Starting phenix.real_space_refine on Mon Oct 26 15:26:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y1q_72403/10_2026/9y1q_72403_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y1q_72403/10_2026/9y1q_72403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y1q_72403/10_2026/9y1q_72403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y1q_72403/10_2026/9y1q_72403.map" model { file = "/net/cci-nas-00/data/ceres_data/9y1q_72403/10_2026/9y1q_72403_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y1q_72403/10_2026/9y1q_72403_trim.cif" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.957 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: 8 Type Number sf(0) Gaussians P 15 5.49 5 Mg 2 5.21 5 S 53 5.16 5 C 6617 2.51 5 N 1583 2.21 5 O 1811 1.98 5 F 2 1.80 5 H 9551 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19634 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 17094 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1038, 16824 Classifications: {'peptide': 1038} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 1012} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 1042, 16901 Classifications: {'peptide': 1042} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 1016} Chain breaks: 6 bond proxies already assigned to first conformer: 16791 Chain: "B" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1785 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 670 Unusual residues: {' MG': 2, '3PH': 3, 'AJP': 1, 'ATP': 2, 'CLR': 4, 'D10': 1, 'D12': 3, 'HEX': 3, 'MYR': 1, 'OCT': 1, 'PC1': 2, 'PLM': 4, 'PTY': 2, 'VX8': 1} Classifications: {'peptide': 2, 'undetermined': 30} Link IDs: {'TRANS': 1, None: 30} Not linked: pdbres="AJP A4001 " pdbres="CLR A4002 " Not linked: pdbres="CLR A4002 " pdbres="CLR A4003 " Not linked: pdbres="CLR A4003 " pdbres="CLR A4004 " Not linked: pdbres="CLR A4004 " pdbres="P5S A4005 " Not linked: pdbres="P5S A4006 " pdbres="PC1 A4007 " ... (remaining 25 not shown) Chain breaks: 1 Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 302 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 3 Residues with excluded nonbonded symmetry interactions: 158 residue: pdb=" N ALYS A 483 " occ=0.50 ... (42 atoms not shown) pdb=" HZ3BLYS A 483 " occ=0.50 residue: pdb=" N ALEU A 541 " occ=0.59 ... (36 atoms not shown) pdb="HD23BLEU A 541 " occ=0.41 residue: pdb=" N AGLY A 542 " occ=0.59 ... (12 atoms not shown) pdb=" HA3BGLY A 542 " occ=0.41 residue: pdb=" N AGLU A 543 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 543 " occ=0.41 residue: pdb=" N AGLY A 544 " occ=0.59 ... (12 atoms not shown) pdb=" HA3BGLY A 544 " occ=0.41 residue: pdb=" N AGLY A 545 " occ=0.59 ... (12 atoms not shown) pdb=" HA3BGLY A 545 " occ=0.41 residue: pdb=" N AILE A 546 " occ=0.59 ... (36 atoms not shown) pdb="HD13BILE A 546 " occ=0.41 residue: pdb=" N ATHR A 547 " occ=0.59 ... (26 atoms not shown) pdb="HG23BTHR A 547 " occ=0.41 residue: pdb=" N ALEU A 548 " occ=0.59 ... (36 atoms not shown) pdb="HD23BLEU A 548 " occ=0.41 residue: pdb=" N BTYR A 913 " occ=0.79 ... (18 atoms not shown) pdb=" HH BTYR A 913 " occ=0.79 residue: pdb=" N BTYR A 914 " occ=0.79 ... (19 atoms not shown) pdb=" HH BTYR A 914 " occ=0.79 residue: pdb=" N BVAL A 915 " occ=0.79 ... (14 atoms not shown) pdb="HG23BVAL A 915 " occ=0.79 ... (remaining 146 not shown) Time building chain proxies: 5.96, per 1000 atoms: 0.30 Number of scatterers: 19634 At special positions: 0 Unit cell: (83.83, 136.95, 136.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 53 16.00 P 15 15.00 Mg 2 11.99 F 2 9.00 O 1811 8.00 N 1583 7.00 C 6617 6.00 H 9551 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 817.6 milliseconds 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2222 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 8 sheets defined 61.0% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 46 through 63 Processing helix chain 'A' and resid 68 through 110 removed outlier: 3.944A pdb=" N ALA A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TRP A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ARG A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Proline residue: A 99 - end of helix removed outlier: 4.151A pdb=" N TYR A 109 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 167 removed outlier: 3.845A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.541A pdb=" N LEU A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 173' Processing helix chain 'A' and resid 176 through 188 removed outlier: 3.517A pdb=" N LEU A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 removed outlier: 3.626A pdb=" N LEU A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 220 Proline residue: A 205 - end of helix removed outlier: 4.122A pdb=" N GLU A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 227 through 268 removed outlier: 4.341A pdb=" N GLY A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 275 Processing helix chain 'A' and resid 277 through 308 removed outlier: 3.647A pdb=" N MET A 281 " --> pdb=" O TRP A 277 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 330 removed outlier: 3.678A pdb=" N VAL A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 332 through 351 removed outlier: 4.114A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 376 Processing helix chain 'A' and resid 465 through 471 Processing helix chain 'A' and resid 501 through 508 Processing helix chain 'A' and resid 514 through 524 Processing helix chain 'A' and resid 526 through 533 