Starting phenix.real_space_refine on Sat Jul 4 00:33:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u5z_63892/07_2026/9u5z_63892.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u5z_63892/07_2026/9u5z_63892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u5z_63892/07_2026/9u5z_63892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u5z_63892/07_2026/9u5z_63892.map" model { file = "/net/cci-nas-00/data/ceres_data/9u5z_63892/07_2026/9u5z_63892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u5z_63892/07_2026/9u5z_63892.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 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: 5 Type Number sf(0) Gaussians Ni 1 6.56 5 S 82 5.16 5 C 10402 2.51 5 N 2876 2.21 5 O 3087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16448 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 5210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5210 Classifications: {'peptide': 669} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 35, 'TRANS': 633} Chain breaks: 7 Chain: "E" Number of atoms: 11237 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1447, 11229 Classifications: {'peptide': 1447} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 1374} Chain breaks: 15 Conformer: "B" Number of residues, atoms: 1447, 11229 Classifications: {'peptide': 1447} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 1374} Chain breaks: 15 bond proxies already assigned to first conformer: 11449 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NI': 1} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AILE E1056 " occ=0.49 ... (14 atoms not shown) pdb=" CD1BILE E1056 " occ=0.51 Time building chain proxies: 5.60, per 1000 atoms: 0.34 Number of scatterers: 16448 At special positions: 0 Unit cell: (164.35, 122.55, 115.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ni 1 28.00 S 82 16.00 O 3087 8.00 N 2876 7.00 C 10402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 64 " distance=2.03 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 84 " distance=2.04 Simple disulfide: pdb=" SG CYS B 89 " - pdb=" SG CYS B 131 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 191 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS B 463 " - pdb=" SG CYS B 581 " distance=2.03 Simple disulfide: pdb=" SG CYS B 492 " - pdb=" SG CYS B 508 " distance=2.03 Simple disulfide: pdb=" SG CYS B 584 " - pdb=" SG CYS B 600 " distance=2.03 Simple disulfide: pdb=" SG CYS B 638 " - pdb=" SG CYS B 665 " distance=2.03 Simple disulfide: pdb=" SG CYS B 675 " - pdb=" SG CYS B 705 " distance=2.03 Simple disulfide: pdb=" SG CYS E1394 " - pdb=" SG CYS E1566 " distance=2.03 Simple disulfide: pdb=" SG CYS E1471 " - pdb=" SG CYS E1535 " distance=2.03 Simple disulfide: pdb=" SG CYS E1583 " - pdb=" SG CYS E1588 " distance=2.03 Simple disulfide: pdb=" SG CYS E1595 " - pdb=" SG CYS E1673 " distance=2.03 Simple disulfide: pdb=" SG CYS E1618 " - pdb=" SG CYS E1742 " distance=2.03 Simple disulfide: pdb=" SG CYS E1718 " - pdb=" SG CYS E1727 " 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=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3902 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 36 sheets defined 16.4% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'B' and resid 212 through 231 Proline residue: B 218 - end of helix removed outlier: 4.604A pdb=" N HIS B 226 " --> pdb=" O THR B 222 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N MET B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.525A pdb=" N LYS B 274 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE B 285 " --> pdb=" O VAL B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 314 removed outlier: 3.657A pdb=" N SER B 313 " --> pdb=" O ASN B 310 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG B 314 " --> pdb=" O ASP B 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 310 through 314' Processing helix chain 'B' and resid 315 through 324 removed outlier: 3.883A pdb=" N VAL B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 333 removed outlier: 4.321A pdb=" N ASN B 333 " --> pdb=" O LYS B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 351 removed outlier: 3.680A pdb=" N ALA B 342 " --> pdb=" O ASN B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 396 removed outlier: 4.211A pdb=" N VAL B 389 " --> pdb=" O PRO B 385 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 396 " --> pdb=" O ILE B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 427 removed outlier: 3.686A pdb=" N LEU B 426 " --> pdb=" O GLU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 450 removed outlier: 3.660A pdb=" N PHE B 449 " --> pdb=" O HIS B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 593 Processing helix chain 'B' and resid 601 through 606 removed outlier: 3.904A pdb=" N GLU B 606 " --> pdb=" O HIS B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 640 removed outlier: 3.666A pdb=" N CYS B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 639 " --> pdb=" O TRP B 635 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU B 640 " --> pdb=" O THR B 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 634 through 640' Processing helix chain 'B' and resid 641 through 645 Processing helix chain 'B' and resid 675 through 679 removed outlier: 3.604A pdb=" N SER B 679 " --> pdb=" O LYS B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 743 removed outlier: 3.740A pdb=" N LEU B 739 " --> pdb=" O MET B 735 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 78 Processing helix chain 'E' and resid 315 through 323 removed outlier: 3.580A pdb=" N PHE E 319 " --> pdb=" O SER E 315 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU E 323 " --> pdb=" O PHE E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 326 No H-bonds generated for 'chain 'E' and resid 324 through 326' Processing helix chain 'E' and resid 534 through 538 removed outlier: 3.508A pdb=" N LEU E 537 " --> pdb=" O ASP E 534 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA E 538 " --> pdb=" O HIS E 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 534 through 538' Processing helix chain 'E' and resid 606 through 612 removed outlier: 3.758A pdb=" N ALA E 610 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA E 611 " --> pdb=" O ALA E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 620 through 630 Processing helix chain 'E' and resid 642 through 651 Processing helix chain 'E' and resid 768 through 772 Processing helix chain 'E' and resid 1018 through 1031 removed outlier: 3.824A pdb=" N LEU E1022 " --> pdb=" O LEU E1018 " (cutoff:3.500A) Processing helix chain 'E' and resid 1040 through 1056 removed outlier: 3.893A pdb=" N HIS E1044 " --> pdb=" O GLU E1040 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY E1052 " --> pdb=" O LEU E1048 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR E1053 " --> pdb=" O ILE E1049 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N MET E1054 " --> pdb=" O GLN E1050 " (cutoff:3.500A) Processing helix chain 'E' and resid 1072 through 1083 removed outlier: 3.846A pdb=" N THR E1076 " --> pdb=" O ARG E1072 " (cutoff:3.500A) Processing helix chain 'E' and resid 1102 through 1107 removed outlier: 3.682A pdb=" N LEU E1107 " --> pdb=" O THR E1103 " (cutoff:3.500A) Processing helix chain 'E' and resid 1139 through 1154 removed outlier: 3.872A pdb=" N ALA E1143 " --> pdb=" O VAL E1139 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE E1147 " --> pdb=" O ALA E1143 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA E1148 " --> pdb=" O PHE E1144 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU E1149 " --> pdb=" O VAL E1145 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N HIS E1150 " --> pdb=" O THR E1146 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N HIS E1151 " --> pdb=" O ILE E1147 " (cutoff:3.500A) Processing helix chain 'E' and resid 1170 through 1182 Processing helix chain 'E' and resid 1189 through 1201 Processing helix chain 'E' and resid 1278 through 1287 removed outlier: 5.057A pdb=" N GLN E1284 " --> pdb=" O GLU E1280 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA E1285 " --> pdb=" O MET E1281 " (cutoff:3.500A) Processing helix chain 'E' and resid 1299 through 1308 removed outlier: 3.632A pdb=" N THR E1305 " --> pdb=" O SER E1301 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL E1306 " --> pdb=" O THR E1302 " (cutoff:3.500A) Processing helix chain 'E' and resid 1310 through 1317 removed outlier: 3.683A pdb=" N ALA E1314 " --> pdb=" O ASP E1310 " (cutoff:3.500A) Processing helix chain 'E' and resid 1497 