Starting phenix.real_space_refine on Sun Dec 29 13:44:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pmi_13535/12_2024/7pmi_13535.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pmi_13535/12_2024/7pmi_13535.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/7pmi_13535/12_2024/7pmi_13535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pmi_13535/12_2024/7pmi_13535.map" model { file = "/net/cci-nas-00/data/ceres_data/7pmi_13535/12_2024/7pmi_13535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pmi_13535/12_2024/7pmi_13535.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 51 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10189 Number of models: 1 Model: "" Number of chains: 7 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: "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: 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: 7.06, per 1000 atoms: 0.69 Number of scatterers: 10189 At special positions: 0 Unit cell: (108.9, 130.9, 151.8, 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: 2.93 Conformation dependent library (CDL) restraints added in 1.5 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: 61 helices and 14 sheets defined 54.8% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.679A pdb=" N GLU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.521A pdb=" N ALA A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 207 removed outlier: 3.519A pdb=" N LYS A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 4.103A 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 246 through 250 Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.166A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 278 removed outlier: 3.560A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 278 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.869A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 4.125A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.756A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 480 Processing helix chain 'A' and resid 492 through 500 Processing helix chain 'A' and resid 504 through 515 removed outlier: 4.009A 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 removed outlier: 3.994A pdb=" N LYS A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.513A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 4.150A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 653 removed outlier: 3.655A pdb=" N ALA A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.861A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 683 " --> pdb=" O VAL A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 723 through 736 removed outlier: 3.821A pdb=" N THR A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 754 through 792 removed outlier: 3.683A pdb=" N TYR A 758 " --> pdb=" O GLY A 754 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.795A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.023A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.758A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.824A pdb=" N THR C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.783A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 232 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.541A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.380A 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 332 through 336 removed outlier: 4.602A pdb=" N LYS C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) 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 removed outlier: 4.006A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.239A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.730A 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: 4.160A 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 sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 7.302A pdb=" N GLN A 39 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 103 removed outlier: 6.399A pdb=" N LEU A 107 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE A 662 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA A 109 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N SER A 158 " --> pdb=" O HIS A 657 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLN A 157 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU A 436 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE A 159 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ILE A 438 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL A 161 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 211 removed outlier: 5.833A pdb=" N ALA A 209 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN A 216 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 342 Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 381 Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA7, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.594A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.820A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 removed outlier: 5.986A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB5, first strand: chain 'B' and resid 26 through 28 504 hydrogen bonds defined for protein. 