Processing helix chain 'A' and resid 549 through 564 removed outlier: 3.890A pdb=" N LYS A 564 " --> pdb=" O ARG A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 590 removed outlier: 3.805A pdb=" N GLU A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 613 Processing helix chain 'A' and resid 629 through 635 Processing helix chain 'A' and resid 826 through 834 Processing helix chain 'A' and resid 845 through 855 removed outlier: 3.638A pdb=" N TYR A 849 " --> pdb=" O THR A 845 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 855 " --> pdb=" O ARG A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 883 removed outlier: 3.912A pdb=" N ILE A 860 " --> pdb=" O HIS A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 921 No H-bonds generated for 'chain 'A' and resid 919 through 921' Processing helix chain 'A' and resid 922 through 927 Processing helix chain 'A' and resid 930 through 959 removed outlier: 3.648A pdb=" N LEU A 935 " --> pdb=" O PHE A 931 " (cutoff:3.500A) Proline residue: A 936 - end of helix Processing helix chain 'A' and resid 960 through 965 Processing helix chain 'A' and resid 968 through 1009 removed outlier: 3.712A pdb=" N ASP A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE A 980 " --> pdb=" O PHE A 976 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) Proline residue: A 988 - end of helix removed outlier: 3.701A pdb=" N VAL A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1033 removed outlier: 4.184A pdb=" N PHE A1016 " --> pdb=" O GLN A1012 " (cutoff:3.500A) Proline residue: A1021 - end of helix Processing helix chain 'A' and resid 1102 through 1119 removed outlier: 3.826A pdb=" N ILE A1119 " --> pdb=" O THR A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1168 removed outlier: 3.548A pdb=" N ILE A1131 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE A1132 " --> pdb=" O ARG A1128 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU A1133 " --> pdb=" O VAL A1129 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP A1145 " --> pdb=" O SER A1141 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A1156 " --> pdb=" O ASP A1152 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1259 Processing helix chain 'A' and resid 1278 through 1285 Processing helix chain 'A' and resid 1299 through 1305 Processing helix chain 'A' and resid 1311 through 1323 Processing helix chain 'A' and resid 1324 through 1331 removed outlier: 3.504A pdb=" N PHE A1331 " --> pdb=" O VAL A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1362 Processing helix chain 'A' and resid 1377 through 1391 Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 3.647A pdb=" N LEU A1430 " --> pdb=" O SER A1426 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 removed outlier: 4.084A pdb=" N THR B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 17 Processing sheet with id=AA1, first strand: chain 'A' and resid 447 through 448 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 399 removed outlier: 4.182A pdb=" N LEU A 441 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 488 through 491 removed outlier: 6.657A pdb=" N TYR A 569 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N VAL A 603 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU A 571 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A 454 " --> pdb=" O LEU A 602 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU A 453 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU A 617 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA A 455 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU A 619 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ALA A 457 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A 616 " --> pdb=" O TYR A 627 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR A 627 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE A 618 " --> pdb=" O TYR A 625 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1230 through 1234 removed outlier: 5.387A pdb=" N ILE A1230 " --> pdb=" O ASP A1214 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A1215 " --> pdb=" O GLU A1264 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU A1264 " --> pdb=" O LEU A1215 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA A1217 " --> pdb=" O ASN A1262 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASN A1262 " --> pdb=" O ALA A1217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1286 through 1289 removed outlier: 6.624A pdb=" N LEU A1367 " --> pdb=" O ILE A1398 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N CYS A1400 " --> pdb=" O LEU A1367 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU A1369 " --> pdb=" O CYS A1400 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A1399 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG A1239 " --> pdb=" O GLN A1412 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N LEU A1414 " --> pdb=" O ARG A1239 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLY A1241 " --> pdb=" O LEU A1414 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE A1416 " --> pdb=" O GLY A1241 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU A1243 " --> pdb=" O ILE A1416 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 7 Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.494A pdb=" N GLY B 10 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N SER B 119 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL B 12 " --> pdb=" O SER B 119 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ARG B 38 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.494A pdb=" N GLY B 10 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N SER B 119 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL B 12 " --> pdb=" O SER B 119 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR B 101 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ALA B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) 548 hydrogen bonds defined for protein. 