Starting phenix.real_space_refine on Fri Sep 11 14:06:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x16_21990/09_2026/6x16_21990.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x16_21990/09_2026/6x16_21990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6x16_21990/09_2026/6x16_21990.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x16_21990/09_2026/6x16_21990.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x16_21990/09_2026/6x16_21990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x16_21990/09_2026/6x16_21990.map" model { file = "/net/cci-nas-00/data/ceres_data/6x16_21990/09_2026/6x16_21990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x16_21990/09_2026/6x16_21990.cif" } resolution = 3.39 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= 0.053 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 54 5.16 5 C 6222 2.51 5 N 1503 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9438 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3087 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 18, 'TRANS': 397} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'6OU': 1, 'TB1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Restraints were copied for chains: A, C Time building chain proxies: 1.97, per 1000 atoms: 0.21 Number of scatterers: 9438 At special positions: 0 Unit cell: (110.545, 109.472, 74.0543, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 3 15.00 O 1656 8.00 N 1503 7.00 C 6222 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: 0.84 Conformation dependent library (CDL) restraints added in 279.9 milliseconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2238 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 82.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 11 through 33 removed outlier: 3.569A pdb=" N LYS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 57 Proline residue: B 45 - end of helix Processing helix chain 'B' and resid 57 through 74 removed outlier: 4.006A pdb=" N ILE B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 107 removed outlier: 3.600A pdb=" N VAL B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR B 88 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 141 through 148 removed outlier: 3.513A pdb=" N ASN B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 169 Processing helix chain 'B' and resid 174 through 220 Proline residue: B 206 - end of helix Processing helix chain 'B' and resid 222 through 254 removed outlier: 4.232A pdb=" N GLY B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU B 227 " --> pdb=" O HIS B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 265 Processing helix chain 'B' and resid 265 through 275 removed outlier: 3.778A pdb=" N ALA B 272 " --> pdb=" O ALA B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.653A pdb=" N LEU B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR B 308 " --> pdb=" O PRO B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 328 removed outlier: 3.586A pdb=" N LEU B 316 " --> pdb=" O ASP B 312 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE B 323 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 326 " --> pdb=" O THR B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 347 removed outlier: 3.521A pdb=" N ILE B 341 " --> pdb=" O GLN B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 371 removed outlier: 3.677A pdb=" N CYS B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER B 369 " --> pdb=" O MET B 365 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 388 removed outlier: 3.648A pdb=" N ALA B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 414 removed outlier: 3.943A pdb=" N MET B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLY B 396 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET B 399 " --> pdb=" O MET B 395 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 400 " --> pdb=" O GLY B 396 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN B 401 " --> pdb=" O ARG B 397 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 406 " --> pdb=" O VAL B 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 11 through 33 removed outlier: 3.569A pdb=" N