Starting phenix.real_space_refine on Sun Sep 13 09:44:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5gjv_9513/09_2026/5gjv_9513.cif Found real_map, /net/cci-nas-00/data/ceres_data/5gjv_9513/09_2026/5gjv_9513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5gjv_9513/09_2026/5gjv_9513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5gjv_9513/09_2026/5gjv_9513.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5gjv_9513/09_2026/5gjv_9513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5gjv_9513/09_2026/5gjv_9513.map" restraint_files = "/net/cci-nas-00/data/ceres_data/5gjv_9513/09_2026/5gjv_9513.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5gjv_9513/09_2026/5gjv_9513.cif" } resolution = 3.6 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 7 5.49 5 S 123 5.16 5 C 14251 2.51 5 N 3550 2.21 5 O 3970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21904 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 10183 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1276, 10141 Classifications: {'peptide': 1276} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 1235} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 3, 'GLU:plan': 4, 'GLN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 94 Conformer: "B" Number of residues, atoms: 1276, 10141 Classifications: {'peptide': 1276} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 1235} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 3, 'GLU:plan': 4, 'GLN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 94 bond proxies already assigned to first conformer: 10343 Chain: "B" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 710 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 91} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1367 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1304 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 7, 'TRANS': 158} Chain breaks: 4 Chain: "F" Number of atoms: 7563 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 941, 7552 Classifications: {'peptide': 941} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 39, 'TRANS': 899} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 941, 7552 Classifications: {'peptide': 941} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 39, 'TRANS': 899} Chain breaks: 6 bond proxies already assigned to first conformer: 7698 Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'ETA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 442 Unusual residues: {' CA': 2, 'NAG': 1, 'PC1': 14} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 331 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 246 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PC1:plan-1': 7, 'PC1:plan-2': 7} Unresolved non-hydrogen planarities: 48 Chain: "F" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 99 Unusual residues: {' CA': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AARG A 794 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 794 " occ=0.50 residue: pdb=" N AARG A 910 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 910 " occ=0.50 residue: pdb=" N ALYS A 912 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 912 " occ=0.50 residue: pdb=" N AARG A1249 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A1249 " occ=0.50 residue: pdb=" N AARG F 315 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG F 315 " occ=0.50 Time building chain proxies: 8.20, per 1000 atoms: 0.37 Number of scatterers: 21904 At special positions: 0 Unit cell: (187.44, 184.8, 157.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 123 16.00 P 7 15.00 O 3970 8.00 N 3550 7.00 C 14251 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 254 " distance=2.01 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=1.93 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 968 " distance=2.03 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 305 " - pdb=" SG CYS F1047 " distance=2.05 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F1062 " distance=2.27 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1074 " distance=1.71 Simple disulfide: pdb=" SG CYS F 907 " - pdb=" SG CYS F 977 " distance=2.04 Simple disulfide: pdb=" SG CYS F 999 " - pdb=" SG CYS F1029 " distance=2.03 Simple disulfide: pdb=" SG CYS F1002 " - pdb=" SG CYS F1027 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " NAG L 3 " NAG-ASN " NAG A1901 " - " ASN A 257 " " NAG D 1 " - " ASN F 350 " " NAG F1203 " - " ASN F 326 " " NAG F1206 " - " ASN F 891 " " NAG F1213 " - " ASN F 94 " " NAG F1214 " - " ASN F 606 " " NAG F1219 " - " ASN F 784 " " NAG F1220 " - " ASN F1001 " " NAG F1221 " - " ASN F 988 " " NAG G 1 " - " ASN F 615 " " NAG H 1 " - " ASN F 186 " " NAG I 1 " - " ASN F 470 " " NAG J 1 " - " ASN F 898 " " NAG K 1 " - " ASN F 678 " " NAG L 1 " - " ASN F 827 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 1.6 seconds 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5048 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 17 sheets defined 55.7% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 41 through 49 removed outlier: 3.811A pdb=" N ILE A 45 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 68 removed outlier: 3.806A pdb=" N ALA A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN A 64 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 108 removed outlier: 3.557A pdb=" N GLU A 87 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.623A pdb=" N HIS A 113 " --> pdb=" O PHE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 120 through 139 removed outlier: 3.561A pdb=" N LEU A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 128 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 170 Processing helix chain 'A' and resid 171 through 179 removed outlier: 3.650A pdb=" N LEU A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 176 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 191 removed outlier: 3.516A pdb=" N VAL A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 219 removed outlier: 3.633A pdb=" N ILE A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 214 " --> pdb=" O TYR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 285 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.898A pdb=" N VAL A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP A 303 " --> pdb=" O TYR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 336 removed outlier: 3.780A pdb=" N PHE A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 333 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY A 335 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 341 removed outlier: 3.541A pdb=" N GLU A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 346 through 375 removed outlier: 3.635A pdb=" N PHE A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 355 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY A 373 " --> pdb=" O TRP A 369 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.840A pdb=" N LYS A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 449 removed outlier: 4.060A pdb=" N VAL A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE A 439 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 440 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 485 removed outlier: 3.768A pdb=" N HIS A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 473 " --> pdb=" O ARG A 469 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 494 removed outlier: 3.597A pdb=" N PHE A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER A 494 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 517 removed outlier: 3.755A pdb=" N VAL A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 removed outlier: 4.058A pdb=" N SER A 525 " --> pdb=" O PRO A 521 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 526 " --> pdb=" O LEU A 522 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 541 Processing helix chain 'A' and resid 544 through 557 removed outlier: 3.584A pdb=" N ALA A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.842A pdb=" N ILE A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 612 removed outlier: 3.607A pdb=" N VAL A 607 " --> pdb=" O ALA A 603 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 608 " --> pdb=" O LEU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 628 removed outlier: 3.799A pdb=" N VAL A 619 " --> pdb=" O ASP A 615 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 622 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET A 625 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 627 " --> pdb=" O GLY A 623 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 628 " --> pdb=" O ILE A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 638 Processing helix chain 'A' and resid 639 through 651 removed outlier: 4.157A pdb=" N PHE A 645 " --> pdb=" O PHE A 641 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN A 649 " --> pdb=" O PHE A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 663 removed outlier: 3.559A pdb=" N ALA A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A 659 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 660 " --> pdb=" O PHE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 669 removed outlier: 3.585A pdb=" N GLU A 668 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 797 removed outlier: 3.582A pdb=" N ILE A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 796 " --> pdb=" O CYS A 792 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN A 797 " --> pdb=" O HIS A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 818 removed outlier: 3.593A pdb=" N PHE A 804 " --> pdb=" O TRP A 800 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 815 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 852 removed outlier: 3.859A pdb=" N GLN A 830 " --> pdb=" O SER A 826 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 831 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU A 832 " --> pdb=" O ARG A 828 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 834 " --> pdb=" O GLN A 830 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA A 838 " --> pdb=" O TYR A 834 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE A 839 " --> pdb=" O PHE A 835 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 841 " --> pdb=" O ILE A 837 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET A 851 " --> pdb=" O ILE A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 860 removed outlier: 4.042A pdb=" N HIS A 859 " --> pdb=" O ALA A 856 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS A 860 " --> pdb=" O PHE A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 885 removed outlier: 3.601A pdb=" N ASN A 866 " --> pdb=" O SER A 862 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A 869 " --> pdb=" O ARG A 865 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP A 872 " --> pdb=" O PHE A 868 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 873 " --> pdb=" O ASN A 869 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL A 878 " --> pdb=" O LEU A 874 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET A 883 " --> pdb=" O SER A 879 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 884 " --> pdb=" O LEU A 880 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 885 " --> pdb=" O ILE A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 899 Processing helix chain 'A' and resid 900 through 902 No H-bonds generated for 'chain 'A' and resid 900 through 902' Processing helix chain 'A' and resid 903 through 909 removed outlier: 3.883A pdb=" N ALA A 907 " --> pdb=" O ARG A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 950 removed outlier: 3.796A pdb=" N VAL A 917 " --> pdb=" O GLY A 913 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG A 926 " --> pdb=" O PHE A 922 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR A 927 " --> pdb=" O VAL A 923 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ASN A 930 " --> pdb=" O ARG A 926 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE A 931 " --> pdb=" O THR A 927 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 