Starting phenix.real_space_refine on Sun May 3 02:10:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nb3_49207/05_2026/9nb3_49207.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nb3_49207/05_2026/9nb3_49207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nb3_49207/05_2026/9nb3_49207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nb3_49207/05_2026/9nb3_49207.map" model { file = "/net/cci-nas-00/data/ceres_data/9nb3_49207/05_2026/9nb3_49207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nb3_49207/05_2026/9nb3_49207.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.040 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 9 5.49 5 Mg 3 5.21 5 S 47 5.16 5 C 6130 2.51 5 N 1766 2.21 5 O 1817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9772 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9592 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1301, 9488 Classifications: {'peptide': 1301} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PCIS': 1, 'PTRANS': 100, 'TRANS': 1199} Chain breaks: 4 Unresolved non-hydrogen bonds: 445 Unresolved non-hydrogen angles: 546 Unresolved non-hydrogen dihedrals: 353 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 41, 'GLN:plan1': 4, 'ASP:plan': 20, 'ASN:plan1': 5, 'PHE:plan': 1, 'ARG:plan': 11, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 325 Conformer: "B" Number of residues, atoms: 1301, 9488 Classifications: {'peptide': 1301} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PCIS': 1, 'PTRANS': 100, 'TRANS': 1199} Chain breaks: 4 Unresolved non-hydrogen bonds: 445 Unresolved non-hydrogen angles: 546 Unresolved non-hydrogen dihedrals: 353 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 41, 'GLN:plan1': 4, 'ASP:plan': 20, 'ASN:plan1': 5, 'PHE:plan': 1, 'ARG:plan': 11, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 325 bond proxies already assigned to first conformer: 9617 Chain: "A" Number of atoms: 180 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 66, 149 Unusual residues: {' MG': 3, 'ADP': 1, 'ANP': 1, 'FGR': 1} Inner-chain residues flagged as termini: ['pdbres="GLN A1404 "'] Classifications: {'peptide': 1, 'undetermined': 6, 'water': 59} Modifications used: {'COO': 1} Link IDs: {None: 65} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:plan1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 66, 149 Unusual residues: {' MG': 3, 'ADP': 1, 'ANP': 1, 'FGR': 1} Inner-chain residues flagged as termini: ['pdbres="GLN A1404 "'] Classifications: {'peptide': 1, 'undetermined': 6, 'water': 59} Modifications used: {'COO': 1} Link IDs: {None: 65} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:plan1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 57 Residues with excluded nonbonded symmetry interactions: 13 residue: pdb=" N ASER A 160 " occ=0.24 ... (10 atoms not shown) pdb=" OG BSER A 160 " occ=0.76 residue: pdb=" N APHE A 161 " occ=0.24 ... (8 atoms not shown) pdb=" CB BPHE A 161 " occ=0.76 residue: pdb=" N ASER A 162 " occ=0.24 ... (10 atoms not shown) pdb=" OG BSER A 162 " occ=0.76 residue: pdb=" N AGLU A 228 " occ=0.53 ... (16 atoms not shown) pdb=" OE2BGLU A 228 " occ=0.47 residue: pdb=" N ALYS A 236 " occ=0.60 ... (16 atoms not shown) pdb=" NZ BLYS A 236 " occ=0.40 residue: pdb=" N AARG A 285 " occ=0.60 ... (20 atoms not shown) pdb=" NH2BARG A 285 " occ=0.40 residue: pdb=" N AGLU A 490 " occ=0.61 ... (16 atoms not shown) pdb=" OE2BGLU A 490 " occ=0.39 residue: pdb=" N AGLN A 560 " occ=0.47 ... (16 atoms not shown) pdb=" NE2BGLN A 560 " occ=0.53 residue: pdb=" N AARG A 568 " occ=0.58 ... (20 atoms not shown) pdb=" NH2BARG A 568 " occ=0.42 residue: pdb=" N AARG A 596 " occ=0.47 ... (20 atoms not shown) pdb=" NH2BARG A 596 " occ=0.53 residue: pdb=" N ALYS A 803 " occ=0.34 ... (16 atoms not shown) pdb=" NZ BLYS A 803 " occ=0.66 residue: pdb=" N AGLN A1324 " occ=0.31 ... (16 atoms not shown) pdb=" NE2BGLN A1324 " occ=0.69 residue: pdb=" C1'AANP A1402 " occ=0.57 ... (60 atoms not shown) pdb=" PG BANP A1402 " occ=0.43 Time building chain proxies: 3.88, per 1000 atoms: 0.40 Number of scatterers: 9772 At special positions: 0 Unit cell: (91.932, 101.712, 101.06, 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 47 16.00 P 9 15.00 Mg 3 11.99 O 1817 8.00 N 1766 7.00 C 6130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 846.0 milliseconds 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2378 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 14 sheets defined 33.7% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 17 through 30 removed outlier: 6.246A pdb=" N ARG A 23 " --> pdb=" O PRO A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 135 through 146 removed outlier: 3.765A pdb=" N HIS A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 182 through 191 removed outlier: 3.721A pdb=" N LYS A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN