Starting phenix.real_space_refine on Sun Sep 13 07:51:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5gjw_9515/09_2026/5gjw_9515.cif Found real_map, /net/cci-nas-00/data/ceres_data/5gjw_9515/09_2026/5gjw_9515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/5gjw_9515/09_2026/5gjw_9515.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5gjw_9515/09_2026/5gjw_9515.cif" model { file = "/net/cci-nas-00/data/ceres_data/5gjw_9515/09_2026/5gjw_9515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5gjw_9515/09_2026/5gjw_9515.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5gjw_9515/09_2026/5gjw_9515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5gjw_9515/09_2026/5gjw_9515.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 124 5.16 5 C 13944 2.51 5 N 3558 2.21 5 O 3932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21561 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 10261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1291, 10261 Classifications: {'peptide': 1291} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 1250} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 22 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 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: {'PTRANS': 12, '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: 7568 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 941, 7552 Classifications: {'peptide': 941} Link IDs: {'PTRANS': 40, 'TRANS': 900} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 941, 7552 Classifications: {'peptide': 941} Link IDs: {'PTRANS': 40, 'TRANS': 900} Chain breaks: 6 bond proxies already assigned to first conformer: 7692 Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'ETA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' CA': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 99 Unusual residues: {' CA': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG F 315 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG F 315 " occ=0.50 Time building chain proxies: 5.97, per 1000 atoms: 0.28 Number of scatterers: 21561 At special positions: 0 Unit cell: (188.76, 171.6, 158.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 3 19.99 S 124 16.00 O 3932 8.00 N 3558 7.00 C 13944 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=2.10 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=2.01 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 968 " distance=2.04 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=2.04 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 80 " distance=2.04 Simple disulfide: pdb=" SG CYS F 305 " - pdb=" SG CYS F1047 " distance=2.04 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F1062 " distance=2.04 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1074 " distance=2.01 Simple disulfide: pdb=" SG CYS F 907 " - pdb=" SG CYS F 977 " distance=2.03 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=2, 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 F1204 " - " ASN F 326 " " NAG F1207 " - " ASN F 891 " " NAG F1214 " - " ASN F 94 " " NAG F1215 " - " ASN F 606 " " NAG F1220 " - " ASN F 784 " " NAG F1221 " - " ASN F1001 " " NAG F1222 " - " 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=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 1.3 seconds 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5072 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 20 sheets defined 55.5% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 40 through 49 removed outlier: 3.856A pdb=" N CYS A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 70 removed outlier: 3.663A pdb=" N LEU A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 108 removed outlier: 3.708A pdb=" N LYS A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 139 removed outlier: 3.666A pdb=" N GLY A 121 " --> pdb=" O TYR A 117 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TRP A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 128 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 172 removed outlier: 4.363A pdb=" N PHE A 167 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG A 168 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 170 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG A 171 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Proline residue: A 172 - end of helix Processing helix chain 'A' and resid 173 through 179 removed outlier: 4.030A pdb=" N SER A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.755A pdb=" N VAL A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU A 194 " --> pdb=" O PHE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 199 through 218 removed outlier: 3.753A pdb=" N VAL A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A 214 " --> pdb=" O TYR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 290 removed outlier: 3.654A pdb=" N SER A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 305 Processing helix chain 'A' and resid 310 through 319 removed outlier: 3.507A pdb=" N PHE A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 343 removed outlier: 4.005A pdb=" N LEU A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY A 335 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 348 Processing helix chain 'A' and resid 348 through 374 removed outlier: 3.865A pdb=" N LYS A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TRP A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 370 " --> pdb=" O TYR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 429 removed outlier: 3.578A pdb=" N ASP A 427 " --> pdb=" O TRP A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 436 removed outlier: 3.870A pdb=" N TYR A 435 " --> pdb=" O SER A 431 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 431 through 436' Processing helix chain 'A' and resid 437 through 447 removed outlier: 3.715A pdb=" N ILE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 485 removed outlier: 3.927A pdb=" N HIS A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 473 " --> pdb=" O ARG A 469 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 removed outlier: 3.518A pdb=" N PHE A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 515 removed outlier: 3.690A pdb=" N ASP A 500 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.586A pdb=" N CYS A 529 " --> pdb=" O SER A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 538 removed outlier: 3.592A pdb=" N LEU A 535 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A 537 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 581 removed outlier: 4.305A pdb=" N ALA A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER A 555 " --> pdb=" O SER A 551 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ARG A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N SER A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 560 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 612 removed outlier: 3.578A pdb=" N VAL A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 611 " --> pdb=" O VAL A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 628 removed outlier: 3.500A pdb=" N TYR A 627 " --> pdb=" O GLY A 623 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY A 628 " --> pdb=" O ILE A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 636 Processing helix chain 'A' and resid 637 through 685 removed outlier: 4.147A pdb=" N PHE A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 651 " --> pdb=" O CYS A 647 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 652 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP A 662 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A 673 " --> pdb=" O SER A 669 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 678 " --> pdb=" O GLN A 674 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 681 " --> pdb=" O LYS A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 797 removed outlier: 3.583A pdb=" N HIS A 793 " --> pdb=" O ARG A 789 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG A 794 " --> pdb=" O VAL A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 818 removed outlier: 4.089A pdb=" N ASN A 803 " --> pdb=" O THR A 799 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE A 804 " --> pdb=" O TRP A 800 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE A 808 " --> pdb=" O PHE A 804 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 852 removed outlier: 3.612A pdb=" N GLN A 830 " --> pdb=" O SER A 826 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 835 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 859 removed outlier: 3.964A pdb=" N HIS A 859 " --> pdb=" O ALA A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 883 removed outlier: 3.674A pdb=" N PHE A 868 " --> pdb=" O CYS A 864 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN A 869 " --> pdb=" O ARG A 865 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 870 " --> pdb=" O ASN A 866 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 876 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE A 881 " --> pdb=" O ALA A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 899 Processing helix