1599 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: 4.65 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9535 1.03 - 1.23: 36 1.23 - 1.42: 4091 1.42 - 1.62: 6060 1.62 - 1.82: 101 Bond restraints: 19823 Sorted by residual: bond pdb=" C17 VX8 A4032 " pdb=" C18 VX8 A4032 " ideal model delta sigma weight residual 1.369 1.602 -0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C16 VX8 A4032 " pdb=" O5 VX8 A4032 " ideal model delta sigma weight residual 1.368 1.564 -0.196 2.00e-02 2.50e+03 9.61e+01 bond pdb=" C15 VX8 A4032 " pdb=" C16 VX8 A4032 " ideal model delta sigma weight residual 1.367 1.528 -0.161 2.00e-02 2.50e+03 6.52e+01 bond pdb=" C17 VX8 A4032 " pdb=" O4 VX8 A4032 " ideal model delta sigma weight residual 1.368 1.240 0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C12 VX8 A4032 " pdb=" N2 VX8 A4032 " ideal model delta sigma weight residual 1.359 1.483 -0.124 2.00e-02 2.50e+03 3.82e+01 ... (remaining 19818 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 35406 4.18 - 8.36: 85 8.36 - 12.55: 5 12.55 - 16.73: 2 16.73 - 20.91: 2 Bond angle restraints: 35500 Sorted by residual: angle pdb=" C14 VX8 A4032 " pdb=" C13 VX8 A4032 " pdb=" C22 VX8 A4032 " ideal model delta sigma weight residual 117.72 138.63 -20.91 3.00e+00 1.11e-01 4.86e+01 angle pdb=" C17 VX8 A4032 " pdb=" O4 VX8 A4032 " pdb=" C20 VX8 A4032 " ideal model delta sigma weight residual 107.00 126.18 -19.18 3.00e+00 1.11e-01 4.09e+01 angle pdb=" C18 VX8 A4032 " pdb=" C17 VX8 A4032 " pdb=" O4 VX8 A4032 " ideal model delta sigma weight residual 129.56 143.45 -13.89 3.00e+00 1.11e-01 2.14e+01 angle pdb=" C15 VX8 A4032 " pdb=" C16 VX8 A4032 " pdb=" O5 VX8 A4032 " ideal model delta sigma weight residual 129.02 142.36 -13.34 3.00e+00 1.11e-01 1.98e+01 angle pdb=" O4 VX8 A4032 " pdb=" C20 VX8 A4032 " pdb=" O5 VX8 A4032 " ideal model delta sigma weight residual 109.47 97.57 11.90 3.00e+00 1.11e-01 1.57e+01 ... (remaining 35495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.94: 9286 30.94 - 61.87: 394 61.87 - 92.81: 25 92.81 - 123.75: 5 123.75 - 154.68: 3 Dihedral angle restraints: 9713 sinusoidal: 5594 harmonic: 4119 Sorted by residual: dihedral pdb=" CA SER A 573 " pdb=" C SER A 573 " pdb=" N PRO A 574 " pdb=" CA PRO A 574 " ideal model delta harmonic sigma weight residual 180.00 152.01 27.99 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 54.79 38.21 1 1.00e+01 1.00e-02 2.06e+01 dihedral pdb=" C17 VX8 A4032 " pdb=" C20 VX8 A4032 " pdb=" O4 VX8 A4032 " pdb=" F1 VX8 A4032 " ideal model delta sinusoidal sigma weight residual 239.99 85.31 154.68 1 3.00e+01 1.11e-03 2.03e+01 ... (remaining 9710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.162: 1555 0.162 - 0.324: 11 0.324 - 0.486: 0 0.486 - 0.648: 0 0.648 - 0.810: 1 Chirality restraints: 1567 Sorted by residual: chirality pdb=" C13 VX8 A4032 " pdb=" C12 VX8 A4032 " pdb=" C14 VX8 A4032 " pdb=" C22 VX8 A4032 " both_signs ideal model delta sigma weight residual True 1.48 0.66 0.81 2.00e-01 2.50e+01 1.64e+01 chirality pdb=" C27 AJP A4001 " pdb=" C26 AJP A4001 " pdb=" C28 AJP A4001 " pdb=" O78 AJP A4001 " both_signs ideal model delta sigma weight residual False -2.44 -2.74 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C3' ATP A4028 " pdb=" C2' ATP A4028 " pdb=" C4' ATP A4028 " pdb=" O3' ATP A4028 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1564 not shown) Planarity restraints: 2780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1030 " -0.337 9.50e-02 1.11e+02 1.16e-01 2.98e+01 pdb=" NE ARG A1030 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A1030 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A1030 " 0.070 2.00e-02 2.50e+03 pdb=" NH2 ARG A1030 " -0.008 2.00e-02 2.50e+03 pdb="HH11 ARG A1030 " -0.016 2.00e-02 2.50e+03 pdb="HH12 ARG A1030 " -0.041 2.00e-02 2.50e+03 pdb="HH21 ARG A1030 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A1030 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 861 " -0.017 2.00e-02 2.50e+03 2.72e-02 2.22e+01 pdb=" CG PHE A 861 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 PHE A 861 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 861 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE A 861 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 861 " -0.078 2.00e-02 2.50e+03 pdb=" CZ PHE A 861 " 0.016 2.00e-02 2.50e+03 pdb=" HD1 PHE A 861 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 861 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 PHE A 861 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE A 861 " 0.020 2.00e-02 2.50e+03 pdb=" HZ PHE A 861 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A1103 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" N GLU A1104 " 0.036 2.00e-02 2.50e+03 pdb=" CA GLU A1104 " -0.009 2.00e-02 2.50e+03 pdb=" H GLU A1104 " -0.016 2.00e-02 2.50e+03 ... (remaining 2777 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 909 2.21 - 2.80: 39781 2.80 - 3.40: 52567 3.40 - 4.00: 67565 4.00 - 4.60: 104916 Nonbonded interactions: 265738 Sorted by model distance: nonbonded pdb="HH12 ARG