through 1506 Processing helix chain 'E' and resid 1612 through 1618 Processing helix chain 'E' and resid 1723 through 1740 removed outlier: 3.512A pdb=" N CYS E1727 " --> pdb=" O GLN E1723 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU E1730 " --> pdb=" O ALA E1726 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR E1737 " --> pdb=" O PHE E1733 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR E1739 " --> pdb=" O GLN E1735 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN E1740 " --> pdb=" O GLU E1736 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 34 through 37 Processing sheet with id=AA2, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 100 Processing sheet with id=AA4, first strand: chain 'B' and resid 122 through 124 removed outlier: 3.685A pdb=" N ILE B 122 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP B 145 " --> pdb=" O ILE B 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 161 through 163 Processing sheet with id=AA6, first strand: chain 'B' and resid 182 through 184 Processing sheet with id=AA7, first strand: chain 'B' and resid 303 through 304 removed outlier: 7.012A pdb=" N LEU B 253 " --> pdb=" O SER B 292 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ALA B 294 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU B 255 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE B 296 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU B 257 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N PHE B 437 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLY B 412 " --> pdb=" O PHE B 437 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 481 through 484 removed outlier: 3.828A pdb=" N GLY B 494 " --> pdb=" O VAL B 482 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 566 " --> pdb=" O GLU B 536 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU B 536 " --> pdb=" O LYS B 566 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 611 through 612 removed outlier: 4.769A pdb=" N CYS B 665 " --> pdb=" O LYS B 630 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP B 727 " --> pdb=" O SER B 666 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE B 730 " --> pdb=" O VAL B 697 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL B 697 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL B 683 " --> pdb=" O VAL B 694 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 616 through 618 Processing sheet with id=AB2, first strand: chain 'E' and resid 80 through 85 removed outlier: 8.942A pdb=" N SER E 38 " --> pdb=" O PRO E 28 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN E 42 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 24 " --> pdb=" O GLN E 42 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 30 through 31 removed outlier: 4.716A pdb=" N VAL E 108 " --> pdb=" O PHE E 134 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL E 56 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL E 66 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU E 58 " --> pdb=" O ASN E 64 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN E 64 " --> pdb=" O LEU E 58 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 30 through 31 removed outlier: 4.716A pdb=" N VAL E 108 " --> pdb=" O PHE E 134 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER E 114 " --> pdb=" O ILE E 127 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE E 127 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 50 through 52 Processing sheet with id=AB6, first strand: chain 'E' and resid 140 through 145 Processing sheet with id=AB7, first strand: chain 'E' and resid 149 through 150 removed outlier: 3.905A pdb=" N ARG E 187 " --> pdb=" O VAL E 178 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 241 through 246 removed outlier: 3.694A pdb=" N MET E 262 " --> pdb=" O LEU E 314 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 252 through 254 removed outlier: 3.743A pdb=" N GLU E 353 " --> pdb=" O ILE E 344 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU E 357 " --> pdb=" O VAL E 340 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL E 340 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER E 359 " --> pdb=" O LEU E 338 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU E 338 " --> pdb=" O SER E 359 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG E 337 " --> pdb=" O LEU E 287 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 252 through 254 removed outlier: 3.743A pdb=" N GLU E 353 " --> pdb=" O ILE E 344 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU E 357 " --> pdb=" O VAL E 340 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL E 340 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER E 359 " --> pdb=" O LEU E 338 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU E 338 " --> pdb=" O SER E 359 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG E 337 " --> pdb=" O LEU E 287 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL E 282 " --> pdb=" O SER E 301 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER E 301 " --> pdb=" O VAL E 282 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 368 through 370 Processing sheet with id=AC3, first strand: chain 'E' and resid 423 through 424 removed outlier: 4.249A pdb=" N GLN E 423 " --> pdb=" O VAL E 403 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU E 460 " --> pdb=" O LEU E 446 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 474 through 477 removed outlier: 3.587A pdb=" N THR E 527 " --> pdb=" O LEU E 493 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 514 through 522 removed outlier: 5.118A pdb=" N ILE E 515 " --> pdb=" O SER E 511 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER E 511 " --> pdb=" O ILE E 515 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE E 517 " --> pdb=" O ILE E 509 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N HIS E 504 " --> pdb=" O TYR E 548 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N TYR E 548 " --> pdb=" O HIS E 504 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU E 510 " --> pdb=" O TYR E 542 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE E 541 " --> pdb=" O VAL E 560 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS E 549 " --> pdb=" O HIS E 552 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 588 through 589 Processing sheet with id=AC7, first strand: chain 'E' and resid 781 through 782 removed outlier: 3.520A pdb=" N LEU E 598 " --> pdb=" O LEU E 813 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 786 through 788 removed outlier: 3.520A pdb=" N LEU E 598 " --> pdb=" O LEU E 813 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 834 through 838 removed outlier: 3.507A pdb=" N HIS E 834 " --> pdb=" O TYR E 856 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG E 838 " --> pdb=" O ARG E 852 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG E 852 " --> pdb=" O ARG E 838 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER E 893 " --> pdb=" O ASN E 857 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 834 through 838 removed outlier: 3.507A pdb=" N HIS E 834 " --> pdb=" O TYR E 856 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG E 838 " --> pdb=" O ARG E 852 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG E 852 " --> pdb=" O ARG E 838 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 842 through 843 Processing sheet with id=AD3, first strand: chain 'E' and resid 938 through 940 Processing sheet with id=AD4, first strand: chain 'E' and resid 944 through 947 removed outlier: 3.524A pdb=" N GLU E1355 " --> pdb=" O VAL E 978 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 956 through 959 Processing sheet with id=AD6, first strand: chain 'E' and resid 1324 through 1327 Processing sheet with id=AD7, first strand: chain 'E' and resid 1397 through 1405 removed outlier: 3.844A pdb=" N LYS E1404 " --> pdb=" O HIS E1467 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 1510 through 1511 Processing sheet with id=AD9, first strand: chain 'E' and resid 1700 through 1702 removed outlier: 6.339A pdb=" N ASN E1666 " --> pdb=" O TYR E1701 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU E1642 " --> pdb=" O GLU E1634 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU E1634 " --> pdb=" O LEU E1642 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLU E1644 " --> pdb=" O LEU E1632 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN E1628 " --> pdb=" O THR E1648 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE E1627 " --> pdb=" O ILE E1685 " (cutoff:3.500A) 496 