chain 'A' and resid 900 through 910 Proline residue: A 904 - end of helix removed outlier: 3.777A pdb=" N ALA A 907 " --> pdb=" O PRO A 904 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE A 908 " --> pdb=" O LEU A 905 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN A 909 " --> pdb=" O ARG A 906 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG A 910 " --> pdb=" O ALA A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 951 removed outlier: 4.899A pdb=" N ARG A 926 " --> pdb=" O PHE A 922 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR A 927 " --> pdb=" O VAL A 923 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN A 930 " --> pdb=" O ARG A 926 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 943 " --> pdb=" O GLN A 939 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 951 " --> pdb=" O VAL A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1012 removed outlier: 3.720A pdb=" N MET A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A1006 " --> pdb=" O SER A1002 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR A1009 " --> pdb=" O MET A1005 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A1010 " --> pdb=" O SER A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1025 removed outlier: 3.858A pdb=" N ARG A1022 " --> pdb=" O GLN A1018 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP A1025 " --> pdb=" O TYR A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1040 No H-bonds generated for 'chain 'A' and resid 1038 through 1040' Processing helix chain 'A' and resid 1041 through 1073 removed outlier: 4.071A pdb=" N PHE A1045 " --> pdb=" O MET A1041 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET A1057 " --> pdb=" O ALA A1053 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE A1063 " --> pdb=" O ILE A1059 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A1064 " --> pdb=" O PHE A1060 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A1066 " --> pdb=" O GLY A1062 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU A1073 " --> pdb=" O GLN A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1078 removed outlier: 4.167A pdb=" N LYS A1077 " --> pdb=" O THR A1074 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A1078 " --> pdb=" O GLU A1075 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1074 through 1078' Processing helix chain 'A' and resid 1083 through 1095 removed outlier: 3.636A pdb=" N LEU A1093 " --> pdb=" O VAL A1089 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A1094 " --> pdb=" O GLN A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1116 removed outlier: 3.579A pdb=" N VAL A1111 " --> pdb=" O TYR A1107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A1114 " --> pdb=" O GLN A1110 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A1116 " --> pdb=" O TRP A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1134 removed outlier: 3.578A pdb=" N ILE A1133 " --> pdb=" O MET A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1172 removed outlier: 3.605A pdb=" N ASN A1147 " --> pdb=" O SER A1143 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A1152 " --> pdb=" O HIS A1148 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN A1154 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR A1158 " --> pdb=" O ASN A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1179 removed outlier: 3.701A pdb=" N GLY A1179 " --> pdb=" O GLY A1176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1176 through 1179' Processing helix chain 'A' and resid 1180 through 1205 removed outlier: 3.522A pdb=" N PHE A1187 " --> pdb=" O ASN A1183 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A1191 " --> pdb=" O PHE A1187 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP A1196 " --> pdb=" O GLY A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1235 Processing helix chain 'A' and resid 1236 through 1241 removed outlier: 4.013A pdb=" N VAL A1240 " --> pdb=" O ARG A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1249 Processing helix chain 'A' and resid 1250 through 1267 removed outlier: 3.886A pdb=" N THR A1255 " --> pdb=" O GLU A1251 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LEU A1256 " --> pdb=" O GLY A1252 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A1265 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA A1266 " --> pdb=" O LYS A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1287 removed outlier: 4.074A pdb=" N ALA A1271 " --> pdb=" O LEU A1267 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A1275 " --> pdb=" O ALA