Starting phenix.real_space_refine on Thu Jul 2 00:58:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pag_13269/07_2026/7pag_13269.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pag_13269/07_2026/7pag_13269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pag_13269/07_2026/7pag_13269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pag_13269/07_2026/7pag_13269.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7pag_13269/07_2026/7pag_13269.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pag_13269/07_2026/7pag_13269.cif" model { file = "/net/cci-nas-00/data/ceres_data/7pag_13269/07_2026/7pag_13269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pag_13269/07_2026/7pag_13269.cif" } resolution = 4.0 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 971 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 28 5.16 5 C 2504 2.51 5 N 746 2.21 5 O 759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4040 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4023 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 23, 'TRANS': 485} Chain breaks: 1 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 3, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.21, per 1000 atoms: 0.30 Number of scatterers: 4040 At special positions: 0 Unit cell: (91.12, 71.02, 171.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 3 19.99 S 28 16.00 O 759 8.00 N 746 7.00 C 2504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 75 " distance=2.03 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 72 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 256 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 380 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 396 " - pdb=" SG CYS A 406 " distance=2.03 Simple disulfide: pdb=" SG CYS A 496 " - pdb=" SG CYS A 509 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 533 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 604 " - " ASN A 204 " Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 147.3 milliseconds 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 956 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 6 sheets defined 15.1% alpha, 54.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 189 through 199 Processing helix chain 'A' and resid 204 through 219 removed outlier: 4.372A pdb=" N HIS A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 320 through 331 removed outlier: 3.726A pdb=" N PHE A 324 " --> pdb=" O THR A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 346 through 349 Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 356 through 373 removed outlier: 3.773A pdb=" N GLN A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47 removed outlier: 3.564A pdb=" N HIS A 221 " --> pdb=" O MET A 47 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 134 removed outlier: 10.294A pdb=" N PHE A 180 " --> pdb=" O PRO A 96 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N SER A 98 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N TYR A 178 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS A 100 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N MET A 142 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER A 264 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA A 144 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN A 262 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL A 146 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLU A 260 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLY A 148 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASN A 258 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N HIS A 150 " --> pdb=" O CYS A 256 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N CYS A 256 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LYS A 152 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY A 254 " --> pdb=" O LYS A 152 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ALA A 154 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU A 252 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N PHE A 156 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA A 250 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ALA A 158 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU A 248 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LYS A 160 " --> pdb=" O ASN A 246 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ASN A 246 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR A 162 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR A 244 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASP A 164 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLN A 242 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TYR A 166 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR A 240 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N PHE A 168 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU A 238 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N SER A 170 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N THR A 236 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N THR A 172 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL A 234 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLU A 174 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE A 232 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ARG A 176 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY A 230 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER A 341 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N VAL A 226 " --> pdb=" O ASP A 339 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASP A 339 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 76 removed outlier: 4.348A pdb=" N THR A 73 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 459 through 460 removed outlier: 4.182A pdb=" N PHE A 421 " --> pdb=" O TRP A 460 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL A 418 " --> pdb=" O HIS A 521 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N HIS A 521 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASN A 420 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER A 519 " --> pdb=" O ASN A 420 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 464 through 470 removed outlier: 5.188A pdb=" N ASP A 465 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A 418 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU A 467 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 416 " --> pdb=" O GLU A 467 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS A 523 " --> pdb=" O HIS A 415 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 448 removed outlier: 6.633A pdb=" N LEU A 477 " --> pdb=" O ASP A 497 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP A 497 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 479 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER A 495 " --> pdb=" O VAL A 479 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL A 481 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP A 491 " --> pdb=" O ASP A 483 " (cutoff:3.500A) 143 hydrogen bonds defined for protein. 405 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: 0.59 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 669 1.32 - 1.45: 1180 1.45 - 1.58: 2251 1.58 - 1.71: 0 1.71 - 1.84: 36 Bond restraints: 4136 Sorted by residual: bond pdb=" C7 NAG A 604 " pdb=" N2 NAG A 604 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" C1 NAG A 604 " pdb=" O5 NAG A 604 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C5 NAG A 604 " pdb=" O5 NAG A 604 " ideal model delta sigma weight residual 1.413 1.474 -0.061 2.00e-02 2.50e+03 9.43e+00 bond pdb=" C2 NAG A 604 " pdb=" N2 NAG A 604 " ideal model delta sigma weight residual 1.439 1.499 -0.060 2.00e-02 2.50e+03 9.08e+00 bond pdb=" C3 NAG A 604 " pdb=" O3 NAG A 604 " ideal model delta sigma weight residual 1.403 1.453 -0.050 2.00e-02 2.50e+03 6.19e+00 ... (remaining 4131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 5355 1.53 - 3.06: 197 3.06 - 4.58: 39 4.58 - 6.11: 19 6.11 - 7.64: 1 Bond angle restraints: 5611 Sorted by residual: angle pdb=" N ARG A 298 " pdb=" CA ARG A 298 " pdb=" C ARG A 298 " ideal model delta sigma weight residual 109.52 101.88 7.64 1.55e+00 4.16e-01 2.43e+01 angle pdb=" CA ARG A 298 " pdb=" C ARG A 298 " pdb=" O ARG A 298 " ideal model delta sigma weight residual 121.44 116.82 4.62 1.17e+00 7.31e-01 1.56e+01 angle pdb=" N ASP A 82 " pdb=" CA ASP A 82 " pdb=" C ASP A 82 " ideal model delta sigma weight residual 111.71 106.85 4.86 1.34e+00 5.57e-01 1.32e+01 angle pdb=" N VAL A 451 " pdb=" CA VAL A 451 " pdb=" C VAL A 451 " ideal model delta sigma weight residual 107.37 111.93 -4.56 1.48e+00 4.57e-01 9.49e+00 angle pdb=" C CYS A 396 " pdb=" N GLN A 397 " pdb=" CA GLN A 397 " ideal model delta sigma weight residual 121.54 126.90 -5.36 1.91e+00 2.74e-01 7.87e+00 ... (remaining 5606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 2228 17.11 - 34.22: 200 34.22 - 51.33: 45 51.33 - 68.44: 7 68.44 - 85.55: 7 Dihedral angle restraints: 2487 sinusoidal: 1009 harmonic: 1478 Sorted by residual: dihedral pdb=" CB CYS A 376 " pdb=" SG CYS A 376 " pdb=" SG CYS A 392 " pdb=" CB CYS A 392 " ideal model delta sinusoidal sigma weight residual -86.00 -4.35 -81.65 1 1.00e+01 1.00e-02 8.21e+01 dihedral pdb=" CB CYS A 396 " pdb=" SG CYS A 396 " pdb=" SG CYS A 406 " pdb=" CB CYS A 406 " ideal model delta sinusoidal sigma weight residual 93.00 146.15 -53.15 1 1.00e+01 1.00e-02 3.84e+01 dihedral pdb=" CA LEU A 359 " pdb=" C LEU A 359 " pdb=" N ARG A 360 " pdb=" CA ARG A 360 " ideal model delta harmonic sigma weight residual -180.00 -153.96 -26.04 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 2484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 370 0.034 - 0.068: 156 0.068 - 0.101: 