937 " --> pdb=" O LEU A 933 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A 939 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE A 940 " --> pdb=" O THR A 936 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 943 " --> pdb=" O GLN A 939 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 948 " --> pdb=" O CYS A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1010 removed outlier: 4.152A pdb=" N SER A1006 " --> pdb=" O SER A1002 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR A1009 " --> pdb=" O MET A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1025 removed outlier: 3.685A pdb=" N LEU A1019 " --> pdb=" O GLY A1015 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP A1025 " --> pdb=" O TYR A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1042 Processing helix chain 'A' and resid 1043 through 1073 removed outlier: 3.605A pdb=" N ILE A1049 " --> pdb=" O PHE A1045 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A1067 " --> pdb=" O PHE A1063 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A1072 " --> pdb=" O PHE A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1093 removed outlier: 4.079A pdb=" N VAL A1089 " --> pdb=" O GLN A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1116 removed outlier: 3.510A pdb=" N GLN A1110 " --> pdb=" O PRO A1106 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A1111 " --> pdb=" O TYR A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1125 removed outlier: 3.511A pdb=" N PHE A1125 " --> pdb=" O GLU A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1137 removed outlier: 3.688A pdb=" N MET A1129 " --> pdb=" O PHE A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1173 removed outlier: 3.629A pdb=" N VAL A1155 " --> pdb=" O ASP A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1204 removed outlier: 3.722A pdb=" N VAL A1184 " --> pdb=" O ASP A1180 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A1191 " --> pdb=" O PHE A1187 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A1199 " --> pdb=" O ILE A1195 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP A1203 " --> pdb=" O LEU A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1235 removed outlier: 3.682A pdb=" N SER A1232 " --> pdb=" O ARG A1229 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A1234 " --> pdb=" O SER A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1241 removed outlier: 3.535A pdb=" N VAL A1240 " --> pdb=" O ARG A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1246 Processing helix chain 'A' and resid 1250 through 1264 removed outlier: 3.534A pdb=" N THR A1255 " --> pdb=" O GLU A1251 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU A1256 " --> pdb=" O GLY A1252 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A1260 " --> pdb=" O LEU A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1289 removed outlier: 4.046A pdb=" N VAL A1270 " --> pdb=" O ALA A1266 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A1273 " --> pdb=" O TYR A1269 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A1285 " --> pdb=" O TYR A1281 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN A1287 " --> pdb=" O VAL A1283 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET A1288 " --> pdb=" O ILE A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1321 removed outlier: 3.608A pdb=" N LEU A1316 " --> pdb=" O ALA A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1332 removed outlier: 4.247A pdb=" N ILE A1328 " --> pdb=" O ALA A1324 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A1330 " --> pdb=" O GLN A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1357 through 1383 removed outlier: 3.882A pdb=" N ILE A1362 " --> pdb=" O TYR A1358 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A1363 " --> pdb=" O TYR A1359 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A1367 " --> pdb=" O SER A1363 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A1371 " --> pdb=" O LEU A1367 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A1374 " --> pdb=" O PHE A1370 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A1380 " --> pdb=" O PHE A1376 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP A1382 " --> pdb=" O ALA A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1388 Processing helix chain 'A' and resid 1395 through 1410 removed outlier: 3.817A pdb=" N LEU A1399 " --> pdb=" O GLY A1395 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A1403 " --> pdb=" O LEU A1399 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA A1404 " --> pdb=" O ASP A1400 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A1405 " --> pdb=" O GLU A1401 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TRP A1406 " --> pdb=" O PHE A1402 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A1407 " --> pdb=" O LYS A1403 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU A1408 " --> pdb=" O ALA A1404 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A1409 " --> pdb=" O ILE A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1421 through 1428 removed outlier: 3.914A pdb=" N ARG A1427 " --> pdb=" O VAL A1423 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG A1428 " --> pdb=" O THR A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1451 Processing helix chain 'A' and resid 1456 through 1458 No H-bonds generated for 'chain 'A' and resid 1456 through 1458' Processing helix chain 'A' and resid 1462 through 1473 removed outlier: 3.660A pdb=" N THR A1466 " --> pdb=" O THR A1462 " (cutoff:3.500A) Processing helix chain 'A' and resid 1481 through 1498 removed outlier: 3.553A pdb=" N GLU A1489 " --> pdb=" O GLN A1485 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1514 Proline residue: A1511 - end of helix Processing helix chain 'B' and resid 77 through 79 No H-bonds generated for 'chain 'B' and resid 77 through 79' Processing helix chain 'B' and resid 80 through 96 removed outlier: 5.065A pdb=" N GLU B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 161 through 174 Processing helix chain 'C' and resid 287 through 305 removed outlier: 3.514A pdb=" N LEU C 297 " --> pdb=" O MET C 293 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS C 303 " --> pdb=" O ASP C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 343 through 358 Processing helix chain 'C' and resid 373 through 377 Processing helix chain 'C' and resid 393 through 404 removed outlier: 3.563A pdb=" N ARG C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 426 through 430 Processing helix chain 'C' and resid 438 through 458 Processing helix chain 'E' and resid 2 through 6 removed outlier: 4.155A pdb=" N ALA E 6 " --> pdb=" O SER E 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2 through 6' Processing helix chain 'E' and resid 6 through 29 removed outlier: 3.859A pdb=" N ARG E 10 " --> pdb=" O ALA E 6 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL E 28 " --> pdb=" O MET E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 129 removed outlier: 3.690A pdb=" N ALA E 109 " --> pdb=" O ILE E 105 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE E 129 " --> pdb=" O ALA E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 165 removed outlier: 3.534A pdb=" N TYR E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL E 162 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS E 163 " --> pdb=" O ARG E 159 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG E 164 " --> pdb=" O GLN E 160 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET E 165 " --> pdb=" O SER E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 204 removed outlier: 3.519A pdb=" N ALA E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 54 removed outlier: 3.507A pdb=" N THR F 48 " --> pdb=" O GLU F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 66 removed outlier: 3.972A pdb=" N ASP F 61 " --> pdb=" O HIS F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 112 removed outlier: 3.634A pdb=" N SER F 96 " --> pdb=" O LEU F 92 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA F 98 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU F 99 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL F 100 " --> pdb=" O SER F 96 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU F 107 " --> pdb=" O ALA F 103 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA F 112 " --> pdb=" O LYS F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 188 removed outlier: 3.518A pdb=" N GLU F 184 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN F 186 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TRP F 187 " --> pdb=" O ASN F 183 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 202 removed outlier: 4.249A pdb=" N VAL F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG F 199 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU F 200 " --> pdb=" O LYS F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 243 Processing helix chain 'F' and resid 268 through 282 removed outlier: 3.975A pdb=" N LYS F 272 " --> pdb=" O GLY F 268 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE F 274 " --> pdb=" O THR F 270 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER F 279 " --> pdb=" O ARG F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 285 No H-bonds generated for 'chain 'F' and resid 283 through 285' Processing helix chain 'F' and resid 315 through 324 removed outlier: 3.720A pdb=" N VAL F 319 " --> pdb=" O AARG F 315 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU F 320 " --> pdb=" O ASN F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 327 No H-bonds generated for 'chain 'F' and resid 325 through 327' Processing helix chain 'F' and resid 335 through 346 removed outlier: 3.835A pdb=" N PHE F 339 " --> pdb=" O TYR F 335 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE F 341 " --> pdb=" O LYS F 337 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU F 344 " --> pdb=" O SER F 340 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN F 345 " --> pdb=" O PHE F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 379 removed outlier: 3.734A pdb=" N PHE F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA F 376 " --> pdb=" O GLN F 372 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS F 377 " --> pdb=" O GLU F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 408 removed outlier: 3.792A pdb=" N ALA F 405 " --> pdb=" O ILE F 401 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS F 406 " --> pdb=" O GLN F 402 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN F 408 " --> pdb=" O MET F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 425 Processing helix chain 'F' and resid 427 through 433 removed outlier: 4.099A pdb=" N VAL F 431 " --> pdb=" O GLU F 427 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU F 432 " --> pdb=" O TYR F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 438 removed outlier: 4.023A pdb=" N LEU F 438 " --> pdb=" O ARG F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 501 Processing helix chain 'F' and resid 562 through 567 removed outlier: 3.809A pdb=" N GLU F 567 " --> pdb=" O PHE F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 581 Processing helix chain 'F' and resid 642 through 651 removed outlier: 3.633A pdb=" N LEU F 651 " --> pdb=" O TYR F 647 " (cutoff:3.500A) Processing helix chain 'F' and resid 652 through 656 removed outlier: 3.979A pdb=" N PHE F 656 " --> pdb=" O PRO F 653 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 694 Processing helix chain 'F' and resid 703 through 723 removed outlier: 3.875A pdb=" N LEU F 709 " --> pdb=" O ILE F 705 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE F 714 " --> pdb=" O LEU F 710 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU F 717 " --> pdb=" O GLY F 713 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU F 718 " --> pdb=" O PHE F 714 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL F 719 " --> pdb=" O THR F 715 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN F 721 " --> pdb=" O GLU F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 