Starting phenix.real_space_refine on Thu Jul 2 13:36:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u7i_63937/07_2026/9u7i_63937.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u7i_63937/07_2026/9u7i_63937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u7i_63937/07_2026/9u7i_63937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u7i_63937/07_2026/9u7i_63937.map" model { file = "/net/cci-nas-00/data/ceres_data/9u7i_63937/07_2026/9u7i_63937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u7i_63937/07_2026/9u7i_63937.cif" } resolution = 3.3 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 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: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 P 4 5.49 5 S 50 5.16 5 C 5488 2.51 5 N 1518 2.21 5 O 1550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8612 Number of models: 1 Model: "" Number of chains: 4 Chain: "a" Number of atoms: 4277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4277 Classifications: {'peptide': 522} Link IDs: {'PCIS': 3, 'PTRANS': 32, 'TRANS': 486} Chain: "A" Number of atoms: 4261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4261 Classifications: {'peptide': 520} Link IDs: {'PCIS': 3, 'PTRANS': 32, 'TRANS': 484} Chain: "a" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Ad-hoc single atom residues: {' MN': 1} Unusual residues: {'GDU': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Ad-hoc single atom residues: {' MN': 1} Unusual residues: {'GDU': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 1.71, per 1000 atoms: 0.20 Number of scatterers: 8612 At special positions: 0 Unit cell: (159.248, 87.156, 126.968, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 50 16.00 P 4 15.00 O 1550 8.00 N 1518 7.00 C 5488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS a 228 " - pdb=" SG CYS a 283 " distance=2.31 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 363.5 milliseconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 9 sheets defined 34.4% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'a' and resid 66 through 75 removed outlier: 3.822A pdb=" N GLY a 72 " --> pdb=" O PRO a 68 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA a 73 " --> pdb=" O THR a 69 " (cutoff:3.500A) Processing helix chain 'a' and resid 80 through 82 No H-bonds generated for 'chain 'a' and resid 80 through 82' Processing helix chain 'a' and resid 96 through 107 removed outlier: 3.668A pdb=" N ARG a 102 " --> pdb=" O SER a 98 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA a 107 " --> pdb=" O GLU a 103 " (cutoff:3.500A) Processing helix chain 'a' and resid 108 through 112 removed outlier: 3.809A pdb=" N TYR a 112 " --> pdb=" O LYS a 109 " (cutoff:3.500A) Processing helix chain 'a' and resid 136 through 156 removed outlier: 3.518A pdb=" N TYR a 140 " --> pdb=" O SER a 136 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU a 141 " --> pdb=" O ASP a 137 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS a 142 " --> pdb=" O SER a 138 " (cutoff:3.500A) Processing helix chain 'a' and resid 175 through 182 Processing helix chain 'a' and resid 216 through 222 removed outlier: 3.753A pdb=" N ILE a 220 " --> pdb=" O ALA a 216 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 249 removed outlier: 4.082A pdb=" N ARG a 248 " --> pdb=" O ALA a 245 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN a 249 " --> pdb=" O ALA a 246 " (cutoff:3.500A) Processing helix chain 'a' and resid 265 through 275 removed outlier: 4.071A pdb=" N PHE a 269 " --> pdb=" O ASP a 265 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA a 270 " --> pdb=" O ILE a 266 " (cutoff:3.500A) Processing helix chain 'a' and resid 300 through 316 removed outlier: 3.755A pdb=" N HIS a 310 " --> pdb=" O GLU a 306 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL a 311 " --> pdb=" O SER a 307 " (cutoff:3.500A) Processing helix chain 'a' and resid 354 through 364 removed outlier: 4.012A pdb=" N MET a 358 " --> pdb=" O ARG a 354 " (cutoff:3.500A) Processing helix chain 'a' and resid 377 through 381 removed outlier: 3.611A pdb=" N MET a 380 " --> pdb=" O GLY a 377 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASN a 381 " --> pdb=" O LYS a 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 377 through 381' Processing helix chain 'a' and resid 384 through 389 removed outlier: 3.594A pdb=" N LEU a 388 " --> pdb=" O GLN a 384 " (cutoff:3.500A) Processing helix chain 'a' and resid 409 through 427 removed outlier: 4.278A pdb=" N PHE a 413 " --> pdb=" O GLU a 409 " (cutoff:3.500A) Processing helix chain 'a' and resid 443 through 457 Processing helix chain 'a' and resid 503 through 510 Processing helix chain 'a' and resid 513 through 518 removed outlier: 3.624A pdb=" N LYS a 517 " --> pdb=" O GLU a 513 " (cutoff:3.500A) Processing helix chain 'a' and resid 520 through 529 Proline residue: a 526 - end of helix removed outlier: 4.031A pdb=" N PHE a 529 " --> pdb=" O LEU a 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 75 removed outlier: 3.692A pdb=" N GLY A 72 " --> pdb=" O PRO A 68 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 98 through 107 removed outlier: 3.602A pdb=" N ARG