Starting phenix.real_space_refine on Fri Sep 11 17:39:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w98_21580/09_2026/6w98_21580_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w98_21580/09_2026/6w98_21580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w98_21580/09_2026/6w98_21580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w98_21580/09_2026/6w98_21580.map" model { file = "/net/cci-nas-00/data/ceres_data/6w98_21580/09_2026/6w98_21580_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w98_21580/09_2026/6w98_21580_neut.cif" } resolution = 2.9 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 2 5.49 5 S 22 5.16 5 C 6573 2.51 5 N 1810 2.21 5 O 1908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10317 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9653 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1312, 9643 Classifications: {'peptide': 1312} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1202} Chain breaks: 6 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 94 Conformer: "B" Number of residues, atoms: 1312, 9643 Classifications: {'peptide': 1312} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1202} Chain breaks: 6 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 94 bond proxies already assigned to first conformer: 9872 Chain: "B" Number of atoms: 605 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 77, 597 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 75} Conformer: "B" Number of residues, atoms: 77, 597 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 75} bond proxies already assigned to first conformer: 592 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 59 Unusual residues: {' CA': 2, '6OU': 1, 'PNS': 1} Classifications: {'undetermined': 4, 'water': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS A 550 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 550 " occ=0.50 residue: pdb=" N AASP B 56 " occ=0.60 ... (14 atoms not shown) pdb=" OD2BASP B 56 " occ=0.40 Time building chain proxies: 4.10, per 1000 atoms: 0.40 Number of scatterers: 10317 At special positions: 0 Unit cell: (143.168, 99.687, 95.445, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 22 16.00 P 2 15.00 O 1908 8.00 N 1810 7.00 C 6573 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 886 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A1104 " - pdb=" SG CYS A1139 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 878.4 milliseconds 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2550 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 14 sheets defined 39.1% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 12 through 27 removed outlier: 3.553A pdb=" N ALA A 16 " --> pdb=" O ARG A 12 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.517A pdb=" N PHE A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.629A pdb=" N ALA A 79 " --> pdb=" O PHE A 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 118 removed outlier: 3.616A pdb=" N VAL A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 135 through 143 removed outlier: 3.834A pdb=" N THR A 141 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 148 removed outlier: 3.782A pdb=" N GLU A 148 " --> pdb=" O ILE A 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 145 through 148' Processing helix chain 'A' and resid 149 through 167 Proline residue: A 156 - end of helix removed outlier: 3.518A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 171 through 186 removed outlier: 3.630A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 198 Processing helix chain 'A' and resid 198 through 207 Processing helix chain 'A' and resid 211 through 243 removed outlier: 3.996A pdb=" N TRP A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix removed outlier: 5.928A pdb=" N TRP A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TRP A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA A 235 " --> pdb=" O TRP A 231 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 288 through 308 removed outlier: 3.502A pdb=" N VAL A 293 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 328 removed outlier: 3.501A pdb=" N VAL A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 361 removed outlier: 3.651A pdb=" N LYS A 361 " --> pdb=" O ASN A 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 358 through 361' Processing helix chain 'A' and resid 362 through 378 removed outlier: 3.661A pdb=" N ILE A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 368 " --> pdb=" O PRO A 364 " (cutoff:3.500A) Proline residue: A 369 - end of helix removed outlier: 3.542A pdb=" N HIS A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.567A pdb=" N ILE A 409 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 removed outlier: 3.838A pdb=" N TRP A 423 " --> pdb=" O THR A 419 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 419 through 424' Processing helix chain 'A' and resid 437 through 450 removed outlier: 3.810A pdb=" N ASN A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 4.093A pdb=" N ALA A 479 " --> pdb=" O GLU A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 