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.11 Time building geometry restraints manager: 1.78 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: 2751 1.30 - 1.43: 4452 1.43 - 1.56: 9451 1.56 - 1.69: 14 1.69 - 1.82: 123 Bond restraints: 16791 Sorted by residual: bond pdb=" CA LYS E1369 " pdb=" C LYS E1369 " ideal model delta sigma weight residual 1.521 1.399 0.123 1.31e-02 5.83e+03 8.75e+01 bond pdb=" CA SER E1361 " pdb=" C SER E1361 " ideal model delta sigma weight residual 1.521 1.422 0.099 1.19e-02 7.06e+03 6.94e+01 bond pdb=" CA SER E1374 " pdb=" C SER E1374 " ideal model delta sigma weight residual 1.528 1.423 0.105 1.34e-02 5.57e+03 6.18e+01 bond pdb=" CA VAL E1370 " pdb=" CB VAL E1370 " ideal model delta sigma weight residual 1.538 1.457 0.080 1.10e-02 8.26e+03 5.32e+01 bond pdb=" CA VAL E1370 " pdb=" C VAL E1370 " ideal model delta sigma weight residual 1.526 1.443 0.083 1.19e-02 7.06e+03 4.90e+01 ... (remaining 16786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.10: 22567 6.10 - 12.19: 161 12.19 - 18.29: 16 18.29 - 24.39: 2 24.39 - 30.48: 1 Bond angle restraints: 22747 Sorted by residual: angle pdb=" N SER E1364 " pdb=" CA SER E1364 " pdb=" C SER E1364 " ideal model delta sigma weight residual 108.75 78.27 30.48 1.71e+00 3.42e-01 3.18e+02 angle pdb=" N SER E1361 " pdb=" CA SER E1361 " pdb=" C SER E1361 " ideal model delta sigma weight residual 108.90 87.77 21.13 1.63e+00 3.76e-01 1.68e+02 angle pdb=" N GLY E1371 " pdb=" CA GLY E1371 " pdb=" C GLY E1371 " ideal model delta sigma weight residual 111.10 95.65 15.45 1.46e+00 4.69e-01 1.12e+02 angle pdb=" N TYR E1620 " pdb=" CA TYR E1620 " pdb=" C TYR E1620 " ideal model delta sigma weight residual 112.75 125.68 -12.93 1.36e+00 5.41e-01 9.04e+01 angle pdb=" N GLY E1372 " pdb=" CA GLY E1372 " pdb=" C GLY E1372 " ideal model delta sigma weight residual 115.36 102.81 12.55 1.33e+00 5.65e-01 8.90e+01 ... (remaining 22742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 8452 17.66 - 35.32: 1208 35.32 - 52.98: 385 52.98 - 70.64: 60 70.64 - 88.31: 10 Dihedral angle restraints: 10115 sinusoidal: 4058 harmonic: 6057 Sorted by residual: dihedral pdb=" CB CYS B 675 " pdb=" SG CYS B 675 " pdb=" SG CYS B 705 " pdb=" CB CYS B 705 " ideal model delta sinusoidal sigma weight residual -86.00 -149.08 63.08 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" CA GLN E1058 " pdb=" C GLN E1058 " pdb=" N PHE E1059 " pdb=" CA PHE E1059 " ideal model delta harmonic sigma weight residual 180.00 -144.45 -35.55 0 5.00e+00 4.00e-02 5.05e+01 dihedral pdb=" CB CYS B 117 " pdb=" SG CYS B 117 " pdb=" SG CYS B 144 " pdb=" CB CYS B 144 " ideal model delta sinusoidal sigma weight residual -86.00 -147.48 61.48 1 1.00e+01 1.00e-02 5.02e+01 ... (remaining 10112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 2437 0.145 - 0.290: 86 0.290 - 0.434: 16 0.434 - 0.579: 1 0.579 - 0.724: 5 Chirality restraints: 2545 Sorted by residual: chirality pdb=" CA PHE B 270 " pdb=" N PHE B 270 " pdb=" C PHE B 270 " pdb=" CB PHE B 270 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA TYR E1620 " pdb=" N TYR E1620 " pdb=" C TYR E1620 " pdb=" CB TYR E1620 " both_signs ideal model delta sigma weight residual False 2.51 1.80 0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CA ASN E1373 " pdb=" N ASN E1373 " pdb=" C ASN E1373 " pdb=" CB ASN E1373 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.89e+00 ... (remaining 2542 not shown) Planarity restraints: 2950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 425 " 0.033 2.00e-02 2.50e+03 7.01e-02 4.91e+01 pdb=" CD GLU B 425 " -0.121 2.00e-02 2.50e+03 pdb=" OE1 GLU B 425 " 0.046 2.00e-02 2.50e+03 pdb=" OE2 GLU B 425 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 852 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO E 853 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO E 853 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO E 853 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 482 " 0.071 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO E 483 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO E 483 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO E 483 " 0.056 5.00e-02 4.00e+02 ... (remaining 2947 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 76 2.52 - 3.12: 10244 3.12 - 3.71: 23483 3.71 - 4.31: 31573 4.31 - 4.90: 54760 Nonbonded interactions: 120136 Sorted by model distance: nonbonded pdb=" N SER E1364 " pdb=" O SER E1364 " model vdw 1.930 2.496 nonbonded pdb=" OG SER B 264 " pdb="NI NI B 801 " model vdw 2.016 2.920 nonbonded pdb=" OG1 THR B 337 " pdb="NI NI B 801 " model vdw 2.083 2.920 nonbonded pdb=" OG SER B 262 " pdb="NI NI B 801 " model vdw 2.157 2.920 nonbonded pdb=" N GLY E1371 " pdb=" O GLY E1371 " model vdw 2.225 2.496 ... (remaining 120131 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=0.49 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: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.890 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.180 16808 Z= 0.497 Angle : 1.255 30.484 22781 Z= 0.705 Chirality : 0.073 0.724 2545 Planarity : 0.009 0.138 2950 Dihedral : 17.910 88.306 6162 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.62 % Favored : 93.33 % Rotamer: Outliers : 2.50 % Allowed : 31.59 % Favored : 65.91 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 1.87 % Twisted General : 0.05 % 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: -2.59 (0.17), residues: 2071 helix: -2.10 (0.25), residues: 280 sheet: -0.19 (0.22), residues: 595 loop : -2.56 (0.15), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 337 TYR 0.031 0.003 TYR B 409 PHE 0.046 0.003 PHE B 689 TRP 0.025 0.002 TRP E 360 HIS 0.010 0.001 HIS E 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00795 / 0.50 (16791) covalent geometry : angle 1.25527 / 0.70 (22747) SS BOND : bond 0.00294 / 0.19 ( 17) SS BOND : angle 1.19121 / 0.76 ( 34) hydrogen bonds : bond 0.24803 / 16.44 ( 468) hydrogen bonds : angle 8.85047 / 6.15 ( 1326) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 305 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 285 PHE cc_start: 0.6679 (OUTLIER) cc_final: 0.6159 (m-80) REVERT: B 316 MET cc_start: 0.7328 (mtp) cc_final: 0.6694 (mtt) REVERT: B 561 ASP cc_start: 0.8213 (t0) cc_final: 0.7990 (t70) REVERT: B 645 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7696 (tm-30) REVERT: B 674 PRO cc_start: 0.7592 (Cg_exo) cc_final: 0.6849 (Cg_endo) REVERT: E 351 GLU cc_start: 0.7830 (tp30) cc_final: 0.7342 (tp30) REVERT: E 841 MET cc_start: 0.8237 (tpt) cc_final: 0.6539 (tpt) REVERT: E 956 ARG cc_start: 0.7648 (ttt90) cc_final: 0.7435 (ttt90) REVERT: E 1356 GLU cc_start: 0.7374 (mp0) cc_final: 0.7045 (mp0) REVERT: E 1369 LYS cc_start: 0.8090 (ptpp) cc_final: 0.7648 (ttmm) REVERT: E 1575 LYS cc_start: 0.6492 (mmmt) cc_final: 0.6170 (pptt) REVERT: E 1620 TYR cc_start: 0.7584 (m-80) cc_final: 0.7382 (m-80) outliers start: 45 outliers final: 17 residues processed: 332 average time/residue: 0.1374 time to fit residues: 66.6947 Evaluate side-chains 302 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 284 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 725 PRO Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 850 GLU Chi-restraints excluded: chain E residue 1302 THR Chi-restraints excluded: chain E residue 1305 THR Chi-restraints excluded: chain E residue 1360 PHE Chi-restraints excluded: chain E residue 1368 VAL Chi-restraints excluded: chain E residue 1375 LYS Chi-restraints excluded: chain E residue 1614 MET Chi-restraints excluded: chain E residue 1619 TYR Chi-restraints excluded: chain E residue 1622 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 0.0870 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 611 GLN E 258 HIS E 430 GLN E 648 GLN ** E 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1303 GLN E1320 HIS E1347 ASN E1359 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.180801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.137908 restraints weight = 55250.905| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 4.56 r_work: 0.3596 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 16808 Z= 0.127 Angle : 0.657 10.448 22781 Z= 0.339 Chirality : 0.044 0.172 2545 Planarity : 0.006 0.079 2950 Dihedral : 7.276 73.711 2308 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.44 % Allowed : 30.71 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.05 % 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: -2.11 (0.17), residues: 2071 helix: -0.94 (0.29), residues: 299 sheet: -0.04 (0.21), residues: 