1407 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: 3.59 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1713 1.31 - 1.44: 2744 1.44 - 1.56: 5835 1.56 - 1.69: 9 1.69 - 1.81: 102 Bond restraints: 10403 Sorted by residual: bond pdb=" O3A ANP A1901 " pdb=" PB ANP A1901 " ideal model delta sigma weight residual 1.700 1.539 0.161 2.00e-02 2.50e+03 6.48e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.436 0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 1.795 1.686 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.192 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" O5' ANP A1901 " pdb=" PA ANP A1901 " ideal model delta sigma weight residual 1.655 1.585 0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 10398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 13910 4.22 - 8.43: 133 8.43 - 12.65: 8 12.65 - 16.87: 1 16.87 - 21.08: 1 Bond angle restraints: 14053 Sorted by residual: angle pdb=" PB ANP A1901 " pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 126.95 105.87 21.08 3.00e+00 1.11e-01 4.94e+01 angle pdb=" N CYS H 5 " pdb=" CA CYS H 5 " pdb=" CB CYS H 5 " ideal model delta sigma weight residual 110.50 100.16 10.34 1.70e+00 3.46e-01 3.70e+01 angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 111.89 9.81 1.80e+00 3.09e-01 2.97e+01 angle pdb=" N DTH H 4 " pdb=" CA DTH H 4 " pdb=" CB DTH H 4 " ideal model delta sigma weight residual 111.50 103.03 8.47 1.70e+00 3.46e-01 2.48e+01 angle pdb=" N GLY A 563 " pdb=" CA GLY A 563 " pdb=" C GLY A 563 " ideal model delta sigma weight residual 113.86 121.03 -7.17 1.50e+00 4.44e-01 2.29e+01 ... (remaining 14048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.26: 6038 27.26 - 54.52: 198 54.52 - 81.78: 50 81.78 - 109.04: 8 109.04 - 136.30: 5 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 300.00 171.94 128.06 1 2.00e+01 2.50e-03 3.88e+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 61.86 -121.86 1 2.00e+01 2.50e-03 3.67e+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 57.07 -117.07 1 2.00e+01 2.50e-03 3.49e+01 ... (remaining 6296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1158 0.076 - 0.152: 334 0.152 - 0.228: 35 0.228 - 0.304: 5 0.304 - 0.380: 2 Chirality restraints: 1534 Sorted by residual: 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 2.13 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CA GLU C 316 " pdb=" N GLU C 316 " pdb=" C GLU C 316 " pdb=" CB GLU C 316 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.89e+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 2.23 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1531 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 784 " -0.284 9.50e-02 1.11e+02 1.55e-01 1.08e+02 pdb=" NE ARG A 784 " 0.077 2.00e-02 2.50e+03 pdb=" CZ ARG A 784 " -0.168 2.00e-02 2.50e+03 pdb=" NH1 ARG A 784 " 0.059 2.00e-02 2.50e+03 pdb=" NH2 ARG A 784 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 564 " -0.044 2.00e-02 2.50e+03 4.36e-02 3.32e+01 pdb=" CG PHE A 564 " 0.101 2.00e-02 2.50e+03 pdb=" CD1 PHE A 564 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE A 564 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 564 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 564 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 564 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 116 " -0.105 9.50e-02 1.11e+02 6.15e-02 2.08e+01 pdb=" NE ARG C 116 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG C 116 " -0.075 2.00e-02 2.50e+03 pdb=" NH1 ARG C 116 " 0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG C 116 " 0.022 2.00e-02 2.50e+03 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 21 2.37 - 3.00: 5889 3.00 - 3.63: 14691 3.63 - 4.27: 22860 4.27 - 4.90: 38693 Nonbonded interactions: 82154 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.733 3.620 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 1.928 2.170 nonbonded pdb=" O2G ANP A1901 " pdb="MG MG A1902 " model vdw 1.940 2.170 nonbonded pdb=" NH1 ARG A 784 " pdb=" O ARG B 37 " model vdw 2.086 3.120 nonbonded pdb=" O LYS B 26 " pdb=" NH2 ARG B 64 " model vdw 2.155 3.120 ... (remaining 82149 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: 2.210 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.130 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 : 0.014 0.161 10403 Z= 0.932 Angle : 1.173 21.081 14053 Z= 0.659 Chirality : 0.069 0.380 1534 Planarity : 0.010 0.155 1792 Dihedral : 15.803 136.295 3911 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.09 % Allowed : 0.28 % Favored : 99.63 % Cbeta Deviations : 0.17 % 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: -1.50 (0.21), residues: 1235 helix: -1.73 (0.16), residues: 627 sheet: 0.33 (0.37), residues: 167 loop : 0.02 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.006 TRP A 484 HIS 0.014 0.003 HIS A 418 PHE 0.101 0.004 PHE A 564 TYR 0.039 0.007 TYR A 477 ARG 0.171 0.015 ARG A 784 *********************** 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 85 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 1.141 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: B 66 ASP cc_start: 0.9297 (p0) cc_final: 0.8919 (p0) outliers start: 1 outliers final: 1 residues processed: 85 average time/residue: 0.3168 time to fit residues: 36.1661 Evaluate side-chains 59 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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: 2.9990 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 37 optimal weight: 0.0050 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 398 ASN A 493 GLN C 162 ASN C 280 ASN C 296 ASN B 75 GLN B 140 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10403 Z= 0.213 Angle : 0.656 7.443 14053 Z= 