ( 3) SS BOND : angle 0.45295 / 0.22 ( 6) hydrogen bonds : bond 0.02964 / 2.00 ( 231) hydrogen bonds : angle 5.19834 / 3.52 ( 621) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.300 Fit side-chains REVERT: A 277 PHE cc_start: 0.7253 (m-10) cc_final: 0.7034 (m-80) REVERT: B 461 LEU cc_start: 0.7967 (mt) cc_final: 0.7680 (tp) REVERT: B 462 ARG cc_start: 0.7793 (tpm170) cc_final: 0.6488 (tpm170) REVERT: B 495 MET cc_start: 0.7372 (mtp) cc_final: 0.7088 (ttt) REVERT: B 552 TRP cc_start: 0.8467 (t60) cc_final: 0.7973 (t60) REVERT: B 581 MET cc_start: 0.7654 (ttp) cc_final: 0.7182 (ttt) REVERT: B 635 TYR cc_start: 0.8219 (p90) cc_final: 0.7788 (p90) REVERT: C 1385 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7140 (mm) REVERT: C 1387 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6650 (tm-30) outliers start: 33 outliers final: 24 residues processed: 149 average time/residue: 0.0721 time to fit residues: 15.5001 Evaluate side-chains 144 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 457 HIS Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 815 ILE Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 845 VAL Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 882 HIS Chi-restraints excluded: chain C residue 1385 ILE Chi-restraints excluded: chain C residue 1387 GLU Chi-restraints excluded: chain C residue 1390 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 882 HIS C1473 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.164954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.114884 restraints weight = 11027.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.118810 restraints weight = 5972.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.121347 restraints weight = 4113.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.122777 restraints weight = 3271.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.123892 restraints weight = 2854.242| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8039 Z= 0.193 Angle : 0.585 8.587 10885 Z= 0.297 Chirality : 0.046 0.161 1265 Planarity : 0.004 0.038 1371 Dihedral : 4.240 27.918 1059 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 5.17 % Allowed : 24.16 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.59 (0.28), residues: 931 helix: 0.49 (0.85), residues: 40 sheet: -0.03 (0.26), residues: 392 loop : -0.70 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 863 TYR 0.028 0.002 TYR A 259 PHE 0.018 0.001 PHE A 326 TRP 0.014 0.002 TRP C 773 HIS 0.004 0.001 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.19 ( 8036) covalent geometry : angle 0.58508 / 0.30 (10879) SS BOND : bond 0.00303 / 0.15 ( 3) SS BOND : angle 0.67687 / 0.34 ( 6) hydrogen bonds : bond 0.03475 / 2.36 ( 231) hydrogen bonds : angle 5.30041 / 3.58 ( 621) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 123 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: A 271 GLU cc_start: 0.8210 (tt0) cc_final: 0.7984 (tp30) REVERT: A 272 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8584 (m-30) REVERT: A 277 PHE cc_start: 0.7294 (m-10) cc_final: 0.7049 (m-80) REVERT: B 66 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7494 (tppt) REVERT: B 225 LYS cc_start: 0.7877 (ttpt) cc_final: 0.7398 (mmtt) REVERT: B 461 LEU cc_start: 0.7984 (mt) cc_final: 0.7673 (tp) REVERT: B 462 ARG cc_start: 0.7948 (tpm170) cc_final: 0.6534 (tpm170) REVERT: B 552 TRP cc_start: 0.8496 (t60) cc_final: 0.7982 (t60) REVERT: B 635 TYR cc_start: 0.8231 (p90) cc_final: 0.7818 (p90) REVERT: C 904 LYS cc_start: 0.7865 (mttt) cc_final: 0.7607 (mtmm) REVERT: C 1385 ILE cc_start: 0.7375 (OUTLIER) cc_final: 0.6954 (mm) REVERT: C 1387 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6592 (tm-30) REVERT: C 1393 ARG cc_start: 0.7262 (ttm110) cc_final: 0.7056 (ttm110) REVERT: C 1485 LEU cc_start: 0.8050 (tt) cc_final: 0.7825 (tt) outliers start: 46 outliers final: 36 residues processed: 160 average time/residue: 0.0715 time to fit residues: 16.1939 Evaluate side-chains 163 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 333 HIS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 457 HIS Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 815 ILE Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 845 VAL Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 882 HIS Chi-restraints excluded: chain C residue 1385 ILE Chi-restraints excluded: chain C residue 1387 GLU Chi-restraints excluded: chain C residue 1390 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 5 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 62 optimal weight: 0.0980 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 18 optimal weight: 30.0000 chunk 17 optimal weight: 20.0000 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 882 HIS C1473 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.168008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.124251 restraints weight = 10795.