A1030 " pdb=" O11 3PH A4023 " model vdw 1.607 1.960 nonbonded pdb="HE22 GLN A 493 " pdb="MG MG A4029 " model vdw 1.695 1.700 nonbonded pdb=" HE2 PHE A 861 " pdb=" C2 D10 A4015 " model vdw 1.818 2.200 nonbonded pdb=" HB3 GLN A1291 " pdb="HE21 GLN A1291 " model vdw 1.874 2.270 nonbonded pdb=" O1B ATP A4030 " pdb="MG MG A4031 " model vdw 1.916 2.050 ... (remaining 265733 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.20 max=1.00 mean=0.95 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 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: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.860 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.050 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 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 : 0.006 0.233 10276 Z= 0.308 Angle : 0.857 20.912 13853 Z= 0.404 Chirality : 0.051 0.810 1567 Planarity : 0.006 0.148 1640 Dihedral : 16.387 154.682 4279 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.24), residues: 1162 helix: 0.38 (0.20), residues: 651 sheet: -0.84 (0.40), residues: 144 loop : -1.34 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A1030 TYR 0.016 0.002 TYR A 627 PHE 0.060 0.002 PHE A 861 TRP 0.018 0.001 TRP A1204 HIS 0.012 0.002 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.31 (10272) covalent geometry : angle 0.85730 / 0.40 (13851) SS BOND : bond 0.00186 / 0.10 ( 1) SS BOND : angle 0.60543 / 0.40 ( 2) hydrogen bonds : bond 0.13492 / 8.98 ( 544) hydrogen bonds : angle 6.25165 / 4.45 ( 1599) Misc. bond : bond 0.02351 / 0.97 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8659 (mm-30) cc_final: 0.7920 (mm-30) REVERT: A 161 TYR cc_start: 0.8178 (t80) cc_final: 0.7841 (t80) REVERT: A 212 MET cc_start: 0.6318 (mmm) cc_final: 0.5839 (mmm) REVERT: A 245 MET cc_start: 0.8886 (tpp) cc_final: 0.8493 (tpp) REVERT: A 336 ILE cc_start: 0.8057 (mm) cc_final: 0.7843 (mm) REVERT: A 607 MET cc_start: 0.6585 (tpp) cc_final: 0.6369 (tpp) REVERT: A 1159 SER cc_start: 0.8664 (m) cc_final: 0.8066 (p) REVERT: B 34 MET cc_start: 0.8497 (mpp) cc_final: 0.7942 (mpp) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1836 time to fit residues: 49.2043 Evaluate side-chains 164 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [108, 49, 97, 113, 53, 5, 33, 65, 62, 51, 100] chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1291 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.177059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.148414 restraints weight = 106002.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.155653 restraints weight = 37575.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.160185 restraints weight = 19304.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.163012 restraints weight = 12344.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.164749 restraints weight = 9065.654| |-----------------------------------------------------------------------------| r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4240 r_free = 0.4240 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4220 r_free = 0.4220 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (9 function evaluations) r_final: 0.4220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10276 Z= 0.150 Angle : 0.562 7.084 13853 Z= 0.292 Chirality : 0.038 0.142 1567 Planarity : 0.003 0.036 1640 Dihedral : 14.875 149.059 2077 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.69 % Allowed : 8.29 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.25), residues: 1162 helix: 0.89 (0.20), residues: 662 sheet: -0.84 (0.40), residues: 151 loop : -1.33 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1030 TYR 0.013 0.001 TYR A 304 PHE 0.022 0.001 PHE A 143 TRP 0.011 0.001 TRP A 865 HIS 0.004 0.001 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (10272) covalent geometry : angle 0.56189 / 0.29 (13851) SS BOND : bond 0.00110 / 0.06 ( 1) SS BOND : angle 0.42000 / 0.28 ( 2) hydrogen bonds : bond 0.04615 / 2.99 ( 544) hydrogen bonds : angle 5.01727 / 3.63 ( 1599) Misc. bond : bond 0.00141 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 169 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8757 (mm-30) cc_final: 0.7936 (mm-30) REVERT: A 143 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7760 (p90) REVERT: A 161 TYR cc_start: 0.8148 (t80) cc_final: 0.7777 (t80) REVERT: A 245 MET cc_start: 0.8948 (tpp) cc_final: 0.8348 (tpp) REVERT: A 490 PHE cc_start: 0.7668 (t80) cc_final: 0.7275 (t80) REVERT: A 924 ASP cc_start: 0.7798 (m-30) cc_final: 0.7585 (m-30) REVERT: A 1159 SER cc_start: 0.8628 (m) cc_final: 0.8427 (m) outliers start: 7 outliers final: 4 residues processed: 173 average time/residue: 0.1760 time to fit residues: 45.6492 Evaluate side-chains 166 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 161 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1280 GLN Chi-restraints excluded: chain B residue 59 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [22, 50, 7, 91, 2, 33, 65, 42, 84, 39, 74] chunk 22 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 GLN ** A 609 HIS ** 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 = 0.4365 r_free = 0.4365 target = 0.174206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.146533 restraints weight = 109625.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.153487 restraints weight = 38035.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.157827 restraints weight = 19405.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.160522 restraints weight = 12398.