Starting phenix.real_space_refine on Wed Mar 4 03:41:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pmf_13531/03_2026/7pmf_13531.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pmf_13531/03_2026/7pmf_13531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pmf_13531/03_2026/7pmf_13531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pmf_13531/03_2026/7pmf_13531.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pmf_13531/03_2026/7pmf_13531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pmf_13531/03_2026/7pmf_13531.map" } resolution = 3.4 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 3 5.21 5 S 63 5.16 5 C 6443 2.51 5 N 1719 2.21 5 O 1892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 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: 10125 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 739, 6041 Classifications: {'peptide': 739} Link IDs: {'PTRANS': 27, 'TRANS': 711} Chain breaks: 6 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.33, per 1000 atoms: 0.23 Number of scatterers: 10125 At special positions: 0 Unit cell: (105.6, 129.8, 150.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 5 15.00 Mg 3 11.99 O 1892 8.00 N 1719 7.00 C 6443 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 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 557.0 milliseconds 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2366 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 14 sheets defined 55.5% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.394A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 116 through 119 removed outlier: 4.458A pdb=" N TYR A 119 " --> pdb=" O LEU A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.651A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 185 Processing helix chain 'A' and resid 191 through 198 removed outlier: 3.669A pdb=" N LYS A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 207 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 259 through 268 removed outlier: 4.230A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 272 through 278 removed outlier: 4.101A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.882A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 314 removed outlier: 3.564A pdb=" N MET A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 338 removed outlier: 3.521A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 375 removed outlier: 3.767A pdb=" N HIS A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 removed outlier: 4.047A pdb=" N ALA A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 480 Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'A' and resid 504 through 515 removed outlier: 3.604A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 563 through 568 Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.537A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 4.227A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 653 Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.848A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 725 through 736 removed outlier: 3.972A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.544A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.943A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.544A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.804A pdb=" N THR C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.591A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.593A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.743A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.610A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.543A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.364A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 16 removed outlier: 4.085A pdb=" N ALA A 11 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 48 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.534A pdb=" N ILE A 662 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN A 157 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU A 436 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE A 159 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE A 438 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL A 161 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 342 removed outlier: 3.510A pdb=" N ALA A 341 " --> pdb=" O ALA A 349 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 381 Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA8, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.811A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.906A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 removed outlier: 5.988A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 241 513 hydrogen bonds defined for protein. 