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.124839 restraints weight = 7150.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.126047 restraints weight = 4861.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.127258 restraints weight = 3719.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.127350 restraints weight = 3323.324| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8039 Z= 0.113 Angle : 0.531 6.797 10885 Z= 0.270 Chirality : 0.045 0.173 1265 Planarity : 0.004 0.038 1371 Dihedral : 4.009 23.725 1059 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.06 % Allowed : 24.83 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.40 (0.28), residues: 931 helix: 1.32 (0.92), residues: 34 sheet: 0.10 (0.26), residues: 392 loop : -0.61 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 148 TYR 0.020 0.001 TYR A 259 PHE 0.010 0.001 PHE A 326 TRP 0.011 0.001 TRP A 319 HIS 0.006 0.001 HIS C 882 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 ( 8036) covalent geometry : angle 0.53077 / 0.27 (10879) SS BOND : bond 0.00234 / 0.12 ( 3) SS BOND : angle 0.83292 / 0.47 ( 6) hydrogen bonds : bond 0.02885 / 1.95 ( 231) hydrogen bonds : angle 5.08083 / 3.45 ( 621) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 124 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 271 GLU cc_start: 0.8250 (tt0) cc_final: 0.8012 (tp30) REVERT: A 311 ARG cc_start: 0.6341 (ptt-90) cc_final: 0.6099 (mpp80) REVERT: B 66 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7319 (tppt) REVERT: B 461 LEU cc_start: 0.7965 (mt) cc_final: 0.7656 (tp) REVERT: B 495 MET cc_start: 0.7347 (mtp) cc_final: 0.7013 (ttt) REVERT: B 635 TYR cc_start: 0.8193 (p90) cc_final: 0.7738 (p90) REVERT: C 1385 ILE cc_start: 0.7343 (OUTLIER) cc_final: 0.6973 (mm) REVERT: C 1387 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6515 (tm-30) outliers start: 45 outliers final: 35 residues processed: 162 average time/residue: 0.0733 time to fit residues: 16.9216 Evaluate side-chains 158 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 333 HIS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 457 HIS Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 815 ILE Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 845 VAL Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 882 HIS Chi-restraints excluded: chain C residue 1385 ILE Chi-restraints excluded: chain C residue 1387 GLU Chi-restraints excluded: chain C residue 1390 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 84 optimal weight: 3.9990 chunk 95 optimal weight: 0.0670 chunk 21 optimal weight: 20.0000 chunk 2 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 18 optimal weight: 30.0000 chunk 26 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 882 HIS C1473 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.167982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.117887 restraints weight = 10918.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.121963 restraints weight = 5843.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.124514 restraints weight = 3982.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.126248 restraints weight = 3149.