Starting phenix.real_space_refine on Wed Feb 12 20:26:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dh7_27431/02_2025/8dh7_27431.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dh7_27431/02_2025/8dh7_27431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dh7_27431/02_2025/8dh7_27431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dh7_27431/02_2025/8dh7_27431.map" model { file = "/net/cci-nas-00/data/ceres_data/8dh7_27431/02_2025/8dh7_27431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dh7_27431/02_2025/8dh7_27431.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 5240 2.51 5 N 1454 2.21 5 O 1546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8274 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4137 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 491} Chain: "A" Number of atoms: 4137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4137 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 491} Time building chain proxies: 5.77, per 1000 atoms: 0.70 Number of scatterers: 8274 At special positions: 0 Unit cell: (113.016, 82.269, 78.945, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1546 8.00 N 1454 7.00 C 5240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 2.00 Conformation dependent library (CDL) restraints added in 1.2 seconds 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 16 sheets defined 39.4% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'B' and resid 4 through 11 Processing helix chain 'B' and resid 13 through 20 removed outlier: 3.964A pdb=" N VAL B 20 " --> pdb=" O LEU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 30 removed outlier: 3.594A pdb=" N ILE B 27 " --> pdb=" O HIS B 24 " (cutoff:3.500A) Proline residue: B 28 - end of helix Processing helix chain 'B' and resid 48 through 62 Processing helix chain 'B' and resid 78 through 87 removed outlier: 3.831A pdb=" N ASN B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 120 through 127 Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 246 through 264 Processing helix chain 'B' and resid 279 through 291 Processing helix chain 'B' and resid 305 through 315 removed outlier: 4.024A pdb=" N LEU B 309 " --> pdb=" O GLN B 305 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 337 Processing helix chain 'B' and resid 338 through 344 removed outlier: 3.567A pdb=" N HIS B 344 " --> pdb=" O GLU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 Processing helix chain 'B' and resid 356 through 364 Processing helix chain 'B' and resid 396 through 404 removed outlier: 3.534A pdb=" N ARG B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 469 Processing helix chain 'B' and resid 471 through 493 removed outlier: 4.566A pdb=" N ALA B 476 " --> pdb=" O PRO B 472 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU B 477 " --> pdb=" O ASP B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 515 Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 13 through 20 removed outlier: 3.929A pdb=" N VAL A 20 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 30 removed outlier: 3.710A pdb=" N ILE A 27 " --> pdb=" O HIS A 24 " (cutoff:3.500A) Proline residue: A 28 - end of helix Processing helix chain 'A' and resid 48 through 62 Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.921A pdb=" N ASN A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 164 through 171 Processing helix chain 'A' and resid 246 through 264 Processing helix chain 'A' and resid 279 through 291 Processing helix chain 'A' and resid 306 through 315 removed outlier: 3.772A pdb=" N ASP A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 338 removed outlier: 3.760A pdb=" N ASN A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 356 through 364 Processing helix chain 'A' and resid 396 through 404 removed outlier: 3.686A pdb=" N ASN A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 469 Processing helix chain 'A' and resid 471 through 493 removed outlier: 4.558A pdb=" N ALA A 476 " --> pdb=" O PRO A 472 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU A 477 " --> pdb=" O ASP A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 515 Processing sheet with id=AA1, first strand: chain 'B' and resid 112 through 113 removed outlier: 6.420A pdb=" N ILE B 91 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N PHE B 69 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ARG B 93 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU B 71 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU B 36 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR B 35 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE B 144 " --> pdb=" O TYR B 35 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY B 37 