LYS A 15 " --> pdb=" O PRO A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 57 Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 57 through 74 removed outlier: 4.006A pdb=" N ILE A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 107 removed outlier: 3.600A pdb=" N VAL A 83 " --> pdb=" O GLY A 79 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 141 through 148 removed outlier: 3.513A pdb=" N ASN A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 169 Processing helix chain 'A' and resid 174 through 220 Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 222 through 254 removed outlier: 4.232A pdb=" N GLY A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'A' and resid 265 through 275 removed outlier: 3.778A pdb=" N ALA A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.653A pdb=" N LEU A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 328 removed outlier: 3.586A pdb=" N LEU A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 326 " --> pdb=" O THR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 347 removed outlier: 3.521A pdb=" N ILE A 341 " --> pdb=" O GLN A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 371 removed outlier: 3.677A pdb=" N CYS A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 388 removed outlier: 3.648A pdb=" N ALA A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 414 removed outlier: 3.943A pdb=" N MET A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET A 399 " --> pdb=" O MET A 395 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 10 Processing helix chain 'C' and resid 11 through 33 removed outlier: 3.569A pdb=" N LYS C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 57 Proline residue: C 45 - end of helix Processing helix chain 'C' and resid 57 through 74 removed outlier: 4.005A pdb=" N ILE C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 107 removed outlier: 3.599A pdb=" N VAL C 83 " --> pdb=" O GLY C 79 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR C 88 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 137 Processing helix chain 'C' and resid 141 through 148 removed outlier: 3.513A pdb=" N ASN C 148 " --> pdb=" O GLY C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 169 Processing helix chain 'C' and resid 174 through 220 Proline residue: C 206 - end of helix Processing helix chain 'C' and resid 222 through 254 removed outlier: 4.232A pdb=" N GLY C 226 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU C 227 " --> pdb=" O HIS C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 265 Processing helix chain 'C' and resid 265 through 275 removed outlier: 3.778A pdb=" N ALA C 272 " --> pdb=" O ALA C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 301 through 310 removed outlier: 3.652A pdb=" N LEU C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR C 308 " --> pdb=" O PRO C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 328 removed outlier: 3.586A pdb=" N LEU C 316 " --> pdb=" O ASP C 312 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE C 323 " --> pdb=" O GLY C 319 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 326 " --> pdb=" O THR C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 347 removed outlier: 3.521A pdb=" N ILE C 341 " --> pdb=" O GLN C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.676A pdb=" N CYS C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER C 369 " --> pdb=" O MET C 365 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 388 removed outlier: 3.648A pdb=" N ALA C 384 " --> pdb=" O ALA C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 414 removed outlier: 3.943A pdb=" N MET C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLY C 396 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET C 399 " --> pdb=" O MET C 395 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL C 400 " --> pdb=" O GLY C 396 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN C 401 " --> pdb=" O ARG C 397 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 406 " --> pdb=" O VAL C 402 " (cutoff:3.500A) 694 hydrogen bonds defined for protein. 