512 removed outlier: 3.576A pdb=" N ILE A 499 " --> pdb=" O PRO A 495 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 525 removed outlier: 3.556A pdb=" N ARG A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 555 removed outlier: 3.695A pdb=" N HIS A 551 " --> pdb=" O ILE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 621 through 632 removed outlier: 3.527A pdb=" N ARG A 630 " --> pdb=" O ASN A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 737 removed outlier: 3.703A pdb=" N SER A 732 " --> pdb=" O PRO A 729 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N THR A 733 " --> pdb=" O GLY A 730 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA A 734 " --> pdb=" O THR A 731 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 736 " --> pdb=" O THR A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 940 removed outlier: 4.176A pdb=" N LEU A 938 " --> pdb=" O GLN A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 964 Processing helix chain 'A' and resid 1091 through 1096 Processing helix chain 'A' and resid 1125 through 1130 Processing helix chain 'A' and resid 1254 through 1267 Processing helix chain 'A' and resid 1268 through 1278 Processing helix chain 'A' and resid 1295 through 1310 removed outlier: 3.542A pdb=" N VAL A1300 " --> pdb=" O PRO A1296 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A1301 " --> pdb=" O ALA A1297 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A1303 " --> pdb=" O GLY A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1328 removed outlier: 3.735A pdb=" N MET A1315 " --> pdb=" O GLY A1311 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A1326 " --> pdb=" O LEU A1322 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP A1327 " --> pdb=" O ALA A1323 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A1328 " --> pdb=" O PHE A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1353 removed outlier: 3.689A pdb=" N THR A1336 " --> pdb=" O LEU A1332 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY A1339 " --> pdb=" O VAL A1335 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A1340 " --> pdb=" O THR A1336 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A1341 " --> pdb=" O ALA A1337 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A1346 " --> pdb=" O LEU A1342 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A1347 " --> pdb=" O ALA A1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 1369 through 1385 removed outlier: 3.663A pdb=" N GLN A1373 " --> pdb=" O SER A1369 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A1377 " --> pdb=" O GLN A1373 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A1378 " --> pdb=" O LEU A1374 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER A1379 " --> pdb=" O LEU A1375 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 16 Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 35 through 51 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 64 through 75 removed outlier: 3.784A pdb=" N TYR B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 455 through 459 removed outlier: 6.697A pdb=" N ARG A 455 " --> pdb=" O TYR A 529 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL A 531 " --> pdb=" O ARG A 455 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU A 457 " --> pdb=" O VAL A 531 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ARG A 533 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A 459 " --> pdb=" O ARG A 533 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLY A 566 " --> pdb=" O PRO A 588 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL A 590 " --> pdb=" O GLN A 564 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLN A 564 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE A 592 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 577 through 579 removed outlier: 6.780A pdb=" N VAL A 578 " --> pdb=" O ARG A1061 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1181 through 1182 removed outlier: 3.663A pdb=" N GLN A1236 " --> pdb=" O VAL A1208 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR A1227 " --> pdb=" O VAL A1239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 641 through 642 removed outlier: 7.119A pdb=" N ARG A 614 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N THR A 659 " --> pdb=" O ARG A 614 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA A 656 " --> pdb=" O GLY A 873 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ASP A 875 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL A 658 " --> pdb=" O ASP A 875 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N GLY A 877 " --> pdb=" O VAL A 658 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL A1163 " --> pdb=" O ARG A 928 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG A 928 " --> pdb=" O VAL A1163 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU A 925 " --> pdb=" O ALA A1136 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLN A1135 " --> pdb=" O THR A1122 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N THR A1122 " --> pdb=" O GLN A1135 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 