643 loop : -2.47 (0.16), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E1325 TYR 0.016 0.001 TYR E 192 PHE 0.016 0.001 PHE E 74 TRP 0.016 0.001 TRP E 798 HIS 0.004 0.001 HIS E1320 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (16791) covalent geometry : angle 0.65646 / 0.34 (22747) SS BOND : bond 0.00216 / 0.15 ( 17) SS BOND : angle 0.80904 / 0.63 ( 34) hydrogen bonds : bond 0.04100 / 2.71 ( 468) hydrogen bonds : angle 5.92531 / 4.14 ( 1326) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 282 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 99 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7654 (tp) REVERT: B 165 PHE cc_start: 0.7543 (t80) cc_final: 0.7236 (t80) REVERT: B 285 PHE cc_start: 0.6869 (OUTLIER) cc_final: 0.6257 (m-80) REVERT: B 348 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8090 (mm) REVERT: B 364 TRP cc_start: 0.7093 (OUTLIER) cc_final: 0.6041 (p90) REVERT: B 561 ASP cc_start: 0.8185 (t0) cc_final: 0.7676 (t70) REVERT: B 645 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7764 (tm-30) REVERT: B 684 PHE cc_start: 0.8325 (m-10) cc_final: 0.8122 (m-10) REVERT: B 710 ASP cc_start: 0.4634 (t0) cc_final: 0.4222 (t0) REVERT: B 722 VAL cc_start: 0.7879 (OUTLIER) cc_final: 0.7673 (m) REVERT: B 725 PRO cc_start: 0.7914 (Cg_exo) cc_final: 0.7611 (Cg_exo) REVERT: E 138 ARG cc_start: 0.7651 (ptm160) cc_final: 0.7312 (ptm160) REVERT: E 193 MET cc_start: 0.6201 (ppp) cc_final: 0.5676 (ppp) REVERT: E 262 MET cc_start: 0.8484 (mmm) cc_final: 0.8251 (mmm) REVERT: E 351 GLU cc_start: 0.8110 (tp30) cc_final: 0.7745 (tp30) REVERT: E 445 GLN cc_start: 0.8026 (mm110) cc_final: 0.7671 (tp-100) REVERT: E 836 HIS cc_start: 0.8264 (t-90) cc_final: 0.7886 (t-90) REVERT: E 1218 MET cc_start: 0.7423 (mmp) cc_final: 0.5896 (ttt) REVERT: E 1356 GLU cc_start: 0.6906 (mp0) cc_final: 0.6697 (mp0) REVERT: E 1616 PHE cc_start: 0.7700 (m-80) cc_final: 0.7356 (m-80) REVERT: E 1622 ARG cc_start: 0.4352 (OUTLIER) cc_final: 0.4025 (mmp80) REVERT: E 1653 PHE cc_start: 0.5660 (t80) cc_final: 0.5409 (t80) REVERT: E 1686 MET cc_start: 0.5065 (OUTLIER) cc_final: 0.4672 (tmm) outliers start: 62 outliers final: 29 residues processed: 319 average time/residue: 0.1522 time to fit residues: 69.3861 Evaluate side-chains 298 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 262 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 199 GLN Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 549 HIS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 769 GLU Chi-restraints excluded: chain E residue 847 GLU Chi-restraints excluded: chain E residue 1015 MET Chi-restraints excluded: chain E residue 1139 VAL Chi-restraints excluded: chain E residue 1302 THR Chi-restraints excluded: chain E residue 1368 VAL Chi-restraints excluded: chain E residue 1375 LYS Chi-restraints excluded: chain E residue 1619 TYR Chi-restraints excluded: chain E residue 1622 ARG Chi-restraints excluded: chain E residue 1623 VAL Chi-restraints excluded: chain E residue 1685 ILE Chi-restraints excluded: chain E residue 1686 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 141 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 207 optimal weight: 0.2980 chunk 20 optimal weight: 5.9990 chunk 91 optimal weight: 0.0970 chunk 158 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 504 HIS E 552 HIS E 648 GLN ** E 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1373 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.176480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.132774 restraints weight = 46400.290| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 4.26 r_work: 0.3525 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16808 Z= 0.172 Angle : 0.675 9.777 22781 Z= 0.348 Chirality : 0.046 0.176 2545 Planarity : 0.006 0.076 2950 Dihedral : 6.958 73.511 2292 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.33 % Allowed : 29.43 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.05 % 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: -1.96 (0.18), residues: 2071 helix: -0.46 (0.30), residues: 303 sheet: -0.05 (0.21), residues: 643 loop : -2.41 (0.16), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E1325 TYR 0.022 0.002 TYR B 409 PHE 0.014 0.002 PHE E 74 TRP 0.012 0.002 TRP E 798 HIS 0.006 0.001 HIS E 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 (16791) covalent geometry : angle 0.67397 / 0.35 (22747) SS BOND : bond 0.00262 / 0.21 ( 17) SS BOND : angle 1.03848 / 0.72 ( 34) hydrogen bonds : bond 0.04047 / 2.66 ( 468) hydrogen bonds : angle 5.46227 / 3.86 ( 1326) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 280 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 285 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.6451 (m-80) REVERT: B 324 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: B 348 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8085 (mm) REVERT: B 364 TRP cc_start: 0.7223 (OUTLIER) cc_final: 0.6302 (p90) REVERT: B 411 ILE cc_start: 0.7095 (mt) cc_final: 0.6771 (mt) REVERT: B 483 THR cc_start: 0.7520 (OUTLIER) cc_final: 0.7132 (p) REVERT: B 645 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7480 (tm-30) REVERT: B 684 PHE cc_start: 0.8552 (m-10) cc_final: 0.8306 (m-80) REVERT: B 721 LYS cc_start: 0.7962 (ttpt) cc_final: 0.7703 (ttpt) REVERT: B 722 VAL cc_start: 0.7948 (OUTLIER) cc_final: 0.7606 (m) REVERT: B 725 PRO cc_start: 0.7959 (Cg_exo) cc_final: 0.7729 (Cg_exo) REVERT: E 138 ARG cc_start: 0.7824 (ptm160) cc_final: 0.7529 (ptm160) REVERT: E 155 ARG cc_start: 0.8091 (ptp90) cc_final: 0.7807 (ptp90) REVERT: E 193 MET cc_start: 0.6590 (ppp) cc_final: 0.5742 (ppp) REVERT: E 351 GLU cc_start: 0.8109 (tp30) cc_final: 0.7879 (tp30) REVERT: E 353 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7646 (tm-30) REVERT: E 836 HIS cc_start: 0.8241 (t-90) cc_final: 0.7890 (t-90) REVERT: E 968 MET cc_start: 0.9173 (ttt) cc_final: 0.8951 (ttm) REVERT: E 1356 GLU cc_start: 0.7118 (mp0) cc_final: 0.6723 (mp0) REVERT: E 1360 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.7196 (t80) REVERT: E 1622 ARG cc_start: 0.4709 (OUTLIER) cc_final: 0.4470 (mmp80) outliers start: 78 outliers final: 46 residues processed: 322 average time/residue: 0.1571 time to fit residues: 72.9135 Evaluate side-chains 323 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 268 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 199 GLN Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 518 MET Chi-restraints excluded: chain E residue 549 HIS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 769 GLU Chi-restraints excluded: chain E residue 777 PHE Chi-restraints excluded: chain E residue 1015 MET Chi-restraints excluded: chain E residue 1302 THR Chi-restraints excluded: chain E residue 1360 PHE Chi-restraints excluded: chain E residue 1368 VAL Chi-restraints excluded: chain E residue 1375 LYS Chi-restraints excluded: chain E residue 1483 MET Chi-restraints excluded: chain E residue 1556 LEU Chi-restraints excluded: chain E residue 1612 TYR Chi-restraints excluded: chain E residue 1619 TYR Chi-restraints excluded: chain E residue 1622 ARG Chi-restraints excluded: chain E residue 1623 VAL Chi-restraints excluded: chain E residue 1686 MET Chi-restraints excluded: chain E residue 1702 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 198 optimal weight: 10.0000 chunk 158 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 172 optimal weight: 5.9990 chunk 144 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 648 GLN E 868 HIS E1350 GLN E1373 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.175058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.131903 restraints weight = 49671.252| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 4.33 r_work: 0.3533 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16808 Z= 0.149 Angle : 0.644 9.370 22781 Z= 0.330 Chirality : 0.045 0.177 2545 Planarity : 0.006 0.072 2950 Dihedral : 6.715 74.558 2292 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 5.33 % Allowed : 29.48 % Favored : 65.