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.127171 restraints weight = 2721.016| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8039 Z= 0.113 Angle : 0.537 7.415 10885 Z= 0.272 Chirality : 0.045 0.158 1265 Planarity : 0.004 0.039 1371 Dihedral : 3.925 23.037 1059 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.17 % Allowed : 24.72 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.35 (0.28), residues: 931 helix: 0.78 (0.85), residues: 40 sheet: 0.15 (0.26), residues: 396 loop : -0.58 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 148 TYR 0.020 0.001 TYR A 259 PHE 0.011 0.001 PHE A 326 TRP 0.015 0.001 TRP B 552 HIS 0.008 0.001 HIS C 882 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.11 ( 8036) covalent geometry : angle 0.53688 / 0.27 (10879) SS BOND : bond 0.00178 / 0.09 ( 3) SS BOND : angle 0.63996 / 0.35 ( 6) hydrogen bonds : bond 0.02908 / 1.93 ( 231) hydrogen bonds : angle 4.93068 / 3.35 ( 621) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 271 GLU cc_start: 0.8302 (tt0) cc_final: 0.7986 (tp30) REVERT: B 66 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7445 (tppt) REVERT: B 225 LYS cc_start: 0.7807 (ttpt) cc_final: 0.7276 (mmtt) REVERT: B 461 LEU cc_start: 0.8010 (mt) cc_final: 0.7655 (tp) REVERT: B 495 MET cc_start: 0.7162 (mtp) cc_final: 0.6867 (ttt) REVERT: B 552 TRP cc_start: 0.8476 (t60) cc_final: 0.7946 (t60) REVERT: B 635 TYR cc_start: 0.8245 (p90) cc_final: 0.7797 (p90) REVERT: C 1385 ILE cc_start: 0.7377 (OUTLIER) cc_final: 0.6980 (mm) REVERT: C 1387 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6485 (tm-30) REVERT: C 1393 ARG cc_start: 0.7305 (ttm110) cc_final: 0.7090 (ttm110) outliers start: 46 outliers final: 37 residues processed: 160 average time/residue: 0.0744 time to fit residues: 16.9394 Evaluate side-chains 157 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 333 HIS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 457 HIS Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 815 ILE Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 845 VAL Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 882 HIS Chi-restraints excluded: chain C residue 1385 ILE Chi-restraints excluded: chain C residue 1387 GLU Chi-restraints excluded: chain C residue 1390 THR Chi-restraints excluded: chain C residue 1434 LEU Chi-restraints excluded: chain C residue 1490 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 64 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 882 HIS C1473 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.167784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.117859 restraints weight = 10837.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.121931 restraints weight = 5806.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.124546 restraints weight = 3950.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.126124 restraints weight = 3124.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.127025 restraints weight = 2714.639| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8039 Z= 0.125 Angle : 0.548 8.789 10885 Z= 0.275 Chirality : 0.045 0.154 1265 Planarity : 0.004 0.039 1371 Dihedral : 3.933 23.788 1059 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.17 % Allowed : 25.06 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.38 (0.28), residues: 931 helix: 0.79 (0.85), residues: 40 sheet: 0.08 (0.26), residues: 404 loop : -0.55 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 881 TYR 0.021 0.001 TYR A 259 PHE 0.012 0.001 PHE A 326 TRP 0.014 0.002 TRP A 319 HIS 0.004 0.001 HIS C 882 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.12 ( 8036) covalent geometry : angle 0.54807 / 0.28 (10879) SS BOND : bond 0.00207 / 0.10 ( 3) SS BOND : angle 0.59088 / 0.32 ( 6) hydrogen bonds : bond 0.02903 / 1.96 ( 231) hydrogen bonds : angle 4.90029 / 3.33 ( 621) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 120 time to evaluate : 0.289 Fit side-chains REVERT: A 271 GLU cc_start: 0.8327 (tt0) cc_final: 0.7985 (tp30) REVERT: B 66 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7428 (tppt) REVERT: B 83 MET cc_start: 0.7517 (pmm) cc_final: 0.5269 (ppp) REVERT: B 225 LYS cc_start: 0.7832 (ttpt) cc_final: 0.7327 (mmtt) REVERT: B 461 LEU cc_start: 0.8010 (mt) cc_final: 0.7651 (tp) REVERT: B 495 MET cc_start: 0.7140 (mtp) cc_final: 0.6842 (ttt) REVERT: B 552 TRP cc_start: 0.8493 (t60) cc_final: 0.7943 (t60) REVERT: B 635 TYR cc_start: 0.8244 (p90) cc_final: 0.7794 (p90) REVERT: C 883 GLN cc_start: 0.7935 (pp30) cc_final: 0.6877 (pt0) REVERT: C 1385 ILE cc_start: 0.7363 (OUTLIER) cc_final: 0.6969 (mm) REVERT: C 1387 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6502 (tm-30) REVERT: C 1393 ARG cc_start: 0.7345 (ttm110) cc_final: 0.7116 (ttm110) outliers