A1271 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A1283 " --> pdb=" O PHE A1279 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A1287 " --> pdb=" O VAL A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1321 removed outlier: 3.809A pdb=" N ALA A1312 " --> pdb=" O THR A1308 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A1314 " --> pdb=" O PRO A1310 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A1321 " --> pdb=" O PHE A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1330 removed outlier: 4.112A pdb=" N ILE A1328 " --> pdb=" O ALA A1324 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU A1330 " --> pdb=" O GLN A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1356 through 1377 removed outlier: 3.794A pdb=" N SER A1363 " --> pdb=" O TYR A1359 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1388 removed outlier: 4.039A pdb=" N MET A1381 " --> pdb=" O VAL A1377 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP A1382 " --> pdb=" O ALA A1378 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP A1385 " --> pdb=" O MET A1381 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TYR A1386 " --> pdb=" O ASP A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1410 removed outlier: 3.750A pdb=" N LYS A1403 " --> pdb=" O LEU A1399 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A1404 " --> pdb=" O ASP A1400 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP A1406 " --> pdb=" O PHE A1402 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A1407 " --> pdb=" O LYS A1403 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A1408 " --> pdb=" O ALA A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1419 through 1428 removed outlier: 4.430A pdb=" N VAL A1423 " --> pdb=" O HIS A1419 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR A1424 " --> pdb=" O LEU A1420 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A1428 " --> pdb=" O THR A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1450 removed outlier: 4.670A pdb=" N LEU A1448 " --> pdb=" O ALA A1444 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1475 removed outlier: 3.704A pdb=" N THR A1473 " --> pdb=" O ALA A1469 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA A1474 " --> pdb=" O LEU A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1481 through 1498 removed outlier: 3.761A pdb=" N GLU A1488 " --> pdb=" O GLU A1484 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A1496 " --> pdb=" O ALA A1492 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1515 removed outlier: 3.851A pdb=" N ASP A1507 " --> pdb=" O MET A1503 " (cutoff:3.500A) Proline residue: A1511 - end of helix Processing helix chain 'B' and resid 83 through 95 removed outlier: 3.855A pdb=" N ARG B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 174 removed outlier: 3.545A pdb=" N ARG B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLN B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 305 removed outlier: 3.920A pdb=" N MET C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 297 " --> pdb=" O MET C 293 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS C 302 " --> pdb=" O PHE C 298 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N HIS C 303 " --> pdb=" O ASP C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 removed outlier: 3.556A pdb=" N LEU C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA C 321 " --> pdb=" O ILE C 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 317 through 321' Processing helix chain 'C' and resid 343 through 358 Processing helix chain 'C' and resid 359 through 361 No H-bonds generated for 'chain 'C' and resid 359 through 361' Processing helix chain 'C' and resid 374 through 378 removed outlier: 3.502A pdb=" N SER C 378 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 404 removed outlier: 3.579A pdb=" N LEU C 397 " --> pdb=" O SER C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 411 through 425 removed outlier: 3.589A pdb=" N GLN C 415 " --> pdb=" O HIS C 411 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA C 418 " --> pdb=" O VAL C 414 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER C 419 " --> pdb=" O GLN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 458 removed outlier: 3.589A pdb=" N TYR C 449 " --> pdb=" O HIS C 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 7 through 29 removed outlier: 3.771A pdb=" N VAL E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL E 28 " --> pdb=" O MET E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 128 removed outlier: 