Starting phenix.real_space_refine on Fri Sep 19 02:48:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5gjv_9513/09_2025/5gjv_9513.cif Found real_map, /net/cci-nas-00/data/ceres_data/5gjv_9513/09_2025/5gjv_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_2025/5gjv_9513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5gjv_9513/09_2025/5gjv_9513.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5gjv_9513/09_2025/5gjv_9513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5gjv_9513/09_2025/5gjv_9513.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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: 312 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 dihedrals: 21 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: 9.10, per 1000 atoms: 0.42 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: 1.94 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.88 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: 4.58 Time building geometry restraints manager: 2.63 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: 13032 27.74 - 55.48: 609 55.48 - 83.22: 98 83.22 - 110.96: 15 110.96 - 138.70: 1 Dihedral angle restraints: 13755 sinusoidal: 5947 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 13752 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: 0.010 Normalize map: mean=0, sd=1: 1.400 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 27.040 Find NCS groups from input model: 0.180 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 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 : 15.741 138.701 8674 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 aren 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 covalent geometry : bond 0.01268 (22369) covalent geometry : angle 1.61517 (30238) SS BOND : bond 0.12470 ( 11) SS BOND : angle 16.32990 ( 22) hydrogen bonds : bond 0.29105 ( 918) hydrogen bonds : angle 9.98465 ( 2607) Misc. bond : bond 0.08345 ( 1) link_BETA1-4 : bond 0.01017 ( 10) link_BETA1-4 : angle 3.06505 ( 30) link_NAG-ASN : bond 0.03201 ( 15) link_NAG-ASN : angle 10.01687 ( 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 : 0.853 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: 0.8361 (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: 0.5870 (m-70) REVERT: A 131 PHE cc_start: 0.7784 (t80) cc_final: 0.7412 (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: 0.8253 (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: 0.5414 (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: 0.6797 (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: 0.8388 (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: 0.5667 (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: 0.5965 (mtp180) 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: 0.7413 (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: 0.6710 (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: 0.7904 (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: 0.7218 (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: 0.8203 (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: 0.6019 (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: 0.1869 time to fit residues: 193.3465 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 : 0.836 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.4268 r_free = 0.4268 target = 0.198557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.157907 restraints weight = 80494.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.153609 restraints weight = 71199.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.150665 restraints weight = 30970.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.150451 restraints weight = 30809.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.151197 restraints weight = 20480.421| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 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 = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22406 Z= 0.194 Angle : 0.936 21.286 30335 Z= 0.462 Chirality : 0.057 1.224 3442 Planarity : 0.006 0.075 3748 Dihedral : 14.000 109.685 3875 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.92 % Allowed : 9.35 % Favored : 89.73 % Rotamer: Outliers : 3.33 % Allowed : 11.50 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.04 % Twisted Proline : 1.87 % Twisted General : 0.43 % 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 aren not related in a simple way. whole: -3.30 (0.15), residues: 2633 helix: -1.71 (0.12), residues: 1335 sheet: -1.13 (0.32), residues: 231 loop : -2.98 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 769 TYR 0.050 0.002 TYR F 647 PHE 0.034 0.002 PHE F 341 TRP 0.038 0.002 TRP F 824 HIS 0.008 0.002 HIS A1397 Details of bonding type rmsd covalent geometry : bond 0.00419 (22369) covalent geometry : angle 0.88967 (30238) SS BOND : bond 0.01065 ( 11) SS BOND : angle 2.57810 ( 22) hydrogen bonds : bond 0.05501 ( 918) hydrogen bonds : angle 5.56944 ( 2607) Misc. bond : bond 0.00230 ( 1) link_BETA1-4 : bond 0.00764 ( 10) link_BETA1-4 : angle 2.13298 ( 30) link_NAG-ASN : bond 0.01276 ( 15) link_NAG-ASN : angle 7.20114 ( 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 541 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 470 time to evaluate : 0.843 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: A 71 TYR cc_start: 0.8158 (t80) cc_final: 0.7800 (t80) REVERT: A 87 GLU cc_start: 0.7669 (tp30) cc_final: 0.7393 (pt0) REVERT: A 99 ILE cc_start: 0.7809 (mt) cc_final: 0.7295 (mt) REVERT: A 131 PHE cc_start: 0.7228 (t80) cc_final: 0.6706 (t80) REVERT: A 177 SER cc_start: 0.7854 (m) cc_final: 0.7619 (p) REVERT: A 376 MET cc_start: 0.1149 (ppp) cc_final: 0.0809 (ppp) REVERT: A 423 TRP cc_start: 0.5464 (m100) cc_final: 0.4797 (m-90) REVERT: A 463 LEU cc_start: 0.8934 (mt) cc_final: 0.8635 (tt) REVERT: A 472 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8731 (mt) REVERT: A 492 PHE cc_start: 0.7228 (OUTLIER) cc_final: 0.6705 (t80) REVERT: A 532 LEU cc_start: 0.9075 (mt) cc_final: 0.8721 (mm) REVERT: A 936 THR cc_start: 0.8580 (t) cc_final: 0.8348 (m) REVERT: A 1022 ARG cc_start: 0.8276 (tpt90) cc_final: 0.8061 (tpt-90) REVERT: A 1056 MET cc_start: 0.7023 (ttm) cc_final: 0.6791 (mtt) REVERT: A 1075 GLU cc_start: 0.7936 (mp0) cc_final: 0.7172 (tp30) REVERT: A 1084 ASN cc_start: 0.6655 (p0) cc_final: 0.6265 (t0) REVERT: A 1120 PHE cc_start: 0.8136 (m-80) cc_final: 0.7764 (m-80) REVERT: A 1153 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8511 (mm) REVERT: A 1201 GLU cc_start: 0.6856 (pt0) cc_final: 0.6603 (pt0) REVERT: A 1334 TYR cc_start: 0.6054 (t80) cc_final: 0.5792 (t80) REVERT: A 1344 TYR cc_start: 0.7453 (p90) cc_final: 0.7231 (p90) REVERT: A 1447 ARG cc_start: 0.7771 (tpm170) cc_final: 0.6985 (tpm170) REVERT: C 301 LEU cc_start: 0.4700 (mt) cc_final: 0.4325 (pp) REVERT: E 10 ARG cc_start: 0.7615 (mmt90) cc_final: 0.7383 (mmm-85) REVERT: E 50 HIS cc_start: 0.6934 (m90) cc_final: 0.6556 (p90) REVERT: E 142 MET cc_start: 0.8124 (mmt) cc_final: 0.7918 (mmt) REVERT: E 155 LEU cc_start: 0.8956 (mp) cc_final: 0.8599 (tt) REVERT: E 206 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7218 (mmp-170) REVERT: F 61 ASP cc_start: 0.7872 (m-30) cc_final: 0.7544 (t0) REVERT: F 281 MET cc_start: 0.9072 (tpp) cc_final: 0.8639 (tpp) REVERT: F 447 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7789 (mm110) REVERT: F 493 ASP cc_start: 0.7683 (m-30) cc_final: 0.7319 (m-30) REVERT: F 528 ASN cc_start: 0.8117 (OUTLIER) cc_final: 0.7519 (t0) REVERT: F 529 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8133 (tt) REVERT: F 656 PHE cc_start: 0.7322 (m-10) cc_final: 0.7084 (m-10) REVERT: F 707 ARG cc_start: 0.7426 (ttt90) cc_final: 0.6537 (tpt-90) REVERT: F 851 MET cc_start: 0.3564 (mtt) cc_final: 0.2707 (ttt) REVERT: F 886 MET cc_start: 0.8086 (tpp) cc_final: 0.7597 (tpp) outliers start: 71 outliers final: 31 residues processed: 509 average time/residue: 0.1647 time to fit residues: 131.1166 Evaluate side-chains 425 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 387 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 E residue 113 PHE Chi-restraints excluded: chain E residue 206 ARG 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 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 744 THR Chi-restraints excluded: chain F residue 895 TYR Chi-restraints excluded: chain F residue 988 ASN Chi-restraints excluded: chain F residue 1036 GLN Chi-restraints excluded: chain F residue 1042 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 201 optimal weight: 0.6980 chunk 215 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 223 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 234 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 202 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 GLN A1287 GLN ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 445 GLN F 644 GLN F 720 GLN F 975 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.201767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.159528 restraints weight = 85689.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.162481 restraints weight = 74552.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.160749 restraints weight = 25648.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.162262 restraints weight = 19740.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.162082 restraints weight = 15994.257| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 22406 Z= 0.152 Angle : 0.850 21.050 30335 Z= 0.414 Chirality : 0.052 0.850 3442 Planarity : 0.005 0.066 3748 Dihedral : 12.185 84.269 3804 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.76 % Allowed : 9.62 % Favored : 89.61 % Rotamer: Outliers : 3.24 % Allowed : 14.56 % Favored : 82.19 % 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 aren not related in a simple way. whole: -2.38 (0.16), residues: 2633 helix: -0.81 (0.13), residues: 1332 sheet: -0.84 (0.32), residues: 244 loop : -2.74 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 469 TYR 0.032 0.002 TYR F 609 PHE 0.030 0.002 PHE E 189 TRP 0.027 0.002 TRP F 824 HIS 0.007 0.001 HIS F 394 Details of bonding type rmsd covalent geometry : bond 0.00328 (22369) covalent geometry : angle 0.80775 (30238) SS BOND : bond 0.00522 ( 11) SS BOND : angle 1.47446 ( 22) hydrogen bonds : bond 0.04501 ( 918) hydrogen bonds : angle 5.00028 ( 2607) Misc. bond : bond 0.00043 ( 1) link_BETA1-4 : bond 0.00500 ( 10) link_BETA1-4 : angle 2.03304 ( 30) link_NAG-ASN : bond 0.00983 ( 15) link_NAG-ASN : angle 6.69581 ( 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 517 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 448 time to evaluate : 0.875 Fit side-chains revert: symmetry clash 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: A 131 PHE cc_start: 0.7089 (t80) cc_final: 0.6654 (t80) REVERT: A 202 LEU cc_start: 0.8663 (tt) cc_final: 0.8461 (tt) REVERT: A 376 MET cc_start: 0.1949 (ppp) cc_final: 0.1530 (ppp) REVERT: A 423 TRP cc_start: 0.5641 (m100) cc_final: 0.4978 (m-90) REVERT: A 436 TRP cc_start: 0.7803 (m100) cc_final: 0.7504 (m100) REVERT: A 463 LEU cc_start: 0.8917 (mt) cc_final: 0.8595 (tt) REVERT: A 469 ARG cc_start: 0.8629 (ttm110) cc_final: 0.8385 (mtt-85) REVERT: A 492 PHE cc_start: 0.7121 (OUTLIER) cc_final: 0.6876 (t80) REVERT: A 936 THR cc_start: 0.8623 (t) cc_final: 0.8373 (m) REVERT: A 945 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8429 (mt) REVERT: A 955 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.8073 (t80) REVERT: A 1075 GLU cc_start: 0.7805 (mp0) cc_final: 0.7311 (tp30) REVERT: A 1084 ASN cc_start: 0.6553 (p0) cc_final: 0.6032 (t0) REVERT: A 1120 PHE cc_start: 0.7723 (m-80) cc_final: 0.7350 (m-80) REVERT: A 1121 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: A 1145 GLU cc_start: 0.7148 (mp0) cc_final: 0.6870 (tp30) REVERT: A 1153 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8504 (mm) REVERT: A 1265 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7672 (tm-30) REVERT: A 1287 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.7140 (mt0) REVERT: A 1303 ASN cc_start: 0.7772 (t0) cc_final: 0.7443 (t0) REVERT: A 1334 TYR cc_start: 0.5909 (t80) cc_final: 0.5610 (t80) REVERT: A 1425 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7211 (tt) REVERT: E 10 ARG cc_start: 0.7365 (mmt90) cc_final: 0.7072 (mtp180) REVERT: E 155 LEU cc_start: 0.8832 (mp) cc_final: 0.8375 (tt) REVERT: E 206 ARG cc_start: 0.7276 (mmp-170) cc_final: 0.6996 (mmp-170) REVERT: F 281 MET cc_start: 0.9026 (tpp) cc_final: 0.8421 (tpp) REVERT: F 426 GLN cc_start: 0.8492 (pt0) cc_final: 0.8163 (pt0) REVERT: F 447 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7822 (mm110) REVERT: F 528 ASN cc_start: 0.7958 (OUTLIER) cc_final: 0.7477 (t0) REVERT: F 851 MET cc_start: 0.3621 (mtt) cc_final: 0.2855 (ttt) REVERT: F 886 MET cc_start: 0.7572 (tpp) cc_final: 0.7253 (tpp) REVERT: F 895 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.7750 (p90) REVERT: F 1013 ASN cc_start: 0.7903 (t0) cc_final: 0.7676 (t0) outliers start: 69 outliers final: 31 residues processed: 491 average time/residue: 0.1593 time to fit residues: 123.4240 Evaluate side-chains 431 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 390 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU 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 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 945 ILE 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 1287 GLN Chi-restraints excluded: chain A residue 1306 PHE Chi-restraints excluded: chain A residue 1338 CYS Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain B residue 115 PRO 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 F residue 305 CYS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 356 CYS 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 544 ARG Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 615 ASN 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 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: 6.9990 chunk 82 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 218 optimal weight: 0.0030 chunk 32 optimal weight: 20.0000 chunk 28 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 654 ASN A 859 HIS A 930 ASN ** A 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 867 HIS F 975 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.199406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.156952 restraints weight = 75925.