0.344 Chirality : 0.043 0.209 1534 Planarity : 0.004 0.040 1792 Dihedral : 10.856 152.322 1429 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.28 % Allowed : 3.78 % Favored : 95.94 % 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: 0.80 (0.23), residues: 1235 helix: 0.56 (0.20), residues: 624 sheet: 0.89 (0.39), residues: 161 loop : 0.63 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 484 HIS 0.006 0.001 HIS A 418 PHE 0.018 0.001 PHE A 564 TYR 0.014 0.002 TYR A 787 ARG 0.007 0.001 ARG A 683 *********************** 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 69 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 1.244 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: A 150 MET cc_start: 0.8018 (ttt) cc_final: 0.7786 (ttt) REVERT: B 66 ASP cc_start: 0.9301 (p0) cc_final: 0.9023 (t0) REVERT: B 120 MET cc_start: 0.7480 (mtm) cc_final: 0.6967 (ptm) outliers start: 3 outliers final: 0 residues processed: 68 average time/residue: 0.2694 time to fit residues: 26.3758 Evaluate side-chains 56 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN B 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10403 Z= 0.201 Angle : 0.572 7.749 14053 Z= 0.296 Chirality : 0.041 0.184 1534 Planarity : 0.004 0.037 1792 Dihedral : 9.732 153.828 1428 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.46 % Allowed : 3.87 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.40 (0.24), residues: 1235 helix: 1.38 (0.21), residues: 614 sheet: 0.69 (0.38), residues: 167 loop : 0.59 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 484 HIS 0.005 0.001 HIS A 418 PHE 0.014 0.001 PHE B 93 TYR 0.013 0.001 TYR A 787 ARG 0.004 0.000 ARG B 37 *********************** 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 60 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.9244 (p0) cc_final: 0.8943 (t0) REVERT: B 120 MET cc_start: 0.7315 (mtm) cc_final: 0.6810 (ptm) outliers start: 5 outliers final: 0 residues processed: 59 average time/residue: 0.2707 time to fit residues: 23.3578 Evaluate side-chains 53 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 0.0980 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN A 474 GLN A 638 HIS A 775 GLN B 140 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10403 Z= 0.230 Angle : 0.561 7.769 14053 Z= 0.286 Chirality : 0.041 0.174 1534 Planarity : 0.003 0.039 1792 Dihedral : 9.389 155.740 1428 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.55 % Allowed : 4.70 % Favored : 94.75 % 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: 1.70 (0.24), residues: 1235 helix: 1.76 (0.22), residues: 605 sheet: 0.59 (0.38), residues: 168 loop : 0.65 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 484 HIS 0.005 0.001 HIS A 418 PHE 0.011 0.001 PHE B 93 TYR 0.010 0.001 TYR A 102 ARG 0.003 0.000 ARG B 64 *********************** 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 62 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 1.227 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 66 ASP cc_start: 0.9258 (p0) cc_final: 0.8955 (t70) REVERT: B 120 MET cc_start: 0.7315 (mtm) cc_final: 0.6780 (ptm) outliers start: 6 outliers final: 1 residues processed: 58 average time/residue: 0.2445 time to fit residues: 21.0017 Evaluate side-chains 56 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 0.1980 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 0.0970 chunk 102 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10403 Z= 0.153 Angle : 0.541 8.799 14053 Z= 0.272 Chirality : 0.040 0.172 1534 Planarity : 0.003 0.044 1792 Dihedral : 9.071 158.695 1428 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.65 % Allowed : 5.71 % 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: 1.77 (0.24), residues: 1235 helix: 1.87 (0.22), residues: 610 sheet: 0.59 (0.40), residues: 153 loop : 0.60 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 781 HIS 0.004 0.001 HIS A 418 PHE 0.011 0.001 PHE B 93 TYR 0.011 0.001 TYR A 102 ARG 0.004 0.000 ARG A 784 *********************** 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 65 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.9191 (p0) cc_final: 0.8930 (t70) outliers start: 7 outliers final: 2 residues processed: 62 average time/residue: 0.2494 time to fit residues: 22.7403 Evaluate side-chains 57 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 239 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3127 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= 0.169 Angle : 0.567 11.050 14053 Z= 0.280 Chirality : 0.040 0.220 1534 Planarity : 0.003 0.045 1792 Dihedral : 8.923 158.296 1428 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.28 % Allowed : 7.47 % Favored : 92.26 % 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: 1.82 (0.24), residues: 1235 helix: 1.93 (0.22), residues: 611 sheet: 0.60 (0.41), residues: 153 loop : 0.60 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 781 HIS 0.006 0.001 HIS A 418 PHE 0.009 0.001 PHE B 93 TYR 0.010 0.001 TYR A 102 ARG 0.003 0.000 ARG B 64 *********************** 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 60 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.9193 (p0) cc_final: 0.8938 (t70) outliers start: 3 outliers final: 1 residues processed: 58 average time/residue: 0.2317 time to fit residues: 20.1075 Evaluate side-chains 55 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN B 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10403 