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.162220 restraints weight = 9181.695| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4215 r_free = 0.4215 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4213 r_free = 0.4213 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.4213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10276 Z= 0.125 Angle : 0.523 7.336 13853 Z= 0.271 Chirality : 0.037 0.144 1567 Planarity : 0.003 0.035 1640 Dihedral : 14.326 146.578 2077 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.49 % Allowed : 9.67 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.25), residues: 1162 helix: 1.12 (0.21), residues: 663 sheet: -0.89 (0.39), residues: 152 loop : -1.23 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1030 TYR 0.014 0.001 TYR A 304 PHE 0.016 0.001 PHE A 315 TRP 0.012 0.001 TRP A 216 HIS 0.005 0.001 HIS A1350 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (10272) covalent geometry : angle 0.52276 / 0.27 (13851) SS BOND : bond 0.00109 / 0.06 ( 1) SS BOND : angle 0.38158 / 0.25 ( 2) hydrogen bonds : bond 0.04308 / 2.79 ( 544) hydrogen bonds : angle 4.71551 / 3.40 ( 1599) Misc. bond : bond 0.00116 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 164 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8703 (mm-30) cc_final: 0.7796 (mm-30) REVERT: A 139 HIS cc_start: 0.7970 (m-70) cc_final: 0.7760 (m-70) REVERT: A 143 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7575 (p90) REVERT: A 245 MET cc_start: 0.8956 (tpp) cc_final: 0.8384 (tpp) REVERT: A 394 MET cc_start: 0.6065 (tmm) cc_final: 0.5811 (tpp) REVERT: A 490 PHE cc_start: 0.7577 (t80) cc_final: 0.7289 (t80) REVERT: A 865 TRP cc_start: 0.8680 (t-100) cc_final: 0.8278 (t-100) outliers start: 5 outliers final: 4 residues processed: 167 average time/residue: 0.1768 time to fit residues: 44.5585 Evaluate side-chains 162 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 157 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1280 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [50, 8, 21, 10, 96, 112, 42, 33, 46, 95, 64] chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 112 optimal weight: 30.0000 chunk 42 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.170103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.142373 restraints weight = 110186.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.149100 restraints weight = 38702.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.153261 restraints weight = 20042.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.155871 restraints weight = 13068.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.157505 restraints weight = 9826.253| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4153 r_free = 0.4153 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4152 r_free = 0.4152 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 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 : 0.004 0.043 10276 Z= 0.190 Angle : 0.591 6.438 13853 Z= 0.308 Chirality : 0.038 0.133 1567 Planarity : 0.003 0.039 1640 Dihedral : 14.724 151.240 2077 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.68 % Allowed : 10.66 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.25), residues: 1162 helix: 0.89 (0.20), residues: 662 sheet: -1.14 (0.38), residues: 157 loop : -1.25 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1030 TYR 0.019 0.001 TYR A 304 PHE 0.014 0.002 PHE A 200 TRP 0.009 0.001 TRP A 216 HIS 0.007 0.002 HIS A1350 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (10272) covalent geometry : angle 0.59071 / 0.31 (13851) SS BOND : bond 0.00099 / 0.05 ( 1) SS BOND : angle 0.43120 / 0.29 ( 2) hydrogen bonds : bond 0.04489 / 2.92 ( 544) hydrogen bonds : angle 4.91878 / 3.52 ( 1599) Misc. bond : bond 0.00117 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 TRP cc_start: 0.7028 (t-100) cc_final: 0.6705 (t-100) REVERT: A 143 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7599 (p90) REVERT: A 245 MET cc_start: 0.9006 (tpp) cc_final: 0.8431 (tpp) REVERT: A 924 ASP cc_start: 0.7947 (m-30) cc_final: 0.7647 (m-30) outliers start: 17 outliers final: 12 residues processed: 172 average time/residue: 0.1895 time to fit residues: 48.7390 Evaluate side-chains 172 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1280 GLN Chi-restraints excluded: chain A residue 1314 GLU Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1419 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [52, 102, 65, 89, 78, 55, 92, 28, 73, 106, 5] chunk 52 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.168262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.139925 restraints weight = 122072.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.146766 restraints weight = 41884.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.151071 restraints weight = 21489.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.153741 restraints weight = 13875.