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.160150 restraints weight = 71152.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.156976 restraints weight = 26974.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.157142 restraints weight = 27866.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.157411 restraints weight = 21861.652| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22406 Z= 0.144 Angle : 0.819 19.855 30335 Z= 0.396 Chirality : 0.052 0.743 3442 Planarity : 0.005 0.060 3748 Dihedral : 11.240 87.649 3793 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.69 % Allowed : 9.81 % Favored : 89.50 % Rotamer: Outliers : 3.20 % Allowed : 15.85 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.04 % Twisted Proline : 1.87 % Twisted General : 0.31 % 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 aren not related in a simple way. whole: -1.90 (0.16), residues: 2633 helix: -0.31 (0.14), residues: 1325 sheet: -0.69 (0.32), residues: 264 loop : -2.67 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 591 TYR 0.030 0.001 TYR F 609 PHE 0.033 0.002 PHE A1356 TRP 0.032 0.001 TRP F 824 HIS 0.014 0.001 HIS F 867 Details of bonding type rmsd covalent geometry : bond 0.00312 (22369) covalent geometry : angle 0.77506 (30238) SS BOND : bond 0.00174 ( 11) SS BOND : angle 1.30630 ( 22) hydrogen bonds : bond 0.03929 ( 918) hydrogen bonds : angle 4.72478 ( 2607) Misc. bond : bond 0.00013 ( 1) link_BETA1-4 : bond 0.00537 ( 10) link_BETA1-4 : angle 1.92185 ( 30) link_NAG-ASN : bond 0.00982 ( 15) link_NAG-ASN : angle 6.68647 ( 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 478 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 410 time to evaluate : 0.913 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: A 99 ILE cc_start: 0.7449 (tp) cc_final: 0.7031 (pt) REVERT: A 106 ILE cc_start: 0.8198 (mm) cc_final: 0.7812 (pt) REVERT: A 376 MET cc_start: 0.1887 (ppp) cc_final: 0.1453 (ppp) REVERT: A 423 TRP cc_start: 0.5680 (m100) cc_final: 0.5362 (m-90) REVERT: A 436 TRP cc_start: 0.7781 (m100) cc_final: 0.7524 (m100) REVERT: A 463 LEU cc_start: 0.8999 (mt) cc_final: 0.8619 (tt) REVERT: A 936 THR cc_start: 0.8620 (t) cc_final: 0.8370 (m) REVERT: A 1075 GLU cc_start: 0.7964 (mp0) cc_final: 0.7285 (tp30) REVERT: A 1084 ASN cc_start: 0.6586 (p0) cc_final: 0.6221 (t0) REVERT: A 1121 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: A 1145 GLU cc_start: 0.7170 (mp0) cc_final: 0.6815 (tp30) REVERT: A 1303 ASN cc_start: 0.7748 (t0) cc_final: 0.7344 (t0) REVERT: A 1334 TYR cc_start: 0.5861 (t80) cc_final: 0.5535 (t80) REVERT: C 301 LEU cc_start: 0.4622 (pp) cc_final: 0.3966 (mm) REVERT: E 155 LEU cc_start: 0.8769 (mp) cc_final: 0.8408 (tt) REVERT: E 206 ARG cc_start: 0.7375 (mmp-170) cc_final: 0.7148 (mpt180) REVERT: F 70 TYR cc_start: 0.7007 (m-80) cc_final: 0.5998 (m-80) REVERT: F 256 MET cc_start: 0.8218 (ttm) cc_final: 0.8010 (ttp) REVERT: F 281 MET cc_start: 0.8986 (tpp) cc_final: 0.8352 (tpp) REVERT: F 528 ASN cc_start: 0.7962 (OUTLIER) cc_final: 0.7496 (t0) REVERT: F 631 PHE cc_start: 0.8069 (m-80) cc_final: 0.7760 (m-80) REVERT: F 792 GLU cc_start: 0.7640 (mp0) cc_final: 0.7433 (tp30) REVERT: F 851 MET cc_start: 0.3773 (mtt) cc_final: 0.3041 (ttt) outliers start: 68 outliers final: 42 residues processed: 443 average time/residue: 0.1591 time to fit residues: 112.2993 Evaluate side-chains 419 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 375 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 266 PRO Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 477 ILE 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 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 1186 ASP Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1306 PHE Chi-restraints excluded: chain A residue 1338 CYS Chi-restraints excluded: chain B residue 115 PRO 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 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 356 CYS 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 718 LEU Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 796 MET Chi-restraints excluded: chain F residue 878 PHE 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 1034 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 260 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 81 optimal weight: 0.4980 chunk 54 optimal weight: 0.0980 chunk 70 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 chunk 153 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 85 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 654 ASN A 930 ASN ** A 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 GLN E 31 HIS ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 GLN F 426 GLN 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 = 0.4308 r_free = 0.4308 target = 0.202343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.161107 restraints weight = 80396.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.158153 restraints weight = 74440.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.152680 restraints weight = 33004.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.153251 restraints weight = 31268.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.153839 restraints weight = 20280.627| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22406 Z= 0.135 Angle : 0.788 19.283 30335 Z= 0.381 Chirality : 0.050 0.626 3442 Planarity : 0.004 0.056 3748 Dihedral : 10.674 83.845 3792 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.57 % Allowed : 10.27 % Favored : 89.16 % Rotamer: Outliers : 3.29 % Allowed : 16.96 % 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 aren not related in a simple way. whole: -1.52 (0.16), residues: 2633 helix: 0.06 (0.14), residues: 1326 sheet: -0.65 (0.32), residues: 270 loop : -2.55 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 591 TYR 0.028 0.001 TYR F 609 PHE 0.032 0.002 PHE A1356 TRP 0.031 0.001 TRP A1258 HIS 0.006 0.001 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.00292 (22369) covalent geometry : angle 0.74599 (30238) SS BOND : bond 0.00250 ( 11) SS BOND : angle 1.19722 ( 22) hydrogen bonds : bond 0.03640 ( 918) hydrogen bonds : angle 4.53070 ( 2607) Misc. bond : bond 0.00025 ( 1) link_BETA1-4 : bond 0.00476 ( 10) link_BETA1-4 : angle 1.77578 ( 30) link_NAG-ASN : bond 0.01091 ( 15) link_NAG-ASN : angle 6.49083 ( 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 481 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 410 time to evaluate : 0.860 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: 0.8349 (t80) cc_final: 0.7736 (t80) REVERT: A 106 ILE cc_start: 0.8110 (mm) cc_final: 0.7728 (pt) REVERT: A 118 LEU cc_start: 0.8380 (mt) cc_final: 0.8130 (tp) REVERT: A 308 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6249 (pm20) REVERT: A 309 TRP cc_start: 0.8516 (m100) cc_final: 0.8247 (m100) REVERT: A 367 MET cc_start: 0.3486 (mtt) cc_final: 0.3187 (mtm) REVERT: A 376 MET cc_start: 0.1492 (ppp) cc_final: 0.1194 (ppp) REVERT: A 423 TRP cc_start: 0.5253 (m100) cc_final: 0.4960 (m-90) REVERT: A 432 ARG cc_start: 0.7008 (tmt170) cc_final: 0.5019 (ptt-90) REVERT: A 447 LEU cc_start: 0.9294 (mt) cc_final: 0.8814 (tt) REVERT: A 463 LEU cc_start: 0.9005 (mt) cc_final: 0.8690 (tt) REVERT: A 466 ILE cc_start: 0.8901 (pp) cc_final: 0.8635 (tp) REVERT: A 821 PRO cc_start: 0.8382 (Cg_endo) cc_final: 0.8162 (Cg_exo) REVERT: A 936 THR cc_start: 0.8645 (t) cc_final: 0.8395 (m) REVERT: A 1075 GLU cc_start: 0.7867 (mp0) cc_final: 0.7183 (tp30) REVERT: A 1084 ASN cc_start: 0.6833 (p0) cc_final: 0.6283 (t0) REVERT: A 1121 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: A 1145 GLU cc_start: 0.7462 (mp0) cc_final: 0.6981 (tp30) REVERT: A 1153 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8425 (mm) REVERT: A 1286 MET cc_start: 0.7445 (tpp) cc_final: 0.6701 (ttt) REVERT: A 1296 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7613 (m-30) REVERT: A 1303 ASN cc_start: 0.7785 (t0) cc_final: 0.7552 (t0) REVERT: A 1334 TYR cc_start: 0.6119 (t80) cc_final: 0.5772 (t80) REVERT: A 1427 ARG cc_start: 0.6712 (mtm-85) cc_final: 0.5798 (mtp180) REVERT: C 301 LEU cc_start: 0.4791 (pp) cc_final: 0.4219 (mm) REVERT: E 155 LEU cc_start: 0.8882 (mp) cc_final: 0.8584 (tt) REVERT: F 70 TYR cc_start: 0.6942 (m-80) cc_final: 0.6021 (m-80) REVERT: F 281 MET cc_start: 0.8934 (tpp) cc_final: 0.8419 (tpp) REVERT: F 302 ASP cc_start: 0.7883 (p0) cc_final: 0.7625 (p0) REVERT: F 528 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.7504 (t0) REVERT: F 598 ASP cc_start: 0.7642 (p0) cc_final: 0.7422 (p0) REVERT: F 631 PHE cc_start: 0.8066 (m-80) cc_final: 0.7793 (m-80) REVERT: F 792 GLU cc_start: 0.7780 (mp0) cc_final: 0.7412 (tp30) REVERT: F 851 MET cc_start: 0.3426 (mtt) cc_final: 0.2646 (ttt) REVERT: F 886 MET cc_start: 0.8230 (tpp) cc_final: 0.7364 (tpp) REVERT: F 987 ASP cc_start: 0.7233 (p0) cc_final: 0.6985 (p0) REVERT: F 1020 MET cc_start: 0.6743 (ptm) cc_final: 0.6507 (ptm) outliers start: 71 outliers final: 44 residues processed: 447 average time/residue: 0.1594 time to fit residues: 113.2357 Evaluate side-chains 430 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 381 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 266 PRO Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 477 ILE 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 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 1186 ASP Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1296 ASP Chi-restraints excluded: chain A residue 1306 PHE Chi-restraints excluded: chain A residue 1338 CYS Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain B residue 115 PRO 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 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 356 CYS 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 680 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 878 PHE Chi-restraints excluded: chain F residue 890 VAL Chi-restraints excluded: chain F residue 895 TYR Chi-restraints excluded: chain F residue 1007 HIS Chi-restraints excluded: chain F residue 1042 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 219 optimal weight: 0.0270 chunk 140 optimal weight: 5.9990 chunk 129 optimal weight: 0.0070 chunk 2 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 240 optimal weight: 0.3980 chunk 138 optimal weight: 5.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 ASN ** A 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 GLN F 208 GLN F 248 GLN F 313 ASN F 316 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 = 0.4311 r_free = 0.4311 target = 0.202663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.159066 restraints weight = 75046.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.157821 restraints weight = 69306.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.151943 restraints weight = 29939.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.152341 restraints weight = 26466.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.153366 restraints weight = 18222.887| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3748 r_free = 0.3748 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3748 r_free = 0.3748 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22406 Z= 0.134 Angle : 0.782 21.137 30335 Z= 0.376 Chirality : 0.049 0.510 3442 Planarity : 0.004 0.054 3748 Dihedral : 10.263 83.491 3790 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.57 % Allowed : 9.89 % Favored : 89.54 % Rotamer: Outliers : 3.37 % Allowed : 17.67 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.04 % Twisted Proline : 0.93 % 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 aren not related in a simple way. whole: -1.29 (0.17), residues: 2633 helix: 0.31 (0.14), residues: 1333 sheet: -0.56 (0.32), residues: 270 loop : -2.53 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 903 TYR 0.027 0.001 TYR F 609 PHE 0.031 0.002 PHE A1356 TRP 0.039 0.001 TRP A1258 HIS 0.012 0.001 HIS F 867 Details of bonding type rmsd covalent geometry : bond 0.00292 (22369) covalent geometry : angle 0.74185 (30238) SS BOND : bond 0.00162 ( 11) SS BOND : angle 1.14275 ( 22) hydrogen bonds : bond 0.03498 ( 918) hydrogen bonds : angle 4.42537 ( 2607) Misc. bond : bond 0.00012 ( 1) link_BETA1-4 : bond 0.00431 ( 10) link_BETA1-4 : angle 1.70217 ( 30) link_NAG-ASN : bond 0.00755 ( 15) link_NAG-ASN : angle 6.34541 ( 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 474 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 401 time to evaluate : 0.904 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: 0.8235 (t80) cc_final: 0.7602 (t80) REVERT: A 106 ILE cc_start: 0.8167 (mm) cc_final: 0.7706 (pt) REVERT: A 118 LEU cc_start: 0.8221 (mt) cc_final: 0.7912 (tp) REVERT: A 309 TRP cc_start: 0.8428 (m100) cc_final: 0.8207 (m100) REVERT: A 376 MET cc_start: 0.1857 (ppp) cc_final: 0.1516 (ppp) REVERT: A 423 TRP cc_start: 0.5587 (m100) cc_final: 0.5269 (m-90) REVERT: A 447 LEU cc_start: 0.9245 (mt) cc_final: 0.8757 (tt) REVERT: A 463 LEU cc_start: 0.9042 (mt) cc_final: 0.8612 (tt) REVERT: A 466 ILE cc_start: 0.8929 (pp) cc_final: 0.8651 (tp) REVERT: A 496 PHE cc_start: 0.6453 (m-80) cc_final: 0.5954 (m-80) REVERT: A 821 PRO cc_start: 0.8322 (Cg_endo) cc_final: 0.7944 (Cg_exo) REVERT: A 851 MET cc_start: 