start: 46 outliers final: 40 residues processed: 157 average time/residue: 0.0676 time to fit residues: 15.4702 Evaluate side-chains 158 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 333 HIS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 457 HIS Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 815 ILE Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 845 VAL Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 1385 ILE Chi-restraints excluded: chain C residue 1387 GLU Chi-restraints excluded: chain C residue 1390 THR Chi-restraints excluded: chain C residue 1426 ASP Chi-restraints excluded: chain C residue 1434 LEU Chi-restraints excluded: chain C residue 1490 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 33 optimal weight: 0.3980 chunk 91 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 882 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.168237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.118404 restraints weight = 10870.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.122415 restraints weight = 5823.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.125030 restraints weight = 3978.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.126519 restraints weight = 3144.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.127607 restraints weight = 2737.224| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8039 Z= 0.122 Angle : 0.558 8.069 10885 Z= 0.279 Chirality : 0.045 0.172 1265 Planarity : 0.004 0.039 1371 Dihedral : 3.923 23.480 1059 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.06 % Allowed : 25.06 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.42 (0.28), residues: 931 helix: 0.65 (0.83), residues: 40 sheet: -0.02 (0.26), residues: 417 loop : -0.50 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 148 TYR 0.020 0.001 TYR A 259 PHE 0.012 0.001 PHE A 326 TRP 0.014 0.002 TRP A 319 HIS 0.005 0.001 HIS C 882 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 ( 8036) covalent geometry : angle 0.55762 / 0.28 (10879) SS BOND : bond 0.00198 / 0.10 ( 3) SS BOND : angle 0.57414 / 0.31 ( 6) hydrogen bonds : bond 0.02932 / 2.01 ( 231) hydrogen bonds : angle 4.91760 / 3.34 ( 621) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 114 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 266 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: A 271 GLU cc_start: 0.8322 (tt0) cc_final: 0.7978 (tp30) REVERT: B 66 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7404 (tppt) REVERT: B 461 LEU cc_start: 0.8033 (mt) cc_final: 0.7683 (tp) REVERT: B 495 MET cc_start: 0.7108 (mtp) cc_final: 0.6824 (ttt) REVERT: B 552 TRP cc_start: 0.8495 (t60) cc_final: 0.7925 (t60) REVERT: B 635 TYR cc_start: 0.8253 (p90) cc_final: 0.7802 (p90) REVERT: C 883 GLN cc_start: 0.7828 (pp30) cc_final: 0.6925 (pt0) REVERT: C 1385 ILE cc_start: 0.7366 (OUTLIER) cc_final: 0.6960 (mm) REVERT: C 1387 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6469 (tm-30) REVERT: C 1393 ARG cc_start: 0.7343 (ttm110) cc_final: 0.7119 (ttm110) outliers start: 45 outliers final: 40 residues processed: 150 average time/residue: 0.0715 time to fit residues: 15.6203 Evaluate side-chains 158 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 114 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 333 HIS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 457 HIS Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 815 ILE Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 845 VAL Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 1385 ILE Chi-restraints excluded: chain C residue 1387 GLU Chi-restraints excluded: chain C residue 1426 ASP Chi-restraints excluded: chain C residue 1434 LEU Chi-restraints excluded: chain C residue 1490 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 61 optimal weight: 0.0670 chunk 96 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 882 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.164553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.116052 restraints weight = 10650.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.119714 restraints weight = 5950.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.122100 restraints weight = 4145.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.123545 restraints weight = 3312.