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N GLU B 146 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASP B 141 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 174 " --> pdb=" O ASP B 141 " (cutoff:3.500A) removed outlier: 10.970A pdb=" N ASP B 173 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 10.088A pdb=" N ALA B 227 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL B 175 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N VAL B 229 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE B 177 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N SER B 231 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VAL B 179 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 149 through 150 removed outlier: 3.713A pdb=" N ALA B 149 " --> pdb=" O VAL B 157 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 190 through 191 removed outlier: 8.429A pdb=" N CYS B 347 " --> pdb=" O ASP B 318 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA B 320 " --> pdb=" O CYS B 347 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ARG B 349 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ALA B 322 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU B 297 " --> pdb=" O ASP B 318 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ALA B 320 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 299 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ALA B 322 " --> pdb=" O VAL B 299 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 274 through 275 removed outlier: 3.865A pdb=" N MET B 368 " --> pdb=" O GLN B 275 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER B 407 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL B 445 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N MET B 409 " --> pdb=" O VAL B 445 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 303 through 304 Processing sheet with id=AA6, first strand: chain 'B' and resid 380 through 381 removed outlier: 6.734A pdb=" N VAL B 374 " --> pdb=" O VAL B 428 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 384 through 385 Processing sheet with id=AA8, first strand: chain 'B' and resid 414 through 415 Processing sheet with id=AA9, first strand: chain 'A' and resid 112 through 113 removed outlier: 6.427A pdb=" N ILE A 91 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N PHE A 69 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARG A 93 " --> pdb=" O PHE A 69 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU A 71 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU A 36 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TYR A 35 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE A 144 " --> pdb=" O TYR A 35 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY A 37 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLU A 146 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ASP A 141 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 10.968A pdb=" N ASP A 173 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N ALA A 227 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL A 175 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N VAL A 229 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE A 177 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N SER A 231 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL A 179 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 149 through 150 removed outlier: 3.653A pdb=" N ALA A 149 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 190 through 191 removed outlier: 8.411A pdb=" N CYS A 347 " --> pdb=" O ASP A 318 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA A 320 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ARG A 349 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA A 322 " --> pdb=" O ARG A 349 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU A 297 " --> pdb=" O ASP A 318 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA A 320 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL A 299 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ALA A 322 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 274 through 275 removed outlier: 5.943A pdb=" N ALA A 367 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N HIS A 410 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASN A 369 " --> pdb=" O HIS A 410 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER A 407 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL A 445 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N MET A 409 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 303 through 304 Processing sheet with id=AB5, first strand: chain 'A' and resid 380 through 381 removed outlier: 6.617A pdb=" N VAL A 374 " --> pdb=" O VAL A 428 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 384 through 385 Processing sheet with id=AB7, first strand: chain 'A' and resid 414 through 415 283 hydrogen bonds defined for protein. 