Starting phenix.real_space_refine on Mon Mar 18 14:43:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmv_29297/03_2024/8fmv_29297_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmv_29297/03_2024/8fmv_29297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmv_29297/03_2024/8fmv_29297.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmv_29297/03_2024/8fmv_29297.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmv_29297/03_2024/8fmv_29297_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmv_29297/03_2024/8fmv_29297_trim_updated.pdb" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.023 sd= 0.049 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: 7 Type Number sf(0) Gaussians P 21 5.49 5 Mg 1 5.21 5 S 41 5.16 5 C 6829 2.51 5 N 1681 2.21 5 O 1928 1.98 5 H 9940 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20441 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 10700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 10700 Classifications: {'peptide': 665} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 651} Chain: "C" Number of atoms: 9038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 9038 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 19, 'TRANS': 549} Chain breaks: 1 Chain: "D" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 376 Unusual residues: {' MG': 1, 'ATP': 1, 'POV': 12} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 4, 'POV:plan-2': 6, 'POV:plan-1': 4} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 327 Unusual residues: {'ATP': 1, 'HT1': 2, 'POV': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 4, 'POV:plan-2': 3, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 9.38, per 1000 atoms: 0.46 Number of scatterers: 20441 At special positions: 0 Unit cell: (71.166, 103.886, 157.056, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 41 16.00 P 21 15.00 Mg 1 11.99 O 1928 8.00 N 1681 7.00 C 6829 6.00 H 9940 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 17.50 Conformation dependent library (CDL) restraints added in 2.4 seconds 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2290 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 8 sheets defined 58.5% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'D' and resid 3 through 12 Processing helix chain 'D' and resid 15 through 45 Proline residue: D 36 - end of helix Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 136 through 141 Processing helix chain 'D' and resid 143 through 193 removed outlier: 4.137A pdb=" N LYS D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY D 148 " --> pdb=" O PRO D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 Processing helix chain 'D' and resid 206 through 229 removed outlier: 4.033A pdb=" N ASP D 216 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR D 217 " --> pdb=" O ILE D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 248 Processing helix chain 'D' and resid 250 through 296 removed outlier: 3.647A pdb=" N VAL D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE D 259 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL D 260 " --> pdb=" O ALA D 256 " (cutoff:3.500A) Proline residue: D 261 - end of helix removed outlier: 3.698A pdb=" N TYR D 276 " --> pdb=" O ARG D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 304 Processing helix chain 'D' and resid 308 through 335 Processing helix chain 'D' and resid 338 through 361 Processing helix chain 'D' and resid 369 through 382 Processing helix chain 'D' and resid 386 through 410 removed outlier: 5.007A pdb=" N GLU D 397 " --> pdb=" O PHE D 393 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU D 398 " --> pdb=" O SER D 394 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 476 removed outlier: 3.894A pdb=" N LEU D 473 " --> pdb=" O LYS D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 496 No H-bonds generated for 'chain 'D' and resid 494 through 496' Processing helix chain 'D' and resid 499 through 503 Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 535 through 540 Processing helix chain 'D' and resid 560 through 562 No H-bonds generated for 'chain 'D' and resid 560 through 562' Processing helix chain 'D' and resid 569 through 583 removed outlier: 3.753A pdb=" N GLN D 573 " --> pdb=" O SER D 569 