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.124533 restraints weight = 2888.428| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8039 Z= 0.172 Angle : 0.608 12.068 10885 Z= 0.302 Chirality : 0.046 0.158 1265 Planarity : 0.004 0.040 1371 Dihedral : 4.198 29.155 1059 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 5.39 % Allowed : 24.83 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.59 (0.28), residues: 931 helix: 0.22 (0.83), residues: 40 sheet: -0.13 (0.26), residues: 417 loop : -0.60 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 148 TYR 0.027 0.001 TYR A 259 PHE 0.017 0.001 PHE A 326 TRP 0.018 0.002 TRP A 319 HIS 0.005 0.001 HIS C 882 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.17 ( 8036) covalent geometry : angle 0.60748 / 0.30 (10879) SS BOND : bond 0.00300 / 0.15 ( 3) SS BOND : angle 0.85024 / 0.47 ( 6) hydrogen bonds : bond 0.03299 / 2.29 ( 231) hydrogen bonds : angle 5.11351 / 3.47 ( 621) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 120 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: A 271 GLU cc_start: 0.8239 (tt0) cc_final: 0.7988 (tp30) REVERT: B 66 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7332 (tppt) REVERT: B 225 LYS cc_start: 0.7958 (ttpt) cc_final: 0.7488 (mmtt) REVERT: B 461 LEU cc_start: 0.8049 (mt) cc_final: 0.7758 (tp) REVERT: B 495 MET cc_start: 0.7237 (mtp) cc_final: 0.6893 (ttt) REVERT: B 552 TRP cc_start: 0.8531 (t60) cc_final: 0.8024 (t60) REVERT: C 826 MET cc_start: 0.6877 (tpp) cc_final: 0.6467 (mmt) REVERT: C 883 GLN cc_start: 0.7712 (pp30) cc_final: 0.6744 (pt0) REVERT: C 904 LYS cc_start: 0.7849 (mttt) cc_final: 0.7495 (mtmm) REVERT: C 1385 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7042 (mm) REVERT: C 1387 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6539 (tm-30) REVERT: C 1393 ARG cc_start: 0.7362 (ttm110) cc_final: 0.7145 (ttm110) outliers start: 48 outliers final: 38 residues processed: 159 average time/residue: 0.0699 time to fit residues: 16.2030 Evaluate side-chains 159 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 117 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 333 HIS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 457 HIS Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 815 ILE Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 845 VAL Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 1385 ILE Chi-restraints excluded: chain C residue 1387 GLU Chi-restraints excluded: chain C residue 1426 ASP Chi-restraints excluded: chain C residue 1434 LEU Chi-restraints excluded: chain C residue 1490 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 80 optimal weight: 2.9990 chunk 82 optimal weight: 0.0770 chunk 10 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 882 HIS C1473 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.169333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.119915 restraints weight = 10765.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.123939 restraints weight = 5752.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.126537 restraints weight = 3930.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.128193 restraints weight = 3110.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.129001 restraints weight = 2687.731| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8039 Z= 0.104 Angle : 0.574 13.711 10885 Z= 0.282 Chirality : 0.045 0.168 1265 Planarity : 0.004 0.039 1371 Dihedral : 3.902 21.662 1059 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.93 % Allowed : 26.40 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.41 (0.28), residues: 931 helix: 0.38 (0.84), residues: 40 sheet: -0.00 (0.26), residues: 417 loop : -0.48 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 148 TYR 0.018 0.001 TYR A 259 PHE 0.012 0.001 PHE B 525 TRP 0.014 0.001 TRP B 552 HIS 0.008 0.001 HIS C 882 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.10 ( 8036) covalent geometry : angle 0.57381 / 0.28 (10879) SS BOND : bond 0.00156 / 0.08 ( 3) SS BOND : angle 0.44423 / 0.22 ( 6) hydrogen bonds : bond 0.02869 / 1.93 ( 231) hydrogen bonds : angle 4.89050 / 3.34 ( 621) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1801.36 seconds wall clock time: 31 minutes 33.35 seconds (1893.35 seconds total)