Starting phenix.real_space_refine on Fri Feb 14 20:53:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pml_13538/02_2025/7pml_13538.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pml_13538/02_2025/7pml_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7pml_13538/02_2025/7pml_13538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pml_13538/02_2025/7pml_13538.map" model { file = "/net/cci-nas-00/data/ceres_data/7pml_13538/02_2025/7pml_13538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pml_13538/02_2025/7pml_13538.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} 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 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: 6.44, per 1000 atoms: 0.63 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: 2.60 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.19 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: 3.55 Time building geometry restraints manager: 2.99 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: 6120 32.20 - 64.40: 134 64.40 - 96.60: 40 96.60 - 128.80: 3 128.80 - 161.00: 2 Dihedral angle restraints: 6299 sinusoidal: 2605 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 6296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1192 0.056 - 0.112: 290 0.112 - 0.167: 48 0.167 - 0.223: 2 0.223 - 0.279: 2 Chirality restraints: 1534 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 -2.64 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA MET A 478 " pdb=" N MET A 478 " pdb=" C MET A 478 " pdb=" CB MET A 478 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+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 2.32 0.19 2.00e-01 2.50e+01 9.50e-01 ... (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: 2.700 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.730 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 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 10403 Z= 0.336 Angle : 0.855 16.267 14053 Z= 0.494 Chirality : 0.049 0.279 1534 Planarity : 0.008 0.124 1792 Dihedral : 15.933 161.004 3911 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.074 0.005 TRP A 484 HIS 0.015 0.002 HIS A 418 PHE 0.060 0.002 PHE A 564 TYR 0.061 0.006 TYR C 306 ARG 0.088 0.012 ARG C 147 *********************** 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 : 1.164 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: 0.3248 time to fit residues: 44.8074 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 : 1.266 ------------------------------------------------------------------------------- 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 104 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 642 ASN C 162 ASN C 280 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.050551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.036740 restraints weight = 52466.188| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.95 r_work: 0.2660 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10403 Z= 0.282 Angle : 0.650 8.075 14053 Z= 0.344 Chirality : 0.043 0.169 1534 Planarity : 0.004 0.038 1792 Dihedral : 11.336 160.727 1429 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.74 % Allowed : 2.67 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.23), residues: 1235 helix: 0.70 (0.20), residues: 610 sheet: 0.91 (0.40), residues: 159 loop : 0.62 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP A 484 HIS 0.009 0.001 HIS A 418 PHE 0.024 0.002 PHE A 564 TYR 0.020 0.002 TYR A 79 ARG 0.009 0.001 ARG A 343 *********************** 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 71 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 1.262 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 93 PHE cc_start: 0.8894 (m-80) cc_final: 0.8503 (m-80) REVERT: A 135 MET cc_start: 0.8510 (mmm) cc_final: 0.8288 (mmm) REVERT: A 364 MET cc_start: 0.9488 (mmm) cc_final: 0.9273 (mmm) REVERT: A 503 MET cc_start: 0.9479 (mmm) cc_final: 0.9211 (mmp) REVERT: C 227 MET cc_start: 0.8343 (mmm) cc_final: 0.8041 (tpp) outliers start: 8 outliers final: 5 residues processed: 67 average time/residue: 0.2713 time to fit residues: 25.8768 Evaluate side-chains 63 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 H residue 5 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 37 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 2 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 HIS A 395 HIS A 410 ASN A 492 ASN A 533 ASN C 161 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.050624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.036880 restraints weight = 52691.803| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.96 r_work: 0.2668 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10403 Z= 0.209 Angle : 0.559 8.119 14053 Z= 0.291 Chirality : 0.041 0.192 1534 Planarity : 0.004 0.035 1792 Dihedral : 10.241 155.095 1429 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.65 % Allowed : 4.24 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.24), residues: 1235 helix: 1.39 (0.21), residues: 622 sheet: 1.08 (0.41), residues: 150 loop : 0.67 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 484 HIS 0.007 0.001 HIS A 418 PHE 0.012 0.001 PHE C 255 TYR 0.014 0.001 TYR A 79 ARG 0.006 0.000 ARG A 343 *********************** 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 68 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 SER cc_start: 0.8436 (m) cc_final: 0.8138 (p) REVERT: B 93 PHE cc_start: 0.8986 (m-80) cc_final: 0.8623 (m-80) REVERT: A 82 GLU cc_start: 0.9120 (mp0) cc_final: 0.8657 (tp30) REVERT: A 150 MET cc_start: 0.9368 (ttp) cc_final: 0.9157 (ttt) REVERT: A 305 MET cc_start: 0.9414 (tpp) cc_final: 0.9066 (tpp) REVERT: C 47 MET cc_start: 0.8945 (tpp) cc_final: 0.8265 (tmm) REVERT: C 176 MET cc_start: 0.9430 (mmm) cc_final: 0.9213 (mmm) outliers start: 7 outliers final: 3 residues processed: 63 average time/residue: 0.2770 time to fit residues: 24.8169 Evaluate side-chains 59 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 49 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS 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 = 0.050260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.036439 restraints weight = 52307.549| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 3.94 r_work: 0.2652 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10403 Z= 0.244 Angle : 0.556 6.298 14053 Z= 0.286 Chirality : 0.041 0.188 1534 Planarity : 0.004 0.039 1792 Dihedral : 9.733 151.541 1429 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.74 % Allowed : 5.62 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.24), residues: 1235 helix: 1.73 (0.21), residues: 616 sheet: 1.07 (0.41), residues: 150 loop : 0.68 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 484 HIS 0.006 0.001 HIS A 418 PHE 0.027 0.001 PHE C 223 TYR 0.014 0.001 TYR A 456 ARG 0.010 0.000 ARG A 343 *********************** 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 : 1.208 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: 0.9472 (mmt) cc_final: 0.9040 (mmt) REVERT: B 62 SER cc_start: 0.8362 (m) cc_final: 0.8059 (p) REVERT: B 93 PHE cc_start: 0.9061 (m-80) cc_final: 0.8651 (m-80) REVERT: A 150 MET cc_start: 0.9375 (ttp) cc_final: 0.9121 (ttt) REVERT: A 305 MET cc_start: 0.9418 (tpp) cc_final: 0.9037 (tpp) REVERT: C 47 MET cc_start: 0.8988 (tpp) cc_final: 0.8137 (tmm) REVERT: C 227 MET cc_start: 0.8978 (tpp) cc_final: 0.8575 (tpp) outliers start: 8 outliers final: 2 residues processed: 65 average time/residue: 0.2917 time to fit residues: 27.3569 Evaluate side-chains 60 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET 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 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.050298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.036449 restraints weight = 52203.187| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.93 r_work: 0.2658 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10403 Z= 0.215 Angle : 0.546 8.339 14053 Z= 0.280 Chirality : 0.041 0.186 1534 Planarity : 0.003 0.037 1792 Dihedral : 9.457 150.212 1428 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.37 % Allowed : 7.10 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.24), residues: 1235 helix: 1.89 (0.22), residues: 617 sheet: 1.06 (0.40), residues: 150 loop : 0.65 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 484 HIS 0.005 0.001 HIS A 418 PHE 0.011 0.001 PHE C 223 TYR 0.013 0.001 TYR A 456 ARG 0.006 0.000 ARG A 343 *********************** 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 62 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 1.171 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: 0.9456 (mmt) cc_final: 0.9062 (mmt) REVERT: B 62 SER cc_start: 0.8396 (m) cc_final: 0.8087 (p) REVERT: B 93 PHE cc_start: 0.9088 (m-80) cc_final: 0.8676 (m-80) REVERT: B 120 MET cc_start: 0.6700 (mpp) cc_final: 0.6343 (pmm) REVERT: A 82 GLU cc_start: 0.9181 (mp0) cc_final: 0.8676 (tp30) REVERT: A 305 MET cc_start: 0.9423 (tpp) cc_final: 0.9086 (tpp) REVERT: A 364 MET cc_start: 0.9384 (mmm) cc_final: 0.9155 (mmp) REVERT: C 227 MET cc_start: 0.8929 (tpp) cc_final: 0.8542 (tpp) outliers start: 4 outliers final: 3 residues processed: 59 average time/residue: 0.2458 time to fit residues: 21.2371 Evaluate side-chains 59 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 740 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 13 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 77 optimal weight: 0.0010 chunk 27 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3324 r_free = 0.3324 target = 0.050486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.036634 restraints weight = 52523.038| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.95 r_work: 0.2662 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10403 Z= 0.191 Angle : 0.539 9.220 14053 Z= 0.272 Chirality : 0.040 0.184 1534 Planarity : 0.003 0.035 1792 Dihedral : 9.288 149.687 1428 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.83 % Allowed : 7.28 