Starting phenix.real_space_refine on Thu Jul 2 22:23:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pml_13538/07_2026/7pml_13538.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pml_13538/07_2026/7pml_13538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7pml_13538/07_2026/7pml_13538.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pml_13538/07_2026/7pml_13538.cif" model { file = "/net/cci-nas-00/data/ceres_data/7pml_13538/07_2026/7pml_13538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pml_13538/07_2026/7pml_13538.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pml_13538/07_2026/7pml_13538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pml_13538/07_2026/7pml_13538.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 6482 2.51 5 N 1730 2.21 5 O 1906 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-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10189 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: 6105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6105 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 5 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 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} 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: 2.25, per 1000 atoms: 0.22 Number of scatterers: 10189 At special positions: 0 Unit cell: (106.7, 126.5, 155.1, 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 1906 8.00 N 1730 7.00 C 6482 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: 1.21 Conformation dependent library (CDL) restraints added in 368.8 milliseconds 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 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: 2382 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 14 sheets defined 55.7% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.220A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.665A 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 96 removed outlier: 4.119A pdb=" N PHE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) 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 73 through 77 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 116 through 119 removed outlier: 4.207A 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 154 removed outlier: 3.958A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 185 removed outlier: 3.630A pdb=" N ALA A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 207 removed outlier: 3.730A pdb=" N LYS A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.099A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 278 Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.577A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 3.878A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 338 removed outlier: 3.509A pdb=" N GLY A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 338 " --> pdb=" O HIS A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 376 removed outlier: 3.835A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 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: 3.825A 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 569 Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.755A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.757A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (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: 3.856A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 683 " --> pdb=" O VAL A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 removed outlier: 3.521A pdb=" N ALA A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) 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 723 through 736 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: 3.699A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.714A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.163A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.732A pdb=" N THR C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.231A 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 347 Processing helix chain 'C' and resid 348 through 349 No H-bonds generated for 'chain 'C' and resid 348 through 349' Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.033A 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: 