A 189 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 318 through 336 Processing helix chain 'A' and resid 377 through 397 removed outlier: 3.961A pdb=" N SER A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN A 387 " --> pdb=" O ILE A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 468 Processing helix chain 'A' and resid 488 through 504 Processing helix chain 'A' and resid 521 through 529 removed outlier: 3.890A pdb=" N VAL A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 550 through 556 Processing helix chain 'A' and resid 571 through 583 Processing helix chain 'A' and resid 629 through 633 Processing helix chain 'A' and resid 660 through 669 removed outlier: 3.636A pdb=" N ARG A 667 " --> pdb=" O GLN A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 734 removed outlier: 3.843A pdb=" N LEU A 733 " --> pdb=" O VAL A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 752 removed outlier: 3.539A pdb=" N ALA A 739 " --> pdb=" O ASP A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 761 Processing helix chain 'A' and resid 776 through 796 removed outlier: 3.598A pdb=" N ALA A 780 " --> pdb=" O GLY A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 872 removed outlier: 3.595A pdb=" N GLN A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 902 removed outlier: 3.782A pdb=" N LEU A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 925 Processing helix chain 'A' and resid 940 through 946 Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 1004 through 1012 Processing helix chain 'A' and resid 1013 through 1020 Processing helix chain 'A' and resid 1024 through 1038 Processing helix chain 'A' and resid 1075 through 1086 Processing helix chain 'A' and resid 1094 through 1100 Processing helix chain 'A' and resid 1117 through 1122 removed outlier: 3.696A pdb=" N ALA A1120 " --> pdb=" O PHE A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1136 Processing helix chain 'A' and resid 1136 through 1148 Processing helix chain 'A' and resid 1158 through 1167 Processing helix chain 'A' and resid 1242 through 1252 removed outlier: 3.550A pdb=" N GLN A1246 " --> pdb=" O SER A1242 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A1248 " --> pdb=" O GLU A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1302 removed outlier: 3.863A pdb=" N VAL A1302 " --> pdb=" O GLU A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1316 removed outlier: 4.522A pdb=" N THR A1316 " --> pdb=" O PRO A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1322 through 1335 removed outlier: 4.085A pdb=" N PHE A1326 " --> pdb=" O TRP A1322 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA A1329 " --> pdb=" O LEU A1325 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG A1330 " --> pdb=" O PHE A1326 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 74 removed outlier: 4.451A pdb=" N ARG A 118 " --> pdb=" O ASN A 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 244 through 245 removed outlier: 3.627A pdb=" N GLN A 244 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N HIS A 240 " --> pdb=" O LEU A 643 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 274 through 286 removed outlier: 5.237A pdb=" N ALA A 275 " --> pdb=" O PHE A 306 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N PHE A 306 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLN A 277 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL A 304 " --> pdb=" O GLN A 277 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A 279 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A 302 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 281 " --> pdb=" O GLY A 300 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 274 through 286 removed outlier: 5.237A pdb=" N ALA A 275 " --> pdb=" O PHE A 306 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N PHE A 306 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLN A 277 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL A 304 " --> pdb=" O GLN A 277 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A 279 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A 302 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 281 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 345 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER A 432 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL A 343 " --> pdb=" O SER A 432 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 410 through 411 Processing sheet with id=AA6, first strand: chain 'A' and resid 511 through 516 removed outlier: 4.548A pdb=" N SER A 513 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 564 " --> pdb=" O HIS A 515 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL A 449 " --> pdb=" O VAL A 589 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL A 589 " --> pdb=" O TYR A 538 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR A 538 " --> pdb=" O VAL A 589 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 692 through 694 removed outlier: 6.392A pdb=" N VAL A 710 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ILE A 719 " --> pdb=" O LEU A 713 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 763 through 764 Processing sheet with id=AA9, first strand: chain 'A' and resid 803 through 804 removed outlier: 3.754A pdb=" N SER A 822 " --> pdb=" O MET A 769 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 811 through 812 Processing sheet with id=AB2, first strand: chain 'A' and resid 904 through 906 removed outlier: 8.363A pdb=" N LEU A 904 " --> pdb=" O GLN A 957 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N GLN A 957 " --> pdb=" O LEU A 904 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLY A 849 " --> pdb=" O HIS A 980 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N HIS A 980 " --> pdb=" O GLY A 849 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU A 851 " --> pdb=" O LEU A 978 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N HIS A 974 " --> pdb=" O ALA A 855 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LEU A 978 " --> pdb=" O ASP A 933 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS A 980 " --> pdb=" O GLN A 931 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N GLY A 929 " --> pdb=" O GLY A 982 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N MET A 989 " --> pdb=" O CYS A 928 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A 930 " --> pdb=" O MET A 989 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL A 990 " --> pdb=" O GLU A1001 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU A1001 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 992 " --> pdb=" O VAL A 999 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1089 through 1091 removed outlier: 6.434A pdb=" N VAL A1065 " --> pdb=" O TRP A1091 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ALA A1112 " --> pdb=" O ARG A1064 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA A1066 " --> pdb=" O ALA A1112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1203 through 1205 Processing sheet with id=AB5, first strand: chain 'A' and resid 1227 through 1228 removed outlier: 3.863A pdb=" N LEU A1227 " --> pdb=" O VAL A1209 " (cutoff:3.500A) 376 hydrogen bonds defined for protein. 1059 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: 2.11 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1587 1.31 - 1.43: 2611 1.43 - 1.56: 5685 1.56 - 1.68: 16 1.68 - 1.81: 69 Bond restraints: 9968 Sorted by residual: bond pdb=" C1 FGR A1401 " pdb=" C2 FGR A1401 " ideal model delta sigma weight residual 1.556 1.266 0.290 2.00e-02 2.50e+03 2.11e+02 bond pdb=" C5 FGR A1401 " pdb=" O4 FGR A1401 " ideal model delta sigma weight residual 1.458 1.278 0.180 2.00e-02 2.50e+03 8.11e+01 bond pdb=" O18 FGR A1401 " pdb=" P15 FGR A1401 " ideal model delta sigma weight residual 1.672 1.512 0.160 2.00e-02 2.50e+03 6.39e+01 bond pdb=" O17 FGR A1401 " pdb=" P15 FGR A1401 " ideal model delta sigma weight residual 1.669 1.509 0.160 2.00e-02 2.50e+03 6.36e+01 bond pdb=" C3 FGR A1401 " pdb=" N19 FGR A1401 " ideal model delta sigma weight residual 1.471 1.314 0.157 2.00e-02 2.50e+03 6.20e+01 ... (remaining 9963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.05: 13652 11.05 - 22.11: 5 22.11 - 33.16: 0 33.16 - 44.21: 0 44.21 - 55.27: 1 Bond angle restraints: 13658 Sorted by residual: angle pdb=" O17 FGR A1401 " pdb=" P15 FGR A1401 " pdb=" O18 FGR A1401 " ideal model delta sigma weight residual 54.40 109.67 -55.27 3.00e+00 1.11e-01 3.39e+02 angle pdb=" N GLU A 444 " pdb=" CA GLU A 444 " pdb=" C GLU A 444 " ideal model delta sigma weight residual 108.07 102.43 5.64 8.90e-01 1.26e+00 4.02e+01 angle pdb=" O16 FGR A1401 " pdb=" P15 FGR A1401 " pdb=" O18 FGR A1401 " ideal model delta sigma weight residual 127.56 109.28 18.28 3.00e+00 1.11e-01 3.71e+01 angle pdb=" O16 FGR A1401 " pdb=" P15 FGR A1401 " pdb=" O17 FGR A1401 " ideal model delta sigma weight residual 128.09 110.07 18.02 3.00e+00 1.11e-01 3.61e+01 angle pdb=" PB BANP A1402 " pdb=" N3BBANP A1402 " pdb=" PG BANP A1402 " ideal model delta sigma weight residual 126.95 109.64 17.31 3.00e+00 1.11e-01 3.33e+01 ... (remaining 13653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.24: 5659 33.24 - 66.49: 266 66.49 - 99.73: 24 99.73 - 132.98: 0 132.98 - 166.22: 2 Dihedral angle restraints: 5951 sinusoidal: 2235 harmonic: 3716 Sorted by residual: dihedral pdb=" CA BPHE A 161 " pdb=" C BPHE A 161 " pdb=" N BSER A 162 " pdb=" CA BSER A 162 " ideal model delta harmonic sigma weight residual 180.00 -154.03 -25.97 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA ASP A 221 " pdb=" C ASP A 221 " pdb=" N LEU A 222 " pdb=" CA LEU A 222 " ideal model delta harmonic sigma weight residual 180.00 154.79 25.21 