48 0.101 - 0.135: 26 0.135 - 0.169: 4 Chirality restraints: 604 Sorted by residual: chirality pdb=" CA ARG A 298 " pdb=" N ARG A 298 " pdb=" C ARG A 298 " pdb=" CB ARG A 298 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA GLU A 446 " pdb=" N GLU A 446 " pdb=" C GLU A 446 " pdb=" CB GLU A 446 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA ILE A 232 " pdb=" N ILE A 232 " pdb=" C ILE A 232 " pdb=" CB ILE A 232 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.82e-01 ... (remaining 601 not shown) Planarity restraints: 739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 499 " 0.050 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO A 500 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 95 " -0.050 5.00e-02 4.00e+02 7.63e-02 9.32e+00 pdb=" N PRO A 96 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 96 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 96 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 407 " 0.041 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO A 408 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 408 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 408 " 0.034 5.00e-02 4.00e+02 ... (remaining 736 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 184 2.72 - 3.27: 3973 3.27 - 3.81: 6105 3.81 - 4.36: 6879 4.36 - 4.90: 12259 Nonbonded interactions: 29400 Sorted by model distance: nonbonded pdb=" OG1 THR A 320 " pdb=" OE1 GLN A 323 " model vdw 2.177 3.040 nonbonded pdb=" O TYR A 366 " pdb=" OG SER A 369 " model vdw 2.185 3.040 nonbonded pdb=" OH TYR A 366 " pdb=" NH1 ARG A 370 " model vdw 2.215 3.120 nonbonded pdb=" OE2 GLU A 395 " pdb=" OG SER A 399 " model vdw 2.222 3.040 nonbonded pdb=" O GLN A 361 " pdb=" OG SER A 364 " model vdw 2.247 3.040 ... (remaining 29395 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 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.810 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 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 : 0.005 0.117 4146 Z= 0.232 Angle : 0.752 7.641 5632 Z= 0.413 Chirality : 0.046 0.169 604 Planarity : 0.006 0.077 738 Dihedral : 13.856 85.555 1504 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.35), residues: 505 helix: -1.61 (0.67), residues: 55 sheet: 0.15 (0.33), residues: 207 loop : -2.22 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 422 TYR 0.012 0.001 TYR A 437 PHE 0.016 0.002 PHE A 447 TRP 0.026 0.002 TRP A 327 HIS 0.003 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.23 ( 4136) covalent geometry : angle 0.74596 / 0.41 ( 5611) SS BOND : bond 0.00212 / 0.12 ( 9) SS BOND : angle 1.81967 / 0.86 ( 18) hydrogen bonds : bond 0.16793 / 11.87 ( 143) hydrogen bonds : angle 7.28566 / 4.82 ( 405) link_NAG-ASN : bond 0.00159 / 0.11 ( 1) link_NAG-ASN : angle 1.14799 / 0.85 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 LEU cc_start: 0.8991 (tp) cc_final: 0.8630 (mp) REVERT: A 231 ARG cc_start: 0.7457 (ttm170) cc_final: 0.7177 (ttt180) REVERT: A 479 VAL cc_start: 0.9503 (t) cc_final: 0.9154 (p) REVERT: A 518 PHE cc_start: 0.8358 (p90) cc_final: 0.8104 (p90) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0900 time to fit residues: 10.0801 Evaluate side-chains 45 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.0020 chunk 48 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 212 HIS ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5575 r_free = 0.5575 target = 0.384600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.5538 r_free = 0.5538 target = 0.273808 restraints weight = 4287.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 83)----------------| | r_work = 0.5593 r_free = 0.5593 target = 0.201695 restraints weight = 2547.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.5594 r_free = 0.5594 target = 0.198728 restraints weight = 3522.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.5593 r_free = 0.5593 target = 0.197389 restraints weight = 3392.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.5594 r_free = 0.5594 target = 0.196205 restraints weight = 3648.111| |-----------------------------------------------------------------------------| r_work (final): 0.5188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4146 Z= 0.231 Angle : 0.736 7.918 5632 Z= 0.391 Chirality : 0.047 0.149 604 Planarity : 0.006 0.058 738 Dihedral : 5.330 20.279 558 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.83 % Allowed : 9.59 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.35), residues: 505 helix: 0.07 (0.70), residues: 53 sheet: -0.61 (0.34), residues: 194 loop : -2.15 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 360 TYR 0.017 0.002 TYR A 166 PHE 0.010 0.002 PHE A 315 TRP 0.032 0.002 TRP A 128 HIS 0.009 0.002 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.23 ( 4136) covalent geometry : angle 0.73193 / 0.39 ( 5611) SS BOND : bond 0.00634 / 0.32 ( 9) SS BOND : angle 