750 through 755 removed outlier: 3.809A pdb=" N GLU F 753 " --> pdb=" O GLU F 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 766 through 773 removed outlier: 3.723A pdb=" N LEU F 771 " --> pdb=" O TYR F 767 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP F 772 " --> pdb=" O LYS F 768 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN F 773 " --> pdb=" O ARG F 769 " (cutoff:3.500A) Processing helix chain 'F' and resid 820 through 831 removed outlier: 3.742A pdb=" N TRP F 824 " --> pdb=" O ASP F 820 " (cutoff:3.500A) Processing helix chain 'F' and resid 877 through 881 Processing helix chain 'F' and resid 882 through 892 removed outlier: 3.563A pdb=" N HIS F 888 " --> pdb=" O SER F 884 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN F 891 " --> pdb=" O ARG F 887 " (cutoff:3.500A) Processing helix chain 'F' and resid 1045 through 1050 Processing sheet with id=AA1, first strand: chain 'A' and resid 955 through 957 Processing sheet with id=AA2, first strand: chain 'A' and resid 971 through 975 Processing sheet with id=AA3, first strand: chain 'A' and resid 1417 through 1418 Processing sheet with id=AA4, first strand: chain 'B' and resid 157 through 160 removed outlier: 7.078A pdb=" N ARG B 148 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE B 136 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA B 104 " --> pdb=" O VAL C 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 309 through 314 removed outlier: 6.215A pdb=" N ILE C 277 " --> pdb=" O LEU C 366 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA C 368 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU C 279 " --> pdb=" O ALA C 368 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE C 278 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE C 389 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL C 280 " --> pdb=" O ILE C 389 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE C 386 " --> pdb=" O ILE C 432 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LEU C 434 " --> pdb=" O ILE C 386 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR C 388 " --> pdb=" O LEU C 434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 78 through 81 removed outlier: 3.680A pdb=" N SER E 81 " --> pdb=" O ILE E 56 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS E 57 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR E 177 " --> pdb=" O VAL E 34 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 73 through 74 Processing sheet with id=AA8, first strand: chain 'F' and resid 152 through 154 Processing sheet with id=AA9, first strand: chain 'F' and resid 167 through 169 removed outlier: 3.893A pdb=" N ALA F 167 " --> pdb=" O TYR F 219 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL F 489 " --> pdb=" O GLY F 211 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL F 468 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL F 489 " --> pdb=" O LEU F 466 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU F 466 " --> pdb=" O VAL F 489 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY F 491 " --> pdb=" O GLY F 464 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY F 464 " --> pdb=" O GLY F 491 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP F 493 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE F 462 " --> pdb=" O ASP F 493 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N SER F 495 " --> pdb=" O LEU F 460 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU F 460 " --> pdb=" O SER F 495 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N THR F 463 " --> pdb=" O ASN F 450 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASN F 450 " --> pdb=" O THR F 463 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR F 465 " --> pdb=" O TRP F 448 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N TRP F 448 " --> pdb=" O THR F 465 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 254 through 255 removed outlier: 3.818A pdb=" N ASP F 261 " --> pdb=" O PHE F 363 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE F 258 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE F 296 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL F 260 " --> pdb=" O PHE F 296 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 254 through 255 removed outlier: 6.454A pdb=" N LYS F 358 " --> pdb=" O ARG F 385 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N PHE F 387 " --> pdb=" O LYS F 358 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE F 360 " --> pdb=" O PHE F 387 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N PHE F 389 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU F 362 " --> pdb=" O PHE F 389 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL F 391 " --> pdb=" O LEU F 362 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N THR F 364 " --> pdb=" O VAL F 391 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N VAL F 386 " --> pdb=" O TYR F 411 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N TYR F 413 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR F 388 " --> pdb=" O TYR F 413 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE F 415 " --> pdb=" O THR F 388 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N SER F 390 " --> pdb=" O ILE F 415 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 517 through 518 Processing sheet with id=AB4, first strand: chain 'F' and resid 586 through 595 removed outlier: 3.820A pdb=" N GLY F 586 " --> pdb=" O TRP F 611 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR F 609 " --> pdb=" O LYS F 588 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 661 through 664 removed outlier: 4.314A pdb=" N ILE F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR F 739 " --> pdb=" O ILE F 743 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 862 through 865 removed outlier: 3.772A pdb=" N MET F 864 " --> pdb=" O ILE F 855 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU F1016 " --> pdb=" O LEU F1011 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 896 through 902 removed outlier: 4.241A pdb=" N ILE F 978 " --> pdb=" O SER F1041 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN F1039 " --> pdb=" O GLU F 980 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 906 through 907 920 hydrogen bonds defined for protein. 2607 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: 4.75 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 3438 1.26 - 1.41: 5652 1.41 - 1.56: 13000 1.56 - 1.70: 90 1.70 - 1.85: 189 Bond restraints: 22369 Sorted by residual: bond pdb=" C ARG A 171 " pdb=" O ARG A 171 " ideal model delta sigma weight residual 1.244 1.480 -0.236 9.80e-03 1.04e+04 5.80e+02 bond pdb=" C TYR F 647 " pdb=" N SER F 648 " ideal model delta sigma weight residual 1.335 1.572 -0.236 1.38e-02 5.25e+03 2.94e+02 bond pdb=" C ALA F 312 " pdb=" O ALA F 312 " ideal model delta sigma weight residual 1.233 1.370 -0.137 1.29e-02 6.01e+03 1.13e+02 bond pdb=" C CYS F1062 " pdb=" O CYS F1062 " ideal model delta sigma weight residual 1.235 1.118 0.117 1.26e-02 6.30e+03 8.67e+01 bond pdb=" CA LYS A 540 " pdb=" C LYS A 540 " ideal model delta sigma weight residual 1.522 1.627 -0.105 1.41e-02 5.03e+03 5.49e+01 ... (remaining 22364 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.49: 29528 4.49 - 8.99: 599 8.99 - 13.48: 82 13.48 - 17.97: 25 17.97 - 22.47: 4 Bond angle restraints: 30238 Sorted by residual: angle pdb=" C ASP F 518 " pdb=" CA ASP F 518 " pdb=" CB ASP F 518 " ideal model delta sigma weight residual 108.87 88.55 20.32 1.41e+00 5.03e-01 2.08e+02 angle pdb=" O SER A1248 " pdb=" C SER A1248 " pdb=" N BARG A1249 " ideal model delta sigma weight residual 122.12 136.97 -14.85 1.06e+00 8.90e-01 1.96e+02 angle pdb=" CA SER A1248 " pdb=" C SER A1248 " pdb=" N BARG A1249 " ideal model delta sigma weight residual 117.30 101.93 15.37 1.16e+00 7.43e-01 1.75e+02 angle pdb=" C GLN F 445 " pdb=" CA GLN F 445 " pdb=" CB GLN F 445 " ideal model delta sigma weight residual 110.45 129.58 -19.13 1.73e+00 3.34e-01 1.22e+02 angle pdb=" N LYS A 540 " pdb=" CA LYS A 540 " pdb=" C LYS A 540 " ideal model delta sigma weight residual 112.38 98.91 13.47 1.22e+00 6.72e-01 1.22e+02 ... (remaining 30233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.74: 12551 27.74 - 55.48: 534 55.48 - 83.22: 80 83.22 - 110.96: 5 110.96 - 138.70: 1 Dihedral angle restraints: 13171 sinusoidal: 5363 harmonic: 7808 Sorted by residual: dihedral pdb=" CA GLU F 476 " pdb=" C GLU F 476 " pdb=" N ASN F 477 " pdb=" CA ASN F 477 " ideal model delta harmonic sigma weight residual -180.00 -113.80 -66.20 0 5.00e+00 4.00e-02 1.75e+02 dihedral pdb=" CA GLY A 629 " pdb=" C GLY A 629 " pdb=" N PRO A 630 " pdb=" CA PRO A 630 " ideal model delta harmonic sigma weight residual 180.00 -114.15 -65.85 0 5.00e+00 4.00e-02 1.73e+02 dihedral pdb=" CA PRO A 266 " pdb=" C PRO A 266 " pdb=" N GLY A 267 " pdb=" CA GLY A 267 " ideal model delta harmonic sigma weight residual 180.00 -122.94 -57.06 0 5.00e+00 4.00e-02 1.30e+02 ... (remaining 13168 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.221: 3380 0.221 - 0.441: 48 0.441 - 0.662: 11 0.662 - 0.883: 1 0.883 - 1.104: 2 Chirality restraints: 3442 Sorted by residual: chirality pdb=" CA TYR F 175 " pdb=" N TYR F 175 " pdb=" C TYR F 175 " pdb=" CB TYR F 175 " both_signs ideal model delta sigma weight residual False 2.51 1.41 1.10 2.00e-01 2.50e+01 3.04e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN F 350 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.49 -0.91 2.00e-01 2.50e+01 2.06e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.75e+01 ... (remaining 3439 not shown) Planarity restraints: 3763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 615 " 0.211 2.00e-02 2.50e+03 2.25e-01 6.33e+02 pdb=" CG ASN F 615 " -0.083 2.00e-02 2.50e+03 pdb=" OD1 ASN F 615 " -0.089 2.00e-02 2.50e+03 pdb=" ND2 ASN F 615 " -0.330 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.291 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " 0.129 2.00e-02 2.50e+03 1.06e-01 1.42e+02 pdb=" C7 NAG G 2 " -0.035 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " 0.097 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " -0.170 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 281 " -0.035 2.00e-02 2.50e+03 7.06e-02 4.99e+01 pdb=" C GLY C 281 " 0.122 2.00e-02 2.50e+03 pdb=" O GLY C 281 " -0.046 2.00e-02 2.50e+03 pdb=" N PRO C 282 " -0.041 2.00e-02 2.50e+03 ... (remaining 3760 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.34: 51 2.34 - 2.98: 10706 2.98 - 3.62: 30510 3.62 - 4.26: 48077 4.26 - 4.90: 77807 Nonbonded interactions: 167151 Sorted by model distance: nonbonded pdb=" CE1 PHE F 515 " pdb=" CB ALA F 623 " model vdw 1.695 3.760 nonbonded pdb=" ND2 ASN F 297 " pdb=" O LYS F 330 " model vdw 1.906 3.120 nonbonded pdb=" OD1 ASP A 362 " pdb=" ND2 ASN C 437 " model vdw 1.930 3.120 nonbonded pdb=" O ASN F 528 " pdb=" ND2 ASN F 528 " model vdw 1.979 3.120 nonbonded pdb=" O SER F 671 " pdb=" OD1 ASP F 672 " model vdw 1.986 3.040 ... (remaining 167146 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 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'K' } ncs_group { reference = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.270 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.080 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 0.013 0.317 22406 Z= 0.647 Angle : 1.718 56.320 30335 Z= 0.951 Chirality : 0.084 1.104 3442 Planarity : 0.008 0.114 3748 Dihedral : 14.847 138.701 8090 Min Nonbonded Distance : 1.695 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 1.99 % Allowed : 11.53 % Favored : 86.48 % Rotamer: Outliers : 4.57 % Allowed : 4.22 % Favored : 91.21 % Cbeta Deviations : 1.27 % Peptide Plane: Cis-proline : 1.87 % Cis-general : 0.04 % Twisted Proline : 3.74 % Twisted General : 0.75 % 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: -5.08 (0.13), residues: 2633 helix: -3.62 (0.09), residues: 1296 sheet: -1.54 (0.32), residues: 233 loop : -3.32 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG F 769 TYR 0.054 0.005 TYR F 609 PHE 0.049 0.004 PHE A 581 TRP 0.040 0.004 TRP F 403 HIS 0.013 0.003 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.01269 / 0.63 (22369) covalent geometry : angle 1.61525 / 0.92 (30238) SS BOND : bond 0.12470 / 5.94 ( 11) SS BOND : angle 16.32990 / 9.14 ( 22) hydrogen bonds : bond 0.29105 / 18.31 ( 918) hydrogen bonds : angle 9.98465 / 6.79 ( 2607) Misc. bond : bond 0.08345 / 4.39 ( 1) link_BETA1-4 : bond 0.01017 / 0.49 ( 10) link_BETA1-4 : angle 3.06505 / 1.78 ( 30) link_NAG-ASN : bond 0.03201 / 1.53 ( 15) link_NAG-ASN : angle 10.01687 / 6.22 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 621 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.8858 (t80) cc_final: 0.8360 (t80) REVERT: A 87 GLU cc_start: 0.8982 (tp30) cc_final: 0.8003 (pt0) REVERT: A 108 TYR cc_start: 0.7975 (m-80) cc_final: 0.7745 (m-80) REVERT: A 113 HIS cc_start: 0.6487 (m-70) cc_final: 0.5868 (m-70) REVERT: A 131 PHE cc_start: 0.7784 (t80) cc_final: 0.7411 (t80) REVERT: A 165 ARG cc_start: 0.8577 (mmt90) cc_final: 0.8040 (mmm-85) REVERT: A 177 SER cc_start: 0.8509 (m) cc_final: 0.8236 (p) REVERT: A 262 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8361 (ptt90) REVERT: A 276 ASP cc_start: 0.8890 (OUTLIER) cc_final: 0.8085 (p0) REVERT: A 292 GLU cc_start: 0.8673 (tp30) cc_final: 0.8243 (tp30) REVERT: A 432 ARG cc_start: 0.6142 (tmt170) cc_final: 0.5413 (ptt-90) REVERT: A 444 LEU cc_start: 0.8916 (tp) cc_final: 0.8641 (tp) REVERT: A 449 ILE cc_start: 0.9113 (tp) cc_final: 0.8894 (tp) REVERT: A 463 LEU cc_start: 0.8969 (mt) cc_final: 0.8593 (tt) REVERT: A 469 ARG cc_start: 0.7623 (mtt180) cc_final: 0.7188 (ttm110) REVERT: A 483 MET cc_start: 0.6796 (mmm) cc_final: 0.6548 (tpp) REVERT: A 532 LEU cc_start: 0.8718 (mt) cc_final: 0.8489 (mm) REVERT: A 535 LEU cc_start: 0.8932 (mt) cc_final: 0.8678 (mp) REVERT: A 591 GLU cc_start: 0.8249 (pm20) cc_final: 0.7802 (tt0) REVERT: A 597 PHE cc_start: 0.9217 (OUTLIER) cc_final: 0.8626 (m-80) REVERT: A 822 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7432 (pt) REVERT: A 936 THR cc_start: 0.8686 (t) cc_final: 0.8485 (m) REVERT: A 965 GLU cc_start: 0.8108 (tp30) cc_final: 0.7398 (tp30) REVERT: A 1022 ARG cc_start: 0.8899 (tpt90) cc_final: 0.8670 (tpp-160) REVERT: A 1028 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8185 (tt0) REVERT: A 1029 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8646 (tp30) REVERT: A 1110 GLN cc_start: 0.7550 (tt0) cc_final: 0.7236 (mm-40) REVERT: A 1122 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.7024 (t80) REVERT: A 1124 MET cc_start: 0.9038 (mmm) cc_final: 0.8837 (mmm) REVERT: A 1145 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6605 (mp0) REVERT: A 1149 ILE cc_start: 0.8865 (mt) cc_final: 0.8589 (mm) REVERT: A 1188 LEU cc_start: 0.9107 (tm) cc_final: 0.8878 (tt) REVERT: A 1234 PHE cc_start: 0.8306 (t80) cc_final: 0.8102 (t80) REVERT: A 1236 ARG cc_start: 0.8353 (mtt180) cc_final: 0.8065 (mtt90) REVERT: A 1241 MET cc_start: 0.8437 (mmm) cc_final: 0.7875 (ttm) REVERT: A 1251 GLU cc_start: 0.8599 (tt0) cc_final: 0.8389 (mt-10) REVERT: A 1269 TYR cc_start: 0.8261 (m-80) cc_final: 0.8056 (m-80) REVERT: A 1304 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.8106 (t0) REVERT: A 1334 TYR cc_start: 0.7673 (t80) cc_final: 0.7042 (t80) REVERT: A 1348 GLU cc_start: 0.7179 (tt0) cc_final: 0.6565 (pm20) REVERT: A 1359 TYR cc_start: 0.8434 (m-10) cc_final: 0.7893 (m-80) REVERT: A 1366 MET cc_start: 0.8807 (mtt) cc_final: 0.8507 (mtp) REVERT: A 1376 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.8152 (t80) REVERT: A 1379 VAL cc_start: 0.8758 (t) cc_final: 0.8193 (p) REVERT: A 1380 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8547 (mp) REVERT: A 1385 ASP cc_start: 0.9234 (m-30) cc_final: 0.8983 (p0) REVERT: A 1427 ARG cc_start: 0.6156 (mtm-85) cc_final: 0.5886 (ptp-110) REVERT: A 1451 MET cc_start: 0.6326 (mmm) cc_final: 0.6065 (mmm) REVERT: B 167 SER cc_start: 0.1790 (OUTLIER) cc_final: 0.1336 (t) REVERT: B 170 LEU cc_start: 0.3427 (OUTLIER) cc_final: 0.2811 (pp) REVERT: C 274 MET cc_start: 0.1637 (mmm) cc_final: 0.0857 (ppp) REVERT: C 301 LEU cc_start: 0.5965 (mt) cc_final: 0.5684 (pp) REVERT: E 8 LYS cc_start: 0.7001 (mttt) cc_final: 0.6797 (mttt) REVERT: E 10 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7173 (mmm-85) REVERT: E 24 MET cc_start: 0.8842 (ttm) cc_final: 0.8637 (ttp) REVERT: E 105 ILE cc_start: 0.8347 (mt) cc_final: 0.8003 (tp) REVERT: E 142 MET cc_start: 0.9103 (mmt) cc_final: 0.8704 (mmt) REVERT: E 156 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7573 (mm-30) REVERT: E 206 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7414 (mmt180) REVERT: E 210 ASN cc_start: 0.8178 (m-40) cc_final: 0.7899 (p0) REVERT: E 212 TRP cc_start: 0.7617 (OUTLIER) cc_final: 0.6709 (p-90) REVERT: F 61 ASP cc_start: 0.8878 (m-30) cc_final: 0.7959 (t0) REVERT: F 107 GLU cc_start: 0.7345 (mt-10) cc_final: 0.7129 (mt-10) REVERT: F 118 ASP cc_start: 0.7973 (p0) cc_final: 0.7747 (p0) REVERT: F 202 ASP cc_start: 0.8205 (t0) cc_final: 0.7905 (t0) REVERT: F 281 MET cc_start: 0.9339 (tpp) cc_final: 0.8780 (tpp) REVERT: F 286 SER cc_start: 0.8322 (p) cc_final: 0.8085 (p) REVERT: F 299 ASN cc_start: 0.7821 (OUTLIER) cc_final: 0.7174 (t0) REVERT: F 311 GLN cc_start: 0.9325 (OUTLIER) cc_final: 0.9082 (tp40) REVERT: F 389 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8925 (m-10) REVERT: F 422 ARG cc_start: 0.8836 (tmm160) cc_final: 0.8440 (ttp80) REVERT: F 427 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7730 (tt0) REVERT: F 445 GLN cc_start: 0.8061 (mt0) cc_final: 0.7672 (pt0) REVERT: F 528 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7766 (t0) REVERT: F 529 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.7919 (tt) REVERT: F 541 ILE cc_start: 0.8267 (mt) cc_final: 0.7987 (tp) REVERT: F 603 ASP cc_start: 0.8563 (m-30) cc_final: 0.8352 (m-30) REVERT: F 646 ARG cc_start: 0.8592 (mtm180) cc_final: 0.8190 (ptp-110) REVERT: F 663 PHE cc_start: 0.8466 (m-80) cc_final: 0.8081 (m-80) REVERT: F 692 ARG cc_start: 0.7451 (ttt-90) cc_final: 0.7217 (ttp80) REVERT: F 707 ARG cc_start: 0.8091 (ttt90) cc_final: 0.7828 (tpt-90) REVERT: F 733 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7266 (tttm) REVERT: F 755 TRP cc_start: 0.8215 (OUTLIER) cc_final: 0.6601 (t60) REVERT: F 763 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8559 (mt-10) REVERT: F 820 ASP cc_start: 0.7956 (t0) cc_final: 0.7624 (t0) REVERT: F 851 MET cc_start: 0.3724 (mtt) cc_final: 0.2483 (ttt) REVERT: F 867 HIS cc_start: 0.8694 (t-90) cc_final: 0.8204 (t-90) REVERT: F 872 ASN cc_start: 0.8648 (m-40) cc_final: 0.8291 (t0) REVERT: F 878 PHE cc_start: 0.8492 (t80) cc_final: 0.8096 (t80) REVERT: F 882 ASP cc_start: 0.8666 (t0) cc_final: 0.7989 (p0) REVERT: F 975 GLN cc_start: 0.6242 (pt0) cc_final: 0.6020 (pt0) REVERT: F 987 ASP cc_start: 0.7774 (t0) cc_final: 0.7540 (p0) REVERT: F 989 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.7700 (t0) REVERT: F 1013 ASN cc_start: 0.8876 (t0) cc_final: 0.8538 (t0) outliers start: 99 outliers final: 24 residues processed: 688 average time/residue: 0.1635 time to fit residues: 170.4812 Evaluate side-chains 467 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 422 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 542 TRP Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 915 LYS Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 1101 TYR Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1122 TYR Chi-restraints excluded: chain A residue 1264 PHE Chi-restraints excluded: chain A residue 1304 ASN Chi-restraints excluded: chain A residue 1376 PHE Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 206 ARG Chi-restraints excluded: chain E residue 212 TRP Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 389 PHE Chi-restraints excluded: chain F residue 428 TYR Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain F residue 528 ASN Chi-restraints excluded: chain F residue 529 LEU Chi-restraints excluded: chain F residue 544 ARG Chi-restraints excluded: chain F residue 615 ASN Chi-restraints excluded: chain F residue 733 LYS Chi-restraints excluded: chain F residue 755 TRP Chi-restraints excluded: chain F residue 895 TYR Chi-restraints excluded: chain F residue 989 ASP Chi-restraints excluded: chain F residue 1036 GLN Chi-restraints excluded: chain F residue 1052 GLN Chi-restraints excluded: chain F residue 1068 LEU Chi-restraints excluded: chain F residue 1071 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN A 426 HIS A 445 ASN A 456 GLN A 464 GLN A 579 GLN ** A 996 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN A1071 GLN A1085 GLN A1139 HIS A1154 ASN A1304 ASN ** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1374 ASN ** A1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1397 HIS E 50 HIS ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN F 311 GLN F 313 ASN F 316 ASN ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 556 GLN F 773 ASN F 904 GLN ** F 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1036 GLN F1052 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.199020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.159267 restraints weight = 80852.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.156537 restraints weight = 74622.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.150590 restraints weight = 35630.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.151283 restraints weight = 34143.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.152052 restraints weight = 21808.281| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22406 Z= 0.195 Angle : 0.940 22.040 30335 Z= 0.466 Chirality : 0.056 1.234 3442 Planarity : 0.006 0.077 3748 Dihedral : 12.845 111.836 3291 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.95 % Allowed : 9.39 % Favored : 89.65 % Rotamer: Outliers : 3.42 % Allowed : 11.59 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.04 % Twisted Proline : 1.87 % Twisted General : 0.39 % 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: -3.33 (0.15), residues: 2633 helix: -1.75 (0.12), residues: 1335 sheet: -1.14 (0.32), residues: 231 loop : -2.98 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 769 TYR 0.047 0.002 TYR F 647 PHE 0.032 0.002 PHE F 341 TRP 0.039 0.002 TRP F 824 HIS 0.008 0.002 HIS A 996 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (22369) covalent geometry : angle 0.89516 / 0.46 (30238) SS BOND : bond 0.01754 / 0.83 ( 11) SS BOND : angle 2.75609 / 1.63 ( 22) hydrogen bonds : bond 0.05885 / 3.71 ( 918) hydrogen bonds : angle 5.64347 / 3.80 ( 2607) Misc. bond : bond 0.00058 / 0.03 ( 1) link_BETA1-4 : bond 0.00756 / 0.35 ( 10) link_BETA1-4 : angle 1.87686 / 1.08 ( 30) link_NAG-ASN : bond 0.01187 / 0.75 ( 15) link_NAG-ASN : angle 7.18185 / 4.67 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 469 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.8158 (t80) cc_final: 0.7816 (t80) REVERT: A 87 GLU cc_start: 0.7667 (tp30) cc_final: 0.7407 (pt0) REVERT: A 99 ILE cc_start: 0.7875 (mt) cc_final: 0.7505 (mt) REVERT: A 131 PHE cc_start: 0.7185 (t80) cc_final: 0.6659 (t80) REVERT: A 177 SER cc_start: 0.7837 (m) cc_final: 0.7604 (p) REVERT: A 423 TRP cc_start: 0.5504 (m100) cc_final: 0.4839 (m-90) REVERT: A 463 LEU cc_start: 0.8938 (mt) cc_final: 0.8642 (tt) REVERT: A 472 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8721 (mt) REVERT: A 492 PHE cc_start: 0.7215 (OUTLIER) cc_final: 0.6717 (t80) REVERT: A 532 LEU cc_start: 0.9089 (mt) cc_final: 0.8765 (mm) REVERT: A 930 ASN cc_start: 0.7012 (m-40) cc_final: 0.6792 (t0) REVERT: A 936 THR cc_start: 0.8620 (t) cc_final: 0.8393 (m) REVERT: A 955 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8196 (t80) REVERT: A 1056 MET cc_start: 0.7056 (ttm) cc_final: 0.6810 (mtt) REVERT: A 1075 GLU cc_start: 0.7952 (mp0) cc_final: 0.7203 (tp30) REVERT: A 1084 ASN cc_start: 0.6638 (p0) cc_final: 0.6194 (t0) REVERT: A 1120 PHE cc_start: 0.8110 (m-80) cc_final: 