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 612 Processing helix chain 'D' and resid 648 through 653 Processing helix chain 'D' and resid 656 through 663 Processing helix chain 'C' and resid 4 through 7 No H-bonds generated for 'chain 'C' and resid 4 through 7' Processing helix chain 'C' and resid 9 through 14 Processing helix chain 'C' and resid 17 through 33 Processing helix chain 'C' and resid 36 through 48 Processing helix chain 'C' and resid 54 through 103 removed outlier: 3.678A pdb=" N THR C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 111 Processing helix chain 'C' and resid 114 through 122 Processing helix chain 'C' and resid 124 through 143 removed outlier: 4.385A pdb=" N ILE C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 156 Processing helix chain 'C' and resid 160 through 165 Processing helix chain 'C' and resid 167 through 206 removed outlier: 4.089A pdb=" N VAL C 171 " --> pdb=" O ILE C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'C' and resid 217 through 269 removed outlier: 3.633A pdb=" N VAL C 221 " --> pdb=" O GLU C 217 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE C 241 " --> pdb=" O LYS C 237 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU C 244 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLU C 246 " --> pdb=" O ASP C 242 " (cutoff:3.500A) Proline residue: C 247 - end of helix removed outlier: 4.000A pdb=" N SER C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 314 removed outlier: 4.906A pdb=" N TRP C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) Proline residue: C 291 - end of helix removed outlier: 3.902A pdb=" N GLY C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 384 removed outlier: 3.757A pdb=" N LEU C 384 " --> pdb=" O ILE C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 428 through 435 removed outlier: 4.803A pdb=" N GLY C 435 " --> pdb=" O ASN C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 450 Processing helix chain 'C' and resid 454 through 459 removed outlier: 3.623A pdb=" N MET C 459 " --> pdb=" O LYS C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 490 Processing helix chain 'C' and resid 507 through 520 Processing helix chain 'C' and resid 533 through 535 No H-bonds generated for 'chain 'C' and resid 533 through 535' Processing helix chain 'C' and resid 556 through 561 Processing sheet with id= A, first strand: chain 'D' and resid 54 through 56 Processing sheet with id= B, first strand: chain 'D' and resid 89 through 93 Processing sheet with id= C, first strand: chain 'D' and resid 116 through 118 Processing sheet with id= D, first strand: chain 'D' and resid 430 through 433 Processing sheet with id= E, first strand: chain 'D' and resid 459 through 462 removed outlier: 7.115A pdb=" N GLN D 633 " --> pdb=" O ALA D 460 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N VAL D 462 " --> pdb=" O GLN D 633 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU D 635 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY D 646 " --> pdb=" O ILE D 634 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL D 636 " --> pdb=" O GLU D 644 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU D 644 " --> pdb=" O VAL D 636 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 506 through 509 removed outlier: 6.388A pdb=" N ILE D 587 " --> pdb=" O GLY D 507 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL D 509 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE D 589 " --> pdb=" O VAL D 509 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 359 through 361 Processing sheet with id= H, first strand: chain 'C' and resid 541 through 544 removed outlier: 6.193A pdb=" N THR C 526 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE C 369 " --> pdb=" O THR C 526 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE C 528 " --> pdb=" O ILE C 369 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1551 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: 7.43 Time building geometry restraints manager: 18.