0.4957 (mmm) cc_final: 0.4097 (mtp) REVERT: A 936 THR cc_start: 0.8629 (t) cc_final: 0.8376 (m) REVERT: A 1071 GLN cc_start: 0.8239 (mm110) cc_final: 0.7351 (mm110) REVERT: A 1075 GLU cc_start: 0.7845 (mp0) cc_final: 0.7219 (tp30) REVERT: A 1121 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: A 1145 GLU cc_start: 0.7438 (mp0) cc_final: 0.6969 (tp30) REVERT: A 1262 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8242 (mtpt) REVERT: A 1296 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7688 (m-30) REVERT: A 1334 TYR cc_start: 0.6033 (t80) cc_final: 0.5720 (t80) REVERT: A 1427 ARG cc_start: 0.6581 (mtm-85) cc_final: 0.5749 (mtp180) REVERT: C 301 LEU cc_start: 0.4863 (pp) cc_final: 0.4298 (mm) REVERT: E 155 LEU cc_start: 0.8869 (mp) cc_final: 0.8622 (tt) REVERT: E 174 ILE cc_start: 0.3479 (OUTLIER) cc_final: 0.2552 (mt) REVERT: F 70 TYR cc_start: 0.6816 (m-80) cc_final: 0.6010 (m-80) REVERT: F 256 MET cc_start: 0.8171 (ttm) cc_final: 0.7783 (ttp) REVERT: F 281 MET cc_start: 0.8890 (tpp) cc_final: 0.8422 (tpp) REVERT: F 426 GLN cc_start: 0.8468 (pt0) cc_final: 0.8251 (pt0) REVERT: F 528 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7416 (t0) REVERT: F 598 ASP cc_start: 0.7668 (p0) cc_final: 0.7424 (p0) REVERT: F 631 PHE cc_start: 0.8078 (m-80) cc_final: 0.7841 (m-80) REVERT: F 711 ASP cc_start: 0.8375 (t0) cc_final: 0.8124 (t70) REVERT: F 824 TRP cc_start: 0.8677 (t60) cc_final: 0.7912 (t60) REVERT: F 826 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6995 (tt0) REVERT: F 851 MET cc_start: 0.3388 (mtt) cc_final: 0.2666 (ttt) REVERT: F 1020 MET cc_start: 0.6575 (ptm) cc_final: 0.6206 (ptm) outliers start: 73 outliers final: 52 residues processed: 438 average time/residue: 0.1560 time to fit residues: 110.3815 Evaluate side-chains 434 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 377 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 434 PHE 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 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 1116 THR Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1186 ASP Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1205 PHE Chi-restraints excluded: chain A residue 1262 LYS Chi-restraints excluded: chain A residue 1296 ASP Chi-restraints excluded: chain A residue 1306 PHE Chi-restraints excluded: chain A residue 1338 CYS Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1352 CYS Chi-restraints excluded: chain B residue 115 PRO 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 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 356 CYS 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 628 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 796 MET Chi-restraints excluded: chain F residue 878 PHE 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 1021 VAL Chi-restraints excluded: chain F residue 1042 ASP 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: 2.9990 chunk 56 optimal weight: 0.6980 chunk 240 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 237 optimal weight: 0.0770 chunk 0 optimal weight: 20.0000 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 277 ASN A 327 ASN A 654 ASN A 993 ASN ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 GLN F 867 HIS ** F 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1013 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.202786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.159387 restraints weight = 73619.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.157785 restraints weight = 67943.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.152513 restraints weight = 28738.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.153093 restraints weight = 23997.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.153908 restraints weight = 17179.802| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22406 Z= 0.132 Angle : 0.774 19.426 30335 Z= 0.375 Chirality : 0.049 0.496 3442 Planarity : 0.004 0.052 3748 Dihedral : 10.030 82.208 3790 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.57 % Allowed : 9.93 % Favored : 89.50 % Rotamer: Outliers : 2.80 % Allowed : 18.87 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.04 % Twisted Proline : 0.93 % Twisted General : 0.16 % 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 aren not related in a simple way. whole: -1.14 (0.17), residues: 2633 helix: 0.49 (0.14), residues: 1332 sheet: -0.53 (0.31), residues: 282 loop : -2.56 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1447 TYR 0.026 0.001 TYR F 609 PHE 0.031 0.002 PHE E 189 TRP 0.033 0.001 TRP A1258 HIS 0.021 0.001 HIS F 867 Details of bonding type rmsd covalent geometry : bond 0.00288 (22369) covalent geometry : angle 0.73752 (30238) SS BOND : bond 0.00154 ( 11) SS BOND : angle 1.08111 ( 22) hydrogen bonds : bond 0.03424 ( 918) hydrogen bonds : angle 4.34642 ( 2607) Misc. bond : bond 0.00021 ( 1) link_BETA1-4 : bond 0.00479 ( 10) link_BETA1-4 : angle 1.62074 ( 30) link_NAG-ASN : bond 0.01164 ( 15) link_NAG-ASN : angle 6.01107 ( 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 453 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 393 time to evaluate : 0.836 Fit side-chains revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 106 ILE cc_start: 0.8208 (mm) cc_final: 0.7804 (pt) REVERT: A 376 MET cc_start: 0.1580 (ppp) cc_final: 0.1272 (ppp) REVERT: A 423 TRP cc_start: 0.5578 (m100) cc_final: 0.5288 (m-90) REVERT: A 447 LEU cc_start: 0.9237 (mt) cc_final: 0.8756 (tt) REVERT: A 463 LEU cc_start: 0.9027 (mt) cc_final: 0.8581 (tt) REVERT: A 466 ILE cc_start: 0.8954 (pp) cc_final: 0.8668 (tp) REVERT: A 496 PHE cc_start: 0.6523 (m-80) cc_final: 0.6046 (m-80) REVERT: A 547 ASN cc_start: 0.7796 (p0) cc_final: 0.7356 (p0) REVERT: A 936 THR cc_start: 0.8626 (t) cc_final: 0.8377 (m) REVERT: A 1034 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.7736 (p) REVERT: A 1071 GLN cc_start: 0.8082 (mm110) cc_final: 0.7229 (mm110) REVERT: A 1075 GLU cc_start: 0.7862 (mp0) cc_final: 0.7248 (tp30) REVERT: A 1121 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: A 1145 GLU cc_start: 0.7455 (mp0) cc_final: 0.6964 (tp30) REVERT: A 1153 LEU cc_start: 0.8804 (mt) cc_final: 0.8525 (mt) REVERT: A 1281 TYR cc_start: 0.9058 (m-80) cc_final: 0.8698 (m-80) REVERT: A 1334 TYR cc_start: 0.6051 (t80) cc_final: 0.5730 (t80) REVERT: A 1427 ARG cc_start: 0.6664 (mtm-85) cc_final: 0.5750 (mtp180) REVERT: C 293 MET cc_start: 0.5134 (mmp) cc_final: 0.3444 (mmp) REVERT: C 301 LEU cc_start: 0.5011 (pp) cc_final: 0.4514 (mm) REVERT: E 155 LEU cc_start: 0.8729 (mp) cc_final: 0.8514 (tt) REVERT: F 41 LYS cc_start: 0.6900 (pttp) cc_final: 0.6688 (tttt) REVERT: F 70 TYR cc_start: 0.6773 (m-80) cc_final: 0.6108 (m-80) REVERT: F 256 MET cc_start: 0.8227 (ttm) cc_final: 0.7829 (ttp) REVERT: F 281 MET cc_start: 0.8929 (tpp) cc_final: 0.8491 (tpp) REVERT: F 426 GLN cc_start: 0.8430 (pt0) cc_final: 0.8200 (pt0) REVERT: F 528 