A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP A 104 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 removed outlier: 3.763A pdb=" N TYR A 112 " --> pdb=" O LYS A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 157 removed outlier: 3.773A pdb=" N TYR A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 182 removed outlier: 3.535A pdb=" N ALA A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 265 through 276 removed outlier: 4.122A pdb=" N PHE A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 317 removed outlier: 3.662A pdb=" N HIS A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 364 removed outlier: 4.043A pdb=" N ARG A 357 " --> pdb=" O ASP A 353 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N MET A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.680A pdb=" N LEU A 388 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 427 removed outlier: 4.247A pdb=" N PHE A 413 " --> pdb=" O GLU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 459 Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 513 through 518 removed outlier: 4.164A pdb=" N LYS A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 529 Proline residue: A 526 - end of helix removed outlier: 3.958A pdb=" N PHE A 529 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 540 removed outlier: 3.643A pdb=" N ALA A 539 " --> pdb=" O GLU A 536 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N HIS A 540 " --> pdb=" O TYR A 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 536 through 540' Processing sheet with id=AA1, first strand: chain 'a' and resid 114 through 118 removed outlier: 4.288A pdb=" N SER a 114 " --> pdb=" O THR a 84 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR a 90 " --> pdb=" O ARG a 118 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU a 55 " --> pdb=" O LEU a 163 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL a 187 " --> pdb=" O TYR a 281 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N CYS a 283 " --> pdb=" O VAL a 187 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA a 189 " --> pdb=" O CYS a 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 201 through 202 removed outlier: 3.594A pdb=" N TRP a 202 " --> pdb=" O MET a 233 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N MET a 233 " --> pdb=" O TRP a 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'a' and resid 344 through 346 removed outlier: 3.545A pdb=" N MET a 345 " --> pdb=" O ARG a 370 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL a 372 " --> pdb=" O MET a 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'a' and resid 430 through 433 removed outlier: 7.026A pdb=" N TYR a 494 " --> pdb=" O ARG a 471 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG a 471 " --> pdb=" O TYR a 494 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N THR a 496 " --> pdb=" O ARG a 469 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ARG a 469 " --> pdb=" O THR a 496 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA a 498 " --> pdb=" O VAL a 467 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY a 468 " --> pdb=" O VAL a 551 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 117 through 120 removed outlier: 8.776A pdb=" N ARG A 118 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL A 88 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ALA A 120 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR A 90 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A 54 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N TRP A 87 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 56 " --> pdb=" O TRP A 87 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ALA A 89 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU A 58 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N ASP A 91 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ALA A 60 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 55 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL A 165 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ALA A 57 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 238 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL A 187 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N CYS A 283 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA A 189 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N MET A 280 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 202 removed outlier: 3.510A pdb=" N MET A 233 " --> pdb=" O TRP A 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 370 through 371 removed outlier: 7.030A pdb=" N PHE A 344 " --> pdb=" O PHE A 434 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 439 through 440 removed outlier: 3.551A pdb=" N TYR A 557 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 487 through 488 removed outlier: 6.815A pdb=" N GLY A 468 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA A 498 " --> pdb=" O VAL A 467 " (cutoff:3.500A) 224 hydrogen bonds defined for protein. 