Starting phenix.real_space_refine on Wed Mar 4 01:03:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x16_21990/03_2026/6x16_21990.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x16_21990/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6x16_21990/03_2026/6x16_21990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x16_21990/03_2026/6x16_21990.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x16_21990/03_2026/6x16_21990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x16_21990/03_2026/6x16_21990.map" } 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-dev-5986/lib/python3.9/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: 2.34, per 1000 atoms: 0.25 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: 0.77 Conformation dependent library (CDL) restraints added in 373.6 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: 0.26 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: 1.49 Time building geometry restraints manager: 1.05 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 - 21.70: 5222 21.70 - 43.39: 409 43.39 - 65.08: 45 65.08 - 86.78: 24 86.78 - 108.47: 3 Dihedral angle restraints: 5703 sinusoidal: 2166 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 5700 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: 0.02 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.910 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 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 : 15.988 108.475 3465 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 covalent geometry : bond 0.00634 ( 9618) covalent geometry : angle 0.99399 (13083) hydrogen bonds : bond 0.12664 ( 694) hydrogen bonds : angle 6.30759 ( 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 : 0.263 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: 0.0667 time to fit residues: 8.7722 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 : 0.322 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3437 r_free = 0.3437 target = 0.137718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.104639 restraints weight = 11168.383| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.23 r_work: 0.2861 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9618 Z= 0.150 Angle : 0.569 7.954 13083 Z= 0.292 Chirality : 0.037 0.121 1620 Planarity : 0.006 0.057 1605 Dihedral : 12.879 98.583 1488 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % 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: -1.09 (0.22), residues: 1242 helix: -0.34 (0.16), residues: 1017 sheet: None (None), residues: 0 loop : -1.86 (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 0.007 0.001 PHE A 50 HIS 0.006 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9618) covalent geometry : angle 0.56899 (13083) hydrogen bonds : bond 0.04630 ( 694) hydrogen bonds : angle 4.66131 ( 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 92 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.313 Fit side-chains REVERT: B 59 MET cc_start: 0.8344 (mmm) cc_final: 0.8094 (mmp) REVERT: B 66 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7659 (mp) REVERT: B 269 MET cc_start: 0.7163 (mtm) cc_final: 0.6880 (mtp) REVERT: B 310 ASN cc_start: 0.9222 (t0) cc_final: 0.8811 (t0) REVERT: B 395 MET cc_start: 0.8490 (mtm) cc_final: 0.8241 (mtp) REVERT: A 310 ASN cc_start: 0.9249 (t0) cc_final: 0.8891 (t0) REVERT: A 399 MET cc_start: 0.7593 (ttp) cc_final: 0.7020 (ttp) REVERT: C 269 MET cc_start: 0.7176 (mtm) cc_final: 0.6780 (mtp) REVERT: C 311 MET cc_start: 0.8940 (mmt) cc_final: 0.8444 (mmt) REVERT: C 399 MET cc_start: 0.7374 (ttp) cc_final: 0.7098 (ttp) outliers start: 10 outliers final: 7 residues processed: 87 average time/residue: 0.0669 time to fit residues: 9.3684 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 : 0.225 ------------------------------------------------------------------------------- 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: 0.9980 chunk 93 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 120 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3405 r_free = 0.3405 target = 0.134917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.102009 restraints weight = 11237.470| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.16 r_work: 