ASN cc_start: 0.7898 (OUTLIER) cc_final: 0.7352 (t0) REVERT: F 598 ASP cc_start: 0.7510 (p0) cc_final: 0.7298 (p0) REVERT: F 711 ASP cc_start: 0.8382 (t0) cc_final: 0.8118 (t70) REVERT: F 824 TRP cc_start: 0.8702 (t60) cc_final: 0.7918 (t60) REVERT: F 826 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6965 (tt0) REVERT: F 828 PHE cc_start: 0.7676 (t80) cc_final: 0.7472 (t80) REVERT: F 851 MET cc_start: 0.4110 (mtt) cc_final: 0.3084 (ttt) REVERT: F 1020 MET cc_start: 0.6581 (ptm) cc_final: 0.6199 (ptm) REVERT: F 1033 LEU cc_start: 0.7942 (mt) cc_final: 0.7565 (pt) outliers start: 60 outliers final: 49 residues processed: 421 average time/residue: 0.1500 time to fit residues: 102.4418 Evaluate side-chains 427 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 375 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 186 LEU 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 327 ASN Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 477 ILE 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 1034 VAL 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 1186 ASP Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1205 PHE Chi-restraints excluded: chain A residue 1306 PHE Chi-restraints excluded: chain A residue 1338 CYS Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1352 CYS Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain B residue 115 PRO 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 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 356 CYS 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 628 THR Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 878 PHE 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 1042 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 69 optimal weight: 30.0000 chunk 167 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 158 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 113 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 263 optimal weight: 0.0980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN ** A 996 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 GLN F 773 ASN F 867 HIS F1013 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.198910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.158787 restraints weight = 79135.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.155116 restraints weight = 72607.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.152180 restraints weight = 31604.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.151349 restraints weight = 27056.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.151523 restraints weight = 24365.191| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 22406 Z= 0.165 Angle : 0.785 15.335 30335 Z= 0.382 Chirality : 0.050 0.452 3442 Planarity : 0.005 0.065 3748 Dihedral : 10.066 79.835 3790 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.61 % Allowed : 10.08 % Favored : 89.31 % Rotamer: Outliers : 2.98 % Allowed : 19.14 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.04 % Twisted Proline : 0.93 % 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 aren not related in a simple way. whole: -1.03 (0.17), residues: 2633 helix: 0.59 (0.15), residues: 1333 sheet: -0.49 (0.32), residues: 273 loop : -2.50 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 591 TYR 0.029 0.002 TYR F 609 PHE 0.039 0.002 PHE A 502 TRP 0.040 0.002 TRP A1258 HIS 0.020 0.001 HIS F 867 Details of bonding type rmsd covalent geometry : bond 0.00379 (22369) covalent geometry : angle 0.75490 (30238) SS BOND : bond 0.00143 ( 11) SS BOND : angle 1.14223 ( 22) hydrogen bonds : bond 0.03488 ( 918) hydrogen bonds : angle 4.37808 ( 2607) Misc. bond : bond 0.00039 ( 1) link_BETA1-4 : bond 0.00439 ( 10) link_BETA1-4 : angle 1.63814 ( 30) link_NAG-ASN : bond 0.00776 ( 15) link_NAG-ASN : angle 5.43902 ( 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 454 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 390 time to evaluate : 0.849 Fit side-chains revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ILE cc_start: 0.8005 (mm) cc_final: 0.7642 (pt) REVERT: A 376 MET cc_start: 0.1409 (ppp) cc_final: 0.1044 (ppp) REVERT: A 423 TRP cc_start: 0.5582 (m100) cc_final: 0.5258 (m-90) REVERT: A 432 ARG cc_start: 0.7217 (tmt170) cc_final: 0.5175 (ptt-90) REVERT: A 463 LEU cc_start: 0.9026 (mt) cc_final: 0.8584 (tt) REVERT: A 466 ILE cc_start: 0.8965 (pp) cc_final: 0.8670 (tp) REVERT: A 496 PHE cc_start: 0.6520 (m-80) cc_final: 0.6036 (m-80) REVERT: A 1034 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.7758 (p) REVERT: A 1071 GLN cc_start: 0.8219 (mm110) cc_final: 0.7216 (mm110) REVERT: A 1075 GLU cc_start: 0.7912 (mp0) cc_final: 0.7234 (tp30) REVERT: A 1084 ASN cc_start: 0.6793 (p0) cc_final: 0.6178 (t0) REVERT: A 1121 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: A 1145 GLU cc_start: 0.7515 (mp0) cc_final: 0.7016 (tp30) REVERT: A 1188 LEU cc_start: 0.9193 (tp) cc_final: 0.8959 (mp) REVERT: A 1286 MET cc_start: 0.7925 (tpp) cc_final: 0.7474 (tpp) REVERT: A 1334 TYR cc_start: 0.6268 (t80) cc_final: 0.5890 (t80) REVERT: C 301 LEU cc_start: 0.5041 (pp) cc_final: 0.4563 (mm) REVERT: F 70 TYR cc_start: 0.6928 (m-80) cc_final: 0.6147 (m-80) REVERT: F 256 MET cc_start: 0.8226 (ttm) cc_final: 0.7822 (ttp) REVERT: F 281 MET cc_start: 0.9032 (tpp) cc_final: 0.8525 (tpp) REVERT: F 528 ASN cc_start: 0.7918 (OUTLIER) cc_final: 0.7257 (t0) REVERT: F 598 ASP cc_start: 0.7582 (p0) cc_final: 0.7353 (p0) REVERT: F 824 TRP cc_start: 0.8718 (t60) cc_final: 0.8359 (t60) REVERT: F 828 PHE cc_start: 0.7668 (t80) cc_final: 0.7453 (t80) REVERT: F 851 MET cc_start: 0.3486 (mtt) cc_final: 0.2604 (ttt) REVERT: F 1033 LEU cc_start: 0.8032 (mt) cc_final: 0.7624 (pt) outliers start: 64 outliers final: 53 residues processed: 422 average time/residue: 0.1528 time to fit residues: 104.2024 Evaluate side-chains 429 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 373 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 229 ILE 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 327 ASN 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 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 1034 VAL 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 1165 MET Chi-restraints excluded: chain A residue 1186 ASP Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1205 PHE Chi-restraints excluded: chain A residue 1306 PHE Chi-restraints excluded: chain A residue 1338 CYS Chi-restraints excluded: chain A residue 1352 CYS 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 E residue 15 CYS 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 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 356 CYS 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 628 THR 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 867 HIS Chi-restraints excluded: chain F residue 878 PHE Chi-restraints excluded: chain F residue 895 TYR Chi-restraints excluded: chain F residue 1006 PHE Chi-restraints excluded: chain F residue 1007 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 251 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 172 optimal weight: 0.4980 chunk 227 optimal weight: 0.7980 chunk 230 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 327 ASN ** A 996 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS E 160 GLN F 248 GLN F 484 GLN 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 = 0.4285 r_free = 0.4285 target = 0.199682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.160294 restraints weight = 75531.