704 through 708 removed outlier: 3.756A pdb=" N ASN A 704 " --> pdb=" O THR A 861 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE A 910 " --> pdb=" O HIS A 858 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA A 860 " --> pdb=" O ILE A 910 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 914 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N THR A1122 " --> pdb=" O GLN A1135 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLN A1135 " --> pdb=" O THR A1122 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU A 925 " --> pdb=" O ALA A1136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 710 through 714 removed outlier: 6.966A pdb=" N THR A 817 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY A 794 " --> pdb=" O THR A 791 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 745 through 746 removed outlier: 6.865A pdb=" N THR A 774 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A 840 " --> pdb=" O THR A 772 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR A 772 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU A 842 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE A 770 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 745 through 746 removed outlier: 4.688A pdb=" N LEU A 842 " --> pdb=" O VAL A 854 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 886 through 887 Processing sheet with id=AB2, first strand: chain 'A' and resid 946 through 948 removed outlier: 6.178A pdb=" N SER A 986 " --> pdb=" O VAL A1052 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL A1052 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N VAL A 988 " --> pdb=" O VAL A1050 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL A1050 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LYS A 990 " --> pdb=" O ILE A1048 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE A1048 " --> pdb=" O LYS A 990 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ASP A1046 " --> pdb=" O PRO A 992 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ILE A1044 " --> pdb=" O PRO A 994 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ALA A 996 " --> pdb=" O PRO A1042 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLY A 998 " --> pdb=" O LEU A1040 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A1002 " --> pdb=" O THR A1036 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR A1036 " --> pdb=" O LEU A1002 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN A1015 " --> pdb=" O THR A1053 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TRP A1055 " --> pdb=" O PRO A1013 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 946 through 948 removed outlier: 3.934A pdb=" N ALA A 999 " --> pdb=" O LEU A1080 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 972 through 973 Processing sheet with id=AB5, first strand: chain 'A' and resid 1192 through 1197 438 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1695 1.30 - 1.43: 2619 1.43 - 1.56: 6208 1.56 - 1.69: 3 1.69 - 1.81: 35 Bond restraints: 10560 Sorted by residual: bond pdb=" C34 PNS A2004 " pdb=" N36 PNS A2004 " ideal model delta sigma weight residual 1.337 1.449 -0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C39 PNS A2004 " pdb=" N41 PNS A2004 " ideal model delta sigma weight residual 1.344 1.447 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C16 6OU A2003 " pdb=" O18 6OU A2003 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C31 6OU A2003 " pdb=" O30 6OU A2003 " ideal model delta sigma weight residual 1.331 1.404 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" O27 PNS A2004 " pdb=" P24 PNS A2004 " ideal model delta sigma weight residual 1.704 1.644 0.060 2.00e-02 2.50e+03 9.04e+00 ... (remaining 10555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 14298 3.04 - 6.09: 187 6.09 - 9.13: 10 9.13 - 12.17: 4 12.17 - 15.22: 1 Bond angle restraints: 14500 Sorted by residual: angle pdb=" O22 6OU A2003 " pdb=" P23 6OU A2003 " pdb=" O26 6OU A2003 " ideal model delta sigma weight residual 93.95 109.17 -15.22 3.00e+00 1.11e-01 2.57e+01 angle pdb=" N GLY A 836 " pdb=" CA GLY A 836 " pdb=" C GLY A 836 " ideal model delta sigma weight residual 110.90 116.21 -5.31 1.53e+00 4.27e-01 1.20e+01 angle pdb=" O23 PNS A2004 " pdb=" P24 PNS A2004 " pdb=" O27 PNS A2004 " ideal model delta sigma weight residual 100.79 110.52 -9.73 3.00e+00 1.11e-01 1.05e+01 angle pdb=" O24 6OU A2003 " pdb=" P23 6OU A2003 " pdb=" O25 6OU A2003 " ideal model delta sigma weight residual 118.72 109.03 9.69 3.00e+00 1.11e-01 1.04e+01 angle pdb=" C33 6OU A2003 " pdb=" C31 6OU A2003 " pdb=" O30 6OU A2003 " ideal model delta sigma weight residual 111.22 120.78 -9.56 3.00e+00 1.11e-01 1.01e+01 ... (remaining 14495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.44: 6086 27.44 - 54.88: 169 54.88 - 82.32: 18 82.32 - 109.75: 2 109.75 - 137.19: 3 Dihedral angle restraints: 6278 sinusoidal: 2328 harmonic: 3950 Sorted by residual: dihedral pdb=" CA PRO A1010 " pdb=" C PRO A1010 " pdb=" N ALA A1011 " pdb=" CA ALA A1011 " ideal model delta harmonic sigma weight residual -180.00 -153.60 -26.40 