651 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2827 1.35 - 1.48: 2245 1.48 - 1.61: 3687 1.61 - 1.74: 2 1.74 - 1.87: 88 Bond restraints: 8849 Sorted by residual: bond pdb=" C4 GDU A 801 " pdb=" N3 GDU A 801 " ideal model delta sigma weight residual 1.388 1.327 0.061 2.00e-02 2.50e+03 9.29e+00 bond pdb=" C4 GDU a 801 " pdb=" N3 GDU a 801 " ideal model delta sigma weight residual 1.388 1.328 0.060 2.00e-02 2.50e+03 8.94e+00 bond pdb=" C4 GDU A 801 " pdb=" C5 GDU A 801 " ideal model delta sigma weight residual 1.440 1.387 0.053 2.00e-02 2.50e+03 6.91e+00 bond pdb=" C4 GDU a 801 " pdb=" C5 GDU a 801 " ideal model delta sigma weight residual 1.440 1.389 0.051 2.00e-02 2.50e+03 6.48e+00 bond pdb=" C2 GDU A 801 " pdb=" N3 GDU A 801 " ideal model delta sigma weight residual 1.373 1.329 0.044 2.00e-02 2.50e+03 4.89e+00 ... (remaining 8844 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 11481 1.89 - 3.79: 465 3.79 - 5.68: 53 5.68 - 7.57: 15 7.57 - 9.47: 5 Bond angle restraints: 12019 Sorted by residual: angle pdb=" C PHE A 434 " pdb=" N GLU A 435 " pdb=" CA GLU A 435 " ideal model delta sigma weight residual 122.44 116.43 6.01 1.19e+00 7.06e-01 2.55e+01 angle pdb=" N MET A 338 " pdb=" CA MET A 338 " pdb=" C MET A 338 " ideal model delta sigma weight residual 114.16 107.88 6.28 1.48e+00 4.57e-01 1.80e+01 angle pdb=" N VAL A 108 " pdb=" CA VAL A 108 " pdb=" C VAL A 108 " ideal model delta sigma weight residual 113.20 109.30 3.90 9.60e-01 1.09e+00 1.65e+01 angle pdb=" N VAL a 108 " pdb=" CA VAL a 108 " pdb=" C VAL a 108 " ideal model delta sigma weight residual 113.20 109.60 3.60 9.60e-01 1.09e+00 1.41e+01 angle pdb=" N HIS a 540 " pdb=" CA HIS a 540 " pdb=" C HIS a 540 " ideal model delta sigma weight residual 114.56 110.04 4.52 1.27e+00 6.20e-01 1.27e+01 ... (remaining 12014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4828 17.76 - 35.52: 482 35.52 - 53.27: 116 53.27 - 71.03: 15 71.03 - 88.79: 6 Dihedral angle restraints: 5447 sinusoidal: 2349 harmonic: 3098 Sorted by residual: dihedral pdb=" CA MET A 338 " pdb=" C MET A 338 " pdb=" N GLY A 339 " pdb=" CA GLY A 339 " ideal model delta harmonic sigma weight residual -180.00 -150.67 -29.33 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA LYS A 337 " pdb=" C LYS A 337 " pdb=" N MET A 338 " pdb=" CA MET A 338 " ideal model delta harmonic sigma weight residual 180.00 152.52 27.48 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ASP A 436 " pdb=" C ASP A 436 " pdb=" N ASP A 437 " pdb=" CA ASP A 437 " ideal model delta harmonic sigma weight residual 180.00 -160.07 -19.93 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 5444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1049 0.056 - 0.112: 208 0.112 - 0.168: 21 0.168 - 0.224: 5 0.224 - 0.280: 3 Chirality restraints: 1286 Sorted by residual: chirality pdb=" C2' GDU A 801 " pdb=" C1' GDU A 801 " pdb=" C3' GDU A 801 " pdb=" O2' GDU A 801 " both_signs ideal model delta sigma weight residual False -2.28 -2.56 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C2' GDU a 801 " pdb=" C1' GDU a 801 " pdb=" C3' GDU a 801 " pdb=" O2' GDU a 801 " both_signs ideal model delta sigma weight residual False -2.28 -2.54 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C1D GDU A 801 " pdb=" C2D GDU A 801 " pdb=" N1 GDU A 801 " pdb=" O4D GDU A 801 " both_signs ideal model delta sigma weight residual False 2.21 2.46 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1283 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP a 202 " -0.030 2.00e-02 2.50e+03 2.06e-02 1.06e+01 pdb=" CG TRP a 202 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP a 202 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP a 202 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP a 202 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP a 202 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP a 202 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 202 " -0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 202 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP a 202 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 202 " 0.026 2.00e-02 2.50e+03 1.89e-02 8.92e+00 pdb=" CG TRP A 202 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 202 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 202 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 202 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 202 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 202 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 202 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 202 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 202 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 256 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO A 257 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 257 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 257 " -0.028 5.00e-02 4.00e+02 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 64 2.57 - 3.16: 6589 3.16 - 3.74: 12344 3.74 - 4.32: 16902 4.32 - 4.90: 29067 Nonbonded interactions: 64966 Sorted by model distance: nonbonded pdb=" OD2 ASP A 168 " pdb="MN MN A 802 " model vdw 1.993 3.060 nonbonded pdb=" N GLU a 121 " pdb=" OE1 GLU a 121 " model vdw 2.078 3.120 nonbonded pdb=" O1B GDU A 801 " pdb="MN MN A 802 " model vdw 2.135 3.060 nonbonded pdb=" NH1 ARG a 61 " pdb=" O HIS a 92 " model vdw 2.198 3.120 