795 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: 2.60 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1668 1.33 - 1.45: 1918 1.45 - 1.57: 4823 1.57 - 1.69: 1 1.69 - 1.81: 60 Bond restraints: 8470 Sorted by residual: bond pdb=" CA ASP B 245 " pdb=" C ASP B 245 " ideal model delta sigma weight residual 1.523 1.455 0.069 1.80e-02 3.09e+03 1.45e+01 bond pdb=" CA ASP A 245 " pdb=" C ASP A 245 " ideal model delta sigma weight residual 1.523 1.456 0.067 1.80e-02 3.09e+03 1.39e+01 bond pdb=" CA GLN B 275 " pdb=" CB GLN B 275 " ideal model delta sigma weight residual 1.527 1.606 -0.078 2.48e-02 1.63e+03 9.99e+00 bond pdb=" N ASP B 245 " pdb=" CA ASP B 245 " ideal model delta sigma weight residual 1.457 1.415 0.042 1.40e-02 5.10e+03 9.02e+00 bond pdb=" N ASP A 245 " pdb=" CA ASP A 245 " ideal model delta sigma weight residual 1.457 1.416 0.041 1.40e-02 5.10e+03 8.45e+00 ... (remaining 8465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 11360 2.30 - 4.61: 122 4.61 - 6.91: 7 6.91 - 9.22: 3 9.22 - 11.52: 2 Bond angle restraints: 11494 Sorted by residual: angle pdb=" N MET B 246 " pdb=" CA MET B 246 " pdb=" C MET B 246 " ideal model delta sigma weight residual 113.41 101.89 11.52 1.22e+00 6.72e-01 8.92e+01 angle pdb=" N MET A 246 " pdb=" CA MET A 246 " pdb=" C MET A 246 " ideal model delta sigma weight residual 113.12 102.23 10.89 1.25e+00 6.40e-01 7.60e+01 angle pdb=" CA GLN B 275 " pdb=" CB GLN B 275 " pdb=" CG GLN B 275 " ideal model delta sigma weight residual 114.10 121.16 -7.06 2.00e+00 2.50e-01 1.25e+01 angle pdb=" CA ASP B 244 " pdb=" C ASP B 244 " pdb=" O ASP B 244 " ideal model delta sigma weight residual 121.78 117.29 4.49 1.28e+00 6.10e-01 1.23e+01 angle pdb=" CA ASP A 244 " pdb=" C ASP A 244 " pdb=" O ASP A 244 " ideal model delta sigma weight residual 121.78 117.38 4.40 1.28e+00 6.10e-01 1.18e+01 ... (remaining 11489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 4711 17.05 - 34.10: 344 34.10 - 51.15: 62 51.15 - 68.19: 16 68.19 - 85.24: 7 Dihedral angle restraints: 5140 sinusoidal: 2096 harmonic: 3044 Sorted by residual: dihedral pdb=" CA ASP B 452 " pdb=" CB ASP B 452 " pdb=" CG ASP B 452 " pdb=" OD1 ASP B 452 " ideal model delta sinusoidal sigma weight residual -30.00 -89.02 59.02 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASP A 447 " pdb=" CB ASP A 447 " pdb=" CG ASP A 447 " pdb=" OD1 ASP A 447 " ideal model delta sinusoidal sigma weight residual -30.00 -86.79 56.79 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA ASP B 447 " pdb=" CB ASP B 447 " pdb=" CG ASP B 447 " pdb=" OD1 ASP B 447 " ideal model delta sinusoidal sigma weight residual -30.00 -86.16 56.16 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 5137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1008 0.053 - 0.107: 212 0.107 - 0.160: 44 0.160 - 0.213: 2 0.213 - 0.266: 2 Chirality restraints: 1268 Sorted by residual: chirality pdb=" CA MET B 246 " pdb=" N MET B 246 " pdb=" C MET B 246 " pdb=" CB MET B 246 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA MET A 246 " pdb=" N MET A 246 " pdb=" C MET A 246 " pdb=" CB MET A 246 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ASP A 245 " pdb=" N ASP A 245 " pdb=" C ASP A 245 " pdb=" CB ASP A 245 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 1265 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 244 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.88e+00 pdb=" C ASP A 244 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP A 244 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP A 245 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 244 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.65e+00 pdb=" C ASP B 244 " -0.045 2.00e-02 2.50e+03 pdb=" O ASP B 244 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP B 245 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 94 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO B 95 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " 0.027 5.00e-02 4.00e+02 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 162 2.67 - 3.23: 7752 3.23 - 3.79: 13074 3.79 - 4.34: 19126 4.34 - 4.90: 31483 Nonbonded interactions: 71597 Sorted by model distance: nonbonded pdb=" O LEU B 317 " pdb=" NH2 ARG B 345 " model vdw 2.117 3.120 nonbonded pdb=" O ASP A 211 " pdb=" NH2 ARG A 349 " model vdw 2.134 3.120 nonbonded pdb=" NZ LYS B 506 " pdb=" O SER B 521 " model vdw 2.178 3.120 nonbonded pdb=" O ASP B 211 " pdb=" NH2 ARG B 349 " model vdw 2.179 3.120 nonbonded pdb=" O PHE B 168 " pdb=" OG SER B 172 " model vdw 2.198 3.040 ... (remaining 71592 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.830 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.780 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:12.