1440 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: 1.48 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1684 1.31 - 1.44: 2737 1.44 - 1.56: 5806 1.56 - 1.69: 8 1.69 - 1.81: 103 Bond restraints: 10338 Sorted by residual: bond pdb=" O3A ANP A1901 " pdb=" PB ANP A1901 " ideal model delta sigma weight residual 1.700 1.546 0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.446 0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" O5' ANP A1901 " pdb=" PA ANP A1901 " ideal model delta sigma weight residual 1.655 1.577 0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.454 0.071 2.10e-02 2.27e+03 1.13e+01 ... (remaining 10333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 13830 3.66 - 7.33: 122 7.33 - 10.99: 11 10.99 - 14.66: 1 14.66 - 18.32: 1 Bond angle restraints: 13965 Sorted by residual: angle pdb=" PB ANP A1901 " pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 126.95 108.63 18.32 3.00e+00 1.11e-01 3.73e+01 angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 110.98 10.72 1.80e+00 3.09e-01 3.55e+01 angle pdb=" N DTH H 4 " pdb=" CA DTH H 4 " pdb=" CB DTH H 4 " ideal model delta sigma weight residual 111.50 101.72 9.78 1.70e+00 3.46e-01 3.31e+01 angle pdb=" N GLY A 563 " pdb=" CA GLY A 563 " pdb=" C GLY A 563 " ideal model delta sigma weight residual 113.86 122.10 -8.24 1.50e+00 4.44e-01 3.02e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 100.45 9.65 1.90e+00 2.77e-01 2.58e+01 ... (remaining 13960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.14: 6049 28.14 - 56.29: 155 56.29 - 84.43: 42 84.43 - 112.57: 6 112.57 - 140.72: 3 Dihedral angle restraints: 6255 sinusoidal: 2586 harmonic: 3669 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 159.28 140.72 1 2.00e+01 2.50e-03 4.26e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 170.09 129.91 1 2.00e+01 2.50e-03 3.94e+01 dihedral pdb=" CA PHE A 593 " pdb=" C PHE A 593 " pdb=" N GLN A 594 " pdb=" CA GLN A 594 " ideal model delta harmonic sigma weight residual -180.00 -151.03 -28.97 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 6252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1097 0.060 - 0.120: 356 0.120 - 0.180: 63 0.180 - 0.241: 7 0.241 - 0.301: 1 Chirality restraints: 1524 Sorted by residual: chirality pdb=" C3' ANP A1901 " pdb=" C2' ANP A1901 " pdb=" C4' ANP A1901 " pdb=" O3' ANP A1901 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA GLU C 316 " pdb=" N GLU C 316 " pdb=" C GLU C 316 " pdb=" CB GLU C 316 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA PHE A 564 " pdb=" N PHE A 564 " pdb=" C PHE A 564 " pdb=" CB PHE A 564 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1521 not shown) Planarity restraints: 1782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 306 " -0.005 2.00e-02 2.50e+03 5.00e-02 5.01e+01 pdb=" CG TYR C 306 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR C 306 " -0.066 2.00e-02 2.50e+03 pdb=" CD2 TYR C 306 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR C 306 " 0.070 2.00e-02 2.50e+03 pdb=" CE2 TYR C 306 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 306 " 0.072 2.00e-02 2.50e+03 pdb=" OH TYR C 306 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 206 " 0.163 9.50e-02 1.11e+02 9.40e-02 4.69e+01 pdb=" NE ARG C 206 " -0.048 2.00e-02 2.50e+03 pdb=" CZ ARG C 206 " 0.113 2.00e-02 2.50e+03 pdb=" NH1 ARG C 206 " -0.040 2.00e-02 2.50e+03 pdb=" NH2 ARG C 206 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 183 " 0.141 9.50e-02 1.11e+02 8.12e-02 3.51e+01 pdb=" NE ARG C 183 