nonbonded pdb=" OD2 ASP a 91 " pdb=" NE2 HIS a 142 " model vdw 2.212 3.120 ... (remaining 64961 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'a' and resid 41 through 802) } 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.640 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 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 : 0.006 0.279 8850 Z= 0.279 Angle : 0.870 12.496 12021 Z= 0.491 Chirality : 0.049 0.280 1286 Planarity : 0.005 0.050 1543 Dihedral : 14.957 88.790 3428 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.67 % Favored : 91.14 % Rotamer: Outliers : 0.87 % Allowed : 0.65 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -2.45 (0.25), residues: 1038 helix: -0.70 (0.30), residues: 328 sheet: -1.47 (0.45), residues: 139 loop : -2.30 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 469 TYR 0.017 0.001 TYR a 288 PHE 0.029 0.002 PHE A 524 TRP 0.055 0.002 TRP a 202 HIS 0.004 0.001 HIS a 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.24 ( 8849) covalent geometry : angle 0.86045 / 0.49 (12019) SS BOND : bond 0.27895 / 18.60 ( 1) SS BOND : angle 9.97242 / 6.76 ( 2) hydrogen bonds : bond 0.23646 / 15.52 ( 224) hydrogen bonds : angle 6.70750 / 4.66 ( 651) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.295 Fit side-chains REVERT: a 418 ASN cc_start: 0.8370 (m-40) cc_final: 0.8158 (m-40) REVERT: a 436 ASP cc_start: 0.7114 (p0) cc_final: 0.6803 (p0) REVERT: a 552 GLU cc_start: 0.7792 (tp30) cc_final: 0.7328 (tp30) REVERT: A 95 ASP cc_start: 0.7568 (m-30) cc_final: 0.7222 (m-30) REVERT: A 429 GLN cc_start: 0.6893 (mp10) cc_final: 0.6385 (mp10) REVERT: A 551 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8148 (m) outliers start: 8 outliers final: 0 residues processed: 134 average time/residue: 0.0828 time to fit residues: 14.8757 Evaluate side-chains 107 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 0.0970 chunk 61 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.171836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.104423 restraints weight = 10393.739| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.37 r_work: 0.2785 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8850 Z= 0.137 Angle : 0.629 12.378 12021 Z= 0.320 Chirality : 0.045 0.245 1286 Planarity : 0.005 0.050 1543 Dihedral : 6.998 46.540 1281 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.84 % Favored : 93.06 % Rotamer: Outliers : 0.76 % Allowed : 7.93 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.03 (0.26), residues: 1038 helix: -0.24 (0.30), residues: 324 sheet: -1.30 (0.43), residues: 150 loop : -2.09 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 61 TYR 0.011 0.001 TYR A 492 PHE 0.016 0.002 PHE a 524 TRP 0.035 0.002 TRP A 202 HIS 0.007 0.001 HIS a 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 8849) covalent geometry : angle 0.62560 / 0.32 (12019) SS BOND : bond 0.02098 / 1.40 ( 1) SS BOND : angle 4.73646 / 3.38 ( 2) hydrogen bonds : bond 0.05385 / 3.49 ( 224) hydrogen bonds : angle 4.83093 / 3.30 ( 651) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.232 Fit side-chains REVERT: a 370 ARG cc_start: 0.7560 (ptm160) cc_final: 0.7234 (ptm160) REVERT: a 436 ASP cc_start: 0.7422 (p0) cc_final: 0.6969 (p0) REVERT: a 518 MET cc_start: 0.7088 (tpp) cc_final: 0.6648 (tpp) REVERT: A 93 ASN cc_start: 0.8568 (m-40) cc_final: 0.8318 (m-40) REVERT: A 95 ASP cc_start: 0.8197 (m-30) cc_final: 0.7713 (m-30) REVERT: A 392 MET cc_start: 0.5517 (mpp) cc_final: 0.3179 (tpt) REVERT: A 429 GLN cc_start: 0.6891 (mp10) cc_final: 0.6431 (mp10) outliers start: 7 outliers final: 6 residues processed: 112 average time/residue: 0.0886 time to fit residues: 13.3087 Evaluate side-chains 104 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 346 ILE Chi-restraints excluded: chain a residue 521 VAL Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 543 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 88 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 77 optimal weight: 0.0040 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.170670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.102887 restraints weight = 10338.309| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.40 r_work: 0.2753 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8850 Z= 0.156 Angle : 0.644 14.643 12021 Z= 0.325 Chirality : 0.046 0.407 1286 Planarity : 0.005 0.046 1543 Dihedral : 6.936 53.045 1280 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.13 % Favored : 92.68 % Rotamer: Outliers : 1.63 % Allowed : 9.67 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.87 (0.26), residues: 1038 helix: 0.06 (0.30), residues: 320 sheet: -1.16 (0.44), residues: 149 loop : -2.10 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 61 TYR 0.012 0.001 TYR a 281 PHE 0.022 0.002 PHE a 229 TRP 0.033 0.002 TRP A 202 HIS 0.004 0.001 HIS a 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 8849) covalent geometry : angle 0.63402 / 0.32 (12019) SS BOND : bond 0.02701 / 1.80 ( 1) SS BOND : angle 8.96845 / 5.95 ( 2) hydrogen bonds : bond 0.04894 / 3.24 ( 224) hydrogen bonds : angle 4.62187 / 3.15 ( 651) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.251 Fit