Z= 0.196 Angle : 0.563 11.517 14053 Z= 0.281 Chirality : 0.040 0.175 1534 Planarity : 0.003 0.045 1792 Dihedral : 8.804 157.987 1428 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.46 % Allowed : 8.02 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.83 (0.24), residues: 1235 helix: 2.00 (0.22), residues: 609 sheet: 0.43 (0.40), residues: 156 loop : 0.58 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 781 HIS 0.007 0.001 HIS A 418 PHE 0.009 0.001 PHE C 255 TYR 0.009 0.001 TYR A 102 ARG 0.003 0.000 ARG B 37 *********************** 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: 5 poor density : 56 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 66 ASP cc_start: 0.9189 (p0) cc_final: 0.8918 (t70) outliers start: 5 outliers final: 2 residues processed: 59 average time/residue: 0.2620 time to fit residues: 23.4156 Evaluate side-chains 53 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain B residue 77 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 11 optimal weight: 0.0270 chunk 93 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10403 Z= 0.260 Angle : 0.601 11.531 14053 Z= 0.301 Chirality : 0.041 0.195 1534 Planarity : 0.003 0.046 1792 Dihedral : 8.783 157.183 1428 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.65 % Allowed : 8.29 % Favored : 91.06 % 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: 1.82 (0.24), residues: 1235 helix: 2.02 (0.22), residues: 607 sheet: 0.39 (0.38), residues: 170 loop : 0.56 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 781 HIS 0.008 0.001 HIS A 418 PHE 0.009 0.001 PHE C 255 TYR 0.010 0.001 TYR A 263 ARG 0.010 0.000 ARG A 231 *********************** 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 60 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.9173 (p0) cc_final: 0.8882 (t70) outliers start: 7 outliers final: 4 residues processed: 58 average time/residue: 0.2171 time to fit residues: 19.5558 Evaluate side-chains 57 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 384 THR 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 114 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10403 Z= 0.193 Angle : 0.579 11.036 14053 Z= 0.289 Chirality : 0.040 0.178 1534 Planarity : 0.003 0.044 1792 Dihedral : 8.710 157.314 1428 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.28 % Allowed : 8.39 % 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: 1.80 (0.24), residues: 1235 helix: 2.02 (0.22), residues: 609 sheet: 0.27 (0.39), residues: 159 loop : 0.57 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 781 HIS 0.006 0.001 HIS A 418 PHE 0.008 0.001 PHE C 255 TYR 0.009 0.001 TYR A 102 ARG 0.003 0.000 ARG A 231 *********************** 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 59 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.9188 (p0) cc_final: 0.8918 (t70) outliers start: 3 outliers final: 3 residues processed: 58 average time/residue: 0.2149 time to fit residues: 19.3071 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 : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 384 THR 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 117 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 0.0980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 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 0.040 10403 Z= 0.272 Angle : 0.623 12.317 14053 Z= 0.309 Chirality : 0.041 0.175 1534 Planarity : 0.003 0.043 1792 Dihedral : 8.722 156.000 1428 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.37 % Allowed : 8.66 % Favored : 90.97 % 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: 1.79 (0.24), residues: 1235 helix: 2.00 (0.22), residues: 607 sheet: 0.34 (0.38), residues: 169 loop : 0.57 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 781 HIS 0.008 0.001 HIS A 418 PHE 0.009 0.001 PHE C 255 TYR 0.010 0.001 TYR A 175 ARG 0.004 0.000 ARG A 231 ********************** 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 57 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.9163 (p0) cc_final: 0.8928 (t0) outliers start: 4 outliers final: 3 residues processed: 56 average time/residue: 0.2214 time to fit residues: 19.3050 Evaluate side-chains 55 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 384 THR 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 104 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 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 = 0.3312 r_free = 0.3312 target = 0.049765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.035516 restraints weight = 54523.882| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 3.93 r_work: 0.2612 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 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 0.044 10403 Z= 0.223 Angle : 0.617 11.292 14053 Z= 0.307 Chirality : 0.041 0.172 1534 Planarity : 0.003 0.043 1792 Dihedral : 8.700 155.857 1428 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.28 % Allowed : 8.76 % Favored : 90.97 % 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: 1.69 (0.24), residues: 1235 helix: 1.96 (0.22), residues: 612 sheet: 0.35 (0.37), residues: 176 loop : 0.39 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 781 HIS 0.006 0.001 HIS A 418 PHE 0.008 0.001 PHE C 255 TYR 0.009 0.001 TYR A 102 ARG 0.003 0.000 ARG A 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1930.30 seconds wall clock time: 36 minutes 55.24 seconds (2215.24 seconds total)