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.156803 restraints weight = 73929.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.153465 restraints weight = 32971.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.152794 restraints weight = 31635.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.153384 restraints weight = 23573.654| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 22406 Z= 0.154 Angle : 0.784 17.254 30335 Z= 0.381 Chirality : 0.050 0.439 3442 Planarity : 0.005 0.085 3748 Dihedral : 9.956 80.208 3790 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.16 % Favored : 89.31 % Rotamer: Outliers : 3.24 % Allowed : 18.92 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.04 % Twisted Proline : 0.93 % 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 aren not related in a simple way. whole: -0.98 (0.17), residues: 2633 helix: 0.65 (0.15), residues: 1330 sheet: -0.50 (0.32), residues: 273 loop : -2.50 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 591 TYR 0.029 0.001 TYR F 609 PHE 0.034 0.002 PHE A 502 TRP 0.035 0.002 TRP A1258 HIS 0.030 0.001 HIS F 867 Details of bonding type rmsd covalent geometry : bond 0.00349 (22369) covalent geometry : angle 0.75069 (30238) SS BOND : bond 0.00136 ( 11) SS BOND : angle 1.09624 ( 22) hydrogen bonds : bond 0.03466 ( 918) hydrogen bonds : angle 4.38028 ( 2607) Misc. bond : bond 0.00037 ( 1) link_BETA1-4 : bond 0.00456 ( 10) link_BETA1-4 : angle 1.60979 ( 30) link_NAG-ASN : bond 0.01011 ( 15) link_NAG-ASN : angle 5.75023 ( 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 460 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 390 time to evaluate : 0.871 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 74 MET cc_start: 0.8813 (mmm) cc_final: 0.8610 (mmt) REVERT: A 106 ILE cc_start: 0.8054 (mm) cc_final: 0.7719 (pt) REVERT: A 376 MET cc_start: 0.1605 (ppp) cc_final: 0.1178 (ppp) REVERT: A 423 TRP cc_start: 0.5642 (m100) cc_final: 0.5343 (m-90) REVERT: A 432 ARG cc_start: 0.7281 (tmt170) cc_final: 0.5269 (ptt-90) REVERT: A 463 LEU cc_start: 0.9013 (mt) cc_final: 0.8564 (tt) REVERT: A 466 ILE cc_start: 0.8949 (pp) cc_final: 0.8663 (tp) REVERT: A 496 PHE cc_start: 0.6393 (m-80) cc_final: 0.5900 (m-80) REVERT: A 547 ASN cc_start: 0.7987 (p0) cc_final: 0.7641 (p0) REVERT: A 1034 VAL cc_start: 0.8335 (OUTLIER) cc_final: 0.7742 (p) REVERT: A 1071 GLN cc_start: 0.8220 (mm110) cc_final: 0.7296 (mm110) REVERT: A 1075 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7269 (tp30) REVERT: A 1084 ASN cc_start: 0.6905 (p0) cc_final: 0.6314 (t0) REVERT: A 1121 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: A 1145 GLU cc_start: 0.7448 (mp0) cc_final: 0.7009 (tp30) REVERT: A 1281 TYR cc_start: 0.8945 (m-80) cc_final: 0.8635 (m-80) REVERT: A 1286 MET cc_start: 0.7981 (tpp) cc_final: 0.7493 (tpp) REVERT: A 1334 TYR cc_start: 0.6308 (t80) cc_final: 0.5973 (t80) REVERT: A 1381 MET cc_start: 0.8022 (mmp) cc_final: 0.7372 (ttt) REVERT: A 1427 ARG cc_start: 0.6705 (mtm-85) cc_final: 0.5809 (mtp180) REVERT: C 301 LEU cc_start: 0.4999 (pp) cc_final: 0.4517 (mm) REVERT: E 174 ILE cc_start: 0.3544 (OUTLIER) cc_final: 0.2578 (mt) REVERT: F 70 TYR cc_start: 0.6836 (m-80) cc_final: 0.6168 (m-80) REVERT: F 256 MET cc_start: 0.8240 (ttm) cc_final: 0.7869 (ttp) REVERT: F 281 MET cc_start: 0.9017 (tpp) cc_final: 0.8605 (tpp) REVERT: F 283 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7579 (mm-30) REVERT: F 528 ASN cc_start: 0.7893 (OUTLIER) cc_final: 0.7206 (t0) REVERT: F 598 ASP cc_start: 0.7545 (p0) cc_final: 0.7295 (p0) REVERT: F 599 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6774 (mp0) REVERT: F 824 TRP cc_start: 0.8615 (t60) cc_final: 0.7837 (t60) REVERT: F 828 PHE cc_start: 0.7547 (t80) cc_final: 0.7343 (t80) REVERT: F 851 MET cc_start: 0.3522 (mtt) cc_final: 0.2673 (ttt) REVERT: F 1033 LEU cc_start: 0.8030 (mt) cc_final: 0.7605 (pt) outliers start: 70 outliers final: 54 residues processed: 423 average time/residue: 0.1547 time to fit residues: 105.6746 Evaluate side-chains 433 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 373 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 243 SER 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 327 ASN Chi-restraints excluded: chain A residue 477 ILE 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 1034 VAL 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 1121 GLU Chi-restraints excluded: chain A residue 1165 MET Chi-restraints excluded: chain A residue 1186 ASP Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1205 PHE Chi-restraints excluded: chain A residue 1306 PHE Chi-restraints excluded: chain A residue 1338 CYS Chi-restraints excluded: chain A residue 1352 CYS 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 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 174 ILE Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain F residue 38 TRP Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 356 CYS 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 599 GLU Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 628 THR 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 867 HIS Chi-restraints excluded: chain F residue 878 PHE Chi-restraints excluded: chain F residue 895 TYR Chi-restraints excluded: chain F residue 1006 PHE Chi-restraints excluded: chain F residue 1007 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 224 optimal weight: 2.9990 chunk 79 optimal weight: 0.0970 chunk 204 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 237 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 133 optimal weight: 20.0000 chunk 22 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 327 ASN A 930 ASN ** 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 867 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1013 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.199318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.160990 restraints weight = 82460.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.155178 restraints weight = 70173.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.150104 restraints weight = 36475.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.150306 restraints weight = 39476.