side-chains REVERT: a 179 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8573 (mp) REVERT: a 370 ARG cc_start: 0.7710 (ptm160) cc_final: 0.7427 (ptm160) REVERT: a 418 ASN cc_start: 0.8489 (m-40) cc_final: 0.8176 (m-40) REVERT: a 436 ASP cc_start: 0.7431 (p0) cc_final: 0.7072 (p0) REVERT: a 518 MET cc_start: 0.7121 (tpp) cc_final: 0.6652 (tpp) REVERT: A 95 ASP cc_start: 0.8220 (m-30) cc_final: 0.7714 (m-30) REVERT: A 141 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8619 (tt0) REVERT: A 314 GLU cc_start: 0.8394 (tp30) cc_final: 0.8155 (tp30) REVERT: A 341 ASP cc_start: 0.7643 (m-30) cc_final: 0.7334 (m-30) REVERT: A 380 MET cc_start: 0.5378 (mmm) cc_final: 0.4733 (tpt) REVERT: A 392 MET cc_start: 0.5509 (mpp) cc_final: 0.3209 (tpt) REVERT: A 429 GLN cc_start: 0.6890 (mp10) cc_final: 0.6386 (mp10) outliers start: 15 outliers final: 8 residues processed: 113 average time/residue: 0.0911 time to fit residues: 13.8686 Evaluate side-chains 104 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 179 LEU Chi-restraints excluded: chain a residue 346 ILE Chi-restraints excluded: chain a residue 366 GLU Chi-restraints excluded: chain a residue 474 VAL Chi-restraints excluded: chain a residue 521 VAL Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 543 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 0.0770 chunk 49 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.169324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.102197 restraints weight = 10397.644| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.24 r_work: 0.2764 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8850 Z= 0.168 Angle : 0.636 15.009 12021 Z= 0.320 Chirality : 0.045 0.321 1286 Planarity : 0.005 0.044 1543 Dihedral : 6.877 58.543 1280 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.61 % Favored : 92.29 % Rotamer: Outliers : 2.72 % Allowed : 11.09 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.80 (0.26), residues: 1038 helix: 0.20 (0.31), residues: 320 sheet: -1.15 (0.45), residues: 145 loop : -2.11 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 53 TYR 0.009 0.001 TYR A 198 PHE 0.015 0.002 PHE a 529 TRP 0.033 0.002 TRP A 202 HIS 0.003 0.001 HIS a 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 ( 8849) covalent geometry : angle 0.62328 / 0.31 (12019) SS BOND : bond 0.02198 / 1.47 ( 1) SS BOND : angle 9.63703 / 6.70 ( 2) hydrogen bonds : bond 0.04560 / 3.02 ( 224) hydrogen bonds : angle 4.49779 / 3.05 ( 651) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.260 Fit side-chains REVERT: a 260 THR cc_start: 0.8730 (m) cc_final: 0.8326 (p) REVERT: a 418 ASN cc_start: 0.8510 (m-40) cc_final: 0.8246 (m110) REVERT: a 436 ASP cc_start: 0.7464 (p0) cc_final: 0.7023 (p0) REVERT: A 93 ASN cc_start: 0.8563 (m-40) cc_final: 0.8345 (m-40) REVERT: A 95 ASP cc_start: 0.8192 (m-30) cc_final: 0.7658 (m-30) REVERT: A 141 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8559 (tt0) REVERT: A 341 ASP cc_start: 0.7777 (m-30) cc_final: 0.7565 (m-30) REVERT: A 380 MET cc_start: 0.5408 (mmm) cc_final: 0.4717 (tpt) REVERT: A 392 MET cc_start: 0.5302 (mpp) cc_final: 0.3014 (tpt) REVERT: A 429 GLN cc_start: 0.6844 (mp10) cc_final: 0.6419 (mp10) outliers start: 25 outliers final: 13 residues processed: 121 average time/residue: 0.0834 time to fit residues: 13.7257 Evaluate side-chains 111 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain a residue 346 ILE Chi-restraints excluded: chain a residue 474 VAL Chi-restraints excluded: chain a residue 521 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 543 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 8 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 61 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 ASN A 347 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.168797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.097382 restraints weight = 10414.560| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.00 r_work: 0.2804 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8850 Z= 0.169 Angle : 0.648 16.514 12021 Z= 0.326 Chirality : 0.047 0.419 1286 Planarity : 0.005 0.046 1543 Dihedral : 6.860 57.806 1280 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.80 % Favored : 92.10 % Rotamer: Outliers : 2.28 % Allowed : 11.63 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.74 (0.26), residues: 1038 helix: 0.29 (0.31), residues: 321 sheet: -1.21 (0.44), residues: 144 loop : -2.06 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 53 TYR 0.010 0.001 TYR A 396 PHE 0.017 0.002 PHE a 529 TRP 0.032 0.002 TRP A 202 HIS 0.003 0.001 HIS a 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 ( 8849) covalent geometry : angle 0.63595 / 0.32 (12019) SS BOND : bond 0.03090 / 2.06 ( 1) SS BOND : angle 9.84435 / 6.41 ( 2) hydrogen bonds : bond 0.04529 / 3.01 ( 224) hydrogen bonds : angle 4.45167 / 3.02 ( 651) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.278 Fit side-chains REVERT: a 144 MET cc_start: 0.8841 (mtp) cc_final: 0.8630 (mtp) REVERT: a 260 THR cc_start: 0.8718 (m) cc_final: 0.8307 (p) REVERT: a 345 MET cc_start: 0.8186 (tpt) cc_final: 0.7930 (tpt) REVERT: a 418 ASN cc_start: 0.8510 (m-40) cc_final: 