1.51941 / 0.71 ( 18) hydrogen bonds : bond 0.03325 / 2.29 ( 143) hydrogen bonds : angle 6.50129 / 4.33 ( 405) link_NAG-ASN : bond 0.00021 / 0.01 ( 1) link_NAG-ASN : angle 1.36615 / 1.17 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 SER cc_start: 0.8020 (OUTLIER) cc_final: 0.7673 (t) REVERT: A 171 ASP cc_start: 0.7275 (OUTLIER) cc_final: 0.6022 (t0) REVERT: A 222 PHE cc_start: 0.8770 (p90) cc_final: 0.8091 (p90) REVERT: A 231 ARG cc_start: 0.7748 (ttm170) cc_final: 0.7331 (ttt90) REVERT: A 343 GLU cc_start: 0.8549 (tp30) cc_final: 0.8287 (tp30) REVERT: A 366 TYR cc_start: 0.8251 (t80) cc_final: 0.7732 (t80) REVERT: A 479 VAL cc_start: 0.9580 (t) cc_final: 0.9125 (t) outliers start: 8 outliers final: 3 residues processed: 69 average time/residue: 0.0826 time to fit residues: 7.0031 Evaluate side-chains 48 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 516 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 0.0010 chunk 34 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 overall best weight: 1.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 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 = 0.5550 r_free = 0.5550 target = 0.383314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.5509 r_free = 0.5509 target = 0.270567 restraints weight = 4315.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.5544 r_free = 0.5544 target = 0.209106 restraints weight = 2742.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 105)---------------| | r_work = 0.5547 r_free = 0.5547 target = 0.201108 restraints weight = 3623.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.5547 r_free = 0.5547 target = 0.200745 restraints weight = 4270.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5547 r_free = 0.5547 target = 0.200455 restraints weight = 3610.382| |-----------------------------------------------------------------------------| r_work (final): 0.5175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4146 Z= 0.188 Angle : 0.702 9.576 5632 Z= 0.363 Chirality : 0.046 0.150 604 Planarity : 0.005 0.050 738 Dihedral : 5.040 17.191 558 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.05 % Allowed : 13.47 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.36), residues: 505 helix: 0.14 (0.72), residues: 53 sheet: -0.96 (0.35), residues: 194 loop : -2.06 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 478 TYR 0.010 0.001 TYR A 275 PHE 0.020 0.002 PHE A 518 TRP 0.027 0.002 TRP A 482 HIS 0.005 0.001 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.19 ( 4136) covalent geometry : angle 0.69770 / 0.36 ( 5611) SS BOND : bond 0.00735 / 0.37 ( 9) SS BOND : angle 1.51721 / 0.65 ( 18) hydrogen bonds : bond 0.03096 / 2.25 ( 143) hydrogen bonds : angle 6.22888 / 4.15 ( 405) link_NAG-ASN : bond 0.00136 / 0.09 ( 1) link_NAG-ASN : angle 1.40933 / 1.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 GLN cc_start: 0.7746 (pt0) cc_final: 0.7246 (tm-30) REVERT: A 222 PHE cc_start: 0.8822 (p90) cc_final: 0.8258 (p90) REVERT: A 231 ARG cc_start: 0.7743 (ttm170) cc_final: 0.7530 (ttt180) REVERT: A 251 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.6990 (t0) REVERT: A 372 ARG cc_start: 0.7260 (ppt170) cc_final: 0.6900 (ppt170) REVERT: A 464 MET cc_start: 0.7049 (tpp) cc_final: 0.6725 (tpp) outliers start: 9 outliers final: 3 residues processed: 56 average time/residue: 0.0897 time to fit residues: 6.1550 Evaluate side-chains 44 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 516 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 35 optimal weight: 40.0000 chunk 30 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 39 optimal weight: 20.0000 chunk 8 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 HIS ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5508 r_free = 0.5508 target = 0.376160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.5460 r_free = 0.5460 target = 0.259129 restraints weight = 4375.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5449 r_free = 0.5449 target = 0.200474 restraints weight = 2810.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 186)---------------| | r_work = 0.5455 r_free = 0.5455 target = 0.178686 restraints weight = 3235.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.5455 r_free = 0.5455 target = 0.178392 restraints weight = 4118.