4.160A pdb=" N ALA A 11 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 103 removed outlier: 7.754A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLN A 157 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU A 436 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE A 159 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE A 438 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N VAL A 161 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.993A 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 211 removed outlier: 5.616A pdb=" N ALA A 209 " --> pdb=" O ASN A 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 342 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 Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.519A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (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: 5.911A 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 241 531 hydrogen bonds defined for protein. 1479 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: 1.84 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1699 1.32 - 1.44: 2746 1.44 - 1.56: 5847 1.56 - 1.69: 8 1.69 - 1.81: 103 Bond restraints: 10403 Sorted by residual: bond pdb=" O3A ANP A1901 " pdb=" PB ANP A1901 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.29e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.451 0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" O5' ANP A1901 " pdb=" PA ANP A1901 " ideal model delta sigma weight residual 1.655 1.582 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.375 -0.046 1.40e-02 5.10e+03 1.08e+01 ... (remaining 10398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 13904 3.25 - 6.51: 137 6.51 - 9.76: 8 9.76 - 13.01: 3 13.01 - 16.27: 1 Bond angle restraints: 14053 Sorted by residual: angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 111.11 10.59 1.80e+00 3.09e-01 3.46e+01 angle pdb=" PB ANP A1901 " pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 126.95 110.68 16.27 3.00e+00 1.11e-01 2.94e+01 angle pdb=" N GLY A 563 " pdb=" CA GLY A 563 " pdb=" C GLY A 563 " ideal model delta sigma weight residual 114.66 120.25 -5.59 1.24e+00 6.50e-01 2.03e+01 angle pdb=" CA TRP A 484 " pdb=" CB TRP A 484 " pdb=" CG TRP A 484 " ideal model delta sigma weight residual 113.60 121.69 -8.09 1.90e+00 2.77e-01 1.81e+01 angle pdb=" N DTH H 4 " pdb=" CA DTH H 4 " pdb=" CB DTH H 4 " ideal model delta sigma weight residual 111.50 104.41 7.09 1.70e+00 3.46e-01 1.74e+01 ... (remaining 14048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.20: 6103 32.20 - 64.40: 120 64.40 - 96.60: 33 96.60 - 128.80: 3 128.80 - 161.00: 2 Dihedral angle restraints: 6261 sinusoidal: 2567 harmonic: 3694 Sorted by residual: 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 300.00 168.16 131.84 1 2.00e+01 2.50e-03 4.00e+01 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 -60.00 55.19 -115.19 1 2.00e+01 2.50e-03 3.42e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 54.36 -114.36 1 2.00e+01 2.50e-03 3.39e+01 ... (remaining 6258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.032: 1532 1.032 - 2.063: 0 2.063 - 3.095: 0 3.095 - 4.127: 0 4.127 - 5.158: 2 Chirality restraints: 1534 Sorted by residual: chirality pdb=" CB DTH H 4 " pdb=" CA DTH H 4 " pdb=" OG1 DTH H 4 " pdb=" CG2 DTH H 4 " both_signs ideal model delta sigma weight residual False 2.55 -2.61 5.16 2.00e-01 2.50e+01 6.65e+02 chirality pdb=" CA DTH H 4 " pdb=" N DTH H 4 " pdb=" C DTH H 4 " pdb=" CB DTH H 4 " both_signs ideal model delta sigma weight residual False 2.53 -2.44 4.97 2.00e-01 2.50e+01 6.17e+02 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 -2.64 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 1531 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 306 " -0.002 2.00e-02 2.50e+03 4.17e-02 3.47e+01 pdb=" CG TYR C 306 " -0.000 2.00e-02 2.50e+03 pdb=" CD1 TYR C 306 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR C 306 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 306 " 0.058 2.00e-02 2.50e+03 pdb=" CE2 TYR C 306 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 306 " 0.060 2.00e-02 2.50e+03 pdb=" OH TYR C 306 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 