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ASP A 977 " pdb=" C ASP A 977 " pdb=" N SER A 978 " pdb=" CA SER A 978 " ideal model delta harmonic sigma weight residual 180.00 154.34 25.66 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA PRO A 653 " pdb=" C PRO A 653 " pdb=" N GLY A 654 " pdb=" CA GLY A 654 " ideal model delta harmonic sigma weight residual 180.00 157.41 22.59 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 6275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 791 0.030 - 0.060: 534 0.060 - 0.090: 237 0.090 - 0.120: 128 0.120 - 0.150: 32 Chirality restraints: 1722 Sorted by residual: chirality pdb=" CA THR A 661 " pdb=" N THR A 661 " pdb=" C THR A 661 " pdb=" CB THR A 661 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA PRO A 62 " pdb=" N PRO A 62 " pdb=" C PRO A 62 " pdb=" CB PRO A 62 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA VAL A1208 " pdb=" N VAL A1208 " pdb=" C VAL A1208 " pdb=" CB VAL A1208 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 1719 not shown) Planarity restraints: 1875 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 974 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO A 975 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 155 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO A 156 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 156 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 156 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 222 " 0.035 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO A 223 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " 0.029 5.00e-02 4.00e+02 ... (remaining 1872 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 84 2.57 - 3.15: 8145 3.15 - 3.74: 15447 3.74 - 4.32: 21800 4.32 - 4.90: 37460 Nonbonded interactions: 82936 Sorted by model distance: nonbonded pdb=" O ALA A 735 " pdb=" OD1 ASP A 738 " model vdw 1.990 3.040 nonbonded pdb=" OD2 ASP A 965 " pdb=" OG1 THR A 970 " model vdw 2.077 3.040 nonbonded pdb=" O ALA A 735 " pdb="CA CA A2001 " model vdw 2.107 2.510 nonbonded pdb=" O ALA A1075 " pdb="CA CA A2002 " model vdw 2.159 2.510 nonbonded pdb=" O ALA A 962 " pdb="CA CA A2002 " model vdw 2.183 2.510 ... (remaining 82931 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.870 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 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 : 0.011 0.560 10563 Z= 0.672 Angle : 0.874 15.215 14504 Z= 0.433 Chirality : 0.051 0.150 1722 Planarity : 0.007 0.056 1875 Dihedral : 13.583 137.191 3722 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.37 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -4.30 (0.17), residues: 1379 helix: -4.11 (0.12), residues: 481 sheet: -1.60 (0.31), residues: 204 loop : -2.21 (0.19), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 764 TYR 0.016 0.002 TYR A 439 PHE 0.018 0.002 PHE A 433 TRP 0.015 0.002 TRP A 232 HIS 0.010 0.002 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00994 / 0.39 (10560) covalent geometry : angle 0.87365 / 0.43 (14500) SS BOND : bond 0.00156 / 0.08 ( 2) SS BOND : angle 0.52563 / 0.26 ( 4) hydrogen bonds : bond 0.28687 / 18.97 ( 427) hydrogen bonds : angle 10.18680 / 7.20 ( 1209) Misc. bond : bond 0.56022 / 29.49 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 ARG cc_start: 0.7993 (ttt90) cc_final: 0.7677 (tpm170) REVERT: A 689 PHE cc_start: 0.8948 (m-80) cc_final: 0.8740 (m-80) REVERT: A 953 VAL cc_start: 0.6943 (m) cc_final: 0.6629 (p) REVERT: A 959 SER cc_start: 0.7810 (p) cc_final: 0.7502 (m) REVERT: A 1014 LYS cc_start: 0.8617 (mtpt) cc_final: 0.8321 (mtpm) REVERT: A 1210 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8338 (mt-10) REVERT: B 4 GLU cc_start: 0.8513 (mp0) cc_final: 0.7864 (mm-30) REVERT: B 44 MET cc_start: 0.7042 (mtm) cc_final: 0.5921 (mtp) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.5515 time to fit residues: 101.4367 Evaluate side-chains 101 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.0270 chunk 55 optimal weight: 0.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 GLN A 360 HIS A 690 ASN A1068 GLN A1151 GLN B 73 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.130489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.091765 restraints weight = 46264.075| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 4.03 r_work: 0.2851 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10563 Z= 0.142 Angle : 0.666 8.021 14504 Z= 0.337 Chirality : 0.045 0.285 1722 Planarity : 0.006 0.051 1875 Dihedral : 8.761 118.504 1519 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.34 % Allowed : 8.87 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.19), residues: 1379 helix: -1.85 (0.19), residues: 494 sheet: -1.06 (0.33), residues: 203 loop : -1.77 (0.20), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 267 TYR 0.015 0.002 TYR B 71 PHE 0.009 0.001 PHE B 50 TRP 0.015 0.001 TRP A 214 HIS 0.005 0.001 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10560) covalent geometry : angle 0.66618 / 0.34 (14500) SS BOND : bond 0.00186 / 0.09 ( 2) SS BOND : angle 0.28936 / 0.14 ( 4) hydrogen bonds : bond 0.04749 / 3.19 ( 427) hydrogen bonds : angle 5.73436 / 4.02 ( 1209) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ARG cc_start: 0.8955 (tpp-160) cc_final: 0.8416 (mmt90) REVERT: A 523 ARG cc_start: 0.8662 (ttm-80) cc_final: 0.8451 (ttm110) REVERT: A 844 GLN cc_start: 0.8242 (tt0) cc_final: 0.7737 (tt0) REVERT: A 953 VAL cc_start: 0.7247 (m) cc_final: 0.6720 (p) REVERT: A 959 SER cc_start: 0.7528 (p) cc_final: 0.7154 (m) REVERT: A 1054 ASP cc_start: 0.8070 (t70) cc_final: 0.7804 (t70) REVERT: A 1198 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7902 (pm20) outliers start: 14 outliers final: 4 residues processed: 129 average time/residue: 0.4476 time to fit residues: 63.4522 Evaluate side-chains 106 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 1198 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 10 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 GLN A 551 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.127436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.090285 restraints weight = 35500.304| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.42 r_work: 0.2836 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 10563 Z= 0.180 Angle : 0.642 8.547 14504 Z= 0.316 Chirality : 0.045 0.294 1722 Planarity : 0.005 0.048 1875 Dihedral : 8.043 94.997 1519 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.00 % Allowed : 10.11 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.21), residues: 1379 helix: -0.56 (0.23), residues: 480 sheet: -0.84 (0.32), residues: 210 loop : -1.42 (0.21), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 267 TYR 0.015 0.001 TYR A 439 PHE 0.009 0.001 PHE A 433 TRP 0.014 0.001 TRP A 214 HIS 0.007 0.001 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (10560) covalent geometry : angle 0.64208 / 0.32 (14500) SS BOND : bond 0.01166 / 0.56 ( 2) SS BOND : angle 0.53541 / 0.29 ( 4) hydrogen bonds : bond 0.04196 / 2.79 ( 427) hydrogen bonds : angle 5.19486 / 3.66 ( 1209) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8840 (mm) REVERT: A 523 ARG cc_start: 0.8742 (ttm-80) cc_final: 0.8420 (ttm110) REVERT: A 676 SER cc_start: 0.9443 (p) cc_final: 0.9186 (t) REVERT: A 844 GLN cc_start: 0.8275 (tt0) cc_final: 0.7785 (tt0) REVERT: A 953 VAL cc_start: 0.7769 (m) cc_final: 0.7156 (p) REVERT: A 959 SER cc_start: 0.7890 (p) cc_final: 0.7424 (m) REVERT: A 1054 ASP cc_start: 0.8089 (t70) cc_final: 0.7863 (t70) REVERT: A 1198 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7918 (pm20) REVERT: B 44 MET cc_start: 0.7266 (mmp) cc_final: 0.6948 (mtt) outliers start: 21 outliers final: 11 residues processed: 115 average time/residue: 0.4153 time to fit residues: 53.0243 Evaluate side-chains 110 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1377 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 45 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 137 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 0.0970 chunk 60 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.091012 restraints weight = 45743.731| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.96 r_work: 0.2845 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10563 Z= 0.122 Angle : 0.590 9.056 14504 Z= 0.286 Chirality : 0.043 0.318 1722 Planarity : 0.005 0.046 1875 Dihedral : 7.412 78.892 1519 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.19 % Allowed : 11.07 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.22), residues: 1379 helix: 0.34 (0.24), residues: 481 sheet: -0.55 (0.33), residues: 210 loop : -1.18 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 267 TYR 0.012 0.001 TYR A 439 PHE 0.008 0.001 PHE A 433 TRP 0.013 0.001 TRP A 232 HIS 0.004 0.001 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (10560) covalent geometry : angle 0.58965 / 0.29 (14500) SS BOND : bond 0.00089 / 0.04 ( 2) SS BOND : angle 0.78350 / 0.45 ( 4) hydrogen bonds : bond 0.03365 / 2.24 ( 427) hydrogen bonds : angle 4.77223 / 3.39 ( 1209) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8869 (mtm-85) cc_final: 0.7594 (mpt180) REVERT: A 137 ARG cc_start: 0.8680 (tpp-160) cc_final: 0.8041 (ttm170) REVERT: A 147 SER cc_start: 0.8362 (OUTLIER) cc_final: 0.8026 (p) REVERT: A 371 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8857 (mm) REVERT: A 844 GLN cc_start: 0.8163 (tt0) cc_final: 0.7801 (tt0) REVERT: A 951 SER cc_start: 0.8180 (p) cc_final: 0.7901 (m) REVERT: A 953 VAL cc_start: 0.7759 (m) cc_final: 0.7479 (p) REVERT: A 959 SER cc_start: 0.7841 (p) cc_final: 0.7429 (m) REVERT: A 1054 ASP cc_start: 0.8144 (t70) cc_final: 0.7907 (t70) REVERT: B 44 MET cc_start: 0.7250 (mmp) cc_final: 0.6855 (mtt) outliers start: 23 outliers final: 7 residues processed: 137 average time/residue: 0.4346 time to fit residues: 65.5906 Evaluate side-chains 119 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 1077 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 HIS A 360 HIS A 626 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.127583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.089446 restraints weight = 33222.876| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.47 