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" C5' ADP A1403 " pdb=" O5' ADP A1403 " pdb=" PA ADP A1403 " pdb=" O2A ADP A1403 " ideal model delta sinusoidal sigma weight residual -60.00 -148.61 88.61 1 2.00e+01 2.50e-03 2.34e+01 ... (remaining 5948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1439 0.096 - 0.193: 84 0.193 - 0.289: 4 0.289 - 0.385: 2 0.385 - 0.482: 2 Chirality restraints: 1531 Sorted by residual: chirality pdb=" CA ALA A 706 " pdb=" N ALA A 706 " pdb=" C ALA A 706 " pdb=" CB ALA A 706 " both_signs ideal model delta sigma weight residual False 2.48 2.00 0.48 2.00e-01 2.50e+01 5.80e+00 chirality pdb=" CA CYS A1158 " pdb=" N CYS A1158 " pdb=" C CYS A1158 " pdb=" CB CYS A1158 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" CA ASP A 800 " pdb=" N ASP A 800 " pdb=" C ASP A 800 " pdb=" CB ASP A 800 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 1528 not shown) Planarity restraints: 1802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A1312 " -0.065 5.00e-02 4.00e+02 9.51e-02 1.45e+01 pdb=" N PRO A1313 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO A1313 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A1313 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 800 " -0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C ASP A 800 " 0.062 2.00e-02 2.50e+03 pdb=" O ASP A 800 " -0.023 2.00e-02 2.50e+03 pdb=" N GLY A 801 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 441 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C GLU A 441 " -0.057 2.00e-02 2.50e+03 pdb=" O GLU A 441 " 0.022 2.00e-02 2.50e+03 pdb=" N ALA A 442 " 0.019 2.00e-02 2.50e+03 ... (remaining 1799 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.29: 17 2.29 - 2.94: 4634 2.94 - 3.59: 14311 3.59 - 4.25: 23385 4.25 - 4.90: 40081 Nonbonded interactions: 82428 Sorted by model distance: nonbonded pdb=" SG CYS A1158 " pdb=" CD GLN A1404 " model vdw 1.634 3.630 nonbonded pdb=" O3B ADP A1403 " pdb="MG MG A1406 " model vdw 1.780 2.170 nonbonded pdb=" OE2 GLU A 727 " pdb="MG MG A1406 " model vdw 1.880 2.170 nonbonded pdb=" OE2 GLU A 746 " pdb="MG MG A1406 " model vdw 2.056 2.170 nonbonded pdb=" O3AAANP A1402 " pdb=" O3GAANP A1402 " model vdw 2.070 3.040 ... (remaining 82423 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.24 max=1.00 mean=0.99 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: 2.800 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.890 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 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 : 0.008 0.290 9968 Z= 0.405 Angle : 0.955 55.266 13658 Z= 0.429 Chirality : 0.049 0.482 1531 Planarity : 0.007 0.095 1802 Dihedral : 18.398 166.222 3573 Min Nonbonded Distance : 1.634 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.22 % Favored : 89.39 % Rotamer: Outliers : 1.17 % Allowed : 27.61 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.23), residues: 1323 helix: 0.20 (0.25), residues: 436 sheet: -1.35 (0.35), residues: 227 loop : -2.29 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 902 TYR 0.027 0.002 TYR A1202 PHE 0.011 0.001 PHE A 426 TRP 0.024 0.002 TRP A 770 HIS 0.015 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00799 ( 9968) covalent geometry : angle 0.95520 (13658) hydrogen bonds : bond 0.17861 ( 367) hydrogen bonds : angle 7.78680 ( 1059) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 169 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 558 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7740 (mt-10) REVERT: A 581 ARG cc_start: 0.8143 (ttp80) cc_final: 0.7777 (ttt90) outliers start: 3 outliers final: 3 residues processed: 171 average time/residue: 0.1028 time to fit residues: 24.2039 Evaluate side-chains 169 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 166 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 1158 CYS Chi-restraints excluded: chain A residue 1404 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 560 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 ASN A1275 ASN A1306 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.128149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.110455 restraints weight = 74102.156| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 5.10 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9968 Z= 0.172 Angle : 0.688 10.444 13658 Z= 0.338 Chirality : 0.046 0.176 1531 Planarity : 0.006 0.078 1802 Dihedral : 9.964 168.905 1525 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.37 % Favored : 91.25 % Rotamer: Outliers : 4.48 % Allowed : 26.01 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.23), residues: 1323 helix: 0.36 (0.25), residues: 441 sheet: -1.16 (0.36), residues: 222 loop : -2.20 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1303 TYR 0.012 0.002 TYR A 559 PHE 0.013 0.002 PHE A 396 TRP 0.025 0.002 TRP A 770 HIS 0.007 0.001 HIS A1297 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 