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.151781 restraints weight = 22181.022| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 22406 Z= 0.156 Angle : 0.794 15.891 30335 Z= 0.385 Chirality : 0.050 0.429 3442 Planarity : 0.005 0.070 3748 Dihedral : 9.949 80.267 3790 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.04 % Favored : 89.42 % Rotamer: Outliers : 2.93 % Allowed : 19.40 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.04 % Twisted Proline : 0.93 % 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 aren not related in a simple way. whole: -1.00 (0.17), residues: 2633 helix: 0.67 (0.15), residues: 1333 sheet: -0.59 (0.31), residues: 278 loop : -2.54 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 591 TYR 0.029 0.001 TYR F 609 PHE 0.033 0.002 PHE A 502 TRP 0.037 0.002 TRP A1258 HIS 0.025 0.001 HIS F 867 Details of bonding type rmsd covalent geometry : bond 0.00355 (22369) covalent geometry : angle 0.76614 (30238) SS BOND : bond 0.00123 ( 11) SS BOND : angle 1.09525 ( 22) hydrogen bonds : bond 0.03482 ( 918) hydrogen bonds : angle 4.40926 ( 2607) Misc. bond : bond 0.00041 ( 1) link_BETA1-4 : bond 0.00405 ( 10) link_BETA1-4 : angle 1.61136 ( 30) link_NAG-ASN : bond 0.00710 ( 15) link_NAG-ASN : angle 5.28341 ( 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 445 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 382 time to evaluate : 0.949 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 106 ILE cc_start: 0.7988 (mm) cc_final: 0.7659 (pt) REVERT: A 376 MET cc_start: 0.1422 (ppp) cc_final: 0.1046 (ppp) REVERT: A 423 TRP cc_start: 0.5582 (m100) cc_final: 0.5269 (m-90) REVERT: A 432 ARG cc_start: 0.7220 (tmt170) cc_final: 0.5181 (ptt-90) REVERT: A 463 LEU cc_start: 0.9020 (mt) cc_final: 0.8561 (tt) REVERT: A 466 ILE cc_start: 0.8943 (pp) cc_final: 0.8662 (tp) REVERT: A 496 PHE cc_start: 0.6532 (m-80) cc_final: 0.6058 (m-80) REVERT: A 547 ASN cc_start: 0.8040 (p0) cc_final: 0.7660 (p0) REVERT: A 1034 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.7728 (p) REVERT: A 1071 GLN cc_start: 0.8274 (mm110) cc_final: 0.7210 (mm110) REVERT: A 1121 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: A 1145 GLU cc_start: 0.7503 (mp0) cc_final: 0.6994 (tp30) REVERT: A 1281 TYR cc_start: 0.8955 (m-80) cc_final: 0.8595 (m-80) REVERT: A 1286 MET cc_start: 0.7977 (tpp) cc_final: 0.7463 (tpp) REVERT: A 1334 TYR cc_start: 0.6336 (t80) cc_final: 0.6040 (t80) REVERT: A 1381 MET cc_start: 0.8022 (mmp) cc_final: 0.7477 (ttt) REVERT: A 1427 ARG cc_start: 0.6766 (mtm-85) cc_final: 0.5792 (mtp180) REVERT: C 301 LEU cc_start: 0.5034 (pp) cc_final: 0.4566 (mm) REVERT: E 174 ILE cc_start: 0.3547 (OUTLIER) cc_final: 0.2629 (mt) REVERT: F 70 TYR cc_start: 0.6788 (m-80) cc_final: 0.6173 (m-80) REVERT: F 280 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7785 (mm-30) REVERT: F 281 MET cc_start: 0.9019 (tpp) cc_final: 0.8579 (tpp) REVERT: F 283 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7432 (mm-30) REVERT: F 528 ASN cc_start: 0.7961 (OUTLIER) cc_final: 0.7218 (t0) REVERT: F 598 ASP cc_start: 0.7570 (p0) cc_final: 0.7356 (p0) REVERT: F 711 ASP cc_start: 0.8322 (t0) cc_final: 0.8117 (t70) REVERT: F 824 TRP cc_start: 0.8676 (t60) cc_final: 0.7853 (t60) REVERT: F 826 GLU cc_start: 0.7749 (tt0) cc_final: 0.7454 (mm-30) REVERT: F 851 MET cc_start: 0.3500 (mtt) cc_final: 0.2566 (ttt) REVERT: F 1033 LEU cc_start: 0.7978 (mt) cc_final: 0.7594 (pt) outliers start: 63 outliers final: 52 residues processed: 411 average time/residue: 0.1520 time to fit residues: 101.6051 Evaluate side-chains 432 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 376 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 243 SER 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 440 LEU Chi-restraints excluded: chain A residue 477 ILE 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 930 ASN Chi-restraints excluded: chain A residue 955 PHE Chi-restraints excluded: chain A residue 1011 SER Chi-restraints excluded: chain A residue 1034 VAL 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 1165 MET Chi-restraints excluded: chain A residue 1186 ASP Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1205 PHE Chi-restraints excluded: chain A residue 1306 PHE Chi-restraints excluded: chain A residue 1338 CYS Chi-restraints excluded: chain A residue 1352 CYS 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 E residue 15 CYS 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 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 356 CYS 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 628 THR 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 878 PHE Chi-restraints excluded: chain F residue 895 TYR Chi-restraints excluded: chain F residue 1006 PHE Chi-restraints excluded: chain F residue 1007 HIS 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: 0.9980 chunk 28 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 198 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 169 optimal weight: 10.0000 chunk 47 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 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 867 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1013 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.199322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.159687 restraints weight = 80859.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.156378 restraints weight = 73855.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.151819 restraints weight = 33265.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.152178 restraints weight = 29566.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.152955 restraints weight = 20704.260| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.292 22406 Z= 0.253 Angle : 0.998 59.198 30335 Z= 0.553 Chirality : 0.063 1.616 3442 Planarity : 0.006 0.162 3748 Dihedral : 10.179 90.272 3790 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.04 % Favored : 89.42 % Rotamer: Outliers : 2.80 % Allowed : 19.67 % Favored : 77.53 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.04 % Twisted Proline : 0.93 % 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 aren not related in a simple way. whole: -1.00 (0.17), residues: 2633 helix: 0.67 (0.15), residues: 1333 sheet: -0.60 (0.31), residues: 278 loop : -2.54 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 591 TYR 0.028 0.001 TYR F 609 PHE 0.032 0.002 PHE A1356 TRP 0.034 0.002 TRP A1258 HIS 0.023 0.001 HIS F 867 Details of bonding type rmsd covalent geometry : bond 0.00509 (22369) covalent geometry : angle 0.97337 (30238) SS BOND : bond 0.00129 ( 11) SS BOND : angle 1.08726 ( 22) hydrogen bonds : bond 0.03510 ( 918) hydrogen bonds : angle 4.41233 ( 2607) Misc. bond : bond 0.00037 ( 1) link_BETA1-4 : bond 0.00413 ( 10) link_BETA1-4 : angle 1.60606 ( 30) link_NAG-ASN : bond 0.02827 ( 15) link_NAG-ASN : angle 5.68028 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5250.00 seconds wall clock time: 91 minutes 1.21 seconds (5461.21 seconds total)