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG C 183 " 0.097 2.00e-02 2.50e+03 pdb=" NH1 ARG C 183 " -0.035 2.00e-02 2.50e+03 pdb=" NH2 ARG C 183 " -0.028 2.00e-02 2.50e+03 ... (remaining 1779 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 18 2.36 - 3.00: 5608 3.00 - 3.63: 14770 3.63 - 4.27: 22588 4.27 - 4.90: 38355 Nonbonded interactions: 81339 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.731 3.620 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 1.916 2.170 nonbonded pdb=" O1A ANP A1901 " pdb="MG MG A1903 " model vdw 1.980 2.170 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 500 " model vdw 2.039 3.040 nonbonded pdb=" O1B ANP A1901 " pdb="MG MG A1903 " model vdw 2.079 2.170 ... (remaining 81334 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.050 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.130 Find NCS groups from input model: 0.140 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 : 0.010 0.154 10340 Z= 0.419 Angle : 1.000 18.321 13971 Z= 0.571 Chirality : 0.059 0.301 1524 Planarity : 0.008 0.094 1780 Dihedral : 15.340 140.715 3883 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.09 % Allowed : 0.00 % Favored : 99.91 % Cbeta Deviations : 0.08 % 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: -1.44 (0.21), residues: 1225 helix: -1.75 (0.16), residues: 602 sheet: 0.15 (0.38), residues: 159 loop : 0.14 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.114 0.012 ARG C 206 TYR 0.074 0.007 TYR C 306 PHE 0.075 0.003 PHE A 564 TRP 0.048 0.005 TRP C 79 HIS 0.014 0.003 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00955 (10338) covalent geometry : angle 0.99642 (13965) hydrogen bonds : bond 0.16220 ( 511) hydrogen bonds : angle 7.10700 ( 1440) link_TRANS : bond 0.01531 ( 2) link_TRANS : angle 4.05156 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 93 average time/residue: 0.1365 time to fit residues: 16.8778 Evaluate side-chains 57 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 430 HIS A 464 GLN A 468 HIS A 474 GLN C 59 GLN C 162 ASN C 280 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.047494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.034214 restraints weight = 56970.720| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 4.01 r_work: 0.2604 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10340 Z= 0.143 Angle : 0.634 7.337 13971 Z= 0.333 Chirality : 0.043 0.212 1524 Planarity : 0.004 0.042 1780 Dihedral : 9.937 120.419 1420 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.28 % Allowed : 3.25 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.23), residues: 1225 helix: 0.49 (0.20), residues: 622 sheet: 0.67 (0.40), residues: 155 loop : 0.62 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 343 TYR 0.012 0.001 TYR A 102 PHE 0.027 0.001 PHE B 12 TRP 0.022 0.002 TRP A 484 HIS 0.007 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00304 (10338) covalent geometry : angle 0.63382 (13965) hydrogen bonds : bond 0.04328 ( 511) hydrogen bonds : angle 4.91233 ( 1440) link_TRANS : bond 0.00225 ( 2) link_TRANS : angle 1.11681 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.3867 (mtt) cc_final: 0.3652 (mtt) REVERT: A 135 MET cc_start: 0.9164 (mmm) cc_final: 0.8949 (mmm) REVERT: C 227 MET cc_start: 0.8093 (mmm) cc_final: 0.7761 (tpp) outliers start: 3 outliers final: 1 residues processed: 70 average time/residue: 0.1004 time to fit residues: 10.1639 Evaluate side-chains 60 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 78 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.047230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.033900 restraints weight = 58250.912| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 4.06 r_work: 0.2601 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10340 Z= 0.135 Angle : 0.561 7.999 13971 Z= 0.289 Chirality : 0.041 0.173 1524 Planarity : 0.003 0.031 1780 Dihedral : 8.703 121.591 1419 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.28 % Allowed : 4.27 % Favored : 95.45 % 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: 1.46 (0.24), residues: 1225 helix: 1.32 (0.21), residues: 618 sheet: 0.73 (0.40), residues: 162 loop : 0.79 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 343 TYR 0.011 0.001 TYR A 79 PHE 0.018 0.001 PHE B 12 TRP 0.023 0.001 TRP A 484 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00296 (10338) covalent geometry : angle 0.56105 (13965) hydrogen bonds : bond 0.03808 ( 511) hydrogen bonds : angle 4.55568 ( 1440) link_TRANS : bond 0.00225 ( 2) link_TRANS : angle 0.83416 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.9212 (tpp) cc_final: 0.8783 (mmt) REVERT: A 132 MET cc_start: 0.8392 (ttp) cc_final: 0.8038 (tmm) REVERT: A 135 MET cc_start: 0.9124 (mmm) cc_final: 0.8913 (mmm) REVERT: A 305 MET cc_start: 0.9141 (tpp) cc_final: 0.8638 (tmm) REVERT: A 478 MET cc_start: 0.8927 (mmp) cc_final: 0.8198 (mmp) REVERT: A 484 TRP cc_start: 0.7500 (m-90) cc_final: 0.7165 (m-90) REVERT: C 57 GLU cc_start: 0.8959 (mp0) cc_final: 0.8710 (mp0) REVERT: C 176 MET cc_start: 0.9353 (mmm) cc_final: 0.9025 (mmt) REVERT: C 205 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8314 (mt-10) REVERT: C 227 MET cc_start: 0.8175 (mmm) cc_final: 0.7793 (tpp) outliers start: 3 outliers final: 2 residues processed: 69 average time/residue: 0.0992 time to fit residues: 9.8566 Evaluate side-chains 60 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 51 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.046687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.033420 restraints weight = 58564.866| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 4.06 r_work: 0.2586 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10340 Z= 0.160 Angle : 0.542 7.761 13971 Z= 0.276 Chirality : 0.041 0.169 1524 Planarity : 0.003 0.029 1780 Dihedral : 8.190 123.582 1419 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.46 % Allowed : 4.64 % Favored : 94.89 % 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: 1.75 (0.24), residues: 1225 helix: 1.70 (0.22), residues: 619 sheet: 0.77 (0.40), residues: 160 loop : 0.71 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 21 TYR 0.010 0.001 TYR A 79 PHE 0.013 0.001 PHE C 255 TRP 0.013 0.001 TRP A 484 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00354 (10338) covalent geometry : angle 0.54153 (13965) hydrogen bonds : bond 0.03665 ( 511) hydrogen bonds : angle 4.35339 ( 1440) link_TRANS : bond 0.00200 ( 2) link_TRANS : angle 0.86294 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.9223 (tpp) cc_final: 0.8727 (mmp) REVERT: B 120 MET cc_start: 0.4399 (mtt) cc_final: 0.3940 (mmt) REVERT: A 305 MET cc_start: 0.9222 (tpp) cc_final: 0.8940 (tpp) REVERT: A 467 MET cc_start: 0.9214 (mmm) cc_final: 0.8926 (mmm) REVERT: A 478 MET cc_start: 0.9031 (mmp) cc_final: 0.8596 (mmp) REVERT: A 484 TRP cc_start: 0.7582 (m-90) cc_final: 0.7278 (m-90) REVERT: C 57 GLU cc_start: 0.9072 (mp0) cc_final: 0.8857 (mp0) REVERT: C 100 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8676 (tm-30) REVERT: C 176 MET cc_start: 0.9410 (mmm) cc_final: 0.9094 (mmt) REVERT: C 227 MET cc_start: 0.8263 (mmm) cc_final: 0.7796 (tpp) REVERT: C 269 MET cc_start: 0.9002 (mtm) cc_final: 0.8736 (mtm) outliers start: 5 outliers final: 3 residues processed: 63 average time/residue: 0.0985 time to fit residues: 9.1210 Evaluate side-chains 59 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.046281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.032878 restraints weight = 59210.053| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 4.07 r_work: 0.2560 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10340 Z= 0.201 Angle : 0.555 7.623 13971 Z= 0.283 Chirality : 0.041 0.167 1524 Planarity : 0.003 0.029 1780 Dihedral : 7.984 128.162 1419 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.65 % Allowed : 4.83 % Favored : 94.52 % 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: 1.84 (0.25), residues: 1225 helix: 1.88 (0.22), residues: 617 sheet: 0.65 (0.41), residues: 154 loop : 0.66 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 177 TYR 0.010 0.001 TYR A 242 PHE 0.013 0.001 PHE C 255 TRP 0.011 0.001 TRP C 79 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00445 (10338) covalent geometry : angle 0.55534 (13965) hydrogen bonds : bond 0.03720 ( 511) hydrogen bonds : angle 4.35252 ( 1440) link_TRANS : bond 0.00200 ( 2) link_TRANS : angle 0.81596 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: B 105 MET cc_start: 0.9242 (tpp) cc_final: 0.8708 (mmp) REVERT: B 120 MET cc_start: 0.4469 (mtt) cc_final: 0.3940 (mmt) REVERT: A 132 MET cc_start: 0.8053 (ttp) cc_final: 0.7805 (tmm) REVERT: A 135 MET cc_start: 0.8957 (mmm) cc_final: 0.8711 (mmt) REVERT: A 305 MET cc_start: 0.9277 (tpp) cc_final: 0.9042 (tpp) REVERT: A 478 MET cc_start: 0.9117 (mmp) cc_final: 0.8846 (mmp) REVERT: A 484 TRP cc_start: 0.7693 (m-90) cc_final: 0.7181 (m-10) REVERT: C 57 GLU cc_start: 0.9098 (mp0) cc_final: 0.8888 (mp0) REVERT: C 100 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8664 (tm-30) REVERT: C 176 MET cc_start: 0.9434 (mmm) cc_final: 0.9130 (mmt) REVERT: C 227 MET cc_start: 0.8398 (mmm) cc_final: 0.7887 (tpp) outliers start: 7 outliers final: 6 residues processed: 60 average time/residue: 0.0926 time to fit residues: 8.4901 Evaluate side-chains 60 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 76 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.045912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.032575 restraints weight = 59861.123| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 4.07 r_work: 0.2547 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10340 Z= 0.222 Angle : 0.566 6.929 13971 Z= 0.288 Chirality : 0.042 0.169 1524 Planarity : 0.004 0.052 1780 Dihedral : 7.688 129.878 1419 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.65 % Allowed : 5.11 % Favored : 94.24 % 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: 1.87 (0.25), residues: 1225 helix: 1.95 (0.22), residues: 617 sheet: 0.67 (0.41), residues: 154 loop : 0.61 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 41 TYR 0.010 0.001 TYR A 242 PHE 0.013 0.001 PHE C 255 TRP 0.010 0.001 TRP C 79 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00490 (10338) covalent geometry : angle 0.56593 (13965) hydrogen bonds : bond 0.03731 ( 511) hydrogen bonds : angle 4.35785 ( 1440) link_TRANS : bond 0.00221 ( 2) link_TRANS : angle 0.81054 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: B 36 MET cc_start: 0.9428 (mmt) cc_final: 0.9175 (mmm) REVERT: B 105 MET cc_start: 0.9250 (tpp) cc_final: 0.8697 (mmp) REVERT: B 120 MET cc_start: 0.4545 (mtt) cc_final: 0.4074 (mmt) REVERT: B 140 ASN cc_start: 0.9553 (p0) cc_final: 0.9317 (t0) REVERT: A 135 MET cc_start: 0.8995 (mmm) cc_final: 0.8782 (mmt) REVERT: A 305 MET cc_start: 0.9322 (tpp) cc_final: 0.8827 (tpp) REVERT: A 478 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8173 (mmp) REVERT: A 484 TRP cc_start: 0.7721 (m-90) cc_final: 0.7039 (m-90) REVERT: C 57 GLU cc_start: 0.9165 (mp0) cc_final: 0.8912 (mp0) REVERT: C 100 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8677 (tm-30) REVERT: C 176 MET cc_start: 0.9425 (mmm) cc_final: 0.8840 (mpp) REVERT: C 227 MET cc_start: 0.8454 (mmm) cc_final: 0.7943 (tpp) outliers start: 7 outliers final: 6 residues processed: 59 average time/residue: 0.0839 time to fit residues: 7.6352 Evaluate side-chains 60 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 19 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 120 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.046823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.033526 restraints weight = 58603.159| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 4.09 r_work: 0.2587 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10340 Z= 0.108 Angle : 0.510 7.408 13971 Z= 0.255 Chirality : 0.040 0.164 1524 Planarity : 0.003 0.031 1780 Dihedral : 7.218 128.625 1419 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.46 % Allowed : 5.76 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.25), residues: 1225 helix: 2.14 (0.22), residues: 609 sheet: 0.63 (0.41), residues: 157 loop : 0.64 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 41 TYR 0.008 0.001 TYR A 79 PHE 0.010 0.001 PHE C 255 TRP 0.012 0.001 TRP C 340 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00237 (10338) covalent geometry : angle 0.50976 (13965) hydrogen bonds : bond 0.03265 ( 