9968) covalent geometry : angle 0.68793 (13658) hydrogen bonds : bond 0.03867 ( 367) hydrogen bonds : angle 5.71368 ( 1059) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 447 MET cc_start: 0.5588 (OUTLIER) cc_final: 0.5174 (mtm) REVERT: A 1039 MET cc_start: 0.7411 (tpp) cc_final: 0.7138 (mpp) REVERT: A 1090 VAL cc_start: 0.7182 (OUTLIER) cc_final: 0.6948 (t) REVERT: A 1152 THR cc_start: 0.8138 (p) cc_final: 0.7767 (t) REVERT: A 1320 SER cc_start: 0.6756 (OUTLIER) cc_final: 0.6486 (t) outliers start: 35 outliers final: 18 residues processed: 197 average time/residue: 0.1023 time to fit residues: 27.9944 Evaluate side-chains 182 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1158 CYS Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1284 ILE Chi-restraints excluded: chain A residue 1320 SER Chi-restraints excluded: chain A residue 1404 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 125 optimal weight: 0.0050 chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 18 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 123 optimal weight: 0.0270 chunk 111 optimal weight: 2.9990 overall best weight: 0.8656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.128330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.110497 restraints weight = 74802.793| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 5.49 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9968 Z= 0.171 Angle : 0.676 9.513 13658 Z= 0.330 Chirality : 0.045 0.174 1531 Planarity : 0.006 0.079 1802 Dihedral : 9.874 179.573 1523 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.06 % Favored : 91.63 % Rotamer: Outliers : 4.05 % Allowed : 26.33 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.23), residues: 1323 helix: 0.37 (0.25), residues: 439 sheet: -1.10 (0.36), residues: 209 loop : -2.14 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 902 TYR 0.010 0.001 TYR A 559 PHE 0.011 0.002 PHE A 426 TRP 0.027 0.002 TRP A 770 HIS 0.007 0.001 HIS A1297 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 9968) covalent geometry : angle 0.67599 (13658) hydrogen bonds : bond 0.03755 ( 367) hydrogen bonds : angle 5.36917 ( 1059) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 447 MET cc_start: 0.5666 (OUTLIER) cc_final: 0.5361 (mtm) REVERT: A 592 ILE cc_start: 0.6971 (mp) cc_final: 0.6734 (mt) REVERT: A 936 VAL cc_start: 0.8192 (t) cc_final: 0.7936 (t) REVERT: A 1039 MET cc_start: 0.7424 (mpp) cc_final: 0.7094 (mpp) REVERT: A 1152 THR cc_start: 0.8108 (OUTLIER) cc_final: 0.7772 (t) REVERT: A 1320 SER cc_start: 0.6720 (OUTLIER) cc_final: 0.6416 (t) outliers start: 31 outliers final: 19 residues processed: 194 average time/residue: 0.0932 time to fit residues: 25.7674 Evaluate side-chains 188 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1158 CYS Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1284 ILE Chi-restraints excluded: chain A residue 1320 SER Chi-restraints excluded: chain A residue 1404 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 59 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 20 optimal weight: 0.0050 chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 86 optimal weight: 0.8980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** A1096 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.129790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.112395 restraints weight = 64750.440| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 4.84 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9968 Z= 0.140 Angle : 0.645 8.615 13658 Z= 0.315 Chirality : 0.044 0.165 1531 Planarity : 0.006 0.081 1802 Dihedral : 9.246 169.079 1523 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.51 % Favored : 92.18 % Rotamer: Outliers : 4.58 % Allowed : 26.23 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.23), residues: 1323 helix: 0.50 (0.25), residues: 440 sheet: -1.04 (0.37), residues: 214 loop : -2.00 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 902 TYR 0.009 0.001 TYR A 559 PHE 0.012 0.001 PHE A1016 TRP 0.028 0.002 TRP A 770 HIS 0.005 0.001 HIS A1297 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9968) covalent geometry : angle 0.64464 (13658) hydrogen bonds : bond 0.03395 ( 367) hydrogen bonds : angle 5.08358 ( 1059) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.326 Fit side-chains REVERT: A 447 MET cc_start: 0.5589 (OUTLIER) cc_final: 0.5345 (mtm) REVERT: A 631 TRP cc_start: 0.7623 (t-100) cc_final: 0.7347 (t-100) REVERT: A 936 VAL cc_start: 0.8198 (t) cc_final: 0.7943 (t) REVERT: A 1039 MET cc_start: 0.7384 (mpp) cc_final: 0.7081 (mpp) REVERT: A 1152 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7731 (t) REVERT: A 1320 SER cc_start: 0.6608 (OUTLIER) cc_final: 0.6385 (t) outliers start: 36 outliers final: 21 residues processed: 198 average time/residue: 0.0977 time to fit residues: 27.1448 