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 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 : 0.003 0.078 8470 Z= 0.234 Angle : 0.594 11.524 11494 Z= 0.339 Chirality : 0.047 0.266 1268 Planarity : 0.005 0.053 1514 Dihedral : 12.958 85.242 3172 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.14 % Rotamer: Outliers : 0.55 % Allowed : 0.11 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.27), residues: 1048 helix: 1.12 (0.28), residues: 384 sheet: 1.15 (0.50), residues: 96 loop : 0.01 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 84 HIS 0.004 0.001 HIS A 492 PHE 0.018 0.001 PHE B 507 TYR 0.006 0.001 TYR B 13 ARG 0.003 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.959 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 121 average time/residue: 1.3935 time to fit residues: 179.0600 Evaluate side-chains 84 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 246 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 HIS A 492 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.141688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.120807 restraints weight = 9602.863| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.80 r_work: 0.3286 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 8470 Z= 0.368 Angle : 0.602 5.823 11494 Z= 0.316 Chirality : 0.049 0.145 1268 Planarity : 0.005 0.052 1514 Dihedral : 5.878 51.280 1140 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.39 % Favored : 97.52 % Rotamer: Outliers : 1.77 % Allowed : 7.96 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.26), residues: 1048 helix: 1.17 (0.27), residues: 364 sheet: 0.65 (0.45), residues: 134 loop : -0.05 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 84 HIS 0.007 0.001 HIS B 410 PHE 0.014 0.002 PHE B 507 TYR 0.009 0.001 TYR B 377 ARG 0.008 0.001 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: B 246 MET cc_start: 0.8157 (ttm) cc_final: 0.7851 (ttt) REVERT: B 327 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7443 (pp) REVERT: B 329 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6839 (tp30) REVERT: A 246 MET cc_start: 0.8206 (ttm) cc_final: 0.7990 (ttt) outliers start: 16 outliers final: 5 residues processed: 95 average time/residue: 1.1721 time to fit residues: 119.6385 Evaluate side-chains 83 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 244 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 6 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 91 optimal weight: 0.0030 chunk 48 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 ASN ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 HIS ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.133067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.113938 restraints weight = 9773.874| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.67 r_work: 0.3212 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8470 Z= 0.192 Angle : 0.518 5.621 11494 Z= 0.269 Chirality : 0.045 0.140 1268 Planarity : 0.005 0.051 1514 Dihedral : 5.477 56.608 1134 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.00 % Favored : 97.90 % Rotamer: Outliers : 1.66 % Allowed : 9.40 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1048 helix: 1.31 (0.27), residues: 366 sheet: 0.65 (0.47), residues: 134 loop : 0.02 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS B 410 PHE 0.011 0.001 PHE A 336 TYR 0.007 0.001 TYR B 127 ARG 0.005 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: B 115 ASP cc_start: 0.8471 (p0) cc_final: 0.8263 (p0) REVERT: B 304 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.7871 (mp) REVERT: B 327 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7154 (pp) REVERT: B 329 GLU cc_start: 0.7363 (pm20) cc_final: 0.6820 (tp30) REVERT: A 115 ASP cc_start: 0.8557 (p0) cc_final: 0.8311 (p0) REVERT: A 172 SER cc_start: 0.9192 (OUTLIER) cc_final: 0.8959 (m) REVERT: A 246 MET cc_start: 0.8103 (ttm) cc_final: 0.7791 (ttt) REVERT: A 304 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.7994 (mp) outliers start: 15 outliers final: 5 residues processed: 93 average time/residue: 1.0018 time to fit residues: 101.0573 Evaluate side-chains 85 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 304 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 1 optimal weight: 0.0010 chunk 97 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 72 optimal weight: 0.0980 chunk 83 optimal weight: 5.9990 chunk 16 optimal weight: 0.2980 chunk 71 optimal weight: 0.1980 chunk 6 