4.035A pdb=" N ALA E 109 " --> pdb=" O ILE E 105 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE E 123 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 164 removed outlier: 4.140A pdb=" N GLY E 148 " --> pdb=" O TYR E 144 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU E 149 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS E 163 " --> pdb=" O ARG E 159 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG E 164 " --> pdb=" O GLN E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 204 removed outlier: 3.711A pdb=" N ALA E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL E 190 " --> pdb=" O CYS E 186 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER E 198 " --> pdb=" O LEU E 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 54 removed outlier: 3.547A pdb=" N THR F 48 " --> pdb=" O GLU F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 64 Processing helix chain 'F' and resid 77 through 112 removed outlier: 3.527A pdb=" N ASN F 94 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL F 100 " --> pdb=" O SER F 96 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA F 106 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN F 110 " --> pdb=" O ALA F 106 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA F 112 " --> pdb=" O LYS F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 188 removed outlier: 3.550A pdb=" N GLU F 184 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TRP F 187 " --> pdb=" O ASN F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 202 removed outlier: 3.697A pdb=" N ARG F 199 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU F 200 " --> pdb=" O LYS F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 242 Processing helix chain 'F' and resid 243 through 249 removed outlier: 3.709A pdb=" N GLN F 248 " --> pdb=" O PRO F 244 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY F 249 " --> pdb=" O TRP F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 267 removed outlier: 3.745A pdb=" N VAL F 266 " --> pdb=" O SER F 263 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER F 267 " --> pdb=" O GLY F 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 263 through 267' Processing helix chain 'F' and resid 268 through 282 removed outlier: 3.673A pdb=" N LYS F 272 " --> pdb=" O GLY F 268 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE F 274 " --> pdb=" O THR F 270 " (cutoff:3.500A) removed outlier: 3.713A 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 313 through 325 removed outlier: 3.675A pdb=" N LYS F 317 " --> pdb=" O ASN F 313 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU F 320 " --> pdb=" O ASN F 316 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS F 321 " --> pdb=" O LYS F 317 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP F 322 " --> pdb=" O LYS F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 346 removed outlier: 3.619A pdb=" N PHE F 339 " --> pdb=" O TYR F 335 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU F 344 " --> pdb=" O SER F 340 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN F 345 " --> pdb=" O PHE F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 379 removed outlier: 3.900A pdb=" N PHE F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 408 removed outlier: 3.725A pdb=" N GLN F 402 " --> pdb=" O ARG F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 425 Processing helix chain 'F' and resid 427 through 432 removed outlier: 3.708A pdb=" N VAL F 431 " --> pdb=" O GLU F 427 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU F 432 " --> pdb=" O TYR F 428 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 427 through 432' Processing helix chain 'F' and resid 433 through 438 Processing helix chain 'F' and resid 496 through 501 Processing helix chain 'F' and resid 562 through 567 removed outlier: 3.764A pdb=" N GLU F 567 " --> pdb=" O PHE F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 581 removed outlier: 3.877A pdb=" N GLU F 575 " --> pdb=" O ASP F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 642 through 652 Processing helix chain 'F' and resid 653 through 656 removed outlier: 3.756A pdb=" N PHE F 656 " --> pdb=" O PRO F 653 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 653 through 656' Processing helix chain 'F' and resid 678 through 694 removed outlier: 3.560A pdb=" N PHE F 689 " --> pdb=" O ASN F 685 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE F 690 " --> pdb=" O PHE F 686 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP F 691 " --> pdb=" O