0.8202 (m-40) REVERT: a 436 ASP cc_start: 0.7469 (p0) cc_final: 0.7149 (p0) REVERT: a 518 MET cc_start: 0.7333 (tpp) cc_final: 0.7073 (tpp) REVERT: A 95 ASP cc_start: 0.8172 (m-30) cc_final: 0.7626 (m-30) REVERT: A 141 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8535 (tt0) REVERT: A 341 ASP cc_start: 0.8063 (m-30) cc_final: 0.7833 (m-30) REVERT: A 380 MET cc_start: 0.5508 (mmm) cc_final: 0.4710 (tpt) REVERT: A 429 GLN cc_start: 0.6781 (mp10) cc_final: 0.6403 (mp10) REVERT: A 552 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7765 (tp30) outliers start: 21 outliers final: 11 residues processed: 119 average time/residue: 0.0911 time to fit residues: 14.6761 Evaluate side-chains 111 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain a residue 346 ILE Chi-restraints excluded: chain a residue 366 GLU Chi-restraints excluded: chain a residue 474 VAL Chi-restraints excluded: chain a residue 521 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 474 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.170115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.101333 restraints weight = 10292.186| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.95 r_work: 0.2773 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8850 Z= 0.165 Angle : 0.651 20.557 12021 Z= 0.326 Chirality : 0.046 0.392 1286 Planarity : 0.005 0.047 1543 Dihedral : 6.809 59.522 1280 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.19 % Favored : 91.71 % Rotamer: Outliers : 2.28 % Allowed : 11.85 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.65 (0.26), residues: 1038 helix: 0.43 (0.31), residues: 321 sheet: -1.20 (0.44), residues: 145 loop : -2.05 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 147 TYR 0.009 0.001 TYR a 288 PHE 0.016 0.001 PHE a 529 TRP 0.030 0.002 TRP A 202 HIS 0.003 0.001 HIS a 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.16 ( 8849) covalent geometry : angle 0.63664 / 0.32 (12019) SS BOND : bond 0.02986 / 1.99 ( 1) SS BOND : angle 10.52504 / 7.05 ( 2) hydrogen bonds : bond 0.04401 / 2.93 ( 224) hydrogen bonds : angle 4.40330 / 2.99 ( 651) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.347 Fit side-chains REVERT: a 260 THR cc_start: 0.8704 (m) cc_final: 0.8290 (p) REVERT: a 345 MET cc_start: 0.8116 (tpt) cc_final: 0.7812 (tpt) REVERT: a 370 ARG cc_start: 0.7467 (ptm160) cc_final: 0.7208 (ptm160) REVERT: a 418 ASN cc_start: 0.8457 (m-40) cc_final: 0.8162 (m-40) REVERT: a 436 ASP cc_start: 0.7434 (p0) cc_final: 0.7106 (p0) REVERT: a 518 MET cc_start: 0.7301 (tpp) cc_final: 0.6985 (tpp) REVERT: A 93 ASN cc_start: 0.8598 (m-40) cc_final: 0.8376 (m-40) REVERT: A 95 ASP cc_start: 0.8174 (m-30) cc_final: 0.7599 (m-30) REVERT: A 141 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8529 (tt0) REVERT: A 202 TRP cc_start: 0.8482 (OUTLIER) cc_final: 0.8199 (p90) REVERT: A 341 ASP cc_start: 0.7997 (m-30) cc_final: 0.7737 (m-30) REVERT: A 380 MET cc_start: 0.5631 (mmm) cc_final: 0.4795 (tpt) REVERT: A 392 MET cc_start: 0.5486 (mpp) cc_final: 0.3178 (tpt) REVERT: A 409 GLU cc_start: 0.6785 (tt0) cc_final: 0.6498 (tt0) REVERT: A 429 GLN cc_start: 0.6741 (mp10) cc_final: 0.6334 (mp10) REVERT: A 552 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7776 (tp30) outliers start: 21 outliers final: 10 residues processed: 122 average time/residue: 0.1027 time to fit residues: 17.1158 Evaluate side-chains 111 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 474 VAL Chi-restraints excluded: chain a residue 521 VAL Chi-restraints excluded: chain a residue 543 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 474 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 103 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.0030 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.169491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.098182 restraints weight = 10386.996| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.97 r_work: 0.2796 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8850 Z= 0.168 Angle : 0.630 14.850 12021 Z= 0.317 Chirality : 0.045 0.334 1286 Planarity : 0.005 0.045 1543 Dihedral : 6.743 57.108 1280 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.90 % Favored : 92.00 % Rotamer: Outliers : 2.50 % Allowed : 12.28 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.62 (0.26), residues: 1038 helix: 0.48 (0.31), residues: 321 sheet: -1.21 (0.45), residues: 144 loop : -2.03 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 147 TYR 0.010 0.001 TYR a 396 PHE 0.016 0.002 PHE a 529 TRP 0.030 0.002 TRP A 202 HIS 0.004 0.001 HIS a 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 ( 8849) covalent geometry : angle 0.61751 / 0.31 (12019) SS BOND : bond 0.02183 / 1.46 ( 1) SS BOND : angle 9.52990 / 6.47 ( 2) hydrogen bonds : bond 0.04373 / 2.92 ( 224) hydrogen bonds : angle 4.40590 / 2.99 ( 651) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.342 Fit side-chains REVERT: a 260 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8354 (p) REVERT: a 345 MET cc_start: 0.8248 (tpt) cc_final: 0.7933 (tpt) REVERT: a 370 ARG cc_start: 0.7514 (ptm160) cc_final: 0.7029 (ptm160) REVERT: a 418 ASN cc_start: 0.8458 (m-40) cc_final: 