0.7789 (m-80) REVERT: A 1153 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8508 (mm) REVERT: A 1168 LYS cc_start: 0.8381 (mttt) cc_final: 0.8156 (mttt) REVERT: A 1334 TYR cc_start: 0.6070 (t80) cc_final: 0.5801 (t80) REVERT: A 1341 GLU cc_start: 0.7137 (mp0) cc_final: 0.6896 (mp0) REVERT: A 1359 TYR cc_start: 0.7775 (m-10) cc_final: 0.7445 (m-10) REVERT: A 1447 ARG cc_start: 0.7751 (tpm170) cc_final: 0.6952 (tpm170) REVERT: C 301 LEU cc_start: 0.4598 (mt) cc_final: 0.4276 (pp) REVERT: E 10 ARG cc_start: 0.7578 (mmt90) cc_final: 0.7366 (mmm-85) REVERT: E 50 HIS cc_start: 0.6864 (m90) cc_final: 0.6495 (p90) REVERT: E 206 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7183 (mmp-170) REVERT: E 212 TRP cc_start: 0.7309 (OUTLIER) cc_final: 0.6537 (p-90) REVERT: F 61 ASP cc_start: 0.7793 (m-30) cc_final: 0.7501 (t0) REVERT: F 281 MET cc_start: 0.9088 (tpp) cc_final: 0.8556 (tpp) REVERT: F 447 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7743 (mm110) REVERT: F 528 ASN cc_start: 0.8047 (OUTLIER) cc_final: 0.7509 (t0) REVERT: F 529 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8203 (tt) REVERT: F 656 PHE cc_start: 0.7326 (m-10) cc_final: 0.7091 (m-10) REVERT: F 707 ARG cc_start: 0.7449 (ttt90) cc_final: 0.6559 (tpt-90) REVERT: F 851 MET cc_start: 0.3512 (mtt) cc_final: 0.2701 (ttt) REVERT: F 886 MET cc_start: 0.8036 (tpp) cc_final: 0.7546 (tpp) outliers start: 73 outliers final: 35 residues processed: 508 average time/residue: 0.1454 time to fit residues: 116.3247 Evaluate side-chains 432 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 388 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 542 TRP Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 955 PHE Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 206 ARG Chi-restraints excluded: chain E residue 212 TRP Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 447 GLN Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain F residue 528 ASN Chi-restraints excluded: chain F residue 529 LEU Chi-restraints excluded: chain F residue 544 ARG Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 615 ASN Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 733 LYS Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 783 PHE Chi-restraints excluded: chain F residue 895 TYR Chi-restraints excluded: chain F residue 988 ASN Chi-restraints excluded: chain F residue 1036 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 201 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 223 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 202 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 HIS ** A 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 445 GLN ** F 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 720 GLN F 975 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.196168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.157293 restraints weight = 85398.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.154186 restraints weight = 73921.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.150105 restraints weight = 34658.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.149697 restraints weight = 36133.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.150561 restraints weight = 22162.950| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 22406 Z= 0.221 Angle : 0.895 21.054 30335 Z= 0.440 Chirality : 0.053 0.787 3442 Planarity : 0.005 0.074 3748 Dihedral : 11.637 83.255 3228 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.80 % Allowed : 10.35 % Favored : 88.85 % Rotamer: Outliers : 4.00 % Allowed : 14.08 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.04 % Twisted Proline : 1.87 % Twisted General : 0.39 % 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: -2.55 (0.16), residues: 2633 helix: -0.94 (0.13), residues: 1331 sheet: -1.08 (0.32), residues: 246 loop : -2.79 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 591 TYR 0.043 0.002 TYR F 609 PHE 0.030 0.002 PHE E 189 TRP 0.027 0.002 TRP F 824 HIS 0.008 0.002 HIS A1141 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.22 (22369) covalent geometry : angle 0.85504 / 0.43 (30238) SS BOND : bond 0.00294 / 0.14 ( 11) SS BOND : angle 1.86031 / 1.14 ( 22) hydrogen bonds : bond 0.04842 / 3.10 ( 918) hydrogen bonds : angle 5.15061 / 3.47 ( 2607) Misc. bond : bond 0.00079 / 0.04 ( 1) link_BETA1-4 : bond 0.00528 / 0.24 ( 10) link_BETA1-4 : angle 1.68701 / 0.98 ( 30) link_NAG-ASN : bond 0.00969 / 0.65 ( 15) link_NAG-ASN : angle 6.70598 / 4.36 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 424 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.8240 (t80) cc_final: 0.7961 (t80) REVERT: A 87 GLU cc_start: 0.7546 (tp30) cc_final: 0.7342 (pt0) REVERT: A 103 MET cc_start: 0.7492 (mmm) cc_final: 0.7195 (mmm) REVERT: A 131 PHE cc_start: 0.7293 (t80) cc_final: 0.6818 (t80) REVERT: A 423 TRP cc_start: 0.5550 (m100) cc_final: 0.4783 (m-90) REVERT: A 436 TRP cc_start: 0.8049 (m100) cc_final: 0.7730 (m100) REVERT: A 463 LEU cc_start: 0.8972 (mt) cc_final: 0.8660 (tt) REVERT: A 492 PHE cc_start: 0.7297 (OUTLIER) cc_final: 0.6968 (t80) REVERT: A 851 MET cc_start: 0.4269 (mmp) cc_final: 0.3548 (ptp) REVERT: A 930 ASN cc_start: 0.7126 (m-40) cc_final: 0.6879 (t0) REVERT: A 937 LEU cc_start: 0.8611 (tp) cc_final: 0.8369 (tt) REVERT: A 948 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8256 (mm110) REVERT: A 1056 MET cc_start: 0.7036 (ttm) cc_final: 0.6816 (mtp) REVERT: A 1075 GLU cc_start: 0.7881 (mp0) cc_final: 0.7233 (tp30) REVERT: A 1084 ASN cc_start: 0.6763 (p0) cc_final: 0.6305 (t0) REVERT: A 1120 PHE cc_start: 0.8018 (m-80) cc_final: 0.7755 (m-80) REVERT: A 1121 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7046 (mp0) REVERT: A 1124 MET cc_start: 0.8515 (mmm) cc_final: 0.8165 (mpp) REVERT: A 1145 GLU cc_start: 0.7232 (mp0) cc_final: 0.6857 (tp30) REVERT: A 1153 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8597 (mm) REVERT: A 1168 LYS cc_start: 0.8375 (mttt) cc_final: 0.8122 (mttt) REVERT: A 1234 PHE cc_start: 0.8272 (t80) cc_final: 0.7907 (t80) REVERT: A 1303 ASN cc_start: 0.7947 (t0) cc_final: 0.7668 (t0) REVERT: A 1334 TYR cc_start: 0.6437 (t80) cc_final: 0.6136 (t80) REVERT: A 1341 GLU cc_start: 0.7108 (mp0) cc_final: 0.6813 (mp0) REVERT: A 1359 TYR cc_start: 0.7912 (m-10) cc_final: 0.7546 (m-10) REVERT: C 301 LEU cc_start: 0.4649 (mt) cc_final: 0.4308 (pp) REVERT: E 50 HIS cc_start: 0.6714 (m90) cc_final: 0.6438 (p90) REVERT: E 155 LEU cc_start: 0.8883 (mp) cc_final: 0.8435 (tt) REVERT: E 206 ARG cc_start: 0.7367 (mmp-170) cc_final: 0.7050 (mmp-170) REVERT: F 61 ASP cc_start: 0.7677 (m-30) cc_final: 0.7406 (t0) REVERT: F 281 MET cc_start: 0.9150 (tpp) cc_final: 0.8375 (tpp) REVERT: F 426 GLN cc_start: 0.8609 (pt0) cc_final: 0.8356 (pt0) REVERT: F 447 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7796 (mm110) REVERT: F 528 ASN cc_start: 0.8006 (OUTLIER) cc_final: 0.7338 (t0) REVERT: F 529 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8260 (tt) REVERT: F 851 MET cc_start: 0.3663 (mtt) cc_final: 0.2749 (ttt) REVERT: F 878 PHE cc_start: 0.7624 (t80) cc_final: 0.7377 (t80) REVERT: F 886 MET cc_start: 0.8096 (tpp) cc_final: 0.7583 (tpp) outliers start: 86 outliers final: 52 residues processed: 475 average time/residue: 0.1385 time to fit residues: 104.9763 Evaluate side-chains 443 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 384 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 266 PRO Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 542 TRP Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 955 PHE Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1264 PHE Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1306 PHE Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 447 GLN Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain F residue 528 ASN Chi-restraints excluded: chain F residue 529 LEU Chi-restraints excluded: chain F residue 544 ARG Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 615 ASN Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 733 LYS Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 770 SER Chi-restraints excluded: chain F residue 796 MET Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 884 SER Chi-restraints excluded: chain F residue 895 TYR Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 988 ASN Chi-restraints excluded: chain F residue 1034 LEU Chi-restraints excluded: chain F residue 1042 ASP Chi-restraints excluded: chain F residue 1048 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 238 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 218 optimal weight: 0.0370 chunk 32 optimal weight: 20.0000 chunk 28 optimal weight: 0.1980 chunk 93 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN A 327 ASN ** A 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 GLN A1148 HIS A1287 GLN E 31 HIS E 160 GLN F 57 HIS ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 357 ASN ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 644 GLN F 726 GLN F 975 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.201143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.159307 restraints weight = 77550.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.157261 restraints weight = 72928.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.152181 restraints weight = 31073.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.152754 restraints weight = 29532.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.153299 restraints weight = 19926.377| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3729 r_free = 0.3729 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3729 r_free = 0.3729 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 22406 Z= 0.143 Angle : 0.823 19.944 30335 Z= 0.400 Chirality : 0.051 0.693 3442 Planarity : 0.005 0.061 3748 Dihedral : 10.759 81.709 3215 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.55 % Favored : 89.73 % Rotamer: Outliers : 3.20 % Allowed : 16.03 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.04 % Twisted Proline : 1.87 % Twisted General : 0.28 % 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: -1.98 (0.16), residues: 2633 helix: -0.39 (0.14), residues: 1332 sheet: -0.74 (0.32), residues: 258 loop : -2.69 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 591 TYR 0.030 0.002 TYR F 609 PHE 0.028 0.002 PHE E 189 TRP 0.031 0.002 TRP F 824 HIS 0.014 0.002 HIS A1148 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (22369) covalent geometry : angle 0.78255 / 0.39 (30238) SS BOND : bond 0.00639 / 0.32 ( 11) SS BOND : angle 1.38322 / 0.88 ( 22) hydrogen bonds : bond 0.04020 / 2.57 ( 918) hydrogen bonds : angle 4.76565 / 3.21 ( 2607) Misc. bond : bond 0.00005 / 0.00 ( 1) link_BETA1-4 : bond 0.00494 / 0.22 ( 10) link_BETA1-4 : angle 1.51564 / 0.87 ( 30) link_NAG-ASN : bond 0.01140 / 0.70 ( 15) link_NAG-ASN : angle 6.54756 / 4.17 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 425 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.8351 (t80) cc_final: 0.7878 (t80) REVERT: A 99 ILE cc_start: 0.7266 (tp) cc_final: 0.6769 (pt) REVERT: A 106 ILE cc_start: 0.8200 (mm) cc_final: 0.7750 (pt) REVERT: A 202 LEU cc_start: 0.8629 (tt) cc_final: 0.8421 (tt) REVERT: A 423 TRP cc_start: 0.5609 (m100) cc_final: 0.5067 (m-90) REVERT: A 436 TRP cc_start: 0.7946 (m100) cc_final: 0.7682 (m100) REVERT: A 463 LEU cc_start: 0.8929 (mt) cc_final: 0.8634 (tt) REVERT: A 482 LYS cc_start: 0.7549 (mttp) cc_final: 0.7238 (mttp) REVERT: A 492 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6974 (t80) REVERT: A 504 VAL cc_start: 0.8304 (t) cc_final: 0.8075 (p) REVERT: A 1075 GLU cc_start: 0.8032 (mp0) cc_final: 0.7227 (tp30) REVERT: A 1084 ASN cc_start: 0.6826 (p0) cc_final: 0.6322 (t0) REVERT: A 1121 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: A 1124 MET cc_start: 0.8395 (mmm) cc_final: 0.8028 (mmm) REVERT: A 1145 GLU cc_start: 0.7396 (mp0) cc_final: 0.6998 (tp30) REVERT: A 1287 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.6956 (mt0) REVERT: A 1303 ASN cc_start: 0.7781 (t0) cc_final: 0.7456 (t0) REVERT: A 1334 TYR cc_start: 0.6357 (t80) cc_final: 0.5944 (t80) REVERT: A 1337 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8478 (tp) REVERT: A 1359 TYR cc_start: 0.7694 (m-10) cc_final: 0.7477 (m-80) REVERT: C 301 LEU cc_start: 0.4702 (mt) cc_final: 0.4305 (pp) REVERT: E 10 ARG cc_start: 0.7403 (mmt90) cc_final: 0.7195 (mtp180) REVERT: E 50 HIS cc_start: 0.6487 (m90) cc_final: 0.6259 (p90) REVERT: E 155 LEU cc_start: 0.8978 (mp) cc_final: 0.8477 (tt) REVERT: F 281 MET cc_start: 0.8957 (tpp) cc_final: 0.8204 (tpp) REVERT: F 426 GLN cc_start: 0.8535 (pt0) cc_final: 0.8281 (pt0) REVERT: F 447 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7874 (mm110) REVERT: F 528 ASN cc_start: 0.7968 (OUTLIER) cc_final: 0.7335 (t0) REVERT: F 826 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7139 (tt0) REVERT: F 851 MET cc_start: 0.3576 (mtt) cc_final: 0.2677 (ttt) REVERT: F 882 ASP cc_start: 0.7872 (p0) cc_final: 0.7539 (t0) outliers start: 68 outliers final: 44 residues processed: 460 average time/residue: 0.1415 time to fit residues: 104.1578 Evaluate side-chains 437 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 387 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 266 PRO Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 542 TRP Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 955 PHE Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1306 PHE Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 447 GLN Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 528 ASN Chi-restraints excluded: chain F residue 544 ARG Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 615 ASN Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 796 MET Chi-restraints excluded: chain F residue 884 SER Chi-restraints excluded: chain F residue 895 TYR Chi-restraints excluded: chain F residue 988 ASN Chi-restraints excluded: chain F residue 1007 HIS Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1034 LEU Chi-restraints excluded: chain F residue 1042 ASP Chi-restraints excluded: chain F residue 1062 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 260 optimal weight: 2.9990 chunk 121 optimal weight: 0.0370 chunk 81 optimal weight: 2.9990 chunk 54 optimal weight: 0.0170 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 153 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 85 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN A 654 ASN A 930 ASN ** A 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 HIS E 160 GLN F 57 HIS F 208 GLN F 248 GLN ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 867 HIS F1013 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.199604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.158985 restraints weight = 82889.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.156738 restraints weight = 74453.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.150909 restraints weight = 33573.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.151778 restraints weight = 30254.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.151882 restraints weight = 23678.755| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 22406 Z= 0.145 Angle : 0.803 19.479 30335 Z= 0.390 Chirality : 0.050 0.614 3442 Planarity : 0.005 0.066 3748 Dihedral : 10.171 83.129 3208 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.89 % Favored : 89.58 % Rotamer: Outliers : 3.51 % Allowed : 16.74 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.04 % Twisted Proline : 1.87 % Twisted General : 0.24 % 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: -1.63 (0.16), residues: 2633 helix: -0.06 (0.14), residues: 1328 sheet: -0.72 (0.32), residues: 268 loop : -2.54 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F1004 TYR 0.031 0.002 TYR F 609 PHE 0.023 0.002 PHE F1006 TRP 0.027 0.001 TRP F 824 HIS 0.013 0.001 HIS F 867 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (22369) covalent geometry : angle 0.76335 / 0.38 (30238) SS BOND : bond 0.00368 / 0.18 ( 11) SS BOND : angle 1.37733 / 0.90 ( 22) hydrogen bonds : bond 0.03788 / 2.42 ( 918) hydrogen bonds : angle 4.63203 / 3.13 ( 2607) Misc. bond : bond 0.00037 / 0.02 ( 1) link_BETA1-4 : bond 0.00490 / 0.22 ( 10) link_BETA1-4 : angle 1.43079 / 0.84 ( 30) link_NAG-ASN : bond 0.01006 / 0.64 ( 15) link_NAG-ASN : angle 6.39693 / 4.01 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 408 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.8286 (t80) cc_final: 0.7820 (t80) REVERT: A 106 ILE cc_start: 0.8169 (mm) cc_final: 0.7745 (pt) REVERT: A 118 LEU cc_start: 0.8265 (mt) cc_final: 0.7977 (tp) REVERT: A 119 ARG cc_start: 0.7800 (ptt90) cc_final: 0.7518 (ptm160) REVERT: A 309 TRP cc_start: 0.8515 (m100) cc_final: 0.8135 (m100) REVERT: A 423 TRP cc_start: 0.5448 (m100) cc_final: 0.5085 (m-90) REVERT: A 436 TRP cc_start: 0.7913 (m100) cc_final: 0.7651 (m100) REVERT: A 463 LEU cc_start: 0.9021 (mt) cc_final: 0.8626 (tt) REVERT: A 482 LYS cc_start: 0.7532 (mttp) cc_final: 0.7205 (mttp) REVERT: A 492 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.6981 (t80) REVERT: A 504 VAL cc_start: 0.8179 (t) cc_final: 0.7912 (p) REVERT: A 1075 GLU cc_start: 0.7986 (mp0) cc_final: 0.7214 (tp30) REVERT: A 1084 ASN cc_start: 0.6861 (p0) cc_final: 0.6342 (t0) REVERT: A 1121 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: A 1124 MET cc_start: 0.8285 (mmm) cc_final: 0.7727 (mmm) REVERT: A 1145 GLU cc_start: 0.7379 (mp0) cc_final: 0.6983 (tp30) REVERT: A 1153 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8538 (mm) REVERT: A 1303 ASN cc_start: 0.7765 (t0) cc_final: 0.7461 (t0) REVERT: A 1334 TYR cc_start: 0.6276 (t80) cc_final: 0.5996 (t80) REVERT: A 1359 TYR cc_start: 0.7656 (m-10) cc_final: 0.7289 (m-10) REVERT: A 1427 ARG cc_start: 0.6743 (mtm-85) cc_final: 0.5895 (mtp180) REVERT: C 293 MET cc_start: 0.5041 (mmp) cc_final: 0.3292 (mmp) REVERT: E 10 ARG cc_start: 0.7390 (mmt90) cc_final: 0.7189 (mtp180) REVERT: E 50 HIS cc_start: 0.6569 (m90) cc_final: 0.6331 (p90) REVERT: E 155 LEU cc_start: 0.8873 (mp) cc_final: 0.8476 (tt) REVERT: F 70 TYR cc_start: 0.7122 (m-80) cc_final: 0.6159 (m-10) REVERT: F 281 MET cc_start: 0.8615 (tpp) cc_final: 0.8227 (tpp) REVERT: F 528 ASN cc_start: 0.8014 (OUTLIER) cc_final: 0.7268 (t0) REVERT: F 826 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6932 (tt0) REVERT: F 851 MET cc_start: 0.3553 (mtt) cc_final: 0.2698 (ttt) REVERT: F 987 ASP cc_start: 0.6996 (p0) cc_final: 0.6648 (p0) REVERT: F 1020 MET cc_start: 0.6624 (ptm) cc_final: 0.6301 (ptm) outliers start: 75 outliers final: 44 residues processed: 446 average time/residue: 0.1374 time to fit residues: 98.3103 Evaluate side-chains 431 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 383 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 266 PRO Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 542 TRP Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1286 MET Chi-restraints excluded: chain A residue 1306 PHE Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 528 ASN Chi-restraints excluded: chain F residue 544 ARG Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 615 ASN Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 796 MET Chi-restraints excluded: chain F residue 890 VAL Chi-restraints excluded: chain F residue 895 TYR Chi-restraints excluded: chain F residue 1006 PHE Chi-restraints excluded: chain F residue 1007 HIS Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1062 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 0.1980 chunk 22 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 219 optimal weight: 0.0470 chunk 140 optimal weight: 9.9990 chunk 129 optimal weight: 0.0370 chunk 2 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 240 optimal weight: 0.0970 chunk 138 optimal weight: 5.9990 overall best weight: 0.6756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 654 ASN ** A 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 GLN F 445 GLN F 578 ASN F 867 HIS F1013 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.199784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.159451 restraints weight = 74728.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.156817 restraints weight = 71269.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.153020 restraints weight = 30317.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.153286 restraints weight = 28059.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.153723 restraints weight = 20898.084| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3766 r_free = 0.3766 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3766 r_free = 0.3766 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 22406 Z= 0.140 Angle : 0.797 22.378 30335 Z= 0.383 Chirality : 0.049 0.499 3442 Planarity : 0.004 0.056 3748 Dihedral : 9.831 83.992 3208 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.00 % Favored : 89.50 % Rotamer: Outliers : 3.06 % Allowed : 17.81 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.04 % Twisted Proline : 1.87 % Twisted General : 0.20 % 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: -1.40 (0.17), residues: 2633 helix: 0.16 (0.14), residues: 1320 sheet: -0.64 (0.32), residues: 270 loop : -2.47 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 591 TYR 0.028 0.001 TYR F 609 PHE 0.033 0.002 PHE A1356 TRP 0.027 0.001 TRP A1258 HIS 0.007 0.001 HIS A 992 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (22369) covalent geometry : angle 0.75997 / 0.37 (30238) SS BOND : bond 0.00142 / 0.08 ( 11) SS BOND : angle 1.13629 / 0.75 ( 22) hydrogen bonds : bond 0.03692 / 2.32 ( 918) hydrogen bonds : angle 4.54051 / 3.06 ( 2607) Misc. bond : bond 0.00024 / 0.01 ( 1) link_BETA1-4 : bond 0.00448 / 0.20 ( 10) link_BETA1-4 : angle 1.39350 / 0.81 ( 30) link_NAG-ASN : bond 0.00988 / 0.64 ( 15) link_NAG-ASN : angle 6.20767 / 3.80 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 405 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.8207 (t80) cc_final: 0.7705 (t80) REVERT: A 106 ILE cc_start: 0.8132 (mm) cc_final: 0.7757 (pt) REVERT: A 309 TRP cc_start: 0.8442 (m100) cc_final: 0.8100 (m100) REVERT: A 367 MET cc_start: 0.3614 (mtt) cc_final: 0.3294 (mtm) REVERT: A 423 TRP cc_start: 0.5413 (m100) cc_final: 0.5095 (m-90) REVERT: A 432 ARG cc_start: 0.7023 (tmt170) cc_final: 0.5367 (ptt-90) REVERT: A 463 LEU cc_start: 0.9018 (mt) cc_final: 0.8607 (tt) REVERT: A 466 ILE cc_start: 0.8902 (pp) cc_final: 0.8656 (tp) REVERT: A 492 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.7026 (t80) REVERT: A 504 VAL cc_start: 0.8282 (t) cc_final: 0.8032 (p) REVERT: A 1075 GLU cc_start: 0.7940 (mp0) cc_final: 0.7235 (tp30) REVERT: A 1084 ASN cc_start: 0.6856 (p0) cc_final: 0.6324 (t0) REVERT: A 1121 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: A 1124 MET cc_start: 0.8164 (mmm) cc_final: 0.7500 (mmm) REVERT: A 1145 GLU cc_start: 0.7425 (mp0) cc_final: 0.6984 (tp30) REVERT: A 1153 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8382 (mm) REVERT: A 1296 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7665 (m-30) REVERT: A 1334 TYR cc_start: 0.6251 (t80) cc_final: 0.5938 (t80) REVERT: A 1359 TYR cc_start: 0.7701 (m-10) cc_final: 0.7264 (m-10) REVERT: C 293 MET cc_start: 0.4517 (mmp) cc_final: 0.3174 (mmp) REVERT: C 301 LEU cc_start: 0.3582 (mm) cc_final: 0.2778 (pt) REVERT: E 155 LEU cc_start: 0.8881 (mp) cc_final: 0.8503 (tt) REVERT: E 174 ILE cc_start: 0.3714 (OUTLIER) cc_final: 0.2717 (mt) REVERT: F 70 TYR cc_start: 0.6965 (m-80) cc_final: 0.5963 (m-80) REVERT: F 281 MET cc_start: 0.8569 (tpp) cc_final: 0.8168 (tpp) REVERT: F 426 GLN cc_start: 0.8363 (pt0) cc_final: 0.8119 (pt0) REVERT: F 528 ASN cc_start: 0.7949 (OUTLIER) cc_final: 0.7386 (t0) REVERT: F 711 ASP cc_start: 0.8253 (t0) cc_final: 0.8042 (t70) REVERT: F 851 MET cc_start: 0.3742 (mtt) cc_final: 0.2880 (ttt) REVERT: F 1020 MET cc_start: 0.6684 (ptm) cc_final: 0.6356 (ptm) outliers start: 66 outliers final: 46 residues processed: 436 average time/residue: 0.1466 time to fit residues: 102.4600 Evaluate side-chains 426 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 374 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 542 TRP Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 955 PHE Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1205 PHE Chi-restraints excluded: chain A residue 1286 MET Chi-restraints excluded: chain A residue 1296 ASP Chi-restraints excluded: chain A residue 1306 PHE Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 528 ASN Chi-restraints excluded: chain F residue 544 ARG Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 615 ASN Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 717 GLU Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 796 MET Chi-restraints excluded: chain F residue 895 TYR Chi-restraints excluded: chain F residue 1006 PHE Chi-restraints excluded: chain F residue 1007 HIS Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1034 LEU Chi-restraints excluded: chain F residue 1062 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 238 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 240 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 244 optimal weight: 5.9990 chunk 237 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 654 ASN ** A 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 GLN F 248 GLN F 313 ASN F 316 ASN F 867 HIS F1013 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.201543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.158622 restraints weight = 73806.