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 3268 1.05 - 1.24: 8003 1.24 - 1.43: 3059 1.43 - 1.63: 6212 1.63 - 1.82: 82 Bond restraints: 20624 Sorted by residual: bond pdb=" NE1 TRP D 266 " pdb=" HE1 TRP D 266 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP D 54 " pdb=" HE1 TRP D 54 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP C 565 " pdb=" HE1 TRP C 565 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP C 10 " pdb=" HE1 TRP C 10 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP C 16 " pdb=" HE1 TRP C 16 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 ... (remaining 20619 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.43: 402 106.43 - 113.39: 23977 113.39 - 120.36: 7016 120.36 - 127.33: 5391 127.33 - 134.30: 97 Bond angle restraints: 36883 Sorted by residual: angle pdb=" PB ATP C 609 " pdb=" O3B ATP C 609 " pdb=" PG ATP C 609 " ideal model delta sigma weight residual 139.87 119.55 20.32 1.00e+00 1.00e+00 4.13e+02 angle pdb=" PA ATP D 713 " pdb=" O3A ATP D 713 " pdb=" PB ATP D 713 " ideal model delta sigma weight residual 136.83 117.71 19.12 1.00e+00 1.00e+00 3.65e+02 angle pdb=" PB ATP D 713 " pdb=" O3B ATP D 713 " pdb=" PG ATP D 713 " ideal model delta sigma weight residual 139.87 130.47 9.40 1.00e+00 1.00e+00 8.83e+01 angle pdb=" PA ATP C 609 " pdb=" O3A ATP C 609 " pdb=" PB ATP C 609 " ideal model delta sigma weight residual 136.83 128.65 8.18 1.00e+00 1.00e+00 6.70e+01 angle pdb=" N GLU D 655 " pdb=" CA GLU D 655 " pdb=" C GLU D 655 " ideal model delta sigma weight residual 108.00 117.55 -9.55 1.48e+00 4.57e-01 4.16e+01 ... (remaining 36878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.69: 9178 27.69 - 55.37: 506 55.37 - 83.06: 100 83.06 - 110.74: 18 110.74 - 138.43: 10 Dihedral angle restraints: 9812 sinusoidal: 5569 harmonic: 4243 Sorted by residual: dihedral pdb=" C29 POV C 608 " pdb="C210 POV C 608 " pdb="C211 POV C 608 " pdb="C212 POV C 608 " ideal model delta sinusoidal sigma weight residual 112.25 -109.32 -138.43 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" C27 POV D 706 " pdb=" C28 POV D 706 " pdb=" C29 POV D 706 " pdb="C210 POV D 706 " ideal model delta sinusoidal sigma weight residual 127.48 -3.34 130.82 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" C29 POV C 605 " pdb="C210 POV C 605 " pdb="C211 POV C 605 " pdb="C212 POV C 605 " ideal model delta sinusoidal sigma weight residual 112.25 -119.19 -128.56 1 3.00e+01 1.11e-03 1.73e+01 ... (remaining 9809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1427 0.075 - 0.151: 112 0.151 - 0.226: 12 0.226 - 0.301: 1 0.301 - 0.377: 1 Chirality restraints: 1553 Sorted by residual: chirality pdb=" CA THR C 466 " pdb=" N THR C 466 " pdb=" C THR C 466 " pdb=" CB THR C 466 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA GLU D 655 " pdb=" N GLU D 655 " pdb=" C GLU D 655 " pdb=" CB GLU D 655 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA THR D 458 " pdb=" N THR D 458 " pdb=" C THR D 458 " pdb=" CB THR D 458 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1550 not shown) Planarity restraints: 2957 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV D 709 " 0.110 2.00e-02 2.50e+03 2.45e-01 6.02e+02 pdb=" C29 POV D 709 " -0.341 2.00e-02 2.50e+03 pdb="C210 POV D 709 " 0.323 2.00e-02 2.50e+03 pdb="C211 POV D 709 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C 606 " 0.224 2.00e-02 2.50e+03 2.44e-01 5.96e+02 pdb=" C29 POV C 606 " -0.182 2.00e-02 2.50e+03 pdb="C210 POV C 606 " -0.299 2.00e-02 2.50e+03 pdb="C211 POV C 606 " 0.257 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 701 " -0.196 2.00e-02 2.50e+03 1.99e-01 3.97e+02 pdb=" C29 POV D 701 " 0.188 2.00e-02 2.50e+03 pdb="C210 POV D 701 " 0.210 2.00e-02 2.50e+03 pdb="C211 POV D 701 " -0.202 2.00e-02 2.50e+03 ... (remaining 2954 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 786 2.08 - 2.71: 32032 2.71 - 3.34: 59717 3.34 - 3.97: 79532 3.97 - 4.60: 121397 Nonbonded interactions: 293464 Sorted by model distance: nonbonded pdb=" HE2 TYR C 179 " pdb=" HG1 THR C 248 " model vdw 1.447 2.100 nonbonded pdb=" HH TYR C 179 " pdb=" HG1 THR C 248 " model vdw 1.477 2.100 nonbonded pdb=" HE2 MET C 144 " pdb=" HG1 THR C 148 " model vdw 1.477 2.270 nonbonded pdb=" HB3 GLU D 420 " pdb=" HG SER D 498 " model vdw 1.482 2.270 nonbonded pdb="HG13 ILE D 119 " pdb=" HG SER D 125 " model vdw 1.535 2.270 ... (remaining 293459 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.920 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: 0.300 Extract box with map and model: 16.750 