147 " -0.134 9.50e-02 1.11e+02 7.53e-02 2.81e+01 pdb=" NE ARG C 147 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG C 147 " -0.087 2.00e-02 2.50e+03 pdb=" NH1 ARG C 147 " 0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG C 147 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 773 " -0.112 9.50e-02 1.11e+02 6.58e-02 2.41e+01 pdb=" NE ARG A 773 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG A 773 " -0.081 2.00e-02 2.50e+03 pdb=" NH1 ARG A 773 " 0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG A 773 " 0.023 2.00e-02 2.50e+03 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 11 2.29 - 2.94: 4427 2.94 - 3.60: 14701 3.60 - 4.25: 23064 4.25 - 4.90: 39502 Nonbonded interactions: 81705 Sorted by model distance: nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 1.641 2.170 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.731 3.620 nonbonded pdb=" O1B ANP A1901 " pdb="MG MG A1903 " model vdw 1.814 2.170 nonbonded pdb=" O3G ANP A1901 " pdb="MG MG A1902 " model vdw 2.129 2.170 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 500 " model vdw 2.155 3.040 ... (remaining 81700 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: 3.260 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.730 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.005 0.145 10405 Z= 0.250 Angle : 0.858 16.267 14059 Z= 0.495 Chirality : 0.189 5.158 1534 Planarity : 0.008 0.124 1792 Dihedral : 15.417 161.004 3873 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.09 % Allowed : 0.18 % Favored : 99.72 % 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: -1.35 (0.20), residues: 1235 helix: -1.72 (0.16), residues: 604 sheet: 0.40 (0.38), residues: 152 loop : 0.15 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.088 0.012 ARG C 147 TYR 0.061 0.006 TYR C 306 PHE 0.060 0.002 PHE A 564 TRP 0.074 0.005 TRP A 484 HIS 0.015 0.002 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.25 (10403) covalent geometry : angle 0.85532 / 0.49 (14053) hydrogen bonds : bond 0.15857 / 10.69 ( 529) hydrogen bonds : angle 6.99780 / 5.08 ( 1479) link_TRANS : bond 0.01144 / 0.59 ( 2) link_TRANS : angle 3.47947 / 2.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.8426 (m-80) cc_final: 0.8212 (m-80) REVERT: A 503 MET cc_start: 0.8521 (mmm) cc_final: 0.8311 (mmt) REVERT: C 270 GLU cc_start: 0.7295 (mt-10) cc_final: 0.7088 (mt-10) outliers start: 1 outliers final: 1 residues processed: 104 average time/residue: 0.1329 time to fit residues: 18.3236 Evaluate side-chains 60 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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: 124 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 147 HIS ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 398 ASN A 463 GLN A 492 ASN A 642 ASN 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 = 0.3313 r_free = 0.3313 target = 0.050293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.036469 restraints weight = 52549.297| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.97 r_work: 0.2648 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10405 Z= 0.211 Angle : 0.658 7.545 14059 Z= 0.349 Chirality : 0.043 0.165 1534 Planarity : 0.004 0.038 1792 Dihedral : 10.093 158.642 1391 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.74 % Allowed : 2.67 % Favored : 96.59 % 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: 0.84 (0.23), residues: 1235 helix: 0.62 (0.20), residues: 610 sheet: 0.88 (0.40), residues: 159 loop : 0.62 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 343 TYR 0.020 0.002 TYR A 79 PHE 0.024 0.002 PHE A 564 TRP 0.046 0.003 TRP A 484 HIS 0.009 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 (10403) covalent geometry : angle 0.65764 / 0.35 (14053) hydrogen bonds : bond 0.04634 / 3.14 ( 529) hydrogen bonds : angle 4.97783 / 3.60 ( 1479) link_TRANS : bond 0.00563 / 0.27 ( 2) link_TRANS : angle 0.67398 / 0.