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.152618 restraints weight = 68501.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.148182 restraints weight = 31961.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.148708 restraints weight = 29528.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.149132 restraints weight = 21203.989| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22406 Z= 0.137 Angle : 0.786 18.464 30335 Z= 0.381 Chirality : 0.049 0.460 3442 Planarity : 0.005 0.072 3748 Dihedral : 9.558 88.012 3208 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.85 % Favored : 89.61 % Rotamer: Outliers : 3.06 % Allowed : 18.21 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.04 % Twisted Proline : 1.87 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.17), residues: 2633 helix: 0.32 (0.14), residues: 1320 sheet: -0.54 (0.32), residues: 276 loop : -2.48 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 591 TYR 0.027 0.001 TYR F 609 PHE 0.032 0.002 PHE A1356 TRP 0.032 0.001 TRP A 50 HIS 0.016 0.001 HIS F 867 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (22369) covalent geometry : angle 0.75383 / 0.37 (30238) SS BOND : bond 0.00136 / 0.07 ( 11) SS BOND : angle 1.05210 / 0.71 ( 22) hydrogen bonds : bond 0.03645 / 2.32 ( 918) hydrogen bonds : angle 4.46173 / 3.01 ( 2607) Misc. bond : bond 0.00026 / 0.01 ( 1) link_BETA1-4 : bond 0.00432 / 0.19 ( 10) link_BETA1-4 : angle 1.37230 / 0.81 ( 30) link_NAG-ASN : bond 0.01008 / 0.68 ( 15) link_NAG-ASN : angle 5.74643 / 3.52 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 393 time to evaluate : 0.803 Fit side-chains revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.8327 (t80) cc_final: 0.7800 (t80) REVERT: A 106 ILE cc_start: 0.7939 (mm) cc_final: 0.7549 (pt) REVERT: A 118 LEU cc_start: 0.8568 (tp) cc_final: 0.8035 (mp) REVERT: A 309 TRP cc_start: 0.8387 (m100) cc_final: 0.8183 (m100) REVERT: A 423 TRP cc_start: 0.5525 (m100) cc_final: 0.5181 (m-90) REVERT: A 463 LEU cc_start: 0.9026 (mt) cc_final: 0.8583 (tt) REVERT: A 466 ILE cc_start: 0.8957 (pp) cc_final: 0.8673 (tp) REVERT: A 482 LYS cc_start: 0.7452 (mttp) cc_final: 0.7135 (mttt) REVERT: A 492 PHE cc_start: 0.7405 (OUTLIER) cc_final: 0.7130 (t80) REVERT: A 504 VAL cc_start: 0.8410 (t) cc_final: 0.8166 (p) REVERT: A 547 ASN cc_start: 0.8262 (p0) cc_final: 0.7850 (p0) REVERT: A 851 MET cc_start: 0.5042 (mmm) cc_final: 0.4075 (mtp) REVERT: A 1071 GLN cc_start: 0.8103 (mm110) cc_final: 0.7246 (mm110) REVERT: A 1075 GLU cc_start: 0.7888 (mp0) cc_final: 0.7145 (tp30) REVERT: A 1084 ASN cc_start: 0.6995 (p0) cc_final: 0.6375 (t0) REVERT: A 1121 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: A 1124 MET cc_start: 0.8251 (mmm) cc_final: 0.7519 (mmm) REVERT: A 1145 GLU cc_start: 0.7546 (mp0) cc_final: 0.6967 (tp30) REVERT: A 1334 TYR cc_start: 0.6182 (t80) cc_final: 0.5885 (t80) REVERT: A 1359 TYR cc_start: 0.7740 (m-10) cc_final: 0.7300 (m-10) REVERT: A 1427 ARG cc_start: 0.6675 (mtm-85) cc_final: 0.5839 (mtp180) REVERT: C 293 MET cc_start: 0.4852 (mmp) cc_final: 0.3699 (mmp) REVERT: C 301 LEU cc_start: 0.3596 (mm) cc_final: 0.2700 (pp) REVERT: E 10 ARG cc_start: 0.7468 (mmt90) cc_final: 0.6902 (mtp180) REVERT: E 155 LEU cc_start: 0.8947 (mp) cc_final: 0.8668 (tt) REVERT: E 174 ILE cc_start: 0.3605 (OUTLIER) cc_final: 0.2767 (mt) REVERT: F 70 TYR cc_start: 0.6908 (m-80) cc_final: 0.6071 (m-80) REVERT: F 280 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7793 (mm-30) REVERT: F 281 MET cc_start: 0.8548 (tpp) cc_final: 0.8160 (tpp) REVERT: F 283 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7424 (mm-30) REVERT: F 528 ASN cc_start: 0.7877 (OUTLIER) cc_final: 0.7232 (t0) REVERT: F 711 ASP cc_start: 0.8496 (t0) cc_final: 0.8216 (t70) REVERT: F 851 MET cc_start: 0.3478 (mtt) cc_final: 0.2403 (ttt) REVERT: F 1020 MET cc_start: 0.6804 (ptm) cc_final: 0.6394 (ptm) outliers start: 66 outliers final: 47 residues processed: 429 average time/residue: 0.1400 time to fit residues: 96.4934 Evaluate side-chains 422 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 371 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 542 TRP Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 955 PHE Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1205 PHE Chi-restraints excluded: chain A residue 1286 MET Chi-restraints excluded: chain A residue 1306 PHE Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1433 LEU Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 528 ASN Chi-restraints excluded: chain F residue 544 ARG Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 615 ASN Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 717 GLU Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 796 MET Chi-restraints excluded: chain F residue 895 TYR Chi-restraints excluded: chain F residue 1004 ARG Chi-restraints excluded: chain F residue 1006 PHE Chi-restraints excluded: chain F residue 1007 HIS Chi-restraints excluded: chain F residue 1036 GLN Chi-restraints excluded: chain F residue 1062 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 69 optimal weight: 8.9990 chunk 167 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 158 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 263 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 654 ASN ** A 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 GLN F 248 GLN F 426 GLN F 484 GLN F 773 ASN F 867 HIS F1013 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.193822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.153744 restraints weight = 80928.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.153452 restraints weight = 73070.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.148602 restraints weight = 33467.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.149734 restraints weight = 30642.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.149713 restraints weight = 21342.923| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 22406 Z= 0.257 Angle : 0.862 14.003 30335 Z= 0.424 Chirality : 0.052 0.440 3442 Planarity : 0.005 0.064 3748 Dihedral : 9.873 88.189 3208 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.57 % Allowed : 11.00 % Favored : 88.43 % Rotamer: Outliers : 3.42 % Allowed : 18.74 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.04 % Twisted Proline : 0.93 % Twisted General : 0.20 % 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: -1.41 (0.16), residues: 2633 helix: 0.16 (0.14), residues: 1331 sheet: -0.47 (0.33), residues: 259 loop : -2.55 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1447 TYR 0.039 0.002 TYR F 609 PHE 0.036 0.003 PHE A1356 TRP 0.031 0.002 TRP A1258 HIS 0.018 0.002 HIS F 867 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.26 (22369) covalent geometry : angle 0.84163 / 0.42 (30238) SS BOND : bond 0.00970 / 0.48 ( 11) SS BOND : angle 1.54008 / 0.96 ( 22) hydrogen bonds : bond 0.04023 / 2.57 ( 918) hydrogen bonds : angle 4.64615 / 3.14 ( 2607) Misc. bond : bond 0.00078 / 0.04 ( 1) link_BETA1-4 : bond 0.00417 / 0.19 ( 10) link_BETA1-4 : angle 1.51708 / 0.92 ( 30) link_NAG-ASN : bond 0.00608 / 0.29 ( 15) link_NAG-ASN : angle 4.74251 / 2.84 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 366 time to evaluate : 0.822 Fit side-chains revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.8495 (t80) cc_final: 0.8035 (t80) REVERT: A 106 ILE cc_start: 0.8220 (mm) cc_final: 0.7958 (pt) REVERT: A 118 LEU cc_start: 0.8361 (tp) cc_final: 0.7836 (mp) REVERT: A 309 TRP cc_start: 0.8212 (m100) cc_final: 0.8009 (m100) REVERT: A 423 TRP cc_start: 0.5662 (m100) cc_final: 0.5374 (m-90) REVERT: A 432 ARG cc_start: 0.7184 (tmt170) cc_final: 0.5493 (ptt-90) REVERT: A 463 LEU cc_start: 0.9032 (mt) cc_final: 0.8629 (tt) REVERT: A 466 ILE cc_start: 0.8977 (pp) cc_final: 0.8682 (tp) REVERT: A 492 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.7092 (t80) REVERT: A 504 VAL cc_start: 0.8484 (t) cc_final: 0.8268 (p) REVERT: A 1071 GLN cc_start: 0.8201 (mm110) cc_final: 0.7845 (mm110) REVERT: A 1075 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7366 (tp30) REVERT: A 1124 MET cc_start: 0.8194 (mmm) cc_final: 0.7955 (mmm) REVERT: A 1145 GLU cc_start: 0.7459 (mp0) cc_final: 0.7085 (tp30) REVERT: A 1153 LEU cc_start: 0.8846 (mt) cc_final: 0.8608 (mt) REVERT: A 1334 TYR cc_start: 0.6597 (t80) cc_final: 0.6265 (t80) REVERT: A 1359 TYR cc_start: 0.8044 (m-10) cc_final: 0.7606 (m-10) REVERT: A 1427 ARG cc_start: 0.6789 (mtm-85) cc_final: 0.5969 (mtp180) REVERT: C 293 MET cc_start: 0.4511 (mmp) cc_final: 0.2779 (mmp) REVERT: E 155 LEU cc_start: 0.8727 (mp) cc_final: 0.8407 (tt) REVERT: F 70 TYR cc_start: 0.7100 (m-80) cc_final: 0.6075 (m-80) REVERT: F 281 MET cc_start: 0.9029 (tpp) cc_final: 0.8477 (tpp) REVERT: F 824 TRP cc_start: 0.8580 (t60) cc_final: 0.8189 (t60) REVERT: F 851 MET cc_start: 0.3733 (mtt) cc_final: 0.2884 (ttt) REVERT: F 864 MET cc_start: 0.7711 (ptm) cc_final: 0.7202 (ptm) outliers start: 74 outliers final: 53 residues processed: 405 average time/residue: 0.1405 time to fit residues: 92.8290 Evaluate side-chains 412 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 357 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 542 TRP Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 955 PHE Chi-restraints excluded: chain A residue 1011 SER Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1075 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1205 PHE Chi-restraints excluded: chain A residue 1264 PHE Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1286 MET Chi-restraints excluded: chain A residue 1306 PHE Chi-restraints excluded: chain A residue 1433 LEU Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain F residue 38 TRP Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 544 ARG Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 717 GLU Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 796 MET Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 895 TYR Chi-restraints excluded: chain F residue 1004 ARG Chi-restraints excluded: chain F residue 1006 PHE Chi-restraints excluded: chain F residue 1007 HIS Chi-restraints excluded: chain F residue 1062 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 251 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 172 optimal weight: 8.9990 chunk 227 optimal weight: 0.0770 chunk 230 optimal weight: 7.9990 chunk 118 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 GLN A 930 ASN ** A 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 GLN F 248 GLN F1013 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.196503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.154751 restraints weight = 74331.