2082 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: 1.62 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1455 1.31 - 1.43: 2347 1.43 - 1.56: 5669 1.56 - 1.68: 45 1.68 - 1.80: 102 Bond restraints: 9618 Sorted by residual: bond pdb=" C16 6OU A 501 " pdb=" O18 6OU A 501 " ideal model delta sigma weight residual 1.327 1.414 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C16 6OU C 501 " pdb=" O18 6OU C 501 " ideal model delta sigma weight residual 1.327 1.413 -0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C16 6OU B 501 " pdb=" O18 6OU B 501 " ideal model delta sigma weight residual 1.327 1.413 -0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C31 6OU B 501 " pdb=" O30 6OU B 501 " ideal model delta sigma weight residual 1.331 1.408 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C31 6OU C 501 " pdb=" O30 6OU C 501 " ideal model delta sigma weight residual 1.331 1.408 -0.077 2.00e-02 2.50e+03 1.48e+01 ... (remaining 9613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 12844 3.11 - 6.22: 191 6.22 - 9.34: 39 9.34 - 12.45: 6 12.45 - 15.56: 3 Bond angle restraints: 13083 Sorted by residual: angle pdb=" O22 6OU C 501 " pdb=" P23 6OU C 501 " pdb=" O26 6OU C 501 " ideal model delta sigma weight residual 93.95 109.51 -15.56 3.00e+00 1.11e-01 2.69e+01 angle pdb=" O22 6OU B 501 " pdb=" P23 6OU B 501 " pdb=" O26 6OU B 501 " ideal model delta sigma weight residual 93.95 109.49 -15.54 3.00e+00 1.11e-01 2.68e+01 angle pdb=" O22 6OU A 501 " pdb=" P23 6OU A 501 " pdb=" O26 6OU A 501 " ideal model delta sigma weight residual 93.95 109.49 -15.54 3.00e+00 1.11e-01 2.68e+01 angle pdb=" N ALA A 205 " pdb=" CA ALA A 205 " pdb=" C ALA A 205 " ideal model delta sigma weight residual 109.81 121.12 -11.31 2.21e+00 2.05e-01 2.62e+01 angle pdb=" N ALA B 205 " pdb=" CA ALA B 205 " pdb=" C ALA B 205 " ideal model delta sigma weight residual 109.81 121.07 -11.26 2.21e+00 2.05e-01 2.59e+01 ... (remaining 13078 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 5028 16.99 - 33.97: 468 33.97 - 50.96: 96 50.96 - 67.95: 18 67.95 - 84.93: 15 Dihedral angle restraints: 5625 sinusoidal: 2088 harmonic: 3537 Sorted by residual: dihedral pdb=" CA VAL B 58 " pdb=" C VAL B 58 " pdb=" N MET B 59 " pdb=" CA MET B 59 " ideal model delta harmonic sigma weight residual -180.00 -160.87 -19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA VAL C 58 " pdb=" C VAL C 58 " pdb=" N MET C 59 " pdb=" CA MET C 59 " ideal model delta harmonic sigma weight residual -180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA VAL A 58 " pdb=" C VAL A 58 " pdb=" N MET A 59 " pdb=" CA MET A 59 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1093 0.039 - 0.079: 378 0.079 - 0.118: 99 0.118 - 0.157: 32 0.157 - 0.196: 18 Chirality restraints: 1620 Sorted by residual: chirality pdb=" C20 6OU C 501 " pdb=" C19 6OU C 501 " pdb=" C21 6OU C 501 " pdb=" O30 6OU C 501 " both_signs ideal model delta sigma weight residual False 2.35 2.54 -0.20 2.00e-01 2.50e+01 9.63e-01 chirality pdb=" C20 6OU B 501 " pdb=" C19 6OU B 501 " pdb=" C21 6OU B 501 " pdb=" O30 6OU B 501 " both_signs ideal model delta sigma weight residual False 2.35 2.54 -0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" C20 6OU A 501 " pdb=" C19 6OU A 501 " pdb=" C21 6OU A 501 " pdb=" O30 6OU A 501 " both_signs ideal model delta sigma weight residual False 2.35 2.54 -0.19 2.00e-01 2.50e+01 9.11e-01 ... (remaining 1617 not shown) Planarity restraints: 1605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " 0.045 5.00e-02 4.00e+02 6.68e-02 7.13e+00 pdb=" N PRO A 45 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 44 " -0.045 5.00e-02 4.00e+02 6.67e-02 7.13e+00 pdb=" N PRO C 45 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 45 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 45 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 44 " 0.045 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO B 45 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 45 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 45 " 0.037 5.00e-02 4.00e+02 ... (remaining 1602 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3012 2.84 - 3.35: 8922 3.35 - 3.87: 15515 3.87 - 4.38: 17713 4.38 - 4.90: 31435 Nonbonded interactions: 76597 Sorted by model distance: nonbonded pdb=" OG SER A 65 " pdb=" OH TYR A 195 " model vdw 2.322 3.040 nonbonded pdb=" OG SER C 65 " pdb=" OH TYR C 195 " model vdw 2.322 3.040 nonbonded pdb=" OG SER B 65 " pdb=" OH TYR B 195 " model vdw 2.322 3.040 nonbonded pdb=" OG SER C 278 " pdb=" O3 TB1 C 502 " model vdw 2.323 3.040 nonbonded pdb=" OG SER B 278 " pdb=" O3 TB1 B 502 " model vdw 2.323 3.040 ... (remaining 76592 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: 0.03 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' } 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: 1.350 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.270 Find NCS groups from input model: 0.080 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 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 0.087 9618 Z= 0.312 Angle : 0.994 15.560 13083 Z= 0.481 Chirality : 0.047 0.196 1620 Planarity : 0.008 0.067 1605 Dihedral : 14.757 84.933 3387 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.31 % Allowed : 7.72 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.86 (0.18), residues: 1242 helix: -2.31 (0.12), residues: 1005 sheet: None (None), residues: 0 loop : -2.56 (0.34), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 105 TYR 0.018 0.001 TYR C 299 PHE 0.013 0.001 PHE A 107 HIS 0.008 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.31 ( 9618) covalent geometry : angle 0.99399 / 0.48 (13083) hydrogen bonds : bond 0.12664 / 8.29 ( 694) hydrogen bonds : angle 6.30759 / 4.43 ( 2082) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.223 Fit side-chains REVERT: B 59 MET cc_start: 0.7758 (mmm) cc_final: 0.7439 (mmp) REVERT: B 169 MET cc_start: 0.8197 (mtm) cc_final: 0.7929 (mtm) REVERT: B 217 MET cc_start: 0.7451 (mmt) cc_final: 0.6728 (mmt) REVERT: B 269 MET cc_start: 0.7008 (mtm) cc_final: 0.6758 (mtp) REVERT: B 310 ASN cc_start: 0.9366 (t0) cc_final: 0.9056 (t0) REVERT: B 395 MET cc_start: 0.8527 (mtm) cc_final: 0.8250 (mtp) REVERT: B 399 MET cc_start: 0.7310 (ttp) cc_final: 0.7054 (ttp) REVERT: A 194 MET cc_start: 0.8359 (mmp) cc_final: 0.7952 (mmp) REVERT: A 269 MET cc_start: 0.7102 (mtm) cc_final: 0.6819 (mtp) REVERT: A 286 MET cc_start: 0.7002 (mtt) cc_final: 0.6524 (mtp) REVERT: A 310 ASN cc_start: 0.9398 (t0) cc_final: 0.9000 (t0) REVERT: A 399 MET cc_start: 0.7646 (ttp) cc_final: 0.7362 (ttp) REVERT: C 217 MET cc_start: 0.7178 (mmt) cc_final: 0.6951 (mmt) REVERT: C 269 MET cc_start: 0.7273 (mtm) cc_final: 0.6993 (mtp) REVERT: C 399 MET cc_start: 0.7319 (ttp) cc_final: 0.6989 (ttp) outliers start: 3 outliers final: 0 residues processed: 81 average time/residue: 0.0695 time to fit residues: 9.1379 Evaluate side-chains 74 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 GLN B 132 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 14 GLN A 132 HIS ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN C 132 HIS C 318 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.137747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.104920 restraints weight = 11155.547| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.22 r_work: 0.2860 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9618 Z= 0.151 Angle : 0.562 7.871 13083 Z= 0.290 Chirality : 0.037 0.118 1620 Planarity : 0.006 0.057 1605 Dihedral : 10.454 90.101 1410 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.03 % Allowed : 10.60 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.22), residues: 1242 helix: -0.32 (0.16), residues: 1017 sheet: None (None), residues: 0 loop : -1.83 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 5 TYR 0.008 0.001 TYR C 299 PHE 0.008 0.001 PHE A 50 HIS 0.006 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 9618) covalent geometry : angle 0.56193 / 0.29 (13083) hydrogen bonds : bond 0.04618 / 3.14 ( 694) hydrogen bonds : angle 4.65534 / 3.24 ( 2082) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.361 Fit side-chains REVERT: B 59 MET cc_start: 0.8373 (mmm) cc_final: 0.8105 (mmp) REVERT: B 66 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7658 (mp) REVERT: B 194 MET cc_start: 0.8515 (mmp) cc_final: 