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 69.960 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 : 0.007 0.165 10684 Z= 0.473 Angle : 0.862 20.320 14342 Z= 0.542 Chirality : 0.044 0.377 1553 Planarity : 0.013 0.245 1758 Dihedral : 19.285 138.429 4196 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.10 % Allowed : 15.17 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.24), residues: 1228 helix: 1.36 (0.19), residues: 766 sheet: -0.35 (0.68), residues: 74 loop : -1.94 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 78 HIS 0.006 0.001 HIS D 307 PHE 0.015 0.001 PHE D 106 TYR 0.020 0.001 TYR D 237 ARG 0.014 0.001 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 106 PHE cc_start: 0.5997 (m-80) cc_final: 0.5684 (m-10) REVERT: C 430 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7788 (mp0) outliers start: 1 outliers final: 1 residues processed: 94 average time/residue: 0.6259 time to fit residues: 79.4588 Evaluate side-chains 88 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 543 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10684 Z= 0.187 Angle : 0.505 5.852 14342 Z= 0.264 Chirality : 0.037 0.145 1553 Planarity : 0.004 0.036 1758 Dihedral : 17.816 127.884 1862 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.57 % Allowed : 15.08 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.25), residues: 1228 helix: 1.54 (0.19), residues: 769 sheet: 0.18 (0.71), residues: 68 loop : -1.79 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 78 HIS 0.002 0.000 HIS D 648 PHE 0.011 0.001 PHE C 187 TYR 0.011 0.001 TYR D 156 ARG 0.002 0.000 ARG D 624 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 430 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7836 (mp0) REVERT: C 467 MET cc_start: 0.7559 (mmm) cc_final: 0.7274 (mmm) outliers start: 6 outliers final: 4 residues processed: 94 average time/residue: 0.6445 time to fit residues: 81.2179 Evaluate side-chains 91 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain C residue 146 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10684 Z= 0.357 Angle : 0.542 7.486 14342 Z= 0.289 Chirality : 0.039 0.136 1553 Planarity : 0.004 0.040 1758 Dihedral : 17.103 148.564 1861 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.15 % Allowed : 16.03 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.24), residues: 1228 helix: 1.38 (0.19), residues: 757 sheet: -0.27 (0.63), residues: 79 loop : -1.81 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 78 HIS 0.003 0.001 HIS C 100 PHE 0.015 0.002 PHE D 356 TYR 0.017 0.002 TYR D 156 ARG 0.003 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 254 PHE cc_start: 0.7815 (m-10) cc_final: 0.7527 (m-10) REVERT: C 430 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7869 (mp0) REVERT: C 467 MET cc_start: 0.7593 (mmm) cc_final: 0.7300 (mmm) outliers start: 12 outliers final: 6 residues processed: 98 average time/residue: 0.6090 time to fit residues: 81.0252 Evaluate side-chains 92 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain C residue 440 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10684 Z= 0.289 Angle : 0.504 6.107 14342 Z= 0.271 Chirality : 0.038 0.137 1553 Planarity : 0.004 0.039 1758 Dihedral : 16.597 153.233 1861 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.43 % Allowed : 15.27 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.24), residues: 1228 helix: 1.36 (0.19), residues: 767 sheet: -0.35 (0.66), residues: 74 loop : -1.75 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 78 HIS 0.007 0.001 HIS D 46 PHE 0.013 0.001 PHE D 356 TYR 0.013 0.001 TYR D 156 ARG 0.002 0.000 ARG D 624 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 287 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.8071 (ptp) REVERT: C 430 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7855 (mp0) REVERT: C 467 MET cc_start: 0.7617 (mmm) cc_final: 0.7348 (mmm) outliers start: 15 outliers final: 9 residues processed: 97 average time/residue: 0.6479 time to fit residues: 85.4385 Evaluate side-chains 95 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 538 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10684 Z= 0.199 Angle : 0.469 5.162 14342 Z= 0.253 Chirality : 0.037 0.138 1553 Planarity : 0.004 0.040 1758 Dihedral : 16.021 161.032 1861 