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.150017 restraints weight = 67815.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.144596 restraints weight = 34780.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.145406 restraints weight = 30700.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.145855 restraints weight = 21815.744| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22406 Z= 0.152 Angle : 0.799 16.498 30335 Z= 0.390 Chirality : 0.053 0.903 3442 Planarity : 0.005 0.066 3748 Dihedral : 9.482 81.388 3201 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.97 % Favored : 89.50 % Rotamer: Outliers : 2.75 % Allowed : 19.80 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.04 % Twisted Proline : 0.93 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.17), residues: 2633 helix: 0.36 (0.14), residues: 1329 sheet: -0.46 (0.33), residues: 263 loop : -2.56 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 591 TYR 0.031 0.002 TYR F 609 PHE 0.035 0.002 PHE A1356 TRP 0.031 0.002 TRP A1258 HIS 0.009 0.001 HIS A 992 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (22369) covalent geometry : angle 0.77455 / 0.38 (30238) SS BOND : bond 0.00132 / 0.06 ( 11) SS BOND : angle 1.20138 / 0.80 ( 22) hydrogen bonds : bond 0.03758 / 2.39 ( 918) hydrogen bonds : angle 4.50957 / 3.04 ( 2607) Misc. bond : bond 0.00040 / 0.02 ( 1) link_BETA1-4 : bond 0.00457 / 0.21 ( 10) link_BETA1-4 : angle 1.32827 / 0.77 ( 30) link_NAG-ASN : bond 0.01021 / 0.68 ( 15) link_NAG-ASN : angle 5.06312 / 3.39 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 377 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.8388 (t80) cc_final: 0.7937 (t80) REVERT: A 106 ILE cc_start: 0.8162 (mm) cc_final: 0.7743 (pt) REVERT: A 118 LEU cc_start: 0.8457 (tp) cc_final: 0.8132 (tp) REVERT: A 240 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7687 (tm-30) REVERT: A 423 TRP cc_start: 0.5691 (m100) cc_final: 0.5325 (m-90) REVERT: A 447 LEU cc_start: 0.9338 (mt) cc_final: 0.8840 (tt) REVERT: A 463 LEU cc_start: 0.9025 (mt) cc_final: 0.8571 (tt) REVERT: A 466 ILE cc_start: 0.8974 (pp) cc_final: 0.8666 (tp) REVERT: A 492 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.6823 (t80) REVERT: A 498 ARG cc_start: 0.7091 (ttt180) cc_final: 0.6779 (mtp180) REVERT: A 504 VAL cc_start: 0.8318 (t) cc_final: 0.8037 (p) REVERT: A 547 ASN cc_start: 0.8296 (p0) cc_final: 0.7951 (p0) REVERT: A 1071 GLN cc_start: 0.8279 (mm110) cc_final: 0.7405 (mm110) REVERT: A 1075 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7223 (tp30) REVERT: A 1124 MET cc_start: 0.8351 (mmm) cc_final: 0.7599 (mmm) REVERT: A 1145 GLU cc_start: 0.7533 (mp0) cc_final: 0.7016 (tp30) REVERT: A 1334 TYR cc_start: 0.6573 (t80) cc_final: 0.6277 (t80) REVERT: A 1381 MET cc_start: 0.8267 (mmp) cc_final: 0.7760 (ttt) REVERT: A 1427 ARG cc_start: 0.6833 (mtm-85) cc_final: 0.5985 (mtp180) REVERT: C 293 MET cc_start: 0.4639 (mmp) cc_final: 0.3438 (mmp) REVERT: E 155 LEU cc_start: 0.8854 (mp) cc_final: 0.8644 (tt) REVERT: E 206 ARG cc_start: 0.7301 (mmt180) cc_final: 0.6996 (mmp-170) REVERT: F 70 TYR cc_start: 0.6924 (m-80) cc_final: 0.5948 (m-80) REVERT: F 281 MET cc_start: 0.8818 (tpp) cc_final: 0.8412 (tpp) REVERT: F 283 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7554 (mm-30) REVERT: F 557 GLU cc_start: 0.5943 (mm-30) cc_final: 0.5740 (mm-30) REVERT: F 851 MET cc_start: 0.3505 (mtt) cc_final: 0.2423 (ttt) REVERT: F 1004 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6531 (mtt-85) outliers start: 59 outliers final: 47 residues processed: 408 average time/residue: 0.1370 time to fit residues: 91.2182 Evaluate side-chains 413 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 362 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 542 TRP Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 930 ASN Chi-restraints excluded: chain A residue 955 PHE Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1075 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1205 PHE Chi-restraints excluded: chain A residue 1286 MET Chi-restraints excluded: chain A residue 1306 PHE Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 160 GLN Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 544 ARG Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 717 GLU Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 796 MET Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 895 TYR Chi-restraints excluded: chain F residue 1004 ARG Chi-restraints excluded: chain F residue 1006 PHE Chi-restraints excluded: chain F residue 1007 HIS Chi-restraints excluded: chain F residue 1062 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 224 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 204 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 106 optimal weight: 0.1980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 GLN F 773 ASN F1013 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.197911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.158556 restraints weight = 82325.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.155091 restraints weight = 74770.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.152116 restraints weight = 32554.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.151513 restraints weight = 29394.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.152210 restraints weight = 20407.030| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 22406 Z= 0.210 Angle : 1.035 59.199 30335 Z= 0.561 Chirality : 0.054 1.076 3442 Planarity : 0.005 0.112 3748 Dihedral : 9.493 81.312 3201 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.04 % Favored : 89.42 % Rotamer: Outliers : 2.62 % Allowed : 20.07 % Favored : 77.31 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.04 % Twisted Proline : 0.93 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.17), residues: 2633 helix: 0.35 (0.14), residues: 1330 sheet: -0.46 (0.33), residues: 263 loop : -2.56 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1447 TYR 0.030 0.002 TYR F 609 PHE 0.033 0.002 PHE A1356 TRP 0.029 0.002 TRP A1258 HIS 0.008 0.001 HIS A 992 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.20 (22369) covalent geometry : angle 1.00874 / 0.55 (30238) SS BOND : bond 0.04015 / 1.91 ( 11) SS BOND : angle 5.18671 / 2.82 ( 22) hydrogen bonds : bond 0.03787 / 2.38 ( 918) hydrogen bonds : angle 4.51721 / 3.05 ( 2607) Misc. bond : bond 0.00399 / 0.21 ( 1) link_BETA1-4 : bond 0.00417 / 0.19 ( 10) link_BETA1-4 : angle 1.34227 / 0.77 ( 30) link_NAG-ASN : bond 0.00885 / 0.55 ( 15) link_NAG-ASN : angle 4.83536 / 3.02 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5266 Ramachandran restraints generated. 2633 Oldfield, 0 Emsley, 2633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 362 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.8439 (t80) cc_final: 0.7902 (t80) REVERT: A 106 ILE cc_start: 0.8201 (mm) cc_final: 0.7788 (pt) REVERT: A 118 LEU cc_start: 0.8422 (tp) cc_final: 0.8095 (tp) REVERT: A 240 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: A 423 TRP cc_start: 0.5718 (m100) cc_final: 0.5375 (m-90) REVERT: A 463 LEU cc_start: 0.9018 (mt) cc_final: 0.8577 (tt) REVERT: A 466 ILE cc_start: 0.8989 (pp) cc_final: 0.8666 (tp) REVERT: A 492 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6844 (t80) REVERT: A 498 ARG cc_start: 0.7092 (ttt180) cc_final: 0.6787 (mtp180) REVERT: A 504 VAL cc_start: 0.8351 (t) cc_final: 0.8021 (p) REVERT: A 547 ASN cc_start: 0.8212 (p0) cc_final: 0.7868 (p0) REVERT: A 1071 GLN cc_start: 0.8265 (mm110) cc_final: 0.7389 (mm110) REVERT: A 1075 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7270 (tp30) REVERT: A 1124 MET cc_start: 0.8285 (mmm) cc_final: 0.7539 (mmm) REVERT: A 1145 GLU cc_start: 0.7492 (mp0) cc_final: 0.7031 (tp30) REVERT: A 1334 TYR cc_start: 0.6541 (t80) cc_final: 0.6283 (t80) REVERT: A 1381 MET cc_start: 0.8165 (mmp) cc_final: 0.7711 (ttt) REVERT: A 1427 ARG cc_start: 0.6800 (mtm-85) cc_final: 0.5983 (mtp180) REVERT: C 293 MET cc_start: 0.4513 (mmp) cc_final: 0.3261 (mmp) REVERT: E 155 LEU cc_start: 0.8793 (mp) cc_final: 0.8577 (tt) REVERT: E 206 ARG cc_start: 0.7312 (mmt180) cc_final: 0.7050 (mmp-170) REVERT: F 70 TYR cc_start: 0.6857 (m-80) cc_final: 0.5921 (m-80) REVERT: F 281 MET cc_start: 0.8839 (tpp) cc_final: 0.8421 (tpp) REVERT: F 283 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7680 (mm-30) REVERT: F 851 MET cc_start: 0.3534 (mtt) cc_final: 0.2471 (ttt) REVERT: F 1004 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6562 (mtt-85) outliers start: 56 outliers final: 47 residues processed: 393 average time/residue: 0.1342 time to fit residues: 86.4368 Evaluate side-chains 411 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 360 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 542 TRP Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 955 PHE Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1075 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1205 PHE Chi-restraints excluded: chain A residue 1286 MET Chi-restraints excluded: chain A residue 1306 PHE Chi-restraints excluded: chain A residue 1433 LEU Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 544 ARG Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 717 GLU Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 796 MET Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 895 TYR Chi-restraints excluded: chain F residue 1004 ARG Chi-restraints excluded: chain F residue 1006 PHE Chi-restraints excluded: chain F residue 1007 HIS Chi-restraints excluded: chain F residue 1062 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 126 optimal weight: 30.0000 chunk 164 optimal weight: 0.6980 chunk 28 optimal weight: 0.0370 chunk 121 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 198 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 930 ASN ** A 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 GLN F 773 ASN ** F 988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1013 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.197932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.158627 restraints weight = 80756.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.155267 restraints weight = 74423.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.152454 restraints weight = 32529.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.151862 restraints weight = 31925.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.152653 restraints weight = 21763.319| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.871 22406 Z= 0.360 Angle : 1.073 59.199 30335 Z= 0.569 Chirality : 0.061 1.618 3442 Planarity : 0.005 0.112 3748 Dihedral : 9.493 81.312 3201 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.04 % Favored : 89.42 % Rotamer: Outliers : 2.49 % Allowed : 20.20 % Favored : 77.31 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.04 % Twisted Proline : 0.93 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.17), residues: 2633 helix: 0.35 (0.14), residues: 1330 sheet: -0.46 (0.33), residues: 263 loop : -2.56 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1447 TYR 0.030 0.002 TYR F 609 PHE 0.033 0.002 PHE A1356 TRP 0.029 0.002 TRP A1258 HIS 0.008 0.001 HIS A 992 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.20 (22369) covalent geometry : angle 1.00880 / 0.55 (30238) SS BOND : bond 0.04778 / 2.31 ( 11) SS BOND : angle 5.49061 / 3.01 ( 22) hydrogen bonds : bond 0.03787 / 2.38 ( 918) hydrogen bonds : angle 4.51721 / 3.05 ( 2607) Misc. bond : bond 0.00399 / 0.21 ( 1) link_BETA1-4 : bond 0.00417 / 0.19 ( 10) link_BETA1-4 : angle 1.34227 / 0.77 ( 30) link_NAG-ASN : bond 0.22500 / 16.79 ( 15) link_NAG-ASN : angle 8.73475 / 5.43 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4828.02 seconds wall clock time: 84 minutes 4.24 seconds (5044.24 seconds total)