0.8098 (mmp) REVERT: B 269 MET cc_start: 0.7169 (mtm) cc_final: 0.6881 (mtp) REVERT: B 310 ASN cc_start: 0.9217 (t0) cc_final: 0.8807 (t0) REVERT: B 395 MET cc_start: 0.8486 (mtm) cc_final: 0.8236 (mtp) REVERT: A 310 ASN cc_start: 0.9231 (t0) cc_final: 0.8873 (t0) REVERT: A 399 MET cc_start: 0.7561 (ttp) cc_final: 0.7006 (ttp) REVERT: C 269 MET cc_start: 0.7185 (mtm) cc_final: 0.6781 (mtp) REVERT: C 311 MET cc_start: 0.8904 (mmt) cc_final: 0.8371 (mmt) REVERT: C 399 MET cc_start: 0.7357 (ttp) cc_final: 0.7092 (ttp) outliers start: 10 outliers final: 7 residues processed: 89 average time/residue: 0.0674 time to fit residues: 9.6933 Evaluate side-chains 87 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 392 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 94 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 318 GLN A 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.133606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.100593 restraints weight = 11248.321| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.16 r_work: 0.2848 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9618 Z= 0.188 Angle : 0.594 7.714 13083 Z= 0.303 Chirality : 0.039 0.125 1620 Planarity : 0.005 0.056 1605 Dihedral : 10.273 94.033 1410 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.34 % Allowed : 12.55 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.23), residues: 1242 helix: 0.23 (0.16), residues: 1026 sheet: None (None), residues: 0 loop : -1.62 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 276 TYR 0.006 0.001 TYR A 236 PHE 0.008 0.001 PHE C 50 HIS 0.006 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 ( 9618) covalent geometry : angle 0.59366 / 0.30 (13083) hydrogen bonds : bond 0.05010 / 3.39 ( 694) hydrogen bonds : angle 4.66058 / 3.26 ( 2082) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.317 Fit side-chains REVERT: B 194 MET cc_start: 0.8461 (mmp) cc_final: 0.8039 (mmp) REVERT: B 269 MET cc_start: 0.7408 (mtm) cc_final: 0.7092 (mtp) REVERT: B 292 MET cc_start: 0.7511 (ttm) cc_final: 0.7303 (mtp) REVERT: B 310 ASN cc_start: 0.9329 (t0) cc_final: 0.9093 (t0) REVERT: B 395 MET cc_start: 0.8541 (mtm) cc_final: 0.8313 (mtp) REVERT: A 269 MET cc_start: 0.7547 (mtm) cc_final: 0.6943 (mtp) REVERT: A 310 ASN cc_start: 0.9314 (t0) cc_final: 0.9075 (t0) REVERT: A 399 MET cc_start: 0.7580 (ttp) cc_final: 0.7245 (ttp) REVERT: C 120 GLN cc_start: 0.7560 (pm20) cc_final: 0.7218 (pm20) REVERT: C 311 MET cc_start: 0.8929 (mmt) cc_final: 0.8410 (mmt) REVERT: C 399 MET cc_start: 0.7499 (ttp) cc_final: 0.7033 (ttp) outliers start: 13 outliers final: 9 residues processed: 91 average time/residue: 0.0750 time to fit residues: 10.8423 Evaluate side-chains 92 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 392 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 116 optimal weight: 0.6980 chunk 73 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.137390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.105027 restraints weight = 11254.711| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.06 r_work: 0.2857 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9618 Z= 0.131 Angle : 0.533 7.725 13083 Z= 0.270 Chirality : 0.037 0.122 1620 Planarity : 0.005 0.054 1605 Dihedral : 9.326 90.863 1410 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.85 % Allowed : 12.86 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.24), residues: 1242 helix: 0.65 (0.17), residues: 1026 sheet: None (None), residues: 0 loop : -1.24 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 77 TYR 0.006 0.001 TYR A 236 PHE 0.006 0.001 PHE C 50 HIS 0.005 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 9618) covalent geometry : angle 0.53288 / 0.27 (13083) hydrogen bonds : bond 0.04161 / 2.83 ( 694) hydrogen bonds : angle 4.42934 / 3.09 ( 2082) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.315 Fit side-chains REVERT: B 269 MET cc_start: 0.7475 (mtm) cc_final: 0.7066 (mtp) REVERT: B 310 ASN cc_start: 0.9302 (t0) cc_final: 0.8962 (t0) REVERT: B 395 MET cc_start: 0.8402 (mtm) cc_final: 0.8185 (mtp) REVERT: B 399 MET cc_start: 0.7768 (ttp) cc_final: 