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 HIS A 117 HIS ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.135689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.116727 restraints weight = 9683.312| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.66 r_work: 0.3243 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8470 Z= 0.142 Angle : 0.491 5.563 11494 Z= 0.253 Chirality : 0.044 0.144 1268 Planarity : 0.005 0.053 1514 Dihedral : 5.315 58.685 1134 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.00 % Favored : 97.90 % Rotamer: Outliers : 2.21 % Allowed : 10.51 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1048 helix: 1.47 (0.27), residues: 378 sheet: 0.57 (0.49), residues: 114 loop : -0.01 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS B 499 PHE 0.010 0.001 PHE A 336 TYR 0.008 0.001 TYR B 377 ARG 0.004 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: B 143 THR cc_start: 0.8952 (t) cc_final: 0.8729 (m) REVERT: B 304 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.7921 (mp) REVERT: B 327 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6974 (pp) REVERT: B 329 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6944 (tp30) REVERT: A 18 LYS cc_start: 0.8751 (mttt) cc_final: 0.8413 (mmtt) REVERT: A 246 MET cc_start: 0.8046 (ttm) cc_final: 0.7741 (ttt) REVERT: A 304 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.7977 (mp) outliers start: 20 outliers final: 5 residues processed: 102 average time/residue: 0.9895 time to fit residues: 109.5231 Evaluate side-chains 89 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 304 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 73 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 HIS ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.132382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.113217 restraints weight = 9715.281| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.67 r_work: 0.3184 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8470 Z= 0.269 Angle : 0.536 5.559 11494 Z= 0.277 Chirality : 0.047 0.151 1268 Planarity : 0.005 0.051 1514 Dihedral : 5.385 53.339 1134 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.10 % Favored : 97.81 % Rotamer: Outliers : 1.77 % Allowed : 12.28 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.26), residues: 1048 helix: 1.49 (0.27), residues: 366 sheet: 0.51 (0.49), residues: 114 loop : 0.00 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.005 0.001 HIS B 492 PHE 0.010 0.001 PHE A 336 TYR 0.008 0.001 TYR B 142 ARG 0.004 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.5255 (tpt) cc_final: 0.3764 (ptt) REVERT: B 304 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8046 (mp) REVERT: B 327 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.6985 (pp) REVERT: B 329 GLU cc_start: 0.7493 (pm20) cc_final: 0.7051 (tp30) REVERT: A 18 LYS cc_start: 0.8761 (mttt) cc_final: 0.8431 (mmtt) REVERT: A 156 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8568 (mt) REVERT: A 246 MET cc_start: 0.8073 (ttm) cc_final: 0.7779 (ttt) REVERT: A 304 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8053 (mp) outliers start: 16 outliers final: 8 residues processed: 98 average time/residue: 1.0616 time to fit residues: 112.7372 Evaluate side-chains 95 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 304 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 99 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 71 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 HIS ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.133630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114509 restraints weight = 9652.044| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.68 r_work: 0.3219 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8470 Z= 0.187 Angle : 0.508 5.605 11494 Z= 0.262 Chirality : 0.045 0.146 1268 Planarity : 0.005 0.051 1514 Dihedral : 5.133 49.181 1134 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.00 % Favored : 97.90 % Rotamer: Outliers : 1.88 % Allowed : 13.38 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1048 helix: 1.65 (0.27), residues: 364 sheet: 0.46 (0.49), residues: 114 loop : 0.03 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.005 0.001 HIS B 492 PHE 0.010 0.001 PHE A 336 TYR 0.006 0.001 TYR A 377 ARG 0.003 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.4854 (tpt) cc_final: 0.3901 (ptt) REVERT: B 115 ASP cc_start: 0.8461 (p0) cc_final: 0.8250 (p0) REVERT: B 143 THR cc_start: 0.8959 (t) cc_final: 0.8696 (m) REVERT: B 304 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.7925 (mp) REVERT: B 327 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.6919 (pp) REVERT: B 329 