0.8148 (m-40) REVERT: a 436 ASP cc_start: 0.7483 (p0) cc_final: 0.7158 (p0) REVERT: a 518 MET cc_start: 0.7352 (tpp) cc_final: 0.7051 (tpp) REVERT: A 95 ASP cc_start: 0.8178 (m-30) cc_final: 0.7619 (m-30) REVERT: A 141 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8525 (tt0) REVERT: A 202 TRP cc_start: 0.8473 (OUTLIER) cc_final: 0.8257 (p90) REVERT: A 318 LYS cc_start: 0.7994 (mttt) cc_final: 0.7614 (ttpt) REVERT: A 341 ASP cc_start: 0.8005 (m-30) cc_final: 0.7726 (m-30) REVERT: A 380 MET cc_start: 0.5587 (mmm) cc_final: 0.4752 (tpt) REVERT: A 392 MET cc_start: 0.5314 (mpp) cc_final: 0.3038 (tpt) REVERT: A 409 GLU cc_start: 0.6799 (tt0) cc_final: 0.6512 (tt0) REVERT: A 429 GLN cc_start: 0.6746 (mp10) cc_final: 0.6313 (mp10) REVERT: A 552 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7714 (tp30) outliers start: 23 outliers final: 14 residues processed: 119 average time/residue: 0.0953 time to fit residues: 15.5794 Evaluate side-chains 115 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 260 THR Chi-restraints excluded: chain a residue 346 ILE Chi-restraints excluded: chain a residue 410 LEU Chi-restraints excluded: chain a residue 474 VAL Chi-restraints excluded: chain a residue 521 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 474 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 0.2980 chunk 45 optimal weight: 9.9990 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.169831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.101111 restraints weight = 10273.090| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.31 r_work: 0.2747 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8850 Z= 0.153 Angle : 0.674 24.269 12021 Z= 0.336 Chirality : 0.046 0.395 1286 Planarity : 0.005 0.046 1543 Dihedral : 6.671 55.289 1280 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.19 % Favored : 91.71 % Rotamer: Outliers : 2.39 % Allowed : 12.83 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.54 (0.26), residues: 1038 helix: 0.58 (0.31), residues: 321 sheet: -1.18 (0.44), residues: 143 loop : -2.00 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 147 TYR 0.010 0.001 TYR a 396 PHE 0.016 0.001 PHE a 529 TRP 0.029 0.001 TRP A 202 HIS 0.003 0.001 HIS a 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 ( 8849) covalent geometry : angle 0.65502 / 0.33 (12019) SS BOND : bond 0.03581 / 2.39 ( 1) SS BOND : angle 12.19219 / 7.83 ( 2) hydrogen bonds : bond 0.04221 / 2.80 ( 224) hydrogen bonds : angle 4.37694 / 2.97 ( 651) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.345 Fit side-chains REVERT: a 260 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8385 (p) REVERT: a 345 MET cc_start: 0.8213 (tpt) cc_final: 0.7870 (tpt) REVERT: a 370 ARG cc_start: 0.7520 (ptm160) cc_final: 0.7219 (ptm160) REVERT: a 436 ASP cc_start: 0.7507 (p0) cc_final: 0.7177 (p0) REVERT: a 518 MET cc_start: 0.7339 (tpp) cc_final: 0.7015 (tpp) REVERT: A 95 ASP cc_start: 0.8224 (m-30) cc_final: 0.7627 (m-30) REVERT: A 141 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8592 (tt0) REVERT: A 202 TRP cc_start: 0.8504 (OUTLIER) cc_final: 0.8216 (p90) REVERT: A 318 LYS cc_start: 0.8046 (mttt) cc_final: 0.7675 (ttpt) REVERT: A 380 MET cc_start: 0.5650 (mmm) cc_final: 0.4796 (tpt) REVERT: A 409 GLU cc_start: 0.6893 (tt0) cc_final: 0.6592 (tt0) REVERT: A 543 LEU cc_start: 0.5741 (OUTLIER) cc_final: 0.5529 (mm) REVERT: A 552 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7639 (tp30) outliers start: 22 outliers final: 13 residues processed: 119 average time/residue: 0.0919 time to fit residues: 14.9080 Evaluate side-chains 116 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 260 THR Chi-restraints excluded: chain a residue 346 ILE Chi-restraints excluded: chain a residue 410 LEU Chi-restraints excluded: chain a residue 474 VAL Chi-restraints excluded: chain a residue 521 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 543 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.169122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.097443 restraints weight = 10222.764| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.99 r_work: 0.2804 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8850 Z= 0.145 Angle : 0.656 22.616 12021 Z= 0.327 Chirality : 0.045 0.385 1286 Planarity : 0.005 0.045 1543 Dihedral : 6.587 54.093 1280 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.00 % Favored : 91.91 % Rotamer: Outliers : 2.07 % Allowed : 13.48 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.50 (0.26), residues: 1038 helix: 0.63 (0.31), residues: 321 sheet: -1.16 (0.44), residues: 143 loop : -1.99 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 147 TYR 0.009 0.001 TYR a 396 PHE 0.016 0.001 PHE a 529 TRP 0.028 0.001 TRP A 202 HIS 0.003 0.001 HIS a 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.14 ( 8849) covalent geometry : angle 0.63819 / 0.32 (12019) SS BOND : bond 0.03032 / 2.02 ( 1) SS BOND : angle 11.64992 / 7.50 ( 2) hydrogen bonds : bond 0.04153 / 2.77 ( 224) hydrogen bonds : angle 4.34635 / 2.95 ( 651) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.271 Fit side-chains REVERT: a 260 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8357 (p) REVERT: a 345 MET cc_start: 0.8189 (tpt) cc_final: 0.7835 (tpt) REVERT: a 436 ASP cc_start: 0.7488 (p0) cc_final: 0.7178 (p0) REVERT: a 518 MET cc_start: 0.7354 (tpp) cc_final: 0.7051 (tpp) REVERT: A 95 ASP cc_start: 0.8168 (m-30) cc_final: 0.7590 (m-30) REVERT: A 141 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8501 (tt0) REVERT: A 202 TRP cc_start: 0.8452 (OUTLIER) cc_final: 0.8196 (p90) REVERT: A 318 LYS cc_start: 0.8012 (mttt) cc_final: 0.7632 (ttpt) REVERT: A 341 ASP cc_start: 0.7646 (m-30) cc_final: 0.7400 (m-30) REVERT: A 380 MET cc_start: 0.5632 (mmm) cc_final: 0.4761 (tpt) REVERT: A 409 GLU cc_start: 0.6887 (tt0) cc_final: 0.6593 (tt0) REVERT: A 429 GLN cc_start: 0.6751 (mp10) cc_final: 0.6451 (mp10) REVERT: A 552 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7651 (tp30) outliers start: 19 outliers final: 13 residues processed: 118 average time/residue: 0.0989 time to fit residues: 15.7943 Evaluate side-chains 113 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 260 THR Chi-restraints excluded: chain a residue 346 ILE Chi-restraints excluded: chain a residue 410 LEU Chi-restraints excluded: chain a residue 474 VAL Chi-restraints excluded: chain a residue 521 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 474 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 61 optimal weight: 0.0010 chunk 87 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.174616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.126000 restraints weight = 10264.116| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.61 r_work: 0.2926 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8850 Z= 0.137 Angle : 0.643 21.304 12021 Z= 0.321 Chirality : 0.045 0.369 1286 Planarity : 0.005 0.045 1543 Dihedral : 6.500 54.280 1280 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.74 % Allowed : 14.02 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.46 (0.26), residues: 1038 helix: 0.69 (0.31), residues: 321 sheet: -1.17 (0.45), residues: 137 loop : -1.96 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 147 TYR 0.012 0.001 TYR a 396 PHE 0.016 0.001 PHE a 529 TRP 0.027 0.001 TRP A 202 HIS 0.003 0.001 HIS a 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 8849) covalent geometry : angle 0.62577 / 0.31 (12019) SS BOND : bond 0.02702 / 1.80 ( 1) SS BOND : angle 11.37334 / 7.33 ( 2) hydrogen bonds : bond 0.04014 / 2.67 ( 224) hydrogen bonds : angle 4.31434 / 2.93 ( 651) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.219 Fit side-chains REVERT: a 260 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8308 (p) REVERT: a 345 MET cc_start: 0.8303 (tpt) cc_final: 0.7987 (tpt) REVERT: a 436 ASP cc_start: 0.7518 (p0) cc_final: 0.7250 (p0) REVERT: a 518 MET cc_start: 0.7506 (tpp) cc_final: 0.7293 (tpp) REVERT: a 552 GLU cc_start: 0.7997 (tp30) cc_final: 0.7686 (tm-30) REVERT: A 95 ASP cc_start: 0.8063 (m-30) cc_final: 0.7573 (m-30) REVERT: A 141 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: A 202 TRP cc_start: 0.8331 (OUTLIER) cc_final: 0.8058 (p90) REVERT: A 318 LYS cc_start: 0.8011 (mttt) cc_final: 0.7618 (ttpt) REVERT: A 341 ASP cc_start: 0.7690 (m-30) cc_final: 0.7427 (m-30) REVERT: A 380 MET cc_start: 0.5563 (mmm) cc_final: 0.4691 (tpt) REVERT: A 392 MET cc_start: 0.5554 (mpp) cc_final: 0.3200 (tmm) REVERT: A 409 GLU cc_start: 0.6909 (tt0) cc_final: 0.6646 (tt0) REVERT: A 429 GLN cc_start: 0.6861 (mp10) cc_final: 0.6580 (mp10) REVERT: A 552 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7671 (tp30) outliers start: 16 outliers final: 13 residues processed: 114 average time/residue: 0.0825 time to fit residues: 12.9315 Evaluate side-chains 112 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 260 THR Chi-restraints excluded: chain a residue 346 ILE Chi-restraints excluded: chain a residue 410 LEU Chi-restraints excluded: chain a residue 474 VAL Chi-restraints excluded: chain a residue 521 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 474 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.175157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.126270 restraints weight = 10289.723| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.67 r_work: 0.2950 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8850 Z= 0.107 Angle : 0.607 19.680 12021 Z= 0.304 Chirality : 0.044 0.351 1286 Planarity : 0.004 0.043 1543 Dihedral : 6.226 53.708 1280 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.63 % Allowed : 14.02 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.28 (0.26), residues: 1038 helix: 0.89 (0.31), residues: 321 sheet: -1.14 (0.45), residues: 138 loop : -1.87 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 370 TYR 0.008 0.001 TYR a 396 PHE 0.014 0.001 PHE a 529 TRP 0.021 0.001 TRP A 202 HIS 0.003 0.001 HIS a 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 8849) covalent geometry : angle 0.59062 / 0.30 (12019) SS BOND : bond 0.02150 / 1.43 ( 1) SS BOND : angle 11.02790 / 7.16 ( 2) hydrogen bonds : bond 0.03593 / 2.41 ( 224) hydrogen bonds : angle 4.20735 / 2.86 ( 651) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2548.14 seconds wall clock time: 44 minutes 6.39 seconds (2646.39 seconds total)