0.7486 (ttp) REVERT: A 269 MET cc_start: 0.7595 (mtm) cc_final: 0.7038 (mtp) REVERT: A 399 MET cc_start: 0.7737 (ttp) cc_final: 0.7406 (ttp) REVERT: C 269 MET cc_start: 0.7520 (mtm) cc_final: 0.6918 (mtp) REVERT: C 311 MET cc_start: 0.9052 (mmt) cc_final: 0.8642 (mmt) outliers start: 18 outliers final: 12 residues processed: 94 average time/residue: 0.0729 time to fit residues: 10.7853 Evaluate side-chains 91 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 299 TYR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 392 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 90 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 120 optimal weight: 0.2980 chunk 43 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 98 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 338 GLN A 338 GLN C 338 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.138146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.106202 restraints weight = 11132.460| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.05 r_work: 0.2893 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9618 Z= 0.116 Angle : 0.515 7.768 13083 Z= 0.260 Chirality : 0.037 0.119 1620 Planarity : 0.005 0.054 1605 Dihedral : 8.768 87.261 1410 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.26 % Allowed : 13.07 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.24), residues: 1242 helix: 0.94 (0.17), residues: 1029 sheet: None (None), residues: 0 loop : -0.87 (0.37), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 77 TYR 0.005 0.001 TYR A 236 PHE 0.005 0.001 PHE C 50 HIS 0.004 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 9618) covalent geometry : angle 0.51543 / 0.26 (13083) hydrogen bonds : bond 0.03845 / 2.61 ( 694) hydrogen bonds : angle 4.29937 / 3.00 ( 2082) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.211 Fit side-chains REVERT: B 269 MET cc_start: 0.7458 (mtm) cc_final: 0.7099 (mtp) REVERT: B 310 ASN cc_start: 0.9300 (t0) cc_final: 0.8945 (t0) REVERT: B 395 MET cc_start: 0.8633 (mtm) cc_final: 0.8404 (mtp) REVERT: A 57 LEU cc_start: 0.8545 (mt) cc_final: 0.8321 (mt) REVERT: A 269 MET cc_start: 0.7758 (mtm) cc_final: 0.7285 (mtp) REVERT: C 269 MET cc_start: 0.7598 (mtm) cc_final: 0.7121 (mtp) REVERT: C 311 MET cc_start: 0.8909 (mmt) cc_final: 0.8523 (mmt) outliers start: 22 outliers final: 16 residues processed: 106 average time/residue: 0.0720 time to fit residues: 12.0778 Evaluate side-chains 105 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 TYR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 299 TYR Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 392 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 45 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 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 = 0.3440 r_free = 0.3440 target = 0.137577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.105561 restraints weight = 11194.487| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.03 r_work: 0.2860 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9618 Z= 0.133 Angle : 0.529 7.718 13083 Z= 0.268 Chirality : 0.037 0.121 1620 Planarity : 0.005 0.054 1605 Dihedral : 8.736 86.155 1410 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.57 % Allowed : 13.48 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.24), residues: 1242 helix: 1.07 (0.16), residues: 1029 sheet: None (None), residues: 0 loop : -0.77 (0.38), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 397 TYR 0.009 0.001 TYR B 254 PHE 0.006 0.001 PHE C 50 HIS 0.005 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 9618) covalent geometry : angle 0.52863 / 0.27 (13083) hydrogen bonds : bond 0.04129 / 2.80 ( 694) hydrogen bonds : angle 4.33612 / 3.02 ( 2082) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.326 Fit side-chains REVERT: B 269 MET cc_start: 0.7443 (mtm) cc_final: 0.7122 (mtp) REVERT: B 310 ASN cc_start: 0.9319 (t0) cc_final: 0.8977 (t0) REVERT: B 395 MET cc_start: 0.8433 (mtm) cc_final: 0.8214 (mtp) REVERT: A 269 MET cc_start: 0.7690 (mtm) cc_final: 0.7270 (mtp) REVERT: C 311 MET cc_start: 0.9048 (mmt) cc_final: 0.8640 (mmt) outliers start: 25 outliers