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8462 (mm-40) REVERT: B 93 PHE cc_start: 0.8912 (m-80) cc_final: 0.8555 (m-80) REVERT: A 135 MET cc_start: 0.8536 (mmm) cc_final: 0.8313 (mmm) REVERT: A 503 MET cc_start: 0.9470 (mmm) cc_final: 0.9201 (mmp) REVERT: C 227 MET cc_start: 0.8354 (mmm) cc_final: 0.8051 (tpp) outliers start: 8 outliers final: 5 residues processed: 69 average time/residue: 0.1039 time to fit residues: 10.0968 Evaluate side-chains 61 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 490 TYR Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain C residue 232 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 64 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 HIS A 395 HIS A 406 HIS A 410 ASN C 161 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.050801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.037052 restraints weight = 52355.251| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.96 r_work: 0.2674 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10405 Z= 0.135 Angle : 0.548 7.379 14059 Z= 0.286 Chirality : 0.041 0.201 1534 Planarity : 0.004 0.036 1792 Dihedral : 9.416 159.849 1390 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.55 % Allowed : 4.61 % Favored : 94.84 % 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: 1.59 (0.24), residues: 1235 helix: 1.46 (0.21), residues: 617 sheet: 1.13 (0.41), residues: 150 loop : 0.67 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 343 TYR 0.013 0.001 TYR A 79 PHE 0.011 0.001 PHE C 255 TRP 0.025 0.002 TRP A 484 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (10403) covalent geometry : angle 0.54836 / 0.29 (14053) hydrogen bonds : bond 0.03782 / 2.54 ( 529) hydrogen bonds : angle 4.51204 / 3.27 ( 1479) link_TRANS : bond 0.00185 / 0.09 ( 2) link_TRANS : angle 0.20616 / 0.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8477 (mm-40) REVERT: B 62 SER cc_start: 0.8433 (m) cc_final: 0.8137 (p) REVERT: B 93 PHE cc_start: 0.9025 (m-80) cc_final: 0.8633 (m-80) REVERT: B 120 MET cc_start: 0.7901 (mpp) cc_final: 0.7478 (mtt) REVERT: A 82 GLU cc_start: 0.9114 (mp0) cc_final: 0.8598 (tp30) REVERT: A 305 MET cc_start: 0.9398 (tpp) cc_final: 0.9073 (tpp) REVERT: C 47 MET cc_start: 0.8914 (tpp) cc_final: 0.8262 (tmm) REVERT: C 176 MET cc_start: 0.9391 (mmm) cc_final: 0.9169 (mmm) outliers start: 6 outliers final: 2 residues processed: 67 average time/residue: 0.1129 time to fit residues: 10.7270 Evaluate side-chains 62 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 740 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 8 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3300 r_free = 0.3300 target = 0.049669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.035945 restraints weight = 52849.469| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 3.95 r_work: 0.2638 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10405 Z= 0.201 Angle : 0.567 7.070 14059 Z= 0.293 Chirality : 0.042 0.191 1534 Planarity : 0.004 0.039 1792 Dihedral : 9.247 156.986 1390 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.74 % Allowed : 6.27 % Favored : 93.00 % 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: 1.69 (0.24), residues: 1235 helix: 1.61 (0.21), residues: 622 sheet: 1.06 (0.41), residues: 150 loop : 0.63 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 343 TYR 0.015 0.001 TYR A 456 PHE 0.012 0.001 PHE A 707 TRP 0.017 0.001 TRP A 484 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (10403) covalent geometry : angle 0.56685 / 0.29 (14053) hydrogen bonds : bond 0.03918 / 2.64 ( 529) hydrogen bonds : angle 4.49793 / 3.26 ( 1479) link_TRANS : bond 0.00292 / 0.14 ( 2) link_TRANS : angle 0.35079 / 0.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8496 (mm-40) REVERT: B 36 MET cc_start: 0.9472 (mmt) cc_final: 0.9035 (mmt) REVERT: B 93 PHE cc_start: 0.9098 (m-80) cc_final: 0.8686 (m-80) REVERT: B 120 MET cc_start: 0.8040 (mpp) cc_final: 0.7474 (pmm) REVERT: A 82 GLU cc_start: 0.9162 (mp0) cc_final: 0.8667 (tp30) REVERT: C 47 MET cc_start: 0.9000 (tpp) cc_final: 0.8111 (tmm) REVERT: C 313 MET cc_start: 0.9509 (mmm) cc_final: 0.9288 (tpt) outliers start: 8 outliers final: 3 residues processed: 66 average time/residue: 0.1173 time to fit residues: 10.9731 Evaluate side-chains 61 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 740 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 11 optimal weight: 5.9990 chunk 114 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.049616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.035786 