Evaluate side-chains 188 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1158 CYS Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1284 ILE Chi-restraints excluded: chain A residue 1320 SER Chi-restraints excluded: chain A residue 1404 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 0.2980 chunk 15 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 22 optimal weight: 0.0170 chunk 69 optimal weight: 0.2980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 HIS ** A 560 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.130506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.112577 restraints weight = 71412.995| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 5.38 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9968 Z= 0.128 Angle : 0.646 14.153 13658 Z= 0.310 Chirality : 0.043 0.187 1531 Planarity : 0.006 0.082 1802 Dihedral : 8.960 164.040 1523 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.74 % Favored : 92.95 % Rotamer: Outliers : 4.05 % Allowed : 26.87 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.24), residues: 1323 helix: 0.61 (0.26), residues: 442 sheet: -1.01 (0.34), residues: 242 loop : -1.96 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 902 TYR 0.008 0.001 TYR A 559 PHE 0.009 0.001 PHE A 542 TRP 0.028 0.002 TRP A 770 HIS 0.005 0.001 HIS A1196 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9968) covalent geometry : angle 0.64559 (13658) hydrogen bonds : bond 0.03242 ( 367) hydrogen bonds : angle 4.85087 ( 1059) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.339 Fit side-chains REVERT: A 631 TRP cc_start: 0.7654 (t-100) cc_final: 0.7349 (t-100) REVERT: A 936 VAL cc_start: 0.8182 (t) cc_final: 0.7934 (t) REVERT: A 1039 MET cc_start: 0.7451 (mpp) cc_final: 0.7142 (mpp) REVERT: A 1152 THR cc_start: 0.8017 (OUTLIER) cc_final: 0.7705 (t) REVERT: A 1320 SER cc_start: 0.6602 (OUTLIER) cc_final: 0.6386 (t) outliers start: 31 outliers final: 22 residues processed: 195 average time/residue: 0.0899 time to fit residues: 24.9049 Evaluate side-chains 190 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 974 HIS Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1158 CYS Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1233 HIS Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1284 ILE Chi-restraints excluded: chain A residue 1320 SER Chi-restraints excluded: chain A residue 1404 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 33 optimal weight: 0.7980 chunk 69 optimal weight: 0.0270 chunk 12 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 118 optimal weight: 0.0970 chunk 109 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 97 optimal weight: 0.0040 chunk 25 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.3448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1275 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 = 0.3743 r_free = 0.3743 target = 0.132056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.113960 restraints weight = 74264.343| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 5.68 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3501 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9968 Z= 0.118 Angle : 0.632 13.710 13658 Z= 0.304 Chirality : 0.042 0.157 1531 Planarity : 0.006 0.083 1802 Dihedral : 8.693 161.157 1523 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.89 % Favored : 92.80 % Rotamer: Outliers : 3.94 % Allowed : 27.08 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.24), residues: 1323 helix: 0.70 (0.26), residues: 442 sheet: -0.92 (0.34), residues: 244 loop : -1.90 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 902 TYR 0.009 0.001 TYR A 559 PHE 0.010 0.001 PHE A 542 TRP 0.028 0.001 TRP A 770 HIS 0.004 0.001 HIS A1297 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9968) covalent geometry : angle 0.63183 (13658) hydrogen bonds : bond 0.03060 ( 367) hydrogen bonds : angle 4.70453 ( 1059) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.317 Fit side-chains REVERT: A 631 TRP cc_start: 0.7665 (t-100) cc_final: 0.7380 (t-100) REVERT: A 702 GLN cc_start: 0.7525 (mm-40) cc_final: 0.7303 (mm110) REVERT: A 936 VAL cc_start: 0.8161 (t) cc_final: 0.7921 (t) REVERT: A 1039 MET cc_start: 0.7400 (mpp) cc_final: 0.7088 (mpp) REVERT: A 1152 THR cc_start: 0.7948 (OUTLIER) cc_final: 0.7661 (t) REVERT: A 1320 SER cc_start: 0.6521 (OUTLIER) cc_final: 0.6294 (t) outliers start: 30 outliers final: 20 residues processed: 183 average time/residue: 0.0962 time to fit residues: 25.0475 Evaluate side-chains 187 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1233 HIS Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1284 ILE Chi-restraints excluded: chain A residue 1320 SER Chi-restraints excluded: chain A residue 1404 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 11 