final: 19 residues processed: 100 average time/residue: 0.0727 time to fit residues: 11.5332 Evaluate side-chains 101 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 299 TYR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 299 TYR Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 392 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 38 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 6 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.137062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.105220 restraints weight = 11142.170| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.03 r_work: 0.2886 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9618 Z= 0.123 Angle : 0.519 7.746 13083 Z= 0.262 Chirality : 0.037 0.121 1620 Planarity : 0.005 0.054 1605 Dihedral : 8.548 84.812 1410 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.67 % Allowed : 13.79 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.24), residues: 1242 helix: 1.21 (0.16), residues: 1032 sheet: None (None), residues: 0 loop : -0.51 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 77 TYR 0.006 0.001 TYR B 254 PHE 0.005 0.001 PHE C 50 HIS 0.005 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 9618) covalent geometry : angle 0.51928 / 0.26 (13083) hydrogen bonds : bond 0.03933 / 2.67 ( 694) hydrogen bonds : angle 4.28475 / 2.99 ( 2082) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.330 Fit side-chains REVERT: B 310 ASN cc_start: 0.9306 (t0) cc_final: 0.8948 (t0) REVERT: B 395 MET cc_start: 0.8595 (mtm) cc_final: 0.8385 (mtp) REVERT: A 269 MET cc_start: 0.7764 (mtm) cc_final: 0.7349 (mtp) REVERT: C 311 MET cc_start: 0.8920 (mmt) cc_final: 0.8533 (mmt) outliers start: 26 outliers final: 21 residues processed: 100 average time/residue: 0.0739 time to fit residues: 11.7364 Evaluate side-chains 104 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 299 TYR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 299 TYR Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 392 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 91 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.137362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.104656 restraints weight = 11133.438| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.18 r_work: 0.2874 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9618 Z= 0.123 Angle : 0.527 7.894 13083 Z= 0.265 Chirality : 0.037 0.120 1620 Planarity : 0.005 0.054 1605 Dihedral : 8.461 83.901 1410 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.78 % Allowed : 13.89 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.24), residues: 1242 helix: 1.36 (0.16), residues: 1029 sheet: None (None), residues: 0 loop : -0.52 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 77 TYR 0.006 0.001 TYR B 254 PHE 0.005 0.001 PHE C 50 HIS 0.005 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 9618) covalent geometry : angle 0.52658 / 0.26 (13083) hydrogen bonds : bond 0.03933 / 2.67 ( 694) hydrogen bonds : angle 4.28096 / 2.98 ( 2082) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.288 Fit side-chains REVERT: B 310 ASN cc_start: 0.9281 (t0) cc_final: 0.8873 (t0) REVERT: B 311 MET cc_start: 0.8882 (mmt) cc_final: 0.7835 (mmt) REVERT: B 395 MET cc_start: 0.8480 (mtm) cc_final: 0.8260 (mtp) REVERT: A 269 MET cc_start: 0.7414 (mtm) cc_final: 0.7012 (mtp) REVERT: C 311 MET cc_start: 0.8923 (mmt) cc_final: 0.8507 (mmt) outliers start: 27 outliers final: 25 residues processed: 97 average time/residue: 0.0705 time to fit residues: 10.8369 Evaluate side-chains 106 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 299 TYR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 299 TYR Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 392 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 33 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 310 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.137255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.104537 restraints weight = 11140.937| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.17 r_work: 0.2861 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9618 