ASN F 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 703 through 722 removed outlier: 3.867A pdb=" N LEU F 709 " --> pdb=" O ILE F 705 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY F 713 " --> pdb=" O LEU F 709 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE F 714 " --> pdb=" O LEU F 710 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU F 718 " --> pdb=" O PHE F 714 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL F 719 " --> pdb=" O THR F 715 " (cutoff:3.500A) Processing helix chain 'F' and resid 764 through 773 removed outlier: 4.235A pdb=" N LYS F 768 " --> pdb=" O ASP F 764 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG F 769 " --> pdb=" O SER F 765 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP F 772 " --> pdb=" O LYS F 768 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN F 773 " --> pdb=" O ARG F 769 " (cutoff:3.500A) Processing helix chain 'F' and resid 820 through 833 removed outlier: 3.507A pdb=" N SER F 832 " --> pdb=" O PHE F 828 " (cutoff:3.500A) Processing helix chain 'F' and resid 877 through 881 Processing helix chain 'F' and resid 882 through 892 removed outlier: 3.509A pdb=" N HIS F 888 " --> pdb=" O SER F 884 " (cutoff:3.500A) removed outlier: 3.841A 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 972 through 975 removed outlier: 3.660A pdb=" N ARG A 986 " --> pdb=" O TYR A 972 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1416 through 1418 Processing sheet with id=AA4, first strand: chain 'B' and resid 156 through 160 removed outlier: 3.560A pdb=" N GLY B 147 " --> pdb=" O GLY B 157 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG B 148 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ILE B 136 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 103 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA B 104 " --> pdb=" O VAL C 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 277 through 280 removed outlier: 6.511A pdb=" N ILE C 278 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE C 389 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL C 280 " --> pdb=" O ILE C 389 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 309 through 314 Processing sheet with id=AA7, first strand: chain 'E' and resid 78 through 81 Processing sheet with id=AA8, first strand: chain 'F' and resid 73 through 74 Processing sheet with id=AA9, first strand: chain 'F' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'F' and resid 217 through 219 removed outlier: 3.798A pdb=" N VAL F 489 " --> pdb=" O GLY F 211 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 217 through 219 removed outlier: 3.798A pdb=" N VAL F 489 " --> pdb=" O GLY F 211 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 254 through 255 removed outlier: 6.098A pdb=" N ASP F 255 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N MET F 361 " --> pdb=" O ASP F 255 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 254 through 255 removed outlier: 6.098A pdb=" N ASP F 255 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N MET F 361 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LYS F 358 " --> pdb=" O ARG F 385 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N PHE F 387 " --> pdb=" O LYS F 358 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ILE F 360 " --> pdb=" O PHE F 387 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N PHE F 389 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU F 362 " --> pdb=" O PHE F 389 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL F 391 " --> pdb=" O LEU F 362 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N TYR F 413 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR F 388 " --> pdb=" O TYR F 413 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ILE F 415 " --> pdb=" O THR F 388 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N SER F 390 " --> pdb=" O ILE F 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 587 through 595 Processing sheet with id=AB6, first strand: chain 'F' and resid 612 through 613 Processing sheet with id=AB7, first strand: chain 'F' and resid 661 through 664 removed outlier: 3.816A pdb=" N ILE F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA F 734 " --> pdb=" O LYS F 818 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 661 through 664 removed outlier: 3.816A pdb=" N ILE F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA F 734 " --> pdb=" O LYS F 818 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 862 through 865 removed outlier: 3.549A pdb=" N MET F 864 " --> pdb=" O ILE F 855 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE F1005 " --> pdb=" O GLU F1022 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 896 through 902 removed outlier: 3.590A pdb=" N SER F 900 " --> pdb=" O GLN F 981 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 906 through 907 954 hydrogen bonds defined for protein. 