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7055 (tp30) REVERT: A 18 LYS cc_start: 0.8746 (mttt) cc_final: 0.8418 (mmtt) REVERT: A 115 ASP cc_start: 0.8570 (p0) cc_final: 0.8316 (p0) REVERT: A 156 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8555 (mt) REVERT: A 246 MET cc_start: 0.8004 (ttm) cc_final: 0.7692 (ttt) REVERT: A 304 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8014 (mp) outliers start: 17 outliers final: 6 residues processed: 98 average time/residue: 0.9940 time to fit residues: 105.8967 Evaluate side-chains 92 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 304 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 2 optimal weight: 0.3980 chunk 84 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 HIS B 356 ASN B 492 HIS ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.131168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.112001 restraints weight = 9768.886| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.68 r_work: 0.3171 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8470 Z= 0.279 Angle : 0.546 5.869 11494 Z= 0.282 Chirality : 0.047 0.143 1268 Planarity : 0.005 0.051 1514 Dihedral : 5.219 53.424 1134 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.00 % Favored : 97.90 % Rotamer: Outliers : 2.10 % Allowed : 13.72 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1048 helix: 1.57 (0.27), residues: 364 sheet: 0.39 (0.49), residues: 114 loop : -0.06 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.005 0.001 HIS B 492 PHE 0.010 0.001 PHE A 336 TYR 0.008 0.001 TYR B 142 ARG 0.003 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.890 Fit side-chains REVERT: B 1 MET cc_start: 0.4961 (tpt) cc_final: 0.3945 (ptt) REVERT: B 304 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8127 (mp) REVERT: B 327 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7064 (pp) REVERT: B 329 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7034 (tp30) REVERT: A 18 LYS cc_start: 0.8754 (mttt) cc_final: 0.8438 (mmtt) REVERT: A 246 MET cc_start: 0.8020 (ttm) cc_final: 0.7704 (ttt) REVERT: A 304 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8051 (mp) outliers start: 19 outliers final: 10 residues processed: 98 average time/residue: 1.0164 time to fit residues: 108.1370 Evaluate side-chains 94 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 304 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 1 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.0270 chunk 24 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 HIS ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.132547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.113559 restraints weight = 9835.147| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.67 r_work: 0.3195 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8470 Z= 0.191 Angle : 0.516 5.646 11494 Z= 0.267 Chirality : 0.045 0.143 1268 Planarity : 0.005 0.051 1514 Dihedral : 5.024 52.696 1134 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.29 % Favored : 97.61 % Rotamer: Outliers : 1.88 % Allowed : 14.82 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.26), residues: 1048 helix: 1.59 (0.27), residues: 376 sheet: 0.45 (0.50), residues: 114 loop : -0.15 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 339 HIS 0.003 0.001 HIS A 492 PHE 0.010 0.001 PHE A 336 TYR 0.006 0.001 TYR B 142 ARG 0.003 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.970 Fit side-chains REVERT: B 1 MET cc_start: 0.4762 (tpt) cc_final: 0.4051 (ptt) REVERT: B 115 ASP cc_start: 0.8467 (p0) cc_final: 0.8201 (p0) REVERT: B 327 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7068 (pp) REVERT: B 329 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7064 (tp30) REVERT: B 375 ASP cc_start: 0.8960 (p0) cc_final: 0.8716 (p0) REVERT: A 18 LYS cc_start: 0.8746 (mttt) cc_final: 0.8437 (mmtt) REVERT: A 115 ASP cc_start: 0.8579 (p0) cc_final: 0.8309 (p0) REVERT: A 246 MET cc_start: 0.7998 (ttm) cc_final: 0.7683 (ttt) REVERT: A 304 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8012 (mp) outliers start: 17 outliers final: 7 residues processed: 98 average time/residue: 0.9684 time to fit residues: 103.0652 Evaluate side-chains 95 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 304 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 74 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 60 optimal weight: 0.1980 chunk 71 optimal weight: 0.0170 chunk 27 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 HIS ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.131185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.112418 restraints weight = 9974.115| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.65 r_work: 0.3206 