restraints weight = 52917.272| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 3.96 r_work: 0.2632 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10405 Z= 0.186 Angle : 0.572 11.030 14059 Z= 0.290 Chirality : 0.041 0.191 1534 Planarity : 0.004 0.038 1792 Dihedral : 9.133 156.857 1390 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.92 % Allowed : 7.10 % Favored : 91.98 % 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: 1.82 (0.24), residues: 1235 helix: 1.83 (0.22), residues: 617 sheet: 0.96 (0.41), residues: 149 loop : 0.59 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 343 TYR 0.014 0.001 TYR A 456 PHE 0.011 0.001 PHE A 707 TRP 0.018 0.001 TRP A 484 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (10403) covalent geometry : angle 0.57185 / 0.29 (14053) hydrogen bonds : bond 0.03801 / 2.56 ( 529) hydrogen bonds : angle 4.42456 / 3.21 ( 1479) link_TRANS : bond 0.00257 / 0.13 ( 2) link_TRANS : angle 0.31920 / 0.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.9459 (mmt) cc_final: 0.9004 (mmt) REVERT: B 93 PHE cc_start: 0.9138 (m-80) cc_final: 0.8708 (m-80) REVERT: A 82 GLU cc_start: 0.9145 (mp0) cc_final: 0.8630 (tp30) REVERT: A 150 MET cc_start: 0.9267 (ttt) cc_final: 0.9024 (ttt) REVERT: A 515 MET cc_start: 0.9277 (tpp) cc_final: 0.9042 (tpt) outliers start: 10 outliers final: 6 residues processed: 63 average time/residue: 0.1049 time to fit residues: 9.6949 Evaluate side-chains 61 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain C residue 194 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 11 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.050186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.036390 restraints weight = 53223.440| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.98 r_work: 0.2655 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10405 Z= 0.126 Angle : 0.547 9.599 14059 Z= 0.274 Chirality : 0.040 0.186 1534 Planarity : 0.003 0.035 1792 Dihedral : 8.946 157.228 1390 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.83 % Allowed : 7.37 % Favored : 91.80 % 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: 1.98 (0.24), residues: 1235 helix: 1.99 (0.22), residues: 612 sheet: 1.05 (0.42), residues: 149 loop : 0.65 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 343 TYR 0.012 0.001 TYR A 456 PHE 0.009 0.001 PHE A 707 TRP 0.016 0.001 TRP A 484 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (10403) covalent geometry : angle 0.54756 / 0.27 (14053) hydrogen bonds : bond 0.03483 / 2.32 ( 529) hydrogen bonds : angle 4.28006 / 3.10 ( 1479) link_TRANS : bond 0.00131 / 0.07 ( 2) link_TRANS : angle 0.20063 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.9428 (mmt) cc_final: 0.9047 (mmt) REVERT: B 62 SER cc_start: 0.8396 (m) cc_final: 0.8092 (p) REVERT: B 93 PHE cc_start: 0.9123 (m-80) cc_final: 0.8708 (m-80) REVERT: A 82 GLU cc_start: 0.9143 (mp0) cc_final: 0.8708 (tp30) REVERT: A 275 LYS cc_start: 0.9434 (OUTLIER) cc_final: 0.9095 (pttm) REVERT: A 305 MET cc_start: 0.9419 (tpp) cc_final: 0.9060 (tpp) REVERT: C 47 MET cc_start: 0.8977 (tpp) cc_final: 0.8408 (tmm) REVERT: C 283 MET cc_start: 0.8921 (mmm) cc_final: 0.8625 (mmm) outliers start: 9 outliers final: 2 residues processed: 59 average time/residue: 0.0902 time to fit residues: 8.1787 Evaluate side-chains 56 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 740 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 113 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.050240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.036420 restraints weight = 52781.556| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.98 r_work: 0.2656 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10405 Z= 0.127 Angle : 0.544 11.960 14059 Z= 0.271 Chirality : 0.040 0.184 1534 Planarity : 0.003 0.036 1792 Dihedral : 8.838 156.132 1390 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.65 % Allowed : 8.29 % Favored : 91.06 % 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: 2.00 (0.24), residues: 1235 helix: 2.02 (0.22), residues: 613 sheet: 1.04 (0.42), residues: 149 loop : 0.64 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 