511) hydrogen bonds : angle 4.20411 ( 1440) link_TRANS : bond 0.00225 ( 2) link_TRANS : angle 0.95016 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.313 Fit side-chains REVERT: B 36 MET cc_start: 0.9433 (mmt) cc_final: 0.9171 (mmm) REVERT: B 105 MET cc_start: 0.9245 (tpp) cc_final: 0.8667 (mmp) REVERT: B 120 MET cc_start: 0.4898 (mtt) cc_final: 0.4534 (mmt) REVERT: B 140 ASN cc_start: 0.9583 (p0) cc_final: 0.9292 (t0) REVERT: A 305 MET cc_start: 0.9289 (tpp) cc_final: 0.8840 (tpp) REVERT: A 478 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8172 (mmp) REVERT: A 484 TRP cc_start: 0.7778 (m-90) cc_final: 0.7099 (m-90) REVERT: C 57 GLU cc_start: 0.9166 (mp0) cc_final: 0.8926 (mp0) REVERT: C 100 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8646 (tm-30) REVERT: C 176 MET cc_start: 0.9400 (mmm) cc_final: 0.8749 (mpp) outliers start: 5 outliers final: 3 residues processed: 58 average time/residue: 0.0884 time to fit residues: 7.9638 Evaluate side-chains 57 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 9 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 81 optimal weight: 0.4980 chunk 60 optimal weight: 0.0060 chunk 118 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.047105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.033833 restraints weight = 57914.405| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 4.07 r_work: 0.2602 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10340 Z= 0.103 Angle : 0.510 10.276 13971 Z= 0.252 Chirality : 0.039 0.165 1524 Planarity : 0.003 0.029 1780 Dihedral : 7.053 128.500 1419 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.56 % Allowed : 5.94 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.25), residues: 1225 helix: 2.32 (0.22), residues: 604 sheet: 0.60 (0.40), residues: 157 loop : 0.66 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 41 TYR 0.009 0.001 TYR A 79 PHE 0.009 0.001 PHE C 255 TRP 0.011 0.001 TRP C 340 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00227 (10338) covalent geometry : angle 0.50934 (13965) hydrogen bonds : bond 0.03087 ( 511) hydrogen bonds : angle 4.12545 ( 1440) link_TRANS : bond 0.00216 ( 2) link_TRANS : angle 0.93561 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: B 36 MET cc_start: 0.9424 (mmt) cc_final: 0.9152 (mmm) REVERT: B 105 MET cc_start: 0.9259 (tpp) cc_final: 0.8645 (mmp) REVERT: B 120 MET cc_start: 0.5423 (mtt) cc_final: 0.5144 (mmt) REVERT: B 140 ASN cc_start: 0.9600 (p0) cc_final: 0.9297 (t0) REVERT: A 305 MET cc_start: 0.9300 (tpp) cc_final: 0.8789 (tpp) REVERT: A 478 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8165 (mmp) REVERT: A 484 TRP cc_start: 0.7871 (m-90) cc_final: 0.7193 (m-90) REVERT: C 57 GLU cc_start: 0.9176 (mp0) cc_final: 0.8930 (mp0) REVERT: C 100 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8639 (tm-30) REVERT: C 132 MET cc_start: 0.9210 (ptm) cc_final: 0.8930 (ptm) REVERT: C 283 MET cc_start: 0.8875 (mmm) cc_final: 0.8523 (mmm) outliers start: 6 outliers final: 5 residues processed: 60 average time/residue: 0.0812 time to fit residues: 7.6440 Evaluate side-chains 61 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.046703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.033425 restraints weight = 58735.761| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 4.04 r_work: 0.2584 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10340 Z= 0.139 Angle : 0.523 10.583 13971 Z= 0.258 Chirality : 0.040 0.167 1524 Planarity : 0.003 0.030 1780 Dihedral : 7.053 129.406 1419 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.65 % Allowed : 6.22 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.25), residues: 1225 helix: 2.38 (0.22), residues: 604 sheet: 0.61 (0.41), residues: 158 loop : 0.64 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 41 TYR 0.009 0.001 TYR A 79 PHE 0.010 0.001 PHE C 255 TRP 0.009 0.001 TRP C 340 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00311 (10338) covalent geometry : angle 0.52256 (13965) hydrogen bonds : bond 0.03230 ( 511) hydrogen bonds : angle 4.13083 ( 1440) link_TRANS : bond 0.00184 ( 2) link_TRANS : angle 0.88875 