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.5456 r_free = 0.5456 target = 0.178126 restraints weight = 3648.456| |-----------------------------------------------------------------------------| r_work (final): 0.5075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.5434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 4146 Z= 0.216 Angle : 0.746 9.886 5632 Z= 0.396 Chirality : 0.049 0.308 604 Planarity : 0.005 0.050 738 Dihedral : 5.394 17.749 558 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.74 % Allowed : 15.98 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.36), residues: 505 helix: 0.07 (0.71), residues: 59 sheet: -1.48 (0.36), residues: 198 loop : -2.09 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 86 TYR 0.014 0.002 TYR A 275 PHE 0.017 0.002 PHE A 156 TRP 0.032 0.002 TRP A 482 HIS 0.006 0.001 HIS A 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.21 ( 4136) covalent geometry : angle 0.73265 / 0.39 ( 5611) SS BOND : bond 0.01160 / 0.58 ( 9) SS BOND : angle 2.53441 / 1.02 ( 18) hydrogen bonds : bond 0.03224 / 2.31 ( 143) hydrogen bonds : angle 6.66542 / 4.48 ( 405) link_NAG-ASN : bond 0.00104 / 0.07 ( 1) link_NAG-ASN : angle 1.32437 / 1.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 GLN cc_start: 0.7791 (pt0) cc_final: 0.7360 (tm-30) REVERT: A 169 ASN cc_start: 0.8218 (OUTLIER) cc_final: 0.7719 (p0) REVERT: A 231 ARG cc_start: 0.7922 (ttm170) cc_final: 0.7391 (ttt90) REVERT: A 251 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.6907 (t70) REVERT: A 279 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7680 (tm-30) REVERT: A 372 ARG cc_start: 0.7592 (ppt170) cc_final: 0.7148 (ppt170) REVERT: A 464 MET cc_start: 0.7096 (tpp) cc_final: 0.6530 (tpp) REVERT: A 488 TRP cc_start: 0.4283 (p90) cc_final: 0.3512 (t60) outliers start: 12 outliers final: 7 residues processed: 61 average time/residue: 0.0893 time to fit residues: 6.6029 Evaluate side-chains 54 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 516 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5485 r_free = 0.5485 target = 0.370270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.5434 r_free = 0.5434 target = 0.207798 restraints weight = 4433.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5408 r_free = 0.5408 target = 0.196014 restraints weight = 6867.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.5404 r_free = 0.5404 target = 0.191146 restraints weight = 5491.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.5406 r_free = 0.5406 target = 0.182039 restraints weight = 4815.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.5405 r_free = 0.5405 target = 0.180957 restraints weight = 5261.770| |-----------------------------------------------------------------------------| r_work (final): 0.5052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.6140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 4146 Z= 0.252 Angle : 0.821 11.121 5632 Z= 0.435 Chirality : 0.050 0.366 604 Planarity : 0.005 0.049 738 Dihedral : 5.683 21.097 558 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 2.97 % Allowed : 18.04 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.35), residues: 505 helix: -0.55 (0.67), residues: 64 sheet: -1.96 (0.34), residues: 208 loop : -2.17 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 478 TYR 0.017 0.002 TYR A 166 PHE 0.024 0.002 PHE A 518 TRP 0.027 0.002 TRP A 482 HIS 0.008 0.002 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.25 ( 4136) covalent geometry : angle 0.80552 / 0.43 ( 5611) SS BOND : bond 0.01316 / 0.66 ( 9) SS BOND : angle 2.91960 / 1.16 ( 18) hydrogen bonds : bond 0.03372 / 2.39 ( 143) hydrogen bonds : angle 7.24595 / 4.88 ( 405) link_NAG-ASN : bond 0.00074 / 0.05 ( 1) link_NAG-ASN : angle 1.25288 / 0.95 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 133 ASP cc_start: 0.8148 (m-30) cc_final: 0.7585 (t0) REVERT: A 163 GLN cc_start: 0.8103 (pt0) cc_final: 0.7492 (tm-30) REVERT: A 251 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7035 (t70) REVERT: A 293 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6763 (mp10) REVERT: A 372 ARG cc_start: 0.7950 (ppt170) cc_final: 0.7489 (ppt170) REVERT: A 464 MET cc_start: 0.7317 (tpp) cc_final: 0.6541 (tpp) REVERT: A 477 LEU cc_start: 0.9174 (tt) cc_final: 0.8761 (mt) REVERT: A 488 TRP cc_start: 0.5266 (p90) cc_final: 0.3667 (t60) outliers start: 13 outliers final: 9 residues processed: 57 average time/residue: 0.0861 time to fit residues: 6.0388 Evaluate side-chains 53 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 516 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 20.0000 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 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 = 0.5431 r_free = 0.5431 target = 0.358356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5327 r_free = 0.5327 target = 0.198623 restraints weight = 4550.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5291 r_free = 0.5291 target = 0.176106 restraints weight = 6484.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.5289 r_free = 0.5289 target = 0.172685 restraints weight = 6224.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.5286 r_free = 0.5286 target = 0.171200 restraints weight = 6106.