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8470 Z= 0.185 Angle : 0.516 6.093 11494 Z= 0.265 Chirality : 0.045 0.142 1268 Planarity : 0.005 0.052 1514 Dihedral : 4.886 53.620 1134 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.00 % Favored : 97.90 % Rotamer: Outliers : 2.10 % Allowed : 15.15 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.27), residues: 1048 helix: 1.55 (0.27), residues: 388 sheet: 0.53 (0.48), residues: 134 loop : -0.14 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 339 HIS 0.004 0.001 HIS A 492 PHE 0.018 0.001 PHE B 312 TYR 0.007 0.001 TYR B 142 ARG 0.004 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.995 Fit side-chains REVERT: B 1 MET cc_start: 0.4771 (tpt) cc_final: 0.4173 (ptt) REVERT: B 143 THR cc_start: 0.8935 (t) cc_final: 0.8702 (m) REVERT: B 246 MET cc_start: 0.7973 (ttp) cc_final: 0.7719 (mtm) REVERT: B 327 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7047 (pp) REVERT: B 329 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7008 (tp30) REVERT: A 18 LYS cc_start: 0.8726 (mttt) cc_final: 0.8387 (mmtt) REVERT: A 115 ASP cc_start: 0.8558 (p0) cc_final: 0.8312 (p0) REVERT: A 156 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8520 (mt) REVERT: A 304 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8004 (mp) REVERT: A 330 LYS cc_start: 0.7819 (tptt) cc_final: 0.7536 (mtmt) outliers start: 19 outliers final: 9 residues processed: 102 average time/residue: 0.9466 time to fit residues: 105.1532 Evaluate side-chains 98 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 304 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 HIS ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.131821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.112868 restraints weight = 9818.401| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.66 r_work: 0.3183 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8470 Z= 0.250 Angle : 0.547 6.217 11494 Z= 0.282 Chirality : 0.046 0.143 1268 Planarity : 0.005 0.051 1514 Dihedral : 4.943 55.799 1132 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.29 % Favored : 97.61 % Rotamer: Outliers : 1.44 % Allowed : 15.93 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.27), residues: 1048 helix: 1.44 (0.27), residues: 388 sheet: 0.46 (0.48), residues: 134 loop : -0.17 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 339 HIS 0.004 0.001 HIS B 410 PHE 0.022 0.001 PHE B 312 TYR 0.008 0.001 TYR B 142 ARG 0.003 0.000 ARG B 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.953 Fit side-chains REVERT: B 1 MET cc_start: 0.4864 (tpt) cc_final: 0.4267 (ptt) REVERT: B 115 ASP cc_start: 0.8415 (p0) cc_final: 0.8165 (p0) REVERT: B 246 MET cc_start: 0.8029 (ttp) cc_final: 0.7770 (mtm) REVERT: B 327 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7206 (pp) REVERT: B 329 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7041 (tp30) REVERT: A 18 LYS cc_start: 0.8733 (mttt) cc_final: 0.8418 (mmtt) REVERT: A 156 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8528 (mt) REVERT: A 304 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8071 (mp) REVERT: A 330 LYS cc_start: 0.7831 (tptt) cc_final: 0.7466 (mtpt) outliers start: 13 outliers final: 6 residues processed: 89 average time/residue: 1.0466 time to fit residues: 101.3302 Evaluate side-chains 89 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 304 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 97 optimal weight: 0.0060 chunk 45 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 21 optimal weight: 0.0030 chunk 71 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 79 optimal weight: 0.0770 overall best weight: 0.2764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 HIS A 61 ASN ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.135224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.116562 restraints weight = 9756.269| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.64 r_work: 0.3244 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8470 Z= 0.156 Angle : 0.500 5.855 11494 Z= 0.258 Chirality : 0.045 0.143 1268 Planarity : 0.005 0.051 1514 Dihedral : 4.657 55.724 1130 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.48 % Favored : 97.42 % Rotamer: Outliers : 1.55 % Allowed : 15.93 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.27), residues: 1048 helix: 1.64 (0.27), residues: 388 sheet: 0.52 (0.48), residues: 134 loop : -0.11 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 339 HIS 0.005 0.001 HIS A 492 PHE 0.019 0.001 PHE B 312 TYR 0.005 0.001 TYR B 127 ARG 0.004 0.000 ARG B 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4793.91 seconds wall clock time: 85 minutes 51.83 seconds (5151.83 seconds total)