r_work: 0.2845 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10563 Z= 0.153 Angle : 0.611 8.166 14504 Z= 0.296 Chirality : 0.044 0.323 1722 Planarity : 0.005 0.057 1875 Dihedral : 6.928 77.398 1519 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.48 % Allowed : 11.83 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -0.59 (0.22), residues: 1379 helix: 0.60 (0.24), residues: 484 sheet: -0.49 (0.34), residues: 211 loop : -1.05 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 764 TYR 0.015 0.001 TYR A 439 PHE 0.009 0.001 PHE A 107 TRP 0.012 0.001 TRP A 232 HIS 0.008 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (10560) covalent geometry : angle 0.61048 / 0.30 (14500) SS BOND : bond 0.00308 / 0.15 ( 2) SS BOND : angle 1.26268 / 0.65 ( 4) hydrogen bonds : bond 0.03517 / 2.34 ( 427) hydrogen bonds : angle 4.75635 / 3.37 ( 1209) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8827 (mtm-85) cc_final: 0.7551 (mpt180) REVERT: A 137 ARG cc_start: 0.8572 (tpp-160) cc_final: 0.7903 (ttm170) REVERT: A 147 SER cc_start: 0.8323 (OUTLIER) cc_final: 0.7941 (p) REVERT: A 371 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8824 (mm) REVERT: A 844 GLN cc_start: 0.8092 (tt0) cc_final: 0.7691 (tt0) REVERT: A 951 SER cc_start: 0.8242 (p) cc_final: 0.7975 (m) REVERT: A 953 VAL cc_start: 0.7845 (m) cc_final: 0.7538 (p) REVERT: A 959 SER cc_start: 0.7838 (p) cc_final: 0.7375 (m) REVERT: A 983 HIS cc_start: 0.6769 (t-170) cc_final: 0.6105 (p90) REVERT: A 1054 ASP cc_start: 0.8169 (t70) cc_final: 0.7917 (t70) REVERT: A 1382 SER cc_start: 0.8909 (m) cc_final: 0.8652 (t) REVERT: B 44 MET cc_start: 0.7259 (mmp) cc_final: 0.6804 (mtt) outliers start: 26 outliers final: 10 residues processed: 128 average time/residue: 0.4086 time to fit residues: 57.8372 Evaluate side-chains 121 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 40 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 GLN A 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.126692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.088192 restraints weight = 42068.930| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.69 r_work: 0.2810 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10563 Z= 0.166 Angle : 0.616 8.161 14504 Z= 0.300 Chirality : 0.045 0.333 1722 Planarity : 0.005 0.057 1875 Dihedral : 6.632 81.867 1519 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.96 % Allowed : 12.12 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -0.43 (0.22), residues: 1379 helix: 0.79 (0.24), residues: 484 sheet: -0.45 (0.34), residues: 211 loop : -0.98 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 764 TYR 0.015 0.001 TYR A 439 PHE 0.009 0.001 PHE A 107 TRP 0.013 0.001 TRP A 232 HIS 0.007 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (10560) covalent geometry : angle 0.61602 / 0.30 (14500) SS BOND : bond 0.00074 / 0.04 ( 2) SS BOND : angle 1.43873 / 0.74 ( 4) hydrogen bonds : bond 0.03528 / 2.35 ( 427) hydrogen bonds : angle 4.73636 / 3.36 ( 1209) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8878 (mtm-85) cc_final: 0.7756 (mmt180) REVERT: A 137 ARG cc_start: 0.8580 (tpp-160) cc_final: 0.7907 (ttm170) REVERT: A 147 SER cc_start: 0.8290 (OUTLIER) cc_final: 0.7906 (p) REVERT: A 844 GLN cc_start: 0.8153 (tt0) cc_final: 0.7744 (tt0) REVERT: A 951 SER cc_start: 0.8314 (p) cc_final: 0.8098 (m) REVERT: A 953 VAL cc_start: 0.8081 (m) cc_final: 0.7736 (p) REVERT: A 959 SER cc_start: 0.8100 (p) cc_final: 0.7586 (m) REVERT: A 983 HIS cc_start: 0.6623 (t-170) cc_final: 0.6208 (p90) REVERT: A 1001 ARG cc_start: 0.6674 (ptp-170) cc_final: 0.6423 (ptm160) REVERT: A 1054 ASP cc_start: 0.8178 (t70) cc_final: 0.7936 (t70) REVERT: A 1097 LYS cc_start: 0.8889 (mtmm) cc_final: 0.8463 (pmtt) REVERT: A 1341 TYR cc_start: 0.8242 (m-10) cc_final: 0.8037 (m-10) REVERT: B 44 MET cc_start: 0.7422 (mmp) cc_final: 0.6909 (mtt) outliers start: 31 outliers final: 16 residues processed: 130 average time/residue: 0.4209 time to fit residues: 60.5371 Evaluate side-chains 123 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1354 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 73 optimal weight: 0.0070 chunk 37 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.127743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.090007 restraints weight = 48006.305| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.89 r_work: 0.2827 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10563 Z= 0.128 Angle : 0.598 8.486 14504 Z= 0.290 Chirality : 0.044 0.309 1722 Planarity : 0.005 0.055 1875 Dihedral : 6.436 85.005 1519 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.19 % Allowed : 13.45 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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 (0.22), residues: 1379 helix: 0.95 (0.24), residues: 491 sheet: -0.40 (0.34), residues: 213 loop : -0.91 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 764 TYR 0.014 0.001 TYR A 439 PHE 0.008 0.001 PHE A 107 TRP 0.013 0.001 TRP A 232 HIS 0.005 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (10560) covalent