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.155409 restraints weight = 10374.728| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4125 r_free = 0.4125 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4125 r_free = 0.4125 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10276 Z= 0.211 Angle : 0.610 6.212 13853 Z= 0.321 Chirality : 0.039 0.138 1567 Planarity : 0.004 0.036 1640 Dihedral : 14.841 155.079 2077 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.28 % Allowed : 13.13 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.24), residues: 1162 helix: 0.75 (0.20), residues: 656 sheet: -1.13 (0.40), residues: 145 loop : -1.34 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1030 TYR 0.019 0.002 TYR A 304 PHE 0.019 0.002 PHE A1337 TRP 0.011 0.001 TRP A 401 HIS 0.007 0.002 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 (10272) covalent geometry : angle 0.61030 / 0.32 (13851) SS BOND : bond 0.00102 / 0.05 ( 1) SS BOND : angle 0.43325 / 0.29 ( 2) hydrogen bonds : bond 0.04602 / 3.00 ( 544) hydrogen bonds : angle 5.03245 / 3.60 ( 1599) Misc. bond : bond 0.00128 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 TRP cc_start: 0.7102 (t-100) cc_final: 0.6777 (t-100) REVERT: A 143 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7862 (p90) REVERT: A 212 MET cc_start: 0.6705 (mmm) cc_final: 0.6063 (mmm) REVERT: A 245 MET cc_start: 0.8998 (tpp) cc_final: 0.8303 (tpt) REVERT: A 448 ILE cc_start: 0.7996 (mt) cc_final: 0.7743 (mt) REVERT: A 924 ASP cc_start: 0.8053 (m-30) cc_final: 0.7772 (m-30) REVERT: A 1259 ARG cc_start: 0.7031 (ttm-80) cc_final: 0.6772 (ttm-80) outliers start: 13 outliers final: 11 residues processed: 167 average time/residue: 0.1858 time to fit residues: 46.7772 Evaluate side-chains 168 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1280 GLN Chi-restraints excluded: chain A residue 1314 GLU Chi-restraints excluded: chain A residue 1359 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [79, 7, 21, 15, 81, 61, 105, 92, 93, 69, 42] chunk 79 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.169034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.141714 restraints weight = 103503.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.148205 restraints weight = 37710.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.152289 restraints weight = 19953.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.154846 restraints weight = 13138.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.156490 restraints weight = 9922.082| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4139 r_free = 0.4139 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4139 r_free = 0.4139 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10276 Z= 0.154 Angle : 0.561 8.479 13853 Z= 0.291 Chirality : 0.038 0.145 1567 Planarity : 0.003 0.035 1640 Dihedral : 14.622 153.731 2077 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.58 % Allowed : 13.82 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.25), residues: 1162 helix: 0.96 (0.20), residues: 659 sheet: -1.20 (0.39), residues: 152 loop : -1.21 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 55 TYR 0.020 0.001 TYR A 109 PHE 0.019 0.002 PHE A 315 TRP 0.010 0.001 TRP A 865 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (10272) covalent geometry : angle 0.56054 / 0.29 (13851) SS BOND : bond 0.00077 / 0.04 ( 1) SS BOND : angle 0.41818 / 0.28 ( 2) hydrogen bonds : bond 0.04311 / 2.82 ( 544) hydrogen bonds : angle 4.80812 / 3.44 ( 1599) Misc. bond : bond 0.00111 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 TRP cc_start: 0.7086 (t-100) cc_final: 0.6702 (t-100) REVERT: A 92 GLU cc_start: 0.8698 (mm-30) cc_final: 0.7755 (mm-30) REVERT: A 143 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7774 (p90) REVERT: A 245 MET cc_start: 0.8981 (tpp) cc_final: 0.8334 (tpt) REVERT: A 448 ILE cc_start: 0.8054 (mt) cc_final: 0.7805 (mt) REVERT: A 924 ASP cc_start: 0.7942 (m-30) cc_final: 0.7638 (m-30) REVERT: A 1259 ARG cc_start: 0.7015 (ttm-80) cc_final: 0.6797 (ttm-80) REVERT: B 34 MET cc_start: 0.8803 (mpp) cc_final: 0.8513 (mpp) outliers start: 16 outliers final: 10 residues processed: 168 average time/residue: 0.1747 time to fit residues: 44.9312 Evaluate side-chains 169 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1280 GLN Chi-restraints excluded: chain A residue 1359 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [41, 97, 83, 108, 68, 67, 107, 37, 103, 113, 36] chunk 41 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 108 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.170392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.142642 restraints weight = 111618.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.149443 restraints weight = 38956.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.153578 restraints weight = 19956.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.156204 restraints weight = 12963.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.157871 restraints weight = 9659.908| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4157 r_free = 0.4157 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4157 r_free = 0.4157 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10276 Z= 0.117 Angle : 0.526 9.488 13853 Z= 0.270 Chirality : 0.037 0.154 1567 Planarity : 0.003 0.034 1640 Dihedral : 14.047 151.428 2077 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.89 % Allowed : 14.51 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.25), residues: 1162 helix: 1.26 (0.21), residues: 659 sheet: -1.12 (0.40), residues: 151 loop : -1.16 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1030 TYR 0.017 0.001 TYR A 109 PHE 0.014 0.001 PHE A 490 TRP 0.010 0.001 TRP A1204 HIS 0.004 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (10272) covalent geometry : angle 0.52595 / 0.27 (13851) SS BOND : bond 0.00081 / 0.04 ( 1) SS BOND : angle 0.37028 / 0.25 ( 2) hydrogen bonds : bond 0.03981 / 2.59 ( 544) hydrogen bonds : angle 