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.5286 r_free = 0.5286 target = 0.169686 restraints weight = 5052.399| |-----------------------------------------------------------------------------| r_work (final): 0.4989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.6989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 4146 Z= 0.333 Angle : 0.996 19.724 5632 Z= 0.537 Chirality : 0.053 0.245 604 Planarity : 0.006 0.049 738 Dihedral : 6.709 28.400 558 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 4.57 % Allowed : 18.49 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.42 (0.35), residues: 505 helix: -0.80 (0.67), residues: 64 sheet: -2.48 (0.32), residues: 214 loop : -2.34 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 86 TYR 0.026 0.003 TYR A 166 PHE 0.030 0.003 PHE A 156 TRP 0.021 0.002 TRP A 482 HIS 0.012 0.002 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.33 ( 4136) covalent geometry : angle 0.97165 / 0.53 ( 5611) SS BOND : bond 0.01428 / 0.72 ( 9) SS BOND : angle 4.01311 / 1.54 ( 18) hydrogen bonds : bond 0.04609 / 3.22 ( 143) hydrogen bonds : angle 8.29169 / 5.60 ( 405) link_NAG-ASN : bond 0.00006 / 0.00 ( 1) link_NAG-ASN : angle 1.20482 / 0.92 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7918 (tt0) cc_final: 0.7134 (tm-30) REVERT: A 114 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8265 (tm-30) REVERT: A 128 TRP cc_start: 0.6160 (OUTLIER) cc_final: 0.5779 (m-10) REVERT: A 169 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8017 (p0) REVERT: A 293 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7033 (mp10) REVERT: A 464 MET cc_start: 0.7441 (tpp) cc_final: 0.6622 (tpp) REVERT: A 477 LEU cc_start: 0.9184 (tt) cc_final: 0.8835 (mt) REVERT: A 488 TRP cc_start: 0.6009 (p90) cc_final: 0.3590 (t60) REVERT: A 490 ASP cc_start: 0.2918 (OUTLIER) cc_final: 0.2386 (t0) outliers start: 20 outliers final: 10 residues processed: 64 average time/residue: 0.0826 time to fit residues: 6.4731 Evaluate side-chains 56 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 TRP Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 516 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 0.0980 chunk 1 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 0.0970 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 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 = 0.5488 r_free = 0.5488 target = 0.372777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.5440 r_free = 0.5440 target = 0.254583 restraints weight = 4453.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.5456 r_free = 0.5456 target = 0.194824 restraints weight = 3216.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 120)---------------| | r_work = 0.5451 r_free = 0.5451 target = 0.181487 restraints weight = 4324.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5451 r_free = 0.5451 target = 0.181487 restraints weight = 4358.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5451 r_free = 0.5451 target = 0.181487 restraints weight = 4357.894| |-----------------------------------------------------------------------------| r_work (final): 0.5085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.6853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4146 Z= 0.170 Angle : 0.888 20.451 5632 Z= 0.450 Chirality : 0.052 0.405 604 Planarity : 0.005 0.053 738 Dihedral : 5.320 20.133 558 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.28 % Allowed : 20.55 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.35), residues: 505 helix: -0.93 (0.63), residues: 63 sheet: -1.98 (0.33), residues: 198 loop : -2.03 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 372 TYR 0.010 0.001 TYR A 295 PHE 0.023 0.002 PHE A 518 TRP 0.020 0.002 TRP A 327 HIS 0.006 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 ( 4136) covalent geometry : angle 0.85887 / 0.44 ( 5611) SS BOND : bond 0.00346 / 0.18 ( 9) SS BOND : angle 4.05101 / 1.56 ( 18) hydrogen bonds : bond 0.03213 / 2.38 ( 143) hydrogen bonds : angle 6.63757 / 4.44 ( 405) link_NAG-ASN : bond 0.00134 / 0.09 ( 1) link_NAG-ASN : angle 1.27047 / 0.96 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7985 (tt0) cc_final: 0.7627 (tm-30) REVERT: A 293 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6812 (mp10) REVERT: A 372 ARG cc_start: 0.7477 (ppt170) cc_final: 0.7219 (pmt-80) REVERT: A 464 MET cc_start: 0.7474 (tpp) cc_final: 0.6706 (tpp) REVERT: A 477 LEU cc_start: 0.9206 (tt) cc_final: 0.8863 (mt) REVERT: A 488 TRP cc_start: 0.5675 (p90) cc_final: 0.3643 (t60) REVERT: A 490 ASP cc_start: 0.2791 (OUTLIER) cc_final: 0.2563 (t0) outliers start: 10 outliers final: 5 residues processed: 51 average time/residue: 0.0897 time to fit residues: 5.5048 Evaluate side-chains 45 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 516 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 43 optimal weight: 0.0170 chunk 28 optimal weight: 0.1980 chunk 47 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 overall best weight: 1.6424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 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 = 0.5481 r_free = 0.5481 target = 0.370751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5420 r_free = 0.5420 target = 0.211057 restraints weight = 4371.