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.129177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.111637 restraints weight = 69303.374| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 4.99 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9968 Z= 0.170 Angle : 0.666 12.791 13658 Z= 0.321 Chirality : 0.045 0.166 1531 Planarity : 0.006 0.082 1802 Dihedral : 8.645 161.452 1522 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.59 % Favored : 92.10 % Rotamer: Outliers : 4.05 % Allowed : 27.08 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.23), residues: 1323 helix: 0.62 (0.25), residues: 441 sheet: -0.76 (0.34), residues: 244 loop : -1.96 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 581 TYR 0.010 0.001 TYR A 679 PHE 0.012 0.002 PHE A 426 TRP 0.037 0.002 TRP A 770 HIS 0.005 0.001 HIS A1196 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 9968) covalent geometry : angle 0.66582 (13658) hydrogen bonds : bond 0.03471 ( 367) hydrogen bonds : angle 4.78094 ( 1059) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.322 Fit side-chains REVERT: A 226 ASN cc_start: 0.7162 (t0) cc_final: 0.6937 (t0) REVERT: A 558 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7238 (mt-10) REVERT: A 936 VAL cc_start: 0.8189 (t) cc_final: 0.7939 (t) REVERT: A 1039 MET cc_start: 0.7336 (mpp) cc_final: 0.7028 (mpp) REVERT: A 1311 PRO cc_start: 0.8533 (Cg_endo) cc_final: 0.8311 (Cg_exo) REVERT: A 1320 SER cc_start: 0.6731 (OUTLIER) cc_final: 0.6424 (t) outliers start: 31 outliers final: 21 residues processed: 193 average time/residue: 0.0939 time to fit residues: 25.9861 Evaluate side-chains 187 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 974 HIS Chi-restraints excluded: chain A residue 1158 CYS Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1233 HIS Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1284 ILE Chi-restraints excluded: chain A residue 1320 SER Chi-restraints excluded: chain A residue 1404 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 123 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 GLN ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 ASN A1159 ASN A1162 GLN ** A1233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.127912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.110797 restraints weight = 63772.347| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 4.73 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9968 Z= 0.196 Angle : 0.687 12.382 13658 Z= 0.333 Chirality : 0.046 0.167 1531 Planarity : 0.006 0.083 1802 Dihedral : 8.750 160.908 1522 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.98 % Favored : 91.71 % Rotamer: Outliers : 3.94 % Allowed : 26.65 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.23), residues: 1323 helix: 0.54 (0.25), residues: 437 sheet: -0.77 (0.35), residues: 227 loop : -2.03 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 581 TYR 0.012 0.002 TYR A 8 PHE 0.014 0.002 PHE A 426 TRP 0.037 0.002 TRP A 770 HIS 0.006 0.001 HIS A1196 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 9968) covalent geometry : angle 0.68716 (13658) hydrogen bonds : bond 0.03648 ( 367) hydrogen bonds : angle 4.87600 ( 1059) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.352 Fit side-chains REVERT: A 220 PHE cc_start: 0.7067 (t80) cc_final: 0.6742 (t80) REVERT: A 558 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7301 (mt-10) REVERT: A 936 VAL cc_start: 0.8165 (t) cc_final: 0.7915 (t) REVERT: A 1039 MET cc_start: 0.7300 (mpp) cc_final: 0.6976 (mpp) REVERT: A 1152 THR cc_start: 0.7952 (p) cc_final: 0.7713 (t) REVERT: A 1320 SER cc_start: 0.6746 (OUTLIER) cc_final: 0.6439 (t) outliers start: 30 outliers final: 25 residues processed: 192 average time/residue: 0.0951 time to fit residues: 26.1033 Evaluate side-chains 196 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 974 HIS Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1158 CYS Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1233 HIS Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1284 ILE Chi-restraints excluded: chain A residue 1320 SER Chi-restraints excluded: chain A residue 1404 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 123 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 GLN ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.128293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.110090 restraints weight = 80514.455| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 5.82 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 9968 Z= 0.196 Angle : 0.944 59.199 13658 Z= 0.516 Chirality : 0.045 0.300 1531 Planarity : 0.006 0.083 1802 Dihedral : 8.769 160.880 1522 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.98 % Favored : 91.71 % Rotamer: Outliers : 3.73 % Allowed : 26.87 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.23), residues: 1323 helix: 0.55 (0.25), residues: 437 sheet: -0.77 (0.35), residues: 