2748 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: 3.93 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6543 1.34 - 1.46: 5687 1.46 - 1.59: 9614 1.59 - 1.72: 0 1.72 - 1.84: 191 Bond restraints: 22035 Sorted by residual: bond pdb=" CA ASP F 239 " pdb=" CB ASP F 239 " ideal model delta sigma weight residual 1.529 1.440 0.088 1.34e-02 5.57e+03 4.34e+01 bond pdb=" N LEU F 102 " pdb=" CA LEU F 102 " ideal model delta sigma weight residual 1.456 1.541 -0.084 1.31e-02 5.83e+03 4.13e+01 bond pdb=" N PRO F 527 " pdb=" CD PRO F 527 " ideal model delta sigma weight residual 1.473 1.562 -0.089 1.40e-02 5.10e+03 4.05e+01 bond pdb=" C PRO A1431 " pdb=" N PRO A1432 " ideal model delta sigma weight residual 1.335 1.409 -0.074 1.19e-02 7.06e+03 3.86e+01 bond pdb=" C ALA F 780 " pdb=" N PRO F 781 " ideal model delta sigma weight residual 1.330 1.407 -0.077 1.25e-02 6.40e+03 3.77e+01 ... (remaining 22030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.54: 29338 4.54 - 9.08: 457 9.08 - 13.62: 50 13.62 - 18.16: 23 18.16 - 22.70: 5 Bond angle restraints: 29873 Sorted by residual: angle pdb=" N TYR F 661 " pdb=" CA TYR F 661 " pdb=" C TYR F 661 " ideal model delta sigma weight residual 109.25 86.55 22.70 1.53e+00 4.27e-01 2.20e+02 angle pdb=" N TYR E 176 " pdb=" CA TYR E 176 " pdb=" C TYR E 176 " ideal model delta sigma weight residual 108.76 87.47 21.29 1.69e+00 3.50e-01 1.59e+02 angle pdb=" N SER F 390 " pdb=" CA SER F 390 " pdb=" C SER F 390 " ideal model delta sigma weight residual 109.24 89.60 19.64 1.67e+00 3.59e-01 1.38e+02 angle pdb=" N GLN F 447 " pdb=" CA GLN F 447 " pdb=" C GLN F 447 " ideal model delta sigma weight residual 108.52 89.51 19.01 1.63e+00 3.76e-01 1.36e+02 angle pdb=" C VAL F 550 " pdb=" N GLN F 551 " pdb=" CA GLN F 551 " ideal model delta sigma weight residual 120.63 138.57 -17.94 1.61e+00 3.86e-01 1.24e+02 ... (remaining 29868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.12: 12524 23.12 - 46.24: 341 46.24 - 69.37: 55 69.37 - 92.49: 8 92.49 - 115.61: 3 Dihedral angle restraints: 12931 sinusoidal: 5090 harmonic: 7841 Sorted by residual: dihedral pdb=" CA VAL F 894 " pdb=" C VAL F 894 " pdb=" N TYR F 895 " pdb=" CA TYR F 895 " ideal model delta harmonic sigma weight residual 180.00 85.90 94.10 0 5.00e+00 4.00e-02 3.54e+02 dihedral pdb=" CA TYR F 220 " pdb=" C TYR F 220 " pdb=" N PRO F 221 " pdb=" CA PRO F 221 " ideal model delta harmonic sigma weight residual 180.00 106.42 73.58 0 5.00e+00 4.00e-02 2.17e+02 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 -106.47 -73.53 0 5.00e+00 4.00e-02 2.16e+02 ... (remaining 12928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 3236 0.136 - 0.273: 185 0.273 - 0.409: 20 0.409 - 0.546: 4 0.546 - 0.682: 4 Chirality restraints: 3449 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN F 827 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" C1 NAG F1220 " pdb=" ND2 ASN F 784 " pdb=" C2 NAG F1220 " pdb=" O5 NAG F1220 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CA PRO A1310 " pdb=" N PRO A1310 " pdb=" C PRO A1310 " pdb=" CB PRO A1310 " both_signs ideal model delta sigma weight residual False 2.72 2.12 0.60 2.00e-01 2.50e+01 8.94e+00 ... (remaining 3446 not shown) Planarity restraints: 3760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 615 " 0.209 2.00e-02 2.50e+03 2.69e-01 9.04e+02 pdb=" CG ASN F 615 " -0.090 2.00e-02 2.50e+03 pdb=" OD1 ASN F 615 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN F 615 " -0.448 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.330 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 350 " -0.117 2.00e-02 2.50e+03 2.24e-01 6.26e+02 pdb=" CG ASN F 350 " 0.065 2.00e-02 2.50e+03 pdb=" OD1 ASN F 350 " -0.092 2.00e-02 2.50e+03 pdb=" ND2 ASN F 350 " 0.399 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.254 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR F 220 " 0.109 5.00e-02 4.00e+02 1.70e-01 4.61e+01 pdb=" N PRO F 221 " -0.294 5.00e-02 4.00e+02 pdb=" CA PRO F 221 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO F 221 " 0.094 5.00e-02 4.00e+02 ... (remaining 3757 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 364 2.62 - 3.19: 19647 3.19 - 3.76: 31651 