Z= 0.129 Angle : 0.532 7.873 13083 Z= 0.268 Chirality : 0.038 0.121 1620 Planarity : 0.005 0.054 1605 Dihedral : 8.492 87.121 1410 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.88 % Allowed : 14.20 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.57 (0.24), residues: 1242 helix: 1.37 (0.16), residues: 1032 sheet: None (None), residues: 0 loop : -0.35 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 77 TYR 0.010 0.001 TYR C 89 PHE 0.005 0.001 PHE C 50 HIS 0.005 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 9618) covalent geometry : angle 0.53238 / 0.27 (13083) hydrogen bonds : bond 0.03998 / 2.72 ( 694) hydrogen bonds : angle 4.29092 / 2.99 ( 2082) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.329 Fit side-chains REVERT: B 310 ASN cc_start: 0.9287 (t0) cc_final: 0.8878 (t0) REVERT: B 311 MET cc_start: 0.8863 (mmt) cc_final: 0.7814 (mmt) REVERT: B 395 MET cc_start: 0.8437 (mtm) cc_final: 0.8214 (mtp) REVERT: A 269 MET cc_start: 0.7377 (mtm) cc_final: 0.6989 (mtp) REVERT: C 311 MET cc_start: 0.8669 (mmt) cc_final: 0.7838 (mmt) outliers start: 28 outliers final: 25 residues processed: 105 average time/residue: 0.0731 time to fit residues: 12.1103 Evaluate side-chains 113 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 299 TYR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 299 TYR Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 392 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.136128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.103426 restraints weight = 11132.541| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.18 r_work: 0.2837 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9618 Z= 0.140 Angle : 0.547 7.737 13083 Z= 0.275 Chirality : 0.038 0.134 1620 Planarity : 0.005 0.055 1605 Dihedral : 8.329 84.194 1410 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.57 % Allowed : 14.71 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.24), residues: 1242 helix: 1.34 (0.16), residues: 1032 sheet: None (None), residues: 0 loop : -0.61 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 397 TYR 0.016 0.001 TYR C 89 PHE 0.005 0.001 PHE C 50 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 9618) covalent geometry : angle 0.54670 / 0.28 (13083) hydrogen bonds : bond 0.04161 / 2.83 ( 694) hydrogen bonds : angle 4.33399 / 3.02 ( 2082) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.349 Fit side-chains REVERT: B 310 ASN cc_start: 0.9301 (t0) cc_final: 0.8914 (t0) REVERT: B 395 MET cc_start: 0.8451 (mtm) cc_final: 0.8239 (mtp) REVERT: A 269 MET cc_start: 0.7428 (mtm) cc_final: 0.7019 (mtp) REVERT: C 311 MET cc_start: 0.8361 (mmt) cc_final: 0.7412 (mmt) outliers start: 25 outliers final: 24 residues processed: 101 average time/residue: 0.0706 time to fit residues: 11.2840 Evaluate side-chains 111 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 299 TYR Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 392 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 66 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 310 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.137115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.104327 restraints weight = 10974.219| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.16 r_work: 0.2867 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9618 Z= 0.129 Angle : 0.540 7.764 13083 Z= 0.271 Chirality : 0.038 0.122 1620 Planarity : 0.005 0.055 1605 Dihedral : 8.178 83.609 1410 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.78 % Allowed : 14.81 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.24), residues: 1242 helix: 1.37 (0.16), residues: 1035 sheet: None (None), residues: 0 loop : -0.44 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 397 TYR 0.014 0.001 TYR C 89 PHE 0.005 0.001 PHE C 50 HIS 0.005 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 9618) covalent geometry : angle 0.53961 / 0.27 (13083) hydrogen bonds : bond 0.03992 / 2.71 ( 694) hydrogen bonds : angle 4.29701 / 2.99 ( 2082) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1790.24 seconds wall clock time: 31 minutes 37.24 seconds (1897.24 seconds total)