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.5402 r_free = 0.5402 target = 0.185779 restraints weight = 5716.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 103)---------------| | r_work = 0.5404 r_free = 0.5404 target = 0.180301 restraints weight = 5267.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5402 r_free = 0.5402 target = 0.178533 restraints weight = 5440.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.5406 r_free = 0.5406 target = 0.177086 restraints weight = 4507.028| |-----------------------------------------------------------------------------| r_work (final): 0.5059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.7059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4146 Z= 0.181 Angle : 0.874 25.357 5632 Z= 0.448 Chirality : 0.052 0.438 604 Planarity : 0.005 0.052 738 Dihedral : 5.297 21.006 558 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.51 % Allowed : 20.09 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.35), residues: 505 helix: -0.82 (0.64), residues: 63 sheet: -1.95 (0.34), residues: 198 loop : -2.01 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 86 TYR 0.012 0.002 TYR A 275 PHE 0.012 0.001 PHE A 156 TRP 0.030 0.002 TRP A 482 HIS 0.006 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.18 ( 4136) covalent geometry : angle 0.84440 / 0.44 ( 5611) SS BOND : bond 0.01059 / 0.53 ( 9) SS BOND : angle 4.05084 / 1.50 ( 18) hydrogen bonds : bond 0.03445 / 2.58 ( 143) hydrogen bonds : angle 6.69886 / 4.47 ( 405) link_NAG-ASN : bond 0.00096 / 0.06 ( 1) link_NAG-ASN : angle 1.27662 / 0.98 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 293 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.6730 (mp10) REVERT: A 464 MET cc_start: 0.7453 (tpp) cc_final: 0.6597 (tpp) REVERT: A 477 LEU cc_start: 0.9220 (tt) cc_final: 0.8874 (mt) REVERT: A 488 TRP cc_start: 0.5572 (p90) cc_final: 0.3614 (t60) REVERT: A 490 ASP cc_start: 0.2858 (OUTLIER) cc_final: 0.2514 (t0) outliers start: 11 outliers final: 7 residues processed: 52 average time/residue: 0.0900 time to fit residues: 5.6367 Evaluate side-chains 47 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 516 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 0.0010 chunk 12 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 46 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 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 = 0.5492 r_free = 0.5492 target = 0.374482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5456 r_free = 0.5456 target = 0.213956 restraints weight = 4426.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.5437 r_free = 0.5437 target = 0.188763 restraints weight = 5718.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 146)---------------| | r_work = 0.5444 r_free = 0.5444 target = 0.181039 restraints weight = 4998.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.5445 r_free = 0.5445 target = 0.179151 restraints weight = 5066.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5445 r_free = 0.5445 target = 0.179148 restraints weight = 4869.232| |-----------------------------------------------------------------------------| r_work (final): 0.5066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.7101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4146 Z= 0.158 Angle : 0.953 29.645 5632 Z= 0.475 Chirality : 0.052 0.428 604 Planarity : 0.004 0.052 738 Dihedral : 4.997 19.125 558 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.05 % Allowed : 20.32 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.35), residues: 505 helix: -1.08 (0.63), residues: 57 sheet: -1.74 (0.33), residues: 209 loop : -2.03 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 70 TYR 0.009 0.001 TYR A 211 PHE 0.023 0.002 PHE A 518 TRP 0.031 0.002 TRP A 482 HIS 0.005 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 ( 4136) covalent geometry : angle 0.92199 / 0.46 ( 5611) SS BOND : bond 0.01133 / 0.57 ( 9) SS BOND : angle 4.37117 / 1.64 ( 18) hydrogen bonds : bond 0.03643 / 2.76 ( 143) hydrogen bonds : angle 6.22582 / 4.17 ( 405) link_NAG-ASN : bond 0.00111 / 0.07 ( 1) link_NAG-ASN : angle 1.28995 / 1.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: A 293 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6583 (mp10) REVERT: A 311 HIS cc_start: 0.7897 (m170) cc_final: 0.7657 (m-70) REVERT: A 314 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.6000 (mm) REVERT: A 464 MET cc_start: 0.7475 (tpp) cc_final: 0.6709 (tpp) REVERT: A 477 LEU cc_start: 0.9230 (tt) cc_final: 0.8893 (mt) REVERT: A 488 TRP cc_start: 0.5556 (p90) cc_final: 0.3561 (t60) REVERT: A 490 ASP cc_start: 0.2744 (OUTLIER) cc_final: 0.2345 (t0) outliers start: 9 outliers final: 6 residues processed: 47 average time/residue: 0.0892 time to fit residues: 5.0314 Evaluate side-chains 47 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 516 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5413 r_free = 0.5413 target = 0.356205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5305 r_free = 0.5305 target = 0.196733 restraints weight = 4473.