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.24), residues: 1235 helix: 1.94 (0.22), residues: 617 sheet: 1.02 (0.41), residues: 150 loop : 0.65 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 484 HIS 0.005 0.001 HIS A 418 PHE 0.010 0.001 PHE C 255 TYR 0.012 0.001 TYR A 456 ARG 0.005 0.000 ARG A 343 *********************** 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 65 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 SER cc_start: 0.8399 (m) cc_final: 0.8091 (p) REVERT: B 93 PHE cc_start: 0.9115 (m-80) cc_final: 0.8707 (m-80) REVERT: B 120 MET cc_start: 0.6615 (mpp) cc_final: 0.6359 (pmm) REVERT: A 82 GLU cc_start: 0.9143 (mp0) cc_final: 0.8807 (tm-30) REVERT: A 305 MET cc_start: 0.9411 (tpp) cc_final: 0.9060 (tpp) REVERT: C 47 MET cc_start: 0.8950 (tpp) cc_final: 0.8331 (tmm) REVERT: C 227 MET cc_start: 0.8914 (tpp) cc_final: 0.8563 (tpp) REVERT: C 283 MET cc_start: 0.8938 (mmm) cc_final: 0.8652 (mmm) outliers start: 9 outliers final: 3 residues processed: 60 average time/residue: 0.2407 time to fit residues: 21.5969 Evaluate side-chains 58 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 7 optimal weight: 10.0000 chunk 76 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3318 r_free = 0.3318 target = 0.050285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.036469 restraints weight = 53137.082| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.97 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: 0.8707 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10403 Z= 0.205 Angle : 0.554 12.708 14053 Z= 0.275 Chirality : 0.041 0.268 1534 Planarity : 0.003 0.036 1792 Dihedral : 9.166 149.187 1428 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.74 % Allowed : 7.65 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.24), residues: 1235 helix: 2.01 (0.22), residues: 617 sheet: 1.02 (0.41), residues: 150 loop : 0.67 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 781 HIS 0.005 0.001 HIS A 418 PHE 0.010 0.001 PHE C 255 TYR 0.012 0.001 TYR A 456 ARG 0.005 0.000 ARG A 343 *********************** 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 65 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 1.286 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: 0.8838 (mm-40) cc_final: 0.8455 (mm-40) REVERT: B 62 SER cc_start: 0.8404 (m) cc_final: 0.8100 (p) REVERT: B 93 PHE cc_start: 0.9104 (m-80) cc_final: 0.8702 (m-80) REVERT: A 82 GLU cc_start: 0.9159 (mp0) cc_final: 0.8844 (tm-30) REVERT: A 132 MET cc_start: 0.7809 (tpp) cc_final: 0.7589 (tpp) REVERT: A 305 MET cc_start: 0.9419 (tpp) cc_final: 0.9024 (tpp) REVERT: A 515 MET cc_start: 0.9212 (tpp) cc_final: 0.8913 (tpt) REVERT: C 47 MET cc_start: 0.8932 (tpp) cc_final: 0.8248 (tmm) REVERT: C 227 MET cc_start: 0.8954 (tpp) cc_final: 0.8614 (tpp) REVERT: C 283 MET cc_start: 0.8913 (mmm) cc_final: 0.8680 (mmm) outliers start: 8 outliers final: 4 residues processed: 62 average time/residue: 0.2452 time to fit residues: 21.8886 Evaluate side-chains 61 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 H residue 5 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 14 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 120 optimal weight: 0.4980 chunk 18 optimal weight: 0.0040 chunk 2 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 43 optimal weight: 0.0870 overall best weight: 0.4370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** 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 = 0.3340 r_free = 0.3340 target = 0.050993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.037181 restraints weight = 52464.231| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.97 r_work: 0.2685 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10403 Z= 0.138 Angle : 0.541 11.165 14053 Z= 0.267 Chirality : 0.040 0.252 1534 Planarity : 0.003 0.034 1792 Dihedral : 8.991 147.653 1428 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.74 % Allowed : 7.93 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.24), residues: 1235 helix: 2.08 (0.22), residues: 618 sheet: 1.07 (0.42), residues: 150 loop : 0.68 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 484 HIS 0.004 0.001 HIS A 418 PHE 0.009 0.001 PHE A 707 TYR 0.012 0.001 TYR A 658 ARG 0.006 0.000 ARG A 792 *********************** 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 66 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8470 (mm-40) REVERT: B 36 MET cc_start: 0.9477 (mmt) cc_final: 0.8787 (mmm) REVERT: B 62 SER cc_start: 0.8322 (m) cc_final: 0.8097 (p) REVERT: B 93 PHE cc_start: 0.9063 (m-80) cc_final: 0.8662 (m-80) REVERT: A 82 GLU cc_start: 0.9158 (mp0) cc_final: 0.8837 (tm-30) REVERT: A 135 MET cc_start: 0.8586 (mmm) cc_final: 0.8372 (mtt) REVERT: A 305 MET cc_start: 0.9390 (tpp) cc_final: 0.9041 (tpp) REVERT: C 47 MET cc_start: 0.8904 (tpp) cc_final: 0.8212 (tmm) REVERT: C 227 MET cc_start: 0.8949 (tpp) cc_final: 0.8640 (tpp) outliers start: 8 outliers final: 6 residues processed: 64 average time/residue: 0.2617 time to fit