227 loop : -2.04 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1205 TYR 0.011 0.001 TYR A 8 PHE 0.013 0.002 PHE A 426 TRP 0.032 0.002 TRP A 770 HIS 0.005 0.001 HIS A1196 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 9968) covalent geometry : angle 0.94371 (13658) hydrogen bonds : bond 0.03627 ( 367) hydrogen bonds : angle 4.87917 ( 1059) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.279 Fit side-chains REVERT: A 220 PHE cc_start: 0.7089 (t80) cc_final: 0.6752 (t80) REVERT: A 558 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7316 (mt-10) REVERT: A 936 VAL cc_start: 0.8176 (t) cc_final: 0.7922 (t) REVERT: A 1039 MET cc_start: 0.7434 (mpp) cc_final: 0.7102 (mpp) REVERT: A 1152 THR cc_start: 0.8007 (p) cc_final: 0.7737 (t) REVERT: A 1320 SER cc_start: 0.6784 (OUTLIER) cc_final: 0.6487 (t) outliers start: 28 outliers final: 24 residues processed: 188 average time/residue: 0.0932 time to fit residues: 24.7990 Evaluate side-chains 195 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 974 HIS Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1158 CYS Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1233 HIS Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1284 ILE Chi-restraints excluded: chain A residue 1320 SER Chi-restraints excluded: chain A residue 1404 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 33 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 83 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 122 optimal weight: 0.2980 chunk 64 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 GLN ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.128247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110288 restraints weight = 75026.933| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 5.24 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3445 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3445 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 9968 Z= 0.196 Angle : 0.944 59.199 13658 Z= 0.516 Chirality : 0.045 0.300 1531 Planarity : 0.006 0.083 1802 Dihedral : 8.769 160.880 1522 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.98 % Favored : 91.71 % Rotamer: Outliers : 3.41 % Allowed : 27.08 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.23), residues: 1323 helix: 0.55 (0.25), residues: 437 sheet: -0.77 (0.35), residues: 227 loop : -2.04 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1205 TYR 0.011 0.001 TYR A 8 PHE 0.013 0.002 PHE A 426 TRP 0.032 0.002 TRP A 770 HIS 0.005 0.001 HIS A1196 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 9968) covalent geometry : angle 0.94371 (13658) hydrogen bonds : bond 0.03627 ( 367) hydrogen bonds : angle 4.87917 ( 1059) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.332 Fit side-chains REVERT: A 220 PHE cc_start: 0.7089 (t80) cc_final: 0.6754 (t80) REVERT: A 558 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7333 (mt-10) REVERT: A 936 VAL cc_start: 0.8179 (t) cc_final: 0.7928 (t) REVERT: A 1039 MET cc_start: 0.7343 (mpp) cc_final: 0.7009 (mpp) REVERT: A 1152 THR cc_start: 0.8003 (p) cc_final: 0.7741 (t) REVERT: A 1320 SER cc_start: 0.6751 (OUTLIER) cc_final: 0.6462 (t) outliers start: 25 outliers final: 24 residues processed: 186 average time/residue: 0.0960 time to fit residues: 25.4207 Evaluate side-chains 195 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 974 HIS Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1158 CYS Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1233 HIS Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1284 ILE Chi-restraints excluded: chain A residue 1320 SER Chi-restraints excluded: chain A residue 1404 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 GLN ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.128254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.110748 restraints weight = 68484.442| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 4.96 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 9968 Z= 0.196 Angle : 0.944 59.200 13658 Z= 0.516 Chirality : 0.045 0.300 1531 Planarity : 0.006 0.083 1802 Dihedral : 8.769 160.880 1522 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.98 % Favored : 91.71 % Rotamer: Outliers : 3.41 % Allowed : 27.08 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.23), residues: 1323 helix: 0.55 (0.25), residues: 437 sheet: -0.77 (0.35), residues: 227 loop : -2.04 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1205 TYR 0.011 0.001 TYR A 8 PHE 0.013 0.002 PHE A 426 TRP 0.032 0.002 TRP A 770 HIS 0.005 0.001 HIS A1196 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 9968) covalent geometry : angle 0.94371 (13658) hydrogen bonds : bond 0.03627 ( 367) hydrogen bonds : angle 4.87917 ( 1059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2047.61 seconds wall clock time: 35 minutes 57.26 seconds (2157.26 seconds total)