343 TYR 0.012 0.001 TYR A 456 PHE 0.010 0.001 PHE A 707 TRP 0.014 0.001 TRP A 484 HIS 0.010 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (10403) covalent geometry : angle 0.54361 / 0.27 (14053) hydrogen bonds : bond 0.03439 / 2.29 ( 529) hydrogen bonds : angle 4.24849 / 3.08 ( 1479) link_TRANS : bond 0.00134 / 0.07 ( 2) link_TRANS : angle 0.19302 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 SER cc_start: 0.8402 (m) cc_final: 0.8093 (p) REVERT: B 93 PHE cc_start: 0.9106 (m-80) cc_final: 0.8692 (m-80) REVERT: B 120 MET cc_start: 0.7339 (mpp) cc_final: 0.7126 (mpp) REVERT: A 150 MET cc_start: 0.9257 (ttt) cc_final: 0.8893 (ttt) REVERT: A 275 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.9080 (pttm) REVERT: A 305 MET cc_start: 0.9413 (tpp) cc_final: 0.9020 (tpp) REVERT: C 47 MET cc_start: 0.8953 (tpp) cc_final: 0.8294 (tmm) REVERT: C 283 MET cc_start: 0.8918 (mmm) cc_final: 0.8652 (mmm) outliers start: 7 outliers final: 4 residues processed: 58 average time/residue: 0.0918 time to fit residues: 8.0709 Evaluate side-chains 59 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 119 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 39 optimal weight: 0.0770 chunk 23 optimal weight: 0.9990 chunk 111 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 ASN A 533 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.050600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.036895 restraints weight = 52421.325| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.96 r_work: 0.2676 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10405 Z= 0.104 Angle : 0.540 12.400 14059 Z= 0.268 Chirality : 0.040 0.181 1534 Planarity : 0.003 0.034 1792 Dihedral : 8.680 155.491 1390 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.92 % Allowed : 8.48 % Favored : 90.60 % 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: 2.05 (0.25), residues: 1235 helix: 2.08 (0.22), residues: 614 sheet: 1.07 (0.42), residues: 149 loop : 0.62 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 343 TYR 0.011 0.001 TYR A 456 PHE 0.009 0.001 PHE A 707 TRP 0.018 0.001 TRP A 781 HIS 0.003 0.001 HIS C 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (10403) covalent geometry : angle 0.54043 / 0.27 (14053) hydrogen bonds : bond 0.03282 / 2.17 ( 529) hydrogen bonds : angle 4.18545 / 3.03 ( 1479) link_TRANS : bond 0.00070 / 0.03 ( 2) link_TRANS : angle 0.13522 / 0.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 SER cc_start: 0.8396 (m) cc_final: 0.8087 (p) REVERT: B 93 PHE cc_start: 0.9097 (m-80) cc_final: 0.8690 (m-80) REVERT: A 82 GLU cc_start: 0.9220 (mp0) cc_final: 0.8767 (tp30) REVERT: A 305 MET cc_start: 0.9404 (tpp) cc_final: 0.9044 (tpp) REVERT: A 783 MET cc_start: 0.9156 (ttt) cc_final: 0.8935 (ppp) REVERT: C 47 MET cc_start: 0.8894 (tpp) cc_final: 0.8216 (tmm) REVERT: C 283 MET cc_start: 0.8938 (mmm) cc_final: 0.8712 (mmm) outliers start: 10 outliers final: 4 residues processed: 64 average time/residue: 0.0970 time to fit residues: 9.0971 Evaluate side-chains 58 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain C residue 17 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 68 optimal weight: 0.0980 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 54 optimal weight: 0.0980 chunk 95 optimal weight: 0.0070 chunk 64 optimal weight: 1.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3336 r_free = 0.3336 target = 0.050933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.037312 restraints weight = 52396.457| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.95 r_work: 0.2691 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10405 Z= 0.099 Angle : 0.547 12.762 14059 Z= 0.271 Chirality : 0.039 0.178 1534 Planarity : 0.004 0.063 1792 Dihedral : 8.540 155.382 1390 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.65 % Allowed : 8.66 % Favored : 90.69 % 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: 2.11 (0.25), residues: 1235 helix: 2.11 (0.22), residues: 614 sheet: 1.11 (0.43), residues: 149 loop : 0.66 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 683 TYR 0.011 0.001 TYR A 658 PHE 0.009 0.001 PHE A 707 TRP 0.013 0.001 TRP A 484 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (10403) covalent