geometry : angle 0.59751 / 0.29 (14500) SS BOND : bond 0.00102 / 0.05 ( 2) SS BOND : angle 1.22855 / 0.61 ( 4) hydrogen bonds : bond 0.03302 / 2.21 ( 427) hydrogen bonds : angle 4.65553 / 3.30 ( 1209) Misc. bond : bond 0.00027 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8876 (mtm-85) cc_final: 0.7644 (mpt180) REVERT: A 137 ARG cc_start: 0.8545 (tpp-160) cc_final: 0.7867 (ttm170) REVERT: A 147 SER cc_start: 0.8186 (OUTLIER) cc_final: 0.7849 (p) REVERT: A 380 ARG cc_start: 0.8193 (mpp-170) cc_final: 0.7766 (mpp-170) REVERT: A 411 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8142 (mm) REVERT: A 844 GLN cc_start: 0.8132 (tt0) cc_final: 0.7759 (tt0) REVERT: A 953 VAL cc_start: 0.8118 (m) cc_final: 0.7804 (p) REVERT: A 959 SER cc_start: 0.8026 (p) cc_final: 0.7536 (m) REVERT: A 983 HIS cc_start: 0.6582 (t-170) cc_final: 0.6188 (p90) REVERT: A 1054 ASP cc_start: 0.8167 (t70) cc_final: 0.7922 (t70) REVERT: B 44 MET cc_start: 0.7564 (mmp) cc_final: 0.6945 (mtt) outliers start: 23 outliers final: 10 residues processed: 121 average time/residue: 0.4069 time to fit residues: 54.7382 Evaluate side-chains 116 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1354 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 63 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 96 optimal weight: 0.0370 chunk 74 optimal weight: 0.0970 chunk 133 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 HIS A 598 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.128853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.091705 restraints weight = 39256.912| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.61 r_work: 0.2856 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10563 Z= 0.117 Angle : 0.590 9.946 14504 Z= 0.286 Chirality : 0.043 0.317 1722 Planarity : 0.005 0.058 1875 Dihedral : 6.279 88.703 1519 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.62 % Allowed : 14.22 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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 (0.23), residues: 1379 helix: 1.19 (0.24), residues: 489 sheet: -0.29 (0.35), residues: 213 loop : -0.83 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 764 TYR 0.014 0.001 TYR A 439 PHE 0.007 0.001 PHE A 107 TRP 0.012 0.001 TRP A 232 HIS 0.006 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (10560) covalent geometry : angle 0.59009 / 0.29 (14500) SS BOND : bond 0.00028 / 0.01 ( 2) SS BOND : angle 1.07203 / 0.53 ( 4) hydrogen bonds : bond 0.03167 / 2.12 ( 427) hydrogen bonds : angle 4.56106 / 3.24 ( 1209) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8848 (mtm-85) cc_final: 0.7630 (tpt170) REVERT: A 41 ASP cc_start: 0.8880 (m-30) cc_final: 0.8655 (m-30) REVERT: A 137 ARG cc_start: 0.8507 (tpp-160) cc_final: 0.7782 (ttm170) REVERT: A 147 SER cc_start: 0.8128 (m) cc_final: 0.7804 (p) REVERT: A 411 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8069 (mm) REVERT: A 844 GLN cc_start: 0.8246 (tt0) cc_final: 0.7831 (tt0) REVERT: A 953 VAL cc_start: 0.8231 (m) cc_final: 0.7823 (p) REVERT: A 959 SER cc_start: 0.7903 (p) cc_final: 0.7503 (m) REVERT: A 983 HIS cc_start: 0.6583 (t-170) cc_final: 0.6189 (p90) REVERT: A 1054 ASP cc_start: 0.8141 (t70) cc_final: 0.7893 (t70) REVERT: A 1097 LYS cc_start: 0.8905 (mtmm) cc_final: 0.8472 (pmtt) REVERT: A 1180 MET cc_start: 0.8951 (ptp) cc_final: 0.8563 (ptt) REVERT: A 1341 TYR cc_start: 0.8246 (m-10) cc_final: 0.8036 (m-10) REVERT: B 44 MET cc_start: 0.7591 (mmp) cc_final: 0.6933 (mtt) outliers start: 17 outliers final: 11 residues processed: 121 average time/residue: 0.4198 time to fit residues: 56.4457 Evaluate side-chains 114 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1354 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 107 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.127807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.090010 restraints weight = 49513.808| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.96 r_work: 0.2845 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10563 Z= 0.119 Angle : 0.597 12.460 14504 Z= 0.288 Chirality : 0.044 0.320 1722 Planarity : 0.005 0.054 1875 Dihedral : 6.092 82.627 1519 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.00 % Allowed : 13.93 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: 0.07 (0.23), residues: 1379 helix: 1.27 (0.24), residues: 491 sheet: -0.15 (0.35), residues: 213 loop : -0.78 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 764 TYR 0.014 0.001 TYR A 439 PHE 0.007 0.001 PHE A 107 TRP 0.012 0.001 TRP A 232 HIS 0.005 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (10560) covalent geometry : angle 0.59686 / 0.29 (14500) SS BOND : bond 0.00214 / 0.10 ( 2) SS BOND : angle 0.97397 / 0.48 ( 4) hydrogen bonds : bond 0.03142 / 2.11 ( 427) hydrogen bonds : angle 4.52057 / 3.20 ( 1209) Misc. bond : bond 0.00026 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8862 (mtm-85) cc_final: 0.7662 (tpt170) REVERT: A 41 ASP cc_start: 0.8895 (m-30) cc_final: 0.8664 (m-30) REVERT: A 137 ARG cc_start: 0.8492 (tpp-160) cc_final: 0.7747 (ttm170) REVERT: A 147 SER cc_start: 0.8113 (OUTLIER) cc_final: 0.7797 (p) REVERT: A 844 GLN cc_start: 0.8130 (tt0) cc_final: 0.7748 (tt0) REVERT: A 953 VAL cc_start: 0.8244 (m) cc_final: 0.7841 (p) REVERT: A 954 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7778 (pp) REVERT: A 959 SER cc_start: 0.7847 (p) cc_final: 0.7461 (m) REVERT: A 983 HIS cc_start: 0.6600 (t-170) cc_final: 0.6170 (p90) REVERT: A 1054 ASP cc_start: 0.8148 (t70) cc_final: 0.7900 (t70) REVERT: A 1097 LYS cc_start: 0.8913 (mtmm) cc_final: 0.8559 (pmtt) REVERT: A 1180 MET cc_start: 0.8952 (ptp) cc_final: 0.8559 (ptt) REVERT: A 1341 TYR cc_start: 0.8265 (m-10) cc_final: 0.8056 (m-10) REVERT: B 44 MET cc_start: 0.7642 (mmp) cc_final: 0.6995 (mtt) outliers start: 21 outliers final: 13 residues processed: 122 average time/residue: 0.4251 time to fit residues: 57.7202 Evaluate side-chains 116 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1354 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 109 optimal weight: 0.0270 chunk 23 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 83 optimal weight: 0.0000 chunk 19 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 120 optimal weight: 0.4980 overall best weight: 0.4844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.129191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.092179 restraints weight = 38287.982| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.55 r_work: 0.2874 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10563 Z= 0.114 Angle : 0.598 13.265 14504 Z= 0.287 Chirality : 0.044 0.320 1722 Planarity : 0.005 0.062 1875 Dihedral : 5.921 77.980 1519 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.53 % Allowed : 14.60 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: 0.15 (0.23), residues: 1379 helix: 1.35 (0.24), residues: 490 sheet: -0.09 (0.36), residues: 213 loop : -0.75 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 764 TYR 0.014 0.001 TYR A 439 PHE 0.006 0.001 PHE A 107 TRP 0.012 0.001 TRP A 232 HIS 0.006 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (10560) covalent geometry : angle 0.59768 / 0.29 (14500) SS BOND : bond 0.00024 / 0.01 ( 2) SS BOND : angle 0.96233 / 0.48 ( 4) hydrogen bonds : bond 0.03118 / 2.10 ( 427) hydrogen bonds : angle 4.47510 / 3.16 ( 1209) Misc. bond : bond 0.00024 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8833 (mtm-85) cc_final: 0.7712 (tpt170) REVERT: A 41 ASP cc_start: 0.8861 (m-30) cc_final: 0.8629 (m-30) REVERT: A 137 ARG cc_start: 0.8529 (tpp-160) cc_final: 0.7777 (ttm170) REVERT: A 147 SER cc_start: 0.8054 (OUTLIER) cc_final: 0.7771 (p) REVERT: A 844 GLN cc_start: 0.8104 (tt0) cc_final: 0.7704 (tt0) REVERT: A 953 VAL cc_start: 0.8255 (m) cc_final: 0.7870 (p) REVERT: A 954 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7791 (pp) REVERT: A 959 SER cc_start: 0.7806 (p) cc_final: 0.7432 (m) REVERT: A 983 HIS cc_start: 0.6586 (t-170) cc_final: 0.6162 (p90) REVERT: A 1054 ASP cc_start: 0.8126 (t70) cc_final: 0.7879 (t70) REVERT: A 1097 LYS cc_start: 0.8909 (mtmm) cc_final: 0.8558 (pmtt) REVERT: A 1180 MET cc_start: 0.8941 (ptp) cc_final: 0.8595 (ptt) REVERT: A 1341 TYR cc_start: 0.8280 (m-10) cc_final: 0.8064 (m-10) REVERT: B 44 MET cc_start: 0.7578 (mmp) cc_final: 0.6838 (mtt) outliers start: 16 outliers final: 10 residues processed: 120 average time/residue: 0.4168 time to fit residues: 55.6948 Evaluate side-chains 117 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1354 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 54 optimal weight: 0.6980 chunk 35 optimal weight: 0.0570 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 87 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 98 optimal weight: 0.0980 chunk 126 optimal weight: 0.0060 overall best weight: 0.2714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 360 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 = 0.3551 r_free = 0.3551 target = 0.130975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.095143 restraints weight = 51386.932| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 4.44 r_work: 0.2868 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10563 Z= 0.102 Angle : 0.591 13.476 14504 Z= 0.282 Chirality : 0.043 0.311 1722 Planarity : 0.005 0.048 1875 Dihedral : 5.693 79.346 1519 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.62 % Allowed : 14.69 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: 0.31 (0.23), residues: 1379 helix: 1.52 (0.24), residues: 488 sheet: -0.06 (0.35), residues: 215 loop : -0.66 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 764 TYR 0.013 0.001 TYR A 439 PHE 0.005 0.001 PHE A 107 TRP 0.011 0.001 TRP A 232 HIS 0.002 0.000 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (10560) covalent geometry : angle 0.59139 / 0.28 (14500) SS BOND : bond 0.00008 / 0.00 ( 2) SS BOND : angle 0.81672 / 0.40 ( 4) hydrogen bonds : bond 0.02910 / 1.96 ( 427) hydrogen bonds : angle 4.39506 / 3.10 ( 1209) Misc. bond : bond 0.00019 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3340.94 seconds wall clock time: 57 minutes 39.13 seconds (3459.13 seconds total)