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -1.83 (0.18), residues: 2071 helix: -0.10 (0.31), residues: 303 sheet: 0.01 (0.21), residues: 626 loop : -2.36 (0.16), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1325 TYR 0.036 0.002 TYR B 409 PHE 0.014 0.001 PHE E 74 TRP 0.014 0.001 TRP E 360 HIS 0.005 0.001 HIS E 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (16791) covalent geometry : angle 0.64339 / 0.33 (22747) SS BOND : bond 0.00256 / 0.19 ( 17) SS BOND : angle 0.94258 / 0.65 ( 34) hydrogen bonds : bond 0.03509 / 2.30 ( 468) hydrogen bonds : angle 5.15010 / 3.66 ( 1326) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 288 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 165 PHE cc_start: 0.7476 (t80) cc_final: 0.7216 (t80) REVERT: B 285 PHE cc_start: 0.7028 (OUTLIER) cc_final: 0.6586 (m-80) REVERT: B 288 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: B 316 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.6811 (mtp) REVERT: B 324 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: B 348 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8095 (mm) REVERT: B 364 TRP cc_start: 0.7203 (OUTLIER) cc_final: 0.6305 (p90) REVERT: B 483 THR cc_start: 0.7486 (OUTLIER) cc_final: 0.7147 (p) REVERT: B 645 GLU cc_start: 0.8407 (tm-30) cc_final: 0.7416 (tm-30) REVERT: B 684 PHE cc_start: 0.8749 (m-10) cc_final: 0.8460 (m-80) REVERT: B 721 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7661 (ttpt) REVERT: B 722 VAL cc_start: 0.7839 (OUTLIER) cc_final: 0.7610 (m) REVERT: E 138 ARG cc_start: 0.7979 (ptm160) cc_final: 0.7745 (ptm160) REVERT: E 155 ARG cc_start: 0.7980 (ptp90) cc_final: 0.7627 (ptp90) REVERT: E 193 MET cc_start: 0.6866 (ppp) cc_final: 0.5854 (ppp) REVERT: E 351 GLU cc_start: 0.8212 (tp30) cc_final: 0.7897 (tp30) REVERT: E 589 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8038 (mp) REVERT: E 835 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8704 (tt) REVERT: E 836 HIS cc_start: 0.8190 (t-90) cc_final: 0.7938 (t-90) REVERT: E 1088 LEU cc_start: 0.5420 (OUTLIER) cc_final: 0.4885 (pp) REVERT: E 1356 GLU cc_start: 0.7166 (mp0) cc_final: 0.6680 (mp0) REVERT: E 1360 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7266 (t80) REVERT: E 1558 ASP cc_start: 0.7972 (t70) cc_final: 0.7749 (t70) REVERT: E 1582 LEU cc_start: 0.8579 (mp) cc_final: 0.8336 (mm) REVERT: E 1622 ARG cc_start: 0.4700 (OUTLIER) cc_final: 0.4466 (mmp80) REVERT: E 1653 PHE cc_start: 0.5672 (t80) cc_final: 0.5430 (t80) outliers start: 96 outliers final: 58 residues processed: 346 average time/residue: 0.1406 time to fit residues: 70.3745 Evaluate side-chains 349 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 277 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 529 TRP Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 678 GLU Chi-restraints excluded: chain B residue 721 LYS Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 199 GLN Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 549 HIS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain E residue 613 SER Chi-restraints excluded: chain E residue 769 GLU Chi-restraints excluded: chain E residue 777 PHE Chi-restraints excluded: chain E residue 835 LEU Chi-restraints excluded: chain E residue 1015 MET Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1088 LEU Chi-restraints excluded: chain E residue 1139 VAL Chi-restraints excluded: chain E residue 1302 THR Chi-restraints excluded: chain E residue 1360 PHE Chi-restraints excluded: chain E residue 1368 VAL Chi-restraints excluded: chain E residue 1375 LYS Chi-restraints excluded: chain E residue 1467 HIS Chi-restraints excluded: chain E residue 1483 MET Chi-restraints excluded: chain E residue 1536 VAL Chi-restraints excluded: chain E residue 1556 LEU Chi-restraints excluded: chain E residue 1619 TYR Chi-restraints excluded: chain E residue 1622 ARG Chi-restraints excluded: chain E residue 1623 VAL Chi-restraints excluded: chain E residue 1686 MET Chi-restraints excluded: chain E residue 1702 LEU Chi-restraints excluded: chain E residue 1744 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 117 optimal weight: 0.1980 chunk 110 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 108 optimal weight: 0.0000 chunk 202 optimal weight: 5.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN ** E 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 836 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.177473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.134073 restraints weight = 55429.729| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 4.63 r_work: 0.3556 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16808 Z= 0.113 Angle : 0.607 9.089 22781 Z= 0.308 Chirality : 0.043 0.166 2545 Planarity : 0.005 0.072 2950 Dihedral : 6.356 76.255 2292 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.78 % Allowed : 30.15 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.18), residues: 2071 helix: 0.16 (0.32), residues: 301 sheet: 0.11 (0.21), residues: 625 loop : -2.24 (0.17), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 187 TYR 0.026 0.001 TYR B 409 PHE 0.013 0.001 PHE E 541 TRP 0.014 0.001 TRP B 529 HIS 0.003 0.001 HIS E 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.11 (16791) covalent geometry : angle 0.60676 / 0.31 (22747) SS BOND : bond 0.00211 / 0.14 ( 17) SS BOND : angle 0.72913 / 0.52 ( 34) hydrogen bonds : bond 0.03043 / 1.98 ( 468) hydrogen bonds : angle 4.90086 / 3.48 ( 1326) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 296 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 285 PHE cc_start: 0.7072 (OUTLIER) cc_final: 0.6388 (m-80) REVERT: B 288 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6980 (mp0) REVERT: B 324 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: B 348 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8097 (mm) REVERT: B 364 TRP cc_start: 0.7187 (OUTLIER) cc_final: 0.6267 (p90) REVERT: B 411 ILE cc_start: 0.7299 (mt) cc_final: 0.6312 (mp) REVERT: B 483 THR cc_start: 0.7557 (OUTLIER) cc_final: 0.7238 (p) REVERT: B 645 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7354 (tm-30) REVERT: B 684 PHE cc_start: 0.8779 (m-10) cc_final: 0.8456 (m-80) REVERT: B 710 ASP cc_start: 0.4461 (t0) cc_final: 0.4124 (t0) REVERT: B 721 LYS cc_start: 0.8114 (ttpt) cc_final: 0.7704 (ttpt) REVERT: B 722 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7295 (m) REVERT: E 155 ARG cc_start: 0.7960 (ptp90) cc_final: 0.7620 (ptp90) REVERT: E 163 LEU cc_start: 0.8641 (mt) cc_final: 0.8382 (mt) REVERT: E 323 LEU cc_start: 0.8465 (tm) cc_final: 0.8264 (pt) REVERT: E 351 GLU cc_start: 0.8230 (tp30) cc_final: 0.7897 (tp30) REVERT: E 353 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7670 (tm-30) REVERT: E 506 TYR cc_start: 0.6920 (m-80) cc_final: 0.6301 (m-80) REVERT: E 956 ARG cc_start: 0.7791 (ttm-80) cc_final: 0.7511 (ttm-80) REVERT: E 1088 LEU cc_start: 0.5317 (OUTLIER) cc_final: 0.4822 (pp) REVERT: E 1356 GLU cc_start: 0.7169 (mp0) cc_final: 0.6704 (mp0) REVERT: E 1365 LYS cc_start: 0.7892 (mtpt) cc_final: 0.7480 (tttp) REVERT: E 1509 ASP cc_start: 0.7566 (p0) cc_final: 0.6265 (m-30) REVERT: E 1558 ASP cc_start: 0.7877 (t70) cc_final: 0.7630 (t70) REVERT: E 1582 LEU cc_start: 0.8607 (mp) cc_final: 0.8362 (mm) REVERT: E 1622 ARG cc_start: 0.4507 (OUTLIER) cc_final: 0.4277 (mmp80) outliers start: 86 outliers final: 49 residues processed: 349 average time/residue: 0.1570 time to fit residues: 78.8271 Evaluate side-chains 336 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 277 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 529 TRP Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 638 CYS Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 678 GLU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 199 GLN Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 549 HIS Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain E residue 613 SER Chi-restraints excluded: chain E residue 769 GLU Chi-restraints excluded: chain E residue 939 ILE Chi-restraints excluded: chain E residue 974 PHE Chi-restraints excluded: chain E residue 1015 MET Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1088 LEU Chi-restraints excluded: chain E residue 1139 VAL Chi-restraints excluded: chain E residue 1368 VAL Chi-restraints excluded: chain E residue 1375 LYS Chi-restraints excluded: chain E residue 1483 MET Chi-restraints excluded: chain E residue 1536 VAL Chi-restraints excluded: chain E residue 1556 LEU Chi-restraints excluded: chain E residue 1619 TYR Chi-restraints excluded: chain E residue 1620 TYR Chi-restraints excluded: chain E residue 1622 ARG Chi-restraints excluded: chain E residue 1623 VAL Chi-restraints excluded: chain E residue 1686 MET Chi-restraints excluded: chain E residue 1744 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 134 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 311 HIS ** E 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN E 836 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.174648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.131587 restraints weight = 41371.500| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 3.99 r_work: 0.3525 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16808 Z= 0.162 Angle : 0.660 8.794 22781 Z= 0.337 Chirality : 0.045 0.193 2545 Planarity : 0.006 0.080 2950 Dihedral : 6.520 74.485 2290 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 5.05 % Allowed : 29.98 % Favored : 64.