geometry : angle 0.54729 / 0.27 (14053) hydrogen bonds : bond 0.03254 / 2.11 ( 529) hydrogen bonds : angle 4.14607 / 3.01 ( 1479) link_TRANS : bond 0.00051 / 0.03 ( 2) link_TRANS : angle 0.11296 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.9489 (mmt) cc_final: 0.8913 (mmm) REVERT: B 62 SER cc_start: 0.8324 (m) cc_final: 0.8100 (p) REVERT: B 93 PHE cc_start: 0.9081 (m-80) cc_final: 0.8686 (m-80) REVERT: B 120 MET cc_start: 0.7122 (mpp) cc_final: 0.6703 (pmm) REVERT: A 82 GLU cc_start: 0.9194 (mp0) cc_final: 0.8673 (tp30) REVERT: A 305 MET cc_start: 0.9402 (tpp) cc_final: 0.9036 (tpp) REVERT: A 783 MET cc_start: 0.9226 (ttt) cc_final: 0.8912 (ppp) REVERT: C 47 MET cc_start: 0.8880 (tpp) cc_final: 0.8218 (tmm) outliers start: 7 outliers final: 5 residues processed: 62 average time/residue: 0.0884 time to fit residues: 8.4023 Evaluate side-chains 60 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain C residue 17 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 103 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.049750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.036144 restraints weight = 52046.227| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 3.92 r_work: 0.2653 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10405 Z= 0.172 Angle : 0.598 13.109 14059 Z= 0.293 Chirality : 0.041 0.183 1534 Planarity : 0.003 0.035 1792 Dihedral : 8.557 157.836 1390 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.55 % Allowed : 9.12 % Favored : 90.32 % 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: 2.09 (0.25), residues: 1235 helix: 2.11 (0.22), residues: 612 sheet: 1.15 (0.44), residues: 147 loop : 0.62 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 683 TYR 0.019 0.001 TYR A 102 PHE 0.010 0.001 PHE C 255 TRP 0.016 0.001 TRP A 484 HIS 0.009 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (10403) covalent geometry : angle 0.59800 / 0.29 (14053) hydrogen bonds : bond 0.03596 / 2.38 ( 529) hydrogen bonds : angle 4.27099 / 3.09 ( 1479) link_TRANS : bond 0.00210 / 0.10 ( 2) link_TRANS : angle 0.28437 / 0.19 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.9510 (mmt) cc_final: 0.8916 (mmm) REVERT: B 62 SER cc_start: 0.8404 (m) cc_final: 0.8112 (p) REVERT: B 93 PHE cc_start: 0.9096 (m-80) cc_final: 0.8694 (m-80) REVERT: B 120 MET cc_start: 0.7137 (mpp) cc_final: 0.6820 (pmm) REVERT: A 82 GLU cc_start: 0.9220 (mp0) cc_final: 0.8756 (tp30) REVERT: A 783 MET cc_start: 0.9217 (ttt) cc_final: 0.8922 (ppp) REVERT: C 176 MET cc_start: 0.9382 (mmm) cc_final: 0.9109 (mmm) REVERT: C 283 MET cc_start: 0.8838 (mmm) cc_final: 0.8541 (mmm) outliers start: 6 outliers final: 6 residues processed: 58 average time/residue: 0.0904 time to fit residues: 8.0282 Evaluate side-chains 59 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain C residue 17 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 6 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 ASN ** 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 = 0.3321 r_free = 0.3321 target = 0.050269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.036662 restraints weight = 52773.014| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.95 r_work: 0.2671 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10405 Z= 0.120 Angle : 0.576 13.214 14059 Z= 0.280 Chirality : 0.040 0.179 1534 Planarity : 0.003 0.034 1792 Dihedral : 8.429 158.488 1390 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.74 % Allowed : 8.94 % Favored : 90.32 % 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: 2.09 (0.25), residues: 1235 helix: 2.12 (0.22), residues: 613 sheet: 1.17 (0.44), residues: 147 loop : 0.59 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 683 TYR 0.011 0.001 TYR A 456 PHE 0.009 0.001 PHE C 255 TRP 0.015 0.001 TRP A 484 HIS 0.008 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (10403) covalent geometry : angle 0.57647 / 0.28 (14053) hydrogen bonds : bond 0.03328 / 2.18 ( 529) hydrogen bonds : angle 4.20198 / 3.04 ( 1479) link_TRANS : bond 0.00106 / 0.05 ( 2) link_TRANS : angle 0.14471 / 0.09 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2403.54 seconds wall clock time: 42 minutes 5.93 seconds (2525.93 seconds total)