0.2860 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9618 Z= 0.164 Angle : 0.571 7.712 13083 Z= 0.290 Chirality : 0.038 0.123 1620 Planarity : 0.005 0.056 1605 Dihedral : 12.032 98.594 1488 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.13 % Allowed : 12.86 % Favored : 86.01 % 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: -0.17 (0.23), residues: 1242 helix: 0.30 (0.16), residues: 1023 sheet: None (None), residues: 0 loop : -1.59 (0.36), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 397 TYR 0.006 0.001 TYR A 299 PHE 0.007 0.001 PHE C 50 HIS 0.006 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 9618) covalent geometry : angle 0.57144 (13083) hydrogen bonds : bond 0.04685 ( 694) hydrogen bonds : angle 4.57650 ( 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 96 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.324 Fit side-chains REVERT: B 269 MET cc_start: 0.7346 (mtm) cc_final: 0.7024 (mtp) REVERT: B 310 ASN cc_start: 0.9288 (t0) cc_final: 0.8903 (t0) REVERT: B 395 MET cc_start: 0.8540 (mtm) cc_final: 0.8316 (mtp) REVERT: A 269 MET cc_start: 0.7411 (mtm) cc_final: 0.6867 (mtp) REVERT: A 310 ASN cc_start: 0.9279 (t0) cc_final: 0.8922 (t0) REVERT: A 399 MET cc_start: 0.7607 (ttp) cc_final: 0.7256 (ttp) REVERT: C 311 MET cc_start: 0.8880 (mmt) cc_final: 0.8599 (mmt) REVERT: C 399 MET cc_start: 0.7504 (ttp) cc_final: 0.7017 (ttp) outliers start: 11 outliers final: 9 residues processed: 90 average time/residue: 0.0706 time to fit residues: 10.1147 Evaluate side-chains 91 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 392 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 116 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3393 r_free = 0.3393 target = 0.133933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.101251 restraints weight = 11309.968| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.06 r_work: 0.2814 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9618 Z= 0.178 Angle : 0.584 7.634 13083 Z= 0.296 Chirality : 0.039 0.128 1620 Planarity : 0.005 0.055 1605 Dihedral : 11.525 97.051 1488 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.65 % Allowed : 13.48 % Favored : 84.88 % 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: 0.18 (0.24), residues: 1242 helix: 0.50 (0.16), residues: 1026 sheet: None (None), residues: 0 loop : -1.29 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 397 TYR 0.006 0.001 TYR A 236 PHE 0.008 0.001 PHE C 50 HIS 0.005 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 9618) covalent geometry : angle 0.58441 (13083) hydrogen bonds : bond 0.04802 ( 694) hydrogen bonds : angle 4.59138 ( 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 100 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.333 Fit side-chains REVERT: B 66 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7905 (mp) REVERT: B 310 ASN cc_start: 0.9312 (t0) cc_final: 0.9052 (t0) REVERT: B 311 MET cc_start: 0.9017 (mmt) cc_final: 0.7999 (mmm) REVERT: B 395 MET cc_start: 0.8413 (mtm) cc_final: 0.8205 (mtp) REVERT: B 399 MET cc_start: 0.7845 (ttp) cc_final: 0.7362 (ttp) REVERT: A 269 MET cc_start: 0.7730 (mtm) cc_final: 0.7108 (mtp) REVERT: A 399 MET cc_start: 0.7820 (ttp) cc_final: 0.7518 (ttp) REVERT: C 120 GLN cc_start: 0.7702 (pm20) cc_final: 0.7355 (pm20) REVERT: C 269 MET cc_start: 0.7568 (mtm) cc_final: 0.6938 (mtp) REVERT: C 311 MET cc_start: 0.9011 (mmt) cc_final: 0.8758 (mmt) outliers start: 16 outliers final: 11 residues processed: 93 average time/residue: 0.0691 time to fit residues: 10.2434 Evaluate side-chains 94 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 198 VAL 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 198 VAL 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: 0.9990 chunk 33 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.135670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.103313 restraints weight = 11195.200| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.05 r_work: 0.2857 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9618 Z= 0.140 Angle : 0.542 7.648 13083 Z= 0.274 Chirality : 0.038 0.123 1620 Planarity : 0.005 0.055 1605 Dihedral : 11.048 95.610 1488 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.98 % Allowed : 12.96 % Favored : 84.05 % 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: 0.58 (0.24), residues: 1242 helix: 0.74 (0.16), residues: 1029 sheet: None (None), residues: 0 loop : -0.94 (0.38), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 77 TYR 0.006 0.001 TYR A 236 PHE 0.006 0.001 PHE C 50 HIS 0.005 0.001 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9618) covalent geometry : angle 0.54185 (13083) hydrogen bonds : bond 0.04256 ( 694) hydrogen bonds : angle 4.43651 ( 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 115 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.272 Fit side-chains REVERT: B 269 MET cc_start: 0.7601 (mtm) cc_final: 0.7174 (mtp) REVERT: B 310 ASN cc_start: 0.9256 (t0) cc_final: 0.8913 (t0) REVERT: B 399 MET cc_start: 0.7744 (ttp) cc_final: 0.7433 (ttp) REVERT: A 269 MET cc_start: 0.7627 (mtm) cc_final: 0.7124 (mtp) REVERT: C 120 GLN cc_start: 0.7602 (pm20) cc_final: 0.7305 (pm20) REVERT: C 311 MET cc_start: 0.8833 (mmt) cc_final: 0.8280 (mmt) outliers start: 29 outliers final: 20 residues processed: 105 average time/residue: 0.0702 time to fit residues: 11.6621 Evaluate side-chains 104 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 245 LEU 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 329 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 72 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 374 LEU 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: 2.9990 chunk 77 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 0.0370 chunk 114 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.136971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.105028 restraints weight = 11247.848| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.01 r_work: 0.2847 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9618 Z= 0.145 Angle : 0.543 7.635 13083 Z= 0.275 Chirality : 0.038 0.123 1620 Planarity : 0.005 0.055 1605 Dihedral : 10.627 94.867 1488 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.19 % Allowed : 13.27 % 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: 0.82 (0.24), residues: 1242 helix: 0.87 (0.16), residues: 1032 sheet: None (None), residues: 0 loop : -0.65 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 397 TYR 0.006 0.001 TYR A 236 PHE 0.006 0.001 PHE C 50 HIS 0.005 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9618) covalent geometry : angle 0.54335 (13083) hydrogen bonds : bond 0.04319 ( 694) hydrogen bonds : angle 4.42594 ( 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 123 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.313 Fit side-chains REVERT: B 269 MET cc_start: 0.7674 (mtm) cc_final: 0.7229 (mtp) REVERT: B 292 MET cc_start: 0.7284 (ttp) cc_final: 0.6951 (ttm) REVERT: B 310 ASN cc_start: 0.9276 (t0) cc_final: 0.8929 (t0) REVERT: B 399 MET cc_start: 0.7876 (ttp) cc_final: 0.7545 (ttp) REVERT: A 269 MET cc_start: 0.7659 (mtm) cc_final: 0.7227 (mtp) REVERT: C 120 GLN cc_start: 0.7679 (pm20) cc_final: 0.7390 (pm20) REVERT: C 311 MET cc_start: 0.8943 (mmt) cc_final: 0.8237 (mmt) outliers start: 31 outliers final: 23 residues processed: 111 average time/residue: 0.0688 time to fit residues: 12.0157 Evaluate side-chains 113 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 198 VAL Chi-restraints excluded: chain B residue 245 LEU 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 169 MET 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 198 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 94 optimal weight: 0.0980 chunk 11 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 HIS C 310 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.138608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.106553 restraints weight = 11142.180| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.07 r_work: 0.2901 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9618 Z= 0.112 Angle : 0.513 7.714 13083 Z= 0.258 Chirality : 0.037 0.118 1620 Planarity : 0.005 0.055 1605 Dihedral : 10.014 93.089 1488 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.98 % Allowed : 14.30 % 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: 1.21 (0.24), residues: 1242 helix: 1.20 (0.17), residues: 1026 sheet: None (None), residues: 0 loop : -0.85 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 77 TYR 0.009 0.001 TYR B 254 PHE 0.005 0.001 PHE A 210 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9618) covalent geometry : angle 0.51310 (13083) hydrogen bonds : bond 0.03722 ( 694) hydrogen bonds : angle 4.24026 ( 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 119 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 0.254 Fit side-chains REVERT: B 202 MET cc_start: 0.7969 (mmm) cc_final: 0.7659 (mmm) REVERT: B 269 MET cc_start: 0.7544 (mtm) cc_final: 0.7173 (mtp) REVERT: B 310 ASN cc_start: 0.9256 (t0) cc_final: 0.8883 (t0) REVERT: B 399 MET cc_start: 0.7774 (ttp) cc_final: 0.7422 (ttp) REVERT: A 269 MET cc_start: 0.7625 (mtm) cc_final: 0.7223 (mtp) REVERT: C 311 MET cc_start: 0.8658 (mmt) cc_final: 0.7888 (mmt) outliers start: 29 outliers final: 17 residues processed: 110 average time/residue: 0.0635 time to fit residues: 10.9763 Evaluate side-chains 104 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 132 HIS 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 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 137 ILE 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: 0.9980 chunk 39 optimal weight: 1.9990 chunk 95 optimal weight: 0.0020 chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 113 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 HIS C 310 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.139161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.107262 restraints weight = 11111.436| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.06 r_work: 0.2901 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9618 Z= 0.110 Angle : 0.517 7.709 13083 Z= 0.259 Chirality : 0.037 0.117 1620 Planarity : 0.004 0.054 1605 Dihedral : 9.879 91.000 1488 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.47 % Allowed : 15.02 % Favored : 82.51 % 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: 1.49 (0.24), residues: 1242 helix: 1.36 (0.17), residues: 1029 sheet: None (None), residues: 0 loop : -0.63 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 77 TYR 0.010 0.001 TYR B 254 PHE 0.004 0.001 PHE A 210 HIS 0.004 0.000 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 9618) covalent geometry : angle 0.51715 (13083) hydrogen bonds : bond 0.03657 ( 694) hydrogen bonds : angle 4.19884 ( 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 107 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.275 Fit side-chains REVERT: B 202 MET cc_start: 0.8062 (mmm) cc_final: 0.7701 (mmm) REVERT: B 269 MET cc_start: 0.7542 (mtm) cc_final: 0.7199 (mtp) REVERT: B 310 ASN cc_start: 0.9269 (t0) cc_final: 0.8888 (t0) REVERT: B 311 MET cc_start: 0.8866 (mmt) cc_final: 0.7942 (mmt) REVERT: B 399 MET cc_start: 0.7748 (ttp) cc_final: 0.7445 (ttp) REVERT: A 269 MET cc_start: 0.7671 (mtm) cc_final: 0.7282 (mtp) REVERT: C 311 MET cc_start: 0.8409 (mmt) cc_final: 0.7586 (mmt) outliers start: 24 outliers final: 20 residues processed: 99 average time/residue: 0.0710 time to fit residues: 11.1876 Evaluate side-chains 103 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 0.6980 chunk 110 optimal weight: 0.6980 chunk 37 optimal weight: 0.0370 chunk 48 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.141182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.109329 restraints weight = 11077.649| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.06 r_work: 0.2922 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9618 Z= 0.107 Angle : 0.516 8.036 13083 Z= 0.258 Chirality : 0.037 0.119 1620 Planarity : 0.004 0.054 1605 Dihedral : 9.713 87.965 1488 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.16 % Allowed : 15.43 % 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: 1.72 (0.24), residues: 1242 helix: 1.52 (0.17), residues: 1026 sheet: None (None), residues: 0 loop : -0.53 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 77 TYR 0.008 0.001 TYR B 254 PHE 0.005 0.001 PHE A 210 HIS 0.004 0.000 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 9618) covalent geometry : angle 0.51635 (13083) hydrogen bonds : bond 0.03551 ( 694) hydrogen bonds : angle 4.14035 ( 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 99 