residues: 24.1117 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 : 1.322 ------------------------------------------------------------------------------- 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 194 THR Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3317 r_free = 0.3317 target = 0.050130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.036436 restraints weight = 52897.415| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.95 r_work: 0.2661 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10403 Z= 0.232 Angle : 0.596 12.764 14053 Z= 0.292 Chirality : 0.041 0.228 1534 Planarity : 0.004 0.057 1792 Dihedral : 8.962 148.645 1428 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.74 % Allowed : 8.48 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.25), residues: 1235 helix: 2.12 (0.22), residues: 612 sheet: 1.08 (0.43), residues: 150 loop : 0.69 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 484 HIS 0.003 0.001 HIS A 81 PHE 0.010 0.001 PHE C 255 TYR 0.012 0.001 TYR A 456 ARG 0.007 0.000 ARG A 683 *********************** 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: 8 poor density : 55 time to evaluate : 1.088 Fit side-chains 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: 0.8472 (mm-40) REVERT: B 36 MET cc_start: 0.9455 (mmt) cc_final: 0.8770 (mmm) REVERT: B 62 SER cc_start: 0.8403 (m) cc_final: 0.8107 (p) REVERT: B 73 MET cc_start: 0.8721 (ttp) cc_final: 0.8495 (ttp) REVERT: B 93 PHE cc_start: 0.9082 (m-80) cc_final: 0.8679 (m-80) REVERT: A 82 GLU cc_start: 0.9185 (mp0) cc_final: 0.8861 (tm-30) REVERT: C 47 MET cc_start: 0.8943 (tpp) cc_final: 0.8193 (tmm) REVERT: C 227 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8560 (tpp) REVERT: C 283 MET cc_start: 0.8878 (mmm) cc_final: 0.8641 (mmm) outliers start: 8 outliers final: 6 residues processed: 61 average time/residue: 0.2426 time to fit residues: 21.9305 Evaluate side-chains 62 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 1.292 ------------------------------------------------------------------------------- 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 194 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 2 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3325 r_free = 0.3325 target = 0.050386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.036692 restraints weight = 52516.755| |-----------------------------------------------------------------------------| 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: 0.8695 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10403 Z= 0.184 Angle : 0.580 13.317 14053 Z= 0.283 Chirality : 0.040 0.229 1534 Planarity : 0.003 0.035 1792 Dihedral : 8.874 147.914 1428 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.92 % Allowed : 8.57 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.25), residues: 1235 helix: 2.11 (0.22), residues: 613 sheet: 1.05 (0.43), residues: 149 loop : 0.62 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 484 HIS 0.009 0.001 HIS A 418 PHE 0.009 0.001 PHE C 255 TYR 0.016 0.001 TYR A 102 ARG 0.006 0.000 ARG A 789 ********************** 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 67 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8431 (mm-40) REVERT: B 36 MET cc_start: 0.9469 (mmt) cc_final: 0.8738 (mmm) REVERT: B 62 SER cc_start: 0.8396 (m) cc_final: 0.8098 (p) REVERT: B 73 MET cc_start: 0.8708 (ttp) cc_final: 0.8502 (ttp) REVERT: B 93 PHE cc_start: 0.9075 (m-80) cc_final: 0.8673 (m-80) REVERT: A 82 GLU cc_start: 0.9175 (mp0) cc_final: 0.8857 (tm-30) REVERT: A 305 MET cc_start: 0.9423 (tpp) cc_final: 0.9021 (tpp) REVERT: C 227 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8614 (tpp) REVERT: C 283 MET cc_start: 0.8911 (mmm) cc_final: 0.8517 (mmm) outliers start: 10 outliers final: 6 residues processed: 65 average time/residue: 0.2326 time to fit residues: 22.3751 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 : 1.200 ------------------------------------------------------------------------------- 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 194 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.049576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.035979 restraints weight = 52595.668| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.92 r_work: 0.2644 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10403 Z= 0.277 Angle : 0.629 16.040 14053 Z= 0.306 Chirality : 0.042 0.214 1534 Planarity : 0.003 0.035 1792 Dihedral : 8.922 149.025 1428 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.01 % Allowed : 8.57 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.25), residues: 1235 helix: 2.13 (0.22), residues: 612 sheet: 1.07 (0.44), residues: 149 loop : 0.58 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 484 HIS 0.010 0.001 HIS A 418 PHE 0.011 0.001 PHE C 255 TYR 0.013 0.001 TYR A 456 ARG 0.005 0.000 ARG A 791 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4865.73 seconds wall clock time: 87 minutes 21.67 seconds (5241.67 seconds total)