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.53 % Allowed : 14.89 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1228 helix: 1.56 (0.19), residues: 766 sheet: -0.37 (0.61), residues: 83 loop : -1.74 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 78 HIS 0.002 0.000 HIS C 100 PHE 0.012 0.001 PHE D 323 TYR 0.013 0.001 TYR D 495 ARG 0.002 0.000 ARG D 624 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 254 PHE cc_start: 0.7818 (m-10) cc_final: 0.7517 (m-10) REVERT: D 329 MET cc_start: 0.8805 (tpt) cc_final: 0.8555 (tpt) REVERT: C 430 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7861 (mp0) REVERT: C 467 MET cc_start: 0.7605 (mmm) cc_final: 0.7364 (mmm) outliers start: 16 outliers final: 14 residues processed: 101 average time/residue: 0.6403 time to fit residues: 88.0336 Evaluate side-chains 100 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 606 GLN Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 440 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10684 Z= 0.311 Angle : 0.501 5.155 14342 Z= 0.271 Chirality : 0.038 0.136 1553 Planarity : 0.004 0.038 1758 Dihedral : 16.151 172.583 1861 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.81 % Allowed : 15.27 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.24), residues: 1228 helix: 1.47 (0.19), residues: 766 sheet: -0.33 (0.66), residues: 74 loop : -1.73 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 78 HIS 0.003 0.001 HIS C 100 PHE 0.013 0.001 PHE D 356 TYR 0.014 0.001 TYR D 156 ARG 0.002 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 287 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.8069 (ptp) REVERT: C 430 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7864 (mp0) REVERT: C 467 MET cc_start: 0.7598 (mmm) cc_final: 0.7358 (mmm) REVERT: C 565 TRP cc_start: 0.5112 (OUTLIER) cc_final: 0.3647 (m100) outliers start: 19 outliers final: 16 residues processed: 102 average time/residue: 0.6015 time to fit residues: 83.4229 Evaluate side-chains 102 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 606 GLN Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 565 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10684 Z= 0.197 Angle : 0.469 5.150 14342 Z= 0.253 Chirality : 0.037 0.138 1553 Planarity : 0.004 0.043 1758 Dihedral : 15.629 172.918 1861 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.72 % Allowed : 15.36 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1228 helix: 1.62 (0.19), residues: 765 sheet: -0.20 (0.66), residues: 73 loop : -1.69 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 78 HIS 0.010 0.001 HIS D 648 PHE 0.011 0.001 PHE C 397 TYR 0.010 0.001 TYR D 156 ARG 0.016 0.000 ARG D 629 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 106 PHE cc_start: 0.6330 (m-80) cc_final: 0.5952 (m-10) REVERT: D 329 MET cc_start: 0.8814 (tpt) cc_final: 0.8548 (tpt) REVERT: C 47 MET cc_start: 0.8361 (mtt) cc_final: 0.8115 (mtt) REVERT: C 430 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7862 (mp0) REVERT: C 467 MET cc_start: 0.7582 (mmm) cc_final: 0.7361 (mmm) REVERT: C 565 TRP cc_start: 0.5098 (OUTLIER) cc_final: 0.3655 (m100) outliers start: 18 outliers final: 14 residues processed: 103 average time/residue: 0.6203 time to fit residues: 86.0564 Evaluate side-chains 101 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 606 GLN Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 565 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 ASN D 384 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10684 Z= 0.356 Angle : 0.522 5.936 14342 Z= 0.281 Chirality : 0.039 0.135 1553 Planarity : 0.004 0.038 1758 Dihedral : 15.904 163.278 1861 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.10 % Allowed : 14.89 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.24), residues: 1228 helix: 1.45 (0.19), residues: 764 sheet: -0.26 (0.62), residues: 79 loop : -1.79 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 78 HIS 0.012 0.001 HIS D 648 PHE 0.016 0.002 PHE C 397 TYR 0.015 0.002 TYR D 156 ARG 0.002 0.000 ARG D 478 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 106 PHE cc_start: 0.6347 (m-80) cc_final: 0.5984 (m-10) REVERT: D 652 MET cc_start: 0.7221 (mmp) cc_final: 0.6898 (mmp) REVERT: C 47 MET cc_start: 0.8438 (mtt) cc_final: 0.8153 (mtt) REVERT: C 430 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7702 (mp0) REVERT: C 467 MET cc_start: 0.7582 (mmm) cc_final: 0.7367 (mmm) REVERT: C 565 TRP cc_start: 0.5156 (OUTLIER) cc_final: 0.3681 (m100) outliers start: 22 outliers final: 17 residues processed: 104 average time/residue: 0.5842 time to fit residues: 82.7439 Evaluate side-chains 102 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 606 GLN Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 565 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 10684 Z= 0.336 Angle : 0.807 59.199 14342 Z= 0.469 Chirality : 0.038 0.154 1553 Planarity : 0.004 0.039 1758 Dihedral : 15.889 162.857 1861 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.62 % Allowed : 15.27 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.24), residues: 1228 helix: 1.43 (0.19), residues: 763 sheet: -0.61 (0.60), residues: 84 loop : -1.78 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 78 HIS 0.015 0.001 HIS D 648 PHE 0.015 0.001 PHE C 397 TYR 0.014 0.001 TYR D 156 ARG 0.002 0.000 ARG D 624 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 106 PHE cc_start: 0.6344 (m-80) cc_final: 0.5983 (m-10) REVERT: D 652 MET cc_start: 0.7220 (mmp) cc_final: 0.6864 (mmp) REVERT: C 47 MET cc_start: 0.8429 (mtt) cc_final: 0.8154 (mtt) REVERT: C 430 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7701 (mp0) REVERT: C 467 MET cc_start: 0.7583 (mmm) cc_final: 0.7366 (mmm) REVERT: C 565 TRP cc_start: 0.5150 (OUTLIER) cc_final: 0.3679 (m100) outliers start: 17 outliers final: 16 residues processed: 100 average time/residue: 0.6023 time to fit residues: 82.1576 Evaluate side-chains 100 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 606 GLN Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 565 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 10 optimal weight: 50.0000 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 0.0670 chunk 103 optimal weight: 3.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 10684 Z= 0.336 Angle : 0.807 59.199 14342 Z= 0.469 Chirality : 0.038 0.154 1553 Planarity : 0.004 0.039 1758 Dihedral : 15.889 162.857 1861 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.62 % Allowed : 15.27 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.24), residues: 1228 helix: 1.43 (0.19), residues: 763 sheet: -0.61 (0.60), residues: 84 loop : -1.78 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 78 HIS 0.015 0.001 HIS D 648 PHE 0.015 0.001 PHE C 397 TYR 0.014 0.001 TYR D 156 ARG 0.002 0.000 ARG D 624 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 106 PHE cc_start: 0.6345 (m-80) cc_final: 0.5983 (m-10) REVERT: D 652 MET cc_start: 0.7221 (mmp) cc_final: 0.6864 (mmp) REVERT: C 47 MET cc_start: 0.8430 (mtt) cc_final: 0.8154 (mtt) REVERT: C 430 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7701 (mp0) REVERT: C 467 MET cc_start: 0.7583 (mmm) cc_final: 0.7366 (mmm) REVERT: C 565 TRP cc_start: 0.5150 (OUTLIER) cc_final: 0.3679 (m100) outliers start: 17 outliers final: 16 residues processed: 98 average time/residue: 0.6297 time to fit residues: 83.9043 Evaluate side-chains 100 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 606 GLN Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 565 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 648 HIS ** 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 = 0.3740 r_free = 0.3740 target = 0.088130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.065642 restraints weight = 72166.410| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.22 r_work: 0.3109 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 10684 Z= 0.336 Angle : 0.807 59.199 14342 Z= 0.469 Chirality : 0.038 0.154 1553 Planarity : 0.004 0.039 1758 Dihedral : 15.889 162.857 1861 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.62 % Allowed : 15.27 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.24), residues: 1228 helix: 1.43 (0.19), residues: 763 sheet: -0.61 (0.60), residues: 84 loop : -1.78 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 78 HIS 0.015 0.001 HIS D 648 PHE 0.015 0.001 PHE C 397 TYR 0.014 0.001 TYR D 156 ARG 0.002 0.000 ARG D 624 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4530.28 seconds wall clock time: 81 minutes 54.64 seconds (4914.64 seconds total)