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.313 Fit side-chains REVERT: B 57 LEU cc_start: 0.8422 (mt) cc_final: 0.8155 (mt) REVERT: B 202 MET cc_start: 0.8109 (mmm) cc_final: 0.7743 (mmm) REVERT: B 269 MET cc_start: 0.7431 (mtm) cc_final: 0.7064 (mtp) REVERT: B 311 MET cc_start: 0.8970 (mmt) cc_final: 0.8187 (mmt) REVERT: B 399 MET cc_start: 0.7787 (ttp) cc_final: 0.7469 (ttp) REVERT: A 56 MET cc_start: 0.8703 (ttp) cc_final: 0.8375 (ttp) REVERT: A 399 MET cc_start: 0.7979 (ttp) cc_final: 0.7674 (ttp) REVERT: C 311 MET cc_start: 0.8561 (mmt) cc_final: 0.7772 (mmt) outliers start: 21 outliers final: 21 residues processed: 90 average time/residue: 0.0701 time to fit residues: 10.1550 Evaluate side-chains 99 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain B residue 132 HIS 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 169 MET 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: 0.8980 chunk 57 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 115 optimal weight: 0.0470 chunk 24 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.138076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.105772 restraints weight = 11161.568| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.16 r_work: 0.2895 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2342 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= 0.126 Angle : 0.541 8.001 13083 Z= 0.270 Chirality : 0.038 0.120 1620 Planarity : 0.005 0.055 1605 Dihedral : 9.813 86.491 1488 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.37 % Allowed : 15.12 % Favored : 82.51 % 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: 1.62 (0.24), residues: 1242 helix: 1.45 (0.16), residues: 1029 sheet: None (None), residues: 0 loop : -0.55 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 397 TYR 0.008 0.001 TYR B 254 PHE 0.005 0.001 PHE C 50 HIS 0.005 0.001 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9618) covalent geometry : angle 0.54119 (13083) hydrogen bonds : bond 0.03919 ( 694) hydrogen bonds : angle 4.23403 ( 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 104 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.276 Fit side-chains REVERT: B 202 MET cc_start: 0.8050 (mmm) cc_final: 0.7684 (mmm) REVERT: B 269 MET cc_start: 0.7224 (mtm) cc_final: 0.6819 (mtp) REVERT: B 310 ASN cc_start: 0.9278 (t0) cc_final: 0.8883 (t0) REVERT: B 311 MET cc_start: 0.8934 (mmt) cc_final: 0.8069 (mmt) REVERT: B 399 MET cc_start: 0.7701 (ttp) cc_final: 0.7346 (ttp) REVERT: A 56 MET cc_start: 0.8659 (ttp) cc_final: 0.8368 (ttp) REVERT: A 292 MET cc_start: 0.7412 (ttm) cc_final: 0.7178 (ttm) REVERT: A 399 MET cc_start: 0.7981 (ttp) cc_final: 0.7425 (ttp) REVERT: C 311 MET cc_start: 0.8581 (mmt) cc_final: 0.7804 (mmt) outliers start: 23 outliers final: 21 residues processed: 94 average time/residue: 0.0683 time to fit residues: 10.2534 Evaluate side-chains 101 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 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 169 MET 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: 3.9990 chunk 57 optimal weight: 0.9990 chunk 52 optimal weight: 0.1980 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.138687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.106454 restraints weight = 10981.386| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.14 r_work: 0.2950 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2361 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= 0.121 Angle : 0.533 7.841 13083 Z= 0.267 Chirality : 0.037 0.120 1620 Planarity : 0.005 0.055 1605 Dihedral : 9.753 85.590 1488 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.26 % Allowed : 15.43 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.66 (0.24), residues: 1242 helix: 1.46 (0.16), residues: 1032 sheet: None (None), residues: 0 loop : -0.48 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 77 TYR 0.008 0.001 TYR B 254 PHE 0.004 0.001 PHE C 50 HIS 0.004 0.001 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9618) covalent geometry : angle 0.53297 (13083) hydrogen bonds : bond 0.03842 ( 694) hydrogen bonds : angle 4.23085 ( 2082) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1881.80 seconds wall clock time: 32 minutes 58.99 seconds (1978.99 seconds total)