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -1.65 (0.18), residues: 2071 helix: 0.25 (0.32), residues: 299 sheet: 0.07 (0.21), residues: 624 loop : -2.25 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 187 TYR 0.019 0.002 TYR E 361 PHE 0.012 0.002 PHE E 541 TRP 0.017 0.001 TRP E 798 HIS 0.007 0.001 HIS E 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 (16791) covalent geometry : angle 0.65896 / 0.34 (22747) SS BOND : bond 0.00375 / 0.29 ( 17) SS BOND : angle 1.00251 / 0.70 ( 34) hydrogen bonds : bond 0.03486 / 2.31 ( 468) hydrogen bonds : angle 5.04337 / 3.59 ( 1326) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 288 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 288 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: B 316 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7123 (mtp) REVERT: B 324 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: B 348 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8055 (mm) REVERT: B 364 TRP cc_start: 0.7199 (OUTLIER) cc_final: 0.6340 (p90) REVERT: B 411 ILE cc_start: 0.7305 (mt) cc_final: 0.6941 (mt) REVERT: B 483 THR cc_start: 0.7491 (OUTLIER) cc_final: 0.7186 (p) REVERT: B 554 ILE cc_start: 0.6923 (mm) cc_final: 0.6616 (mt) REVERT: B 645 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7443 (tm-30) REVERT: B 684 PHE cc_start: 0.8765 (m-10) cc_final: 0.8491 (m-80) REVERT: B 721 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7580 (ttpt) REVERT: E 155 ARG cc_start: 0.7844 (ptp90) cc_final: 0.7636 (ptp90) REVERT: E 351 GLU cc_start: 0.8220 (tp30) cc_final: 0.7784 (tp30) REVERT: E 353 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7617 (tm-30) REVERT: E 506 TYR cc_start: 0.6801 (m-80) cc_final: 0.6078 (m-80) REVERT: E 570 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8364 (ttmm) REVERT: E 589 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7996 (mp) REVERT: E 616 HIS cc_start: 0.6041 (OUTLIER) cc_final: 0.5283 (p-80) REVERT: E 1356 GLU cc_start: 0.7459 (mp0) cc_final: 0.7023 (mp0) REVERT: E 1360 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.7298 (t80) REVERT: E 1365 LYS cc_start: 0.7974 (mtpt) cc_final: 0.7548 (tttp) REVERT: E 1465 ARG cc_start: 0.8217 (mpp80) cc_final: 0.7950 (mpp80) REVERT: E 1558 ASP cc_start: 0.8007 (t70) cc_final: 0.7735 (t70) REVERT: E 1582 LEU cc_start: 0.8554 (mp) cc_final: 0.8337 (mm) outliers start: 91 outliers final: 56 residues processed: 337 average time/residue: 0.1619 time to fit residues: 78.5144 Evaluate side-chains 346 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 278 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 529 TRP Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 638 CYS Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 678 GLU Chi-restraints excluded: chain B residue 721 LYS Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 199 GLN Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 361 TYR Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 549 HIS Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 570 LYS Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain E residue 613 SER Chi-restraints excluded: chain E residue 616 HIS Chi-restraints excluded: chain E residue 777 PHE Chi-restraints excluded: chain E residue 974 PHE Chi-restraints excluded: chain E residue 1015 MET Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1139 VAL Chi-restraints excluded: chain E residue 1360 PHE Chi-restraints excluded: chain E residue 1368 VAL Chi-restraints excluded: chain E residue 1375 LYS Chi-restraints excluded: chain E residue 1467 HIS Chi-restraints excluded: chain E residue 1483 MET Chi-restraints excluded: chain E residue 1536 VAL Chi-restraints excluded: chain E residue 1553 SER Chi-restraints excluded: chain E residue 1556 LEU Chi-restraints excluded: chain E residue 1619 TYR Chi-restraints excluded: chain E residue 1623 VAL Chi-restraints excluded: chain E residue 1686 MET Chi-restraints excluded: chain E residue 1702 LEU Chi-restraints excluded: chain E residue 1744 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 101 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 40 optimal weight: 0.0770 chunk 208 optimal weight: 10.0000 chunk 166 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 422 GLN ** E 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN E 836 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.175071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.132408 restraints weight = 49017.756| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 4.21 r_work: 0.3535 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16808 Z= 0.132 Angle : 0.632 15.860 22781 Z= 0.319 Chirality : 0.044 0.189 2545 Planarity : 0.005 0.072 2950 Dihedral : 5.998 74.899 2282 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.61 % Allowed : 30.21 % Favored : 65.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -1.61 (0.18), residues: 2071 helix: 0.25 (0.32), residues: 301 sheet: 0.05 (0.21), residues: 634 loop : -2.20 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E1622 TYR 0.018 0.001 TYR E 192 PHE 0.014 0.001 PHE E 134 TRP 0.014 0.001 TRP B 529 HIS 0.005 0.001 HIS E 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 (16791) covalent geometry : angle 0.63126 / 0.32 (22747) SS BOND : bond 0.00227 / 0.15 ( 17) SS BOND : angle 0.86648 / 0.59 ( 34) hydrogen bonds : bond 0.03122 / 2.05 ( 468) hydrogen bonds : angle 4.91984 / 3.50 ( 1326) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 289 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 288 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: B 348 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8149 (mm) REVERT: B 364 TRP cc_start: 0.7189 (OUTLIER) cc_final: 0.6327 (p90) REVERT: B 411 ILE cc_start: 0.7415 (mt) cc_final: 0.7035 (mt) REVERT: B 422 GLU cc_start: 0.8263 (mt-10) cc_final: 0.8025 (mt-10) REVERT: B 483 THR cc_start: 0.7392 (OUTLIER) cc_final: 0.7110 (p) REVERT: B 554 ILE cc_start: 0.7091 (mm) cc_final: 0.6806 (mt) REVERT: B 645 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7743 (tm-30) REVERT: B 684 PHE cc_start: 0.8765 (m-10) cc_final: 0.8539 (m-80) REVERT: B 710 ASP cc_start: 0.4555 (t0) cc_final: 0.4230 (t0) REVERT: B 721 LYS cc_start: 0.8046 (ttpt) cc_final: 0.7714 (ttpt) REVERT: E 155 ARG cc_start: 0.7828 (ptp90) cc_final: 0.7597 (ptp90) REVERT: E 163 LEU cc_start: 0.8709 (mt) cc_final: 0.8500 (mt) REVERT: E 351 GLU cc_start: 0.8222 (tp30) cc_final: 0.7824 (tp30) REVERT: E 353 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: E 506 TYR cc_start: 0.6614 (m-80) cc_final: 0.5870 (m-80) REVERT: E 570 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8372 (ttmm) REVERT: E 589 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8009 (mp) REVERT: E 616 HIS cc_start: 0.5966 (OUTLIER) cc_final: 0.5192 (p-80) REVERT: E 1356 GLU cc_start: 0.7340 (mp0) cc_final: 0.6986 (mp0) REVERT: E 1360 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7318 (t80) REVERT: E 1365 LYS cc_start: 0.7943 (mtpt) cc_final: 0.7499 (tttp) REVERT: E 1465 ARG cc_start: 0.8218 (mpp80) cc_final: 0.7964 (mpp80) REVERT: E 1558 ASP cc_start: 0.7958 (t70) cc_final: 0.7697 (t70) REVERT: E 1688 LEU cc_start: 0.4172 (OUTLIER) cc_final: 0.3908 (tt) outliers start: 83 outliers final: 59 residues processed: 337 average time/residue: 0.1603 time to fit residues: 77.8936 Evaluate side-chains 350 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 281 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 529 TRP Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 638 CYS Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 678 GLU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 199 GLN Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 361 TYR Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 549 HIS Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 570 LYS Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain E residue 613 SER Chi-restraints excluded: chain E residue 616 HIS Chi-restraints excluded: chain E residue 974 PHE Chi-restraints excluded: chain E residue 1015 MET Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1139 VAL Chi-restraints excluded: chain E residue 1360 PHE Chi-restraints excluded: chain E residue 1368 VAL Chi-restraints excluded: chain E residue 1375 LYS Chi-restraints excluded: chain E residue 1467 HIS Chi-restraints excluded: chain E residue 1483 MET Chi-restraints excluded: chain E residue 1536 VAL Chi-restraints excluded: chain E residue 1556 LEU Chi-restraints excluded: chain E residue 1619 TYR Chi-restraints excluded: chain E residue 1620 TYR Chi-restraints excluded: chain E residue 1622 ARG Chi-restraints excluded: chain E residue 1623 VAL Chi-restraints excluded: chain E residue 1686 MET Chi-restraints excluded: chain E residue 1688 LEU Chi-restraints excluded: chain E residue 1705 SER Chi-restraints excluded: chain E residue 1744 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 197 optimal weight: 8.9990 chunk 172 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 8.9990 chunk 140 optimal weight: 0.9980 chunk 205 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 199 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN ** E 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 836 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.177730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.134245 restraints weight = 49724.246| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 4.31 r_work: 0.3547 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 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 0.047 16808 Z= 0.117 Angle : 0.615 14.503 22781 Z= 0.310 Chirality : 0.043 0.187 2545 Planarity : 0.005 0.068 2950 Dihedral : 5.803 75.810 2282 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 4.33 % Allowed : 30.82 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -1.54 (0.18), residues: 2071 helix: 0.31 (0.32), residues: 302 sheet: 0.10 (0.21), residues: 628 loop : -2.16 (0.17), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E1622 TYR 0.018 0.001 TYR E1027 PHE 0.015 0.001 PHE B 649 TRP 0.015 0.001 TRP B 529 HIS 0.005 0.001 HIS E 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (16791) covalent geometry : angle 0.61467 / 0.31 (22747) SS BOND : bond 0.00210 / 0.14 ( 17) SS BOND : angle 0.77092 / 0.54 ( 34) hydrogen bonds : bond 0.02917 / 1.93 ( 468) hydrogen bonds : angle 4.79257 / 3.41 ( 1326) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 288 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 285 PHE cc_start: 0.7045 (t80) cc_final: 0.6563 (m-80) REVERT: B 288 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: B 316 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6615 (mtp) REVERT: B 348 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8152 (mm) REVERT: B 364 TRP cc_start: 0.7081 (OUTLIER) cc_final: 0.6153 (p90) REVERT: B 422 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7995 (mt-10) REVERT: B 483 THR cc_start: 0.7424 (OUTLIER) cc_final: 0.7160 (p) REVERT: B 554 ILE cc_start: 0.7126 (mm) cc_final: 0.6885 (mt) REVERT: B 645 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7764 (tm-30) REVERT: B 684 PHE cc_start: 0.8837 (m-10) cc_final: 0.8578 (m-80) REVERT: B 721 LYS cc_start: 0.8038 (ttpt) cc_final: 0.7736 (ttpt) REVERT: E 155 ARG cc_start: 0.7836 (ptp90) cc_final: 0.7616 (ptp90) REVERT: E 163 LEU cc_start: 0.8701 (mt) cc_final: 0.8488 (mt) REVERT: E 351 GLU cc_start: 0.8224 (tp30) cc_final: 0.7817 (tp30) REVERT: E 353 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: E 570 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8048 (tppt) REVERT: E 589 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.7992 (mp) REVERT: E 616 HIS cc_start: 0.5801 (OUTLIER) cc_final: 0.5051 (p-80) REVERT: E 1356 GLU cc_start: 0.7232 (mp0) cc_final: 0.6808 (mp0) REVERT: E 1360 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.7302 (t80) REVERT: E 1365 LYS cc_start: 0.7960 (mtpt) cc_final: 0.7514 (tttp) REVERT: E 1465 ARG cc_start: 0.8231 (mpp80) cc_final: 0.7995 (mpp80) REVERT: E 1558 ASP cc_start: 0.7918 (t70) cc_final: 0.7656 (t70) REVERT: E 1688 LEU cc_start: 0.4155 (OUTLIER) cc_final: 0.3856 (tt) outliers start: 78 outliers final: 56 residues processed: 335 average time/residue: 0.1642 time to fit residues: 78.7810 Evaluate side-chains 346 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 279 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 529 TRP Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 638 CYS Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 678 GLU Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 199 GLN Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 361 TYR Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 549 HIS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 570 LYS Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain E residue 613 SER Chi-restraints excluded: chain E residue 616 HIS Chi-restraints excluded: chain E residue 777 PHE Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1139 VAL Chi-restraints excluded: chain E residue 1360 PHE Chi-restraints excluded: chain E residue 1368 VAL Chi-restraints excluded: chain E residue 1375 LYS Chi-restraints excluded: chain E residue 1467 HIS Chi-restraints excluded: chain E residue 1483 MET Chi-restraints excluded: chain E residue 1536 VAL Chi-restraints excluded: chain E residue 1553 SER Chi-restraints excluded: chain E residue 1556 LEU Chi-restraints excluded: chain E residue 1619 TYR Chi-restraints excluded: chain E residue 1620 TYR Chi-restraints excluded: chain E residue 1623 VAL Chi-restraints excluded: chain E residue 1686 MET Chi-restraints excluded: chain E residue 1688 LEU Chi-restraints excluded: chain E residue 1705 SER Chi-restraints excluded: chain E residue 1744 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 5 optimal weight: 0.3980 chunk 110 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 56 optimal weight: 0.0170 chunk 123 optimal weight: 5.9990 chunk 158 optimal weight: 20.0000 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 0.0030 chunk 189 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 155 optimal weight: 20.0000 overall best weight: 1.4832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 311 HIS ** E 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN ** E 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 836 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.175756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.132785 restraints weight = 43273.053| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 4.00 r_work: 0.3543 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16808 Z= 0.148 Angle : 0.647 14.272 22781 Z= 0.327 Chirality : 0.045 0.191 2545 Planarity : 0.005 0.073 2950 Dihedral : 5.934 74.377 2282 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 4.39 % Allowed : 30.82 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -1.57 (0.18), residues: 2071 helix: 0.27 (0.32), residues: 302 sheet: 0.04 (0.21), residues: 634 loop : -2.15 (0.17), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E1622 TYR 0.018 0.002 TYR E 192 PHE 0.014 0.001 PHE B 35 TRP 0.019 0.001 TRP E 798 HIS 0.007 0.001 HIS E 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (16791) covalent geometry : angle 0.64614 / 0.33 (22747) SS BOND : bond 0.00232 / 0.16 ( 17) SS BOND : angle 0.93091 / 0.63 ( 34) hydrogen bonds : bond 0.03221 / 2.13 ( 468) hydrogen bonds : angle 4.83166 / 3.43 ( 1326) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 284 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 285 PHE cc_start: 0.7028 (t80) cc_final: 0.6554 (m-80) REVERT: B 288 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: B 316 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.6643 (mtp) REVERT: B 348 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8137 (mm) REVERT: B 364 TRP cc_start: 0.7092 (OUTLIER) cc_final: 0.6251 (p90) REVERT: B 422 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7980 (mt-10) REVERT: B 483 THR cc_start: 0.7333 (OUTLIER) cc_final: 0.7056 (p) REVERT: B 645 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7745 (tm-30) REVERT: B 684 PHE cc_start: 0.8845 (m-10) cc_final: 0.8556 (m-80) REVERT: B 721 LYS cc_start: 0.8021 (ttpt) cc_final: 0.7692 (ttpt) REVERT: E 48 ARG cc_start: 0.6973 (ptt90) cc_final: 0.6203 (ppt170) REVERT: E 74 PHE cc_start: 0.7338 (t80) cc_final: 0.7077 (t80) REVERT: E 155 ARG cc_start: 0.7866 (ptp90) cc_final: 0.7641 (ptp90) REVERT: E 168 ARG cc_start: 0.7846 (mtm110) cc_final: 0.7643 (mtm180) REVERT: E 351 GLU cc_start: 0.8212 (tp30) cc_final: 0.7761 (tp30) REVERT: E 353 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: E 502 PHE cc_start: 0.6378 (m-80) cc_final: 0.6134 (m-80) REVERT: E 506 TYR cc_start: 0.6450 (m-80) cc_final: 0.5714 (m-80) REVERT: E 570 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8382 (ttmm) REVERT: E 616 HIS cc_start: 0.5893 (OUTLIER) cc_final: 0.5109 (p-80) REVERT: E 1356 GLU cc_start: 0.7313 (mp0) cc_final: 0.6852 (mp0) REVERT: E 1360 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.7377 (t80) REVERT: E 1365 LYS cc_start: 0.7984 (mtpt) cc_final: 0.7478 (tttp) REVERT: E 1465 ARG cc_start: 0.8233 (mpp80) cc_final: 0.8001 (mpp80) REVERT: E 1558 ASP cc_start: 0.8013 (t70) cc_final: 0.7729 (t70) REVERT: E 1688 LEU cc_start: 0.4195 (OUTLIER) cc_final: 0.3865 (tt) outliers start: 79 outliers final: 60 residues processed: 330 average time/residue: 0.1630 time to fit residues: 77.3434 Evaluate side-chains 350 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 280 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 529 TRP Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 638 CYS Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 678 GLU Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 199 GLN Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 361 TYR Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 549 HIS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 570 LYS Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain E residue 613 SER Chi-restraints excluded: chain E residue 616 HIS Chi-restraints excluded: chain E residue 1015 MET Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1139 VAL Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1360 PHE Chi-restraints excluded: chain E residue 1368 VAL Chi-restraints excluded: chain E residue 1375 LYS Chi-restraints excluded: chain E residue 1467 HIS Chi-restraints excluded: chain E residue 1483 MET Chi-restraints excluded: chain E residue 1536 VAL Chi-restraints excluded: chain E residue 1553 SER Chi-restraints excluded: chain E residue 1556 LEU Chi-restraints excluded: chain E residue 1619 TYR Chi-restraints excluded: chain E residue 1620 TYR Chi-restraints excluded: chain E residue 1623 VAL Chi-restraints excluded: chain E residue 1686 MET Chi-restraints excluded: chain E residue 1688 LEU Chi-restraints excluded: chain E residue 1702 LEU Chi-restraints excluded: chain E residue 1705 SER Chi-restraints excluded: chain E residue 1744 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 80 optimal weight: 0.1980 chunk 99 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 175 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 77 optimal weight: 0.0970 chunk 89 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 163 optimal weight: 20.0000 chunk 154 optimal weight: 7.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN E 836 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.177946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.137889 restraints weight = 32254.906| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 3.35 r_work: 0.3618 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16808 Z= 0.106 Angle : 0.609 14.198 22781 Z= 0.305 Chirality : 0.043 0.187 2545 Planarity : 0.005 0.067 2950 Dihedral : 5.665 76.066 2282 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.50 % Allowed : 32.04 % Favored : 64.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -1.47 (0.18), residues: 2071 helix: 0.37 (0.31), residues: 302 sheet: 0.13 (0.21), residues: 634 loop : -2.11 (0.17), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E1622 TYR 0.019 0.001 TYR E1027 PHE 0.016 0.001 PHE B 649 TRP 0.017 0.001 TRP B 529 HIS 0.004 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (16791) covalent geometry : angle 0.60877 / 0.31 (22747) SS BOND : bond 0.00212 / 0.14 ( 17) SS BOND : angle 0.68462 / 0.48 ( 34) hydrogen bonds : bond 0.02741 / 1.81 ( 468) hydrogen bonds : angle 4.66457 / 3.32 ( 1326) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 290 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 99 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7654 (tp) REVERT: B 285 PHE cc_start: 0.6958 (t80) cc_final: 0.6292 (m-80) REVERT: B 288 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: B 348 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8078 (mm) REVERT: B 362 MET cc_start: 0.6865 (ptm) cc_final: 0.6339 (ptt) REVERT: B 364 TRP cc_start: 0.7046 (OUTLIER) cc_final: 0.6154 (p90) REVERT: B 390 ASP cc_start: 0.8079 (t0) cc_final: 0.7695 (t0) REVERT: B 422 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7908 (mt-10) REVERT: B 483 THR cc_start: 0.7353 (OUTLIER) cc_final: 0.7100 (p) REVERT: B 645 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7725 (tm-30) REVERT: B 710 ASP cc_start: 0.4362 (t0) cc_final: 0.3909 (t70) REVERT: B 721 LYS cc_start: 0.8043 (ttpt) cc_final: 0.7658 (ttpt) REVERT: E 74 PHE cc_start: 0.7309 (t80) cc_final: 0.7073 (t80) REVERT: E 351 GLU cc_start: 0.8132 (tp30) cc_final: 0.7687 (tp30) REVERT: E 353 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7512 (tm-30) REVERT: E 502 PHE cc_start: 0.6240 (m-80) cc_final: 0.6035 (m-80) REVERT: E 506 TYR cc_start: 0.6374 (m-80) cc_final: 0.5660 (m-80) REVERT: E 570 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8153 (ttmm) REVERT: E 616 HIS cc_start: 0.5765 (OUTLIER) cc_final: 0.5021 (p-80) REVERT: E 1356 GLU cc_start: 0.7152 (mp0) cc_final: 0.6804 (mp0) REVERT: E 1360 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.7304 (t80) REVERT: E 1365 LYS cc_start: 0.7958 (mtpt) cc_final: 0.7470 (tttp) REVERT: E 1465 ARG cc_start: 0.8239 (mpp80) cc_final: 0.8018 (mpp80) REVERT: E 1558 ASP cc_start: 0.7843 (t70) cc_final: 0.7589 (t70) REVERT: E 1688 LEU cc_start: 0.3933 (OUTLIER) cc_final: 0.3630 (tt) outliers start: 63 outliers final: 48 residues processed: 324 average time/residue: 0.1600 time to fit residues: 74.5575 Evaluate side-chains 341 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 283 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 529 TRP Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 638 CYS Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 678 GLU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 199 GLN Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 549 HIS Chi-restraints excluded: chain E residue 570 LYS Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain E residue 613 SER Chi-restraints excluded: chain E residue 616 HIS Chi-restraints excluded: chain E residue 1015 MET Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1139 VAL Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1360 PHE Chi-restraints excluded: chain E residue 1368 VAL Chi-restraints excluded: chain E residue 1375 LYS Chi-restraints excluded: chain E residue 1536 VAL Chi-restraints excluded: chain E residue 1553 SER Chi-restraints excluded: chain E residue 1556 LEU Chi-restraints excluded: chain E residue 1619 TYR Chi-restraints excluded: chain E residue 1620 TYR Chi-restraints excluded: chain E residue 1623 VAL Chi-restraints excluded: chain E residue 1686 MET Chi-restraints excluded: chain E residue 1688 LEU Chi-restraints excluded: chain E residue 1744 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 145 optimal weight: 4.9990 chunk 2 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 152 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 422 GLN ** E 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN E 836 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.177236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.135166 restraints weight = 47253.600| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 4.14 r_work: 0.3567 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16808 Z= 0.115 Angle : 0.617 14.031 22781 Z= 0.308 Chirality : 0.043 0.203 2545 Planarity : 0.005 0.069 2950 Dihedral : 5.650 75.901 2282 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.78 % Allowed : 31.65 % Favored : 64.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.45 (0.18), residues: 2071 helix: 0.28 (0.31), residues: 314 sheet: 0.06 (0.21), residues: 645 loop : -2.05 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E1622 TYR 0.018 0.001 TYR E 192 PHE 0.015 0.001 PHE B 35 TRP 0.017 0.001 TRP E 798 HIS 0.004 0.001 HIS E 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (16791) covalent geometry : angle 0.61687 / 0.31 (22747) SS BOND : bond 0.00187 / 0.11 ( 17) SS BOND : angle 0.73674 / 0.51 ( 34) hydrogen bonds : bond 0.02859 / 1.89 ( 468) hydrogen bonds : angle 4.58507 / 3.26 ( 1326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5231.98 seconds wall clock time: 90 minutes 4.98 seconds (5404.98 seconds total)