4.54422 / 3.26 ( 1599) Misc. bond : bond 0.00103 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 TRP cc_start: 0.7037 (t-100) cc_final: 0.6611 (t-100) REVERT: A 92 GLU cc_start: 0.8668 (mm-30) cc_final: 0.7729 (mm-30) REVERT: A 264 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8442 (mm-30) REVERT: A 448 ILE cc_start: 0.8115 (mt) cc_final: 0.7862 (mt) REVERT: A 924 ASP cc_start: 0.7917 (m-30) cc_final: 0.7657 (m-30) REVERT: A 1169 MET cc_start: 0.6792 (mmt) cc_final: 0.6575 (mmt) REVERT: B 34 MET cc_start: 0.8792 (mpp) cc_final: 0.8486 (mpp) outliers start: 9 outliers final: 9 residues processed: 167 average time/residue: 0.1900 time to fit residues: 47.3157 Evaluate side-chains 167 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 158 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 1104 GLU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1280 GLN Chi-restraints excluded: chain A residue 1359 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [35, 2, 74, 108, 87, 93, 26, 10, 23, 102, 115] chunk 35 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.169469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.141837 restraints weight = 107092.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.148507 restraints weight = 38161.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.152641 restraints weight = 19765.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.155135 restraints weight = 12852.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.156794 restraints weight = 9710.357| |-----------------------------------------------------------------------------| r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4143 r_free = 0.4143 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4143 r_free = 0.4143 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10276 Z= 0.143 Angle : 0.553 9.676 13853 Z= 0.285 Chirality : 0.038 0.147 1567 Planarity : 0.003 0.045 1640 Dihedral : 14.004 153.060 2077 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.18 % Allowed : 14.51 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.25), residues: 1162 helix: 1.26 (0.20), residues: 659 sheet: -1.08 (0.40), residues: 151 loop : -1.22 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 289 TYR 0.013 0.001 TYR A 304 PHE 0.022 0.001 PHE A 315 TRP 0.008 0.001 TRP A1204 HIS 0.004 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (10272) covalent geometry : angle 0.55277 / 0.29 (13851) SS BOND : bond 0.00101 / 0.05 ( 1) SS BOND : angle 0.39362 / 0.26 ( 2) hydrogen bonds : bond 0.04027 / 2.61 ( 544) hydrogen bonds : angle 4.62358 / 3.31 ( 1599) Misc. bond : bond 0.00110 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 TRP cc_start: 0.7002 (t-100) cc_final: 0.6647 (t-100) REVERT: A 92 GLU cc_start: 0.8673 (mm-30) cc_final: 0.7744 (mm-30) REVERT: A 264 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8469 (mm-30) REVERT: A 448 ILE cc_start: 0.8088 (mt) cc_final: 0.7826 (mt) REVERT: A 924 ASP cc_start: 0.7909 (m-30) cc_final: 0.7622 (m-30) REVERT: A 1169 MET cc_start: 0.6850 (mmt) cc_final: 0.6603 (mmt) REVERT: A 1259 ARG cc_start: 0.6960 (ttm-80) cc_final: 0.6746 (ttm110) REVERT: B 34 MET cc_start: 0.8827 (mpp) cc_final: 0.8511 (mpp) outliers start: 12 outliers final: 11 residues processed: 170 average time/residue: 0.1920 time to fit residues: 48.8616 Evaluate side-chains 172 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1104 GLU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1280 GLN Chi-restraints excluded: chain A residue 1359 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [10, 66, 40, 74, 65, 104, 100, 0, 2, 37, 77] chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.169450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.141917 restraints weight = 105174.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.148562 restraints weight = 37696.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.152659 restraints weight = 19534.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.155160 restraints weight = 12707.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.156815 restraints weight = 9581.987| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4146 r_free = 0.4146 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4146 r_free = 0.4146 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.4146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10276 Z= 0.140 Angle : 0.551 9.821 13853 Z= 0.284 Chirality : 0.038 0.159 1567 Planarity : 0.003 0.035 1640 Dihedral : 13.885 153.243 2077 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.38 % Allowed : 14.91 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.25), residues: 1162 helix: 1.26 (0.20), residues: 660 sheet: -1.04 (0.41), residues: 146 loop : -1.20 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1030 TYR 0.013 0.001 TYR A 304 PHE 0.037 0.002 PHE A 490 TRP 0.010 0.001 TRP A1204 HIS 0.004 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (10272) covalent geometry : angle 0.55144 / 0.28 (13851) SS BOND : bond 0.00092 / 0.05 ( 1) SS BOND : angle 0.38158 / 0.25 ( 2) hydrogen bonds : bond 0.03998 / 2.59 ( 544) hydrogen bonds : angle 4.59127 / 3.29 ( 1599) Misc. bond : bond 0.00120 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 TRP cc_start: 0.6975 (t-100) cc_final: 0.6699 (t-100) REVERT: A 92 GLU cc_start: 0.8655 (mm-30) cc_final: 0.7739 (mm-30) REVERT: A 153 ARG cc_start: 0.8131 (mtp-110) cc_final: 0.7908 (mtp180) REVERT: A 264 