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5255 r_free = 0.5255 target = 0.173801 restraints weight = 6471.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.5248 r_free = 0.5248 target = 0.162405 restraints weight = 5076.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.5239 r_free = 0.5239 target = 0.158402 restraints weight = 5688.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.5239 r_free = 0.5239 target = 0.155561 restraints weight = 5843.065| |-----------------------------------------------------------------------------| r_work (final): 0.4950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.7675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 4146 Z= 0.342 Angle : 1.118 28.923 5632 Z= 0.583 Chirality : 0.056 0.437 604 Planarity : 0.007 0.050 738 Dihedral : 6.619 30.576 558 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 2.28 % Allowed : 20.55 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -3.50 (0.35), residues: 505 helix: -1.34 (0.58), residues: 64 sheet: -2.66 (0.32), residues: 208 loop : -2.10 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 81 TYR 0.028 0.003 TYR A 166 PHE 0.027 0.003 PHE A 156 TRP 0.037 0.002 TRP A 482 HIS 0.012 0.002 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.34 ( 4136) covalent geometry : angle 1.09328 / 0.57 ( 5611) SS BOND : bond 0.01425 / 0.72 ( 9) SS BOND : angle 4.31042 / 1.65 ( 18) hydrogen bonds : bond 0.05068 / 3.60 ( 143) hydrogen bonds : angle 8.25864 / 5.58 ( 405) link_NAG-ASN : bond 0.00025 / 0.02 ( 1) link_NAG-ASN : angle 1.18787 / 0.92 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.098 Fit side-chains REVERT: A 45 GLU cc_start: 0.7861 (tt0) cc_final: 0.7566 (tm-30) REVERT: A 114 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8039 (tm-30) REVERT: A 163 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7769 (tm-30) REVERT: A 281 LYS cc_start: 0.8565 (tttp) cc_final: 0.8344 (tttp) REVERT: A 293 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7249 (mp10) REVERT: A 343 GLU cc_start: 0.8387 (tp30) cc_final: 0.8172 (tp30) REVERT: A 464 MET cc_start: 0.7544 (tpp) cc_final: 0.6750 (tpp) REVERT: A 477 LEU cc_start: 0.9186 (tt) cc_final: 0.8899 (mt) REVERT: A 488 TRP cc_start: 0.5559 (p90) cc_final: 0.3537 (t60) REVERT: A 490 ASP cc_start: 0.3313 (OUTLIER) cc_final: 0.2616 (t0) outliers start: 10 outliers final: 8 residues processed: 50 average time/residue: 0.0511 time to fit residues: 3.2531 Evaluate side-chains 48 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 516 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 18 optimal weight: 0.0020 chunk 6 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5463 r_free = 0.5463 target = 0.367173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5435 r_free = 0.5435 target = 0.204196 restraints weight = 4384.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.5420 r_free = 0.5420 target = 0.195387 restraints weight = 6505.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5416 r_free = 0.5416 target = 0.191195 restraints weight = 5725.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.5416 r_free = 0.5416 target = 0.187728 restraints weight = 5232.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.5419 r_free = 0.5419 target = 0.185641 restraints weight = 4794.101| |-----------------------------------------------------------------------------| r_work (final): 0.5075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.7570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4146 Z= 0.177 Angle : 0.982 27.117 5632 Z= 0.492 Chirality : 0.053 0.408 604 Planarity : 0.004 0.050 738 Dihedral : 5.576 31.237 558 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.28 % Allowed : 21.23 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -3.14 (0.35), residues: 505 helix: -1.14 (0.62), residues: 57 sheet: -2.18 (0.33), residues: 209 loop : -2.11 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 70 TYR 0.012 0.002 TYR A 162 PHE 0.024 0.002 PHE A 156 TRP 0.029 0.002 TRP A 482 HIS 0.006 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 ( 4136) covalent geometry : angle 0.95286 / 0.48 ( 5611) SS BOND : bond 0.01134 / 0.57 ( 9) SS BOND : angle 4.30631 / 1.61 ( 18) hydrogen bonds : bond 0.03754 / 2.85 ( 143) hydrogen bonds : angle 6.84372 / 4.58 ( 405) link_NAG-ASN : bond 0.00073 / 0.05 ( 1) link_NAG-ASN : angle 1.35668 / 1.07 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 954.63 seconds wall clock time: 17 minutes 4.29 seconds (1024.29 seconds total)