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.9442 (mmt) cc_final: 0.9167 (mmm) REVERT: B 105 MET cc_start: 0.9260 (tpp) cc_final: 0.8643 (mmp) REVERT: B 120 MET cc_start: 0.5509 (mtt) cc_final: 0.5218 (mmt) REVERT: B 140 ASN cc_start: 0.9592 (p0) cc_final: 0.9387 (p0) REVERT: A 382 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8531 (p) REVERT: A 478 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8174 (mmp) REVERT: A 484 TRP cc_start: 0.7895 (m-90) cc_final: 0.7195 (m-90) REVERT: C 57 GLU cc_start: 0.9200 (mp0) cc_final: 0.8926 (mp0) REVERT: C 100 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8635 (tm-30) REVERT: C 283 MET cc_start: 0.8911 (mmm) cc_final: 0.8558 (mmm) outliers start: 7 outliers final: 5 residues processed: 59 average time/residue: 0.0840 time to fit residues: 7.8154 Evaluate side-chains 60 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 118 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 7 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.046723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.033461 restraints weight = 57618.039| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 4.01 r_work: 0.2586 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10340 Z= 0.138 Angle : 0.528 10.298 13971 Z= 0.260 Chirality : 0.040 0.167 1524 Planarity : 0.003 0.029 1780 Dihedral : 7.055 130.079 1419 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.65 % Allowed : 6.50 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.25), residues: 1225 helix: 2.36 (0.22), residues: 605 sheet: 0.65 (0.42), residues: 156 loop : 0.59 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 41 TYR 0.010 0.001 TYR A 79 PHE 0.010 0.001 PHE C 255 TRP 0.009 0.001 TRP C 340 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00309 (10338) covalent geometry : angle 0.52787 (13965) hydrogen bonds : bond 0.03196 ( 511) hydrogen bonds : angle 4.11877 ( 1440) link_TRANS : bond 0.00194 ( 2) link_TRANS : angle 0.89271 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.9450 (mmt) cc_final: 0.9212 (mmm) REVERT: B 105 MET cc_start: 0.9262 (tpp) cc_final: 0.8642 (mmp) REVERT: B 120 MET cc_start: 0.5582 (mtt) cc_final: 0.5222 (mmt) REVERT: A 132 MET cc_start: 0.8617 (tmm) cc_final: 0.8232 (tpp) REVERT: A 382 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8397 (p) REVERT: A 478 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8207 (mmp) REVERT: A 484 TRP cc_start: 0.7946 (m-90) cc_final: 0.7237 (m-90) REVERT: C 57 GLU cc_start: 0.9204 (mp0) cc_final: 0.8919 (mp0) REVERT: C 100 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8646 (tm-30) REVERT: C 176 MET cc_start: 0.9381 (tpp) cc_final: 0.8739 (mpp) REVERT: C 283 MET cc_start: 0.8897 (mmm) cc_final: 0.8553 (mmm) outliers start: 7 outliers final: 5 residues processed: 61 average time/residue: 0.0873 time to fit residues: 8.2420 Evaluate side-chains 59 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 119 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 0.0020 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.047361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.034086 restraints weight = 58074.139| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 4.08 r_work: 0.2613 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10340 Z= 0.097 Angle : 0.523 11.583 13971 Z= 0.257 Chirality : 0.040 0.230 1524 Planarity : 0.003 0.031 1780 Dihedral : 6.924 128.705 1419 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.46 % Allowed : 6.78 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.25), residues: 1225 helix: 2.38 (0.22), residues: 605 sheet: 0.64 (0.42), residues: 156 loop : 0.62 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 41 TYR 0.011 0.001 TYR A 79 PHE 0.009 0.001 PHE B 12 TRP 0.011 0.001 TRP C 340 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00212 (10338) covalent geometry : angle 0.52258 (13965) hydrogen bonds : bond 0.02984 ( 511) hydrogen bonds : angle 4.08216 ( 1440) link_TRANS : bond 0.00231 ( 2) link_TRANS : angle 0.95341 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2259.21 seconds wall clock time: 39 minutes 29.76 seconds (2369.76 seconds total)