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8492 (mm-30) REVERT: A 448 ILE cc_start: 0.8107 (mt) cc_final: 0.7836 (mt) REVERT: A 827 GLU cc_start: 0.7696 (tp30) cc_final: 0.6683 (tp30) REVERT: A 924 ASP cc_start: 0.7941 (m-30) cc_final: 0.7672 (m-30) REVERT: A 1169 MET cc_start: 0.6950 (mmt) cc_final: 0.6673 (mmt) REVERT: A 1259 ARG cc_start: 0.6944 (ttm-80) cc_final: 0.6735 (ttm-80) REVERT: B 34 MET cc_start: 0.8818 (mpp) cc_final: 0.8516 (mpp) outliers start: 14 outliers final: 14 residues processed: 169 average time/residue: 0.1853 time to fit residues: 46.7518 Evaluate side-chains 173 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1033 PHE Chi-restraints excluded: chain A residue 1104 GLU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1280 GLN Chi-restraints excluded: chain A residue 1359 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [85, 2, 102, 22, 83, 10, 35, 65, 50, 7, 61] chunk 85 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 7 optimal weight: 0.0670 chunk 61 optimal weight: 3.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1303 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 = 0.4319 r_free = 0.4319 target = 0.170559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.142505 restraints weight = 111298.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.149416 restraints weight = 38437.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.153676 restraints weight = 19565.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.156294 restraints weight = 12559.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.157947 restraints weight = 9373.303| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4160 r_free = 0.4160 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4160 r_free = 0.4160 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.4160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10276 Z= 0.115 Angle : 0.534 9.924 13853 Z= 0.274 Chirality : 0.037 0.149 1567 Planarity : 0.003 0.034 1640 Dihedral : 13.619 151.457 2077 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.09 % Allowed : 15.50 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.25), residues: 1162 helix: 1.41 (0.21), residues: 659 sheet: -0.93 (0.41), residues: 146 loop : -1.15 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1030 TYR 0.012 0.001 TYR A 304 PHE 0.031 0.001 PHE A 131 TRP 0.014 0.001 TRP A 57 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (10272) covalent geometry : angle 0.53395 / 0.27 (13851) SS BOND : bond 0.00081 / 0.04 ( 1) SS BOND : angle 0.37991 / 0.25 ( 2) hydrogen bonds : bond 0.03831 / 2.48 ( 544) hydrogen bonds : angle 4.46460 / 3.19 ( 1599) Misc. bond : bond 0.00112 / 0.05 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 TRP cc_start: 0.7037 (t-100) cc_final: 0.6441 (t-100) REVERT: A 80 ARG cc_start: 0.7568 (tpt170) cc_final: 0.7360 (tpt90) REVERT: A 92 GLU cc_start: 0.8606 (mm-30) cc_final: 0.7685 (mm-30) REVERT: A 153 ARG cc_start: 0.8093 (mtp-110) cc_final: 0.7742 (mtp180) REVERT: A 264 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8516 (mm-30) REVERT: A 448 ILE cc_start: 0.8090 (mt) cc_final: 0.7823 (mt) REVERT: A 924 ASP cc_start: 0.7886 (m-30) cc_final: 0.7611 (m-30) REVERT: A 1169 MET cc_start: 0.6917 (mmt) cc_final: 0.6636 (mmt) REVERT: B 34 MET cc_start: 0.8840 (mpp) cc_final: 0.8527 (mpp) outliers start: 11 outliers final: 10 residues processed: 172 average time/residue: 0.1927 time to fit residues: 49.1673 Evaluate side-chains 171 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1104 GLU Chi-restraints excluded: chain A residue 1280 GLN Chi-restraints excluded: chain A residue 1359 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [32, 69, 10, 19, 112, 23, 37, 82, 76, 43, 109] chunk 32 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 82 optimal weight: 0.0770 chunk 76 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.169716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.141853 restraints weight = 107043.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.148616 restraints weight = 38112.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.152815 restraints weight = 19724.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.155367 restraints weight = 12808.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.156970 restraints weight = 9640.193| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4147 r_free = 0.4147 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4147 r_free = 0.4147 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10276 Z= 0.137 Angle : 0.545 9.696 13853 Z= 0.283 Chirality : 0.038 0.142 1567 Planarity : 0.003 0.035 1640 Dihedral : 13.591 152.943 2077 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.18 % Allowed : 15.60 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.25), residues: 1162 helix: 1.36 (0.20), residues: 659 sheet: -0.96 (0.41), residues: 146 loop : -1.19 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1259 TYR 0.013 0.001 TYR A 304 PHE 0.030 0.002 PHE A 490 TRP 0.010 0.001 TRP A 57 HIS 0.004 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (10272) covalent geometry : angle 0.54545 / 0.28 (13851) SS BOND : bond 0.00085 / 0.04 ( 1) SS BOND : angle 0.39418 / 0.26 ( 2) hydrogen bonds : bond 0.03889 / 2.51 ( 544) hydrogen bonds : angle 4.54197 / 3.24 ( 1599) Misc. bond : bond 0.00112 / 0.05 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3695.01 seconds wall clock time: 63 minutes 29.58 seconds (3809.58 seconds total)