3.76 - 4.33: 44149 4.33 - 4.90: 68780 Nonbonded interactions: 164591 Sorted by model distance: nonbonded pdb=" O PRO F 531 " pdb=" CG LYS F 532 " model vdw 2.056 3.440 nonbonded pdb=" CG2 ILE A1380 " pdb=" CE2 PHE A1384 " model vdw 2.141 3.760 nonbonded pdb=" OH TYR A 71 " pdb=" NH2 ARG A 165 " model vdw 2.169 3.120 nonbonded pdb=" CG ARG A 165 " pdb=" NH2 ARG A 168 " model vdw 2.179 3.520 nonbonded pdb=" O LEU A 580 " pdb=" OH TYR A 627 " model vdw 2.205 3.040 ... (remaining 164586 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'K' } ncs_group { reference = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.940 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 : 0.012 0.414 22073 Z= 0.612 Angle : 1.589 44.105 29970 Z= 0.888 Chirality : 0.077 0.682 3449 Planarity : 0.009 0.170 3745 Dihedral : 11.560 115.611 7826 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 1.75 % Allowed : 12.76 % Favored : 85.50 % Rotamer: Outliers : 1.50 % Allowed : 3.27 % Favored : 95.22 % Cbeta Deviations : 0.79 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 5.61 % Twisted General : 1.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.28 (0.12), residues: 2638 helix: -3.69 (0.08), residues: 1283 sheet: -1.86 (0.29), residues: 271 loop : -3.55 (0.16), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG F 769 TYR 0.067 0.005 TYR F 609 PHE 0.038 0.004 PHE F 363 TRP 0.037 0.004 TRP A 459 HIS 0.012 0.003 HIS A 992 Details of bonding type rmsd/Z covalent geometry : bond 0.01158 / 0.54 (22035) covalent geometry : angle 1.51368 / 0.86 (29873) SS BOND : bond 0.02403 / 1.26 ( 11) SS BOND : angle 14.36723 / 11.24 ( 22) hydrogen bonds : bond 0.30440 / 19.53 ( 929) hydrogen bonds : angle 10.36651 / 6.96 ( 2748) Misc. bond : bond 0.29398 / 15.46 ( 2) link_BETA1-4 : bond 0.00994 / 0.51 ( 10) link_BETA1-4 : angle 3.84674 / 2.40 ( 30) link_NAG-ASN : bond 0.00998 / 0.49 ( 15) link_NAG-ASN : angle 7.02614 / 4.07 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 727 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8008 (tp30) REVERT: A 91 TYR cc_start: 0.9088 (m-10) cc_final: 0.8383 (t80) REVERT: A 112 PHE cc_start: 0.5265 (m-10) cc_final: 0.4699 (m-10) REVERT: A 123 ASN cc_start: 0.9190 (m-40) cc_final: 0.8967 (t0) REVERT: A 162 LYS cc_start: 0.7254 (tptm) cc_final: 0.6825 (mptt) REVERT: A 240 GLU cc_start: 0.8431 (tt0) cc_final: 0.7807 (pt0) REVERT: A 260 GLU cc_start: 0.9034 (tp30) cc_final: 0.8431 (pm20) REVERT: A 295 THR cc_start: 0.9344 (p) cc_final: 0.9030 (t) REVERT: A 327 ASN cc_start: 0.9125 (m-40) cc_final: 0.8920 (m-40) REVERT: A 343 LYS cc_start: 0.7642 (mttm) cc_final: 0.7290 (tptt) REVERT: A 423 TRP cc_start: 0.7502 (t-100) cc_final: 0.7295 (t-100) REVERT: A 427 ASP cc_start: 0.8156 (t70) cc_final: 0.7183 (m-30) REVERT: A 436 TRP cc_start: 0.7606 (m100) cc_final: 0.7047 (t60) REVERT: A 444 LEU cc_start: 0.9418 (mt) cc_final: 0.9206 (tt) REVERT: A 465 ASP cc_start: 0.9258 (t70) cc_final: 0.8962 (m-30) REVERT: A 501 CYS cc_start: 0.9102 (m) cc_final: 0.8697 (p) REVERT: A 588 GLU cc_start: 0.9278 (tt0) cc_final: 0.8728 (tp30) REVERT: A 598 ASP cc_start: 0.9216 (t0) cc_final: 0.8983 (t0) REVERT: A 615 ASP cc_start: 0.9194 (t0) cc_final: 0.8862 (t0) REVERT: A 632 TYR cc_start: 0.8093 (t80) cc_final: 0.7891 (t80) REVERT: A 641 PHE cc_start: 0.8962 (m-10) cc_final: 0.8619 (m-10) REVERT: A 808 PHE cc_start: 0.8365 (m-10) cc_final: 0.8108 (m-10) REVERT: A 828 ARG cc_start: 0.8053 (mtp85) cc_final: 0.7456 (mmt180) REVERT: A 843 PHE cc_start: 0.7028 (t80) cc_final: 0.6507 (t80) REVERT: A 851 MET cc_start: 0.7794 (tpp) cc_final: 0.7486 (mmp) REVERT: A 906 ARG cc_start: 0.8306 (ptp-170) cc_final: 0.7100 (tpt-90) REVERT: A 967 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8747 (mt-10) REVERT: A 1014 GLU cc_start: 0.8857 (tp30) cc_final: 0.8490 (tm-30) REVERT: A 1029 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8760 (mm-30) REVERT: A 1057 MET cc_start: 0.7953 (mtm) cc_final: 0.7601 (mtm) REVERT: A 1110 GLN cc_start: 0.8133 (tt0) cc_final: 0.7440 (tp40) REVERT: A 1146 MET cc_start: 0.8649 (mmm) cc_final: 0.8425 (mtm) REVERT: A 1183 ASN cc_start: 0.9306 (m-40) cc_final: 0.9023 (m110) REVERT: A 1258 TRP cc_start: 0.8801 (t60) cc_final: 0.8455 (t60) REVERT: A 1307 GLN cc_start: 0.8501 (mt0) cc_final: 0.8243 (mt0) REVERT: A 1381 MET cc_start: 0.9071 (mtt) cc_final: 0.8868 (mtp) REVERT: A 1401 GLU cc_start: 0.8967 (tt0) cc_final: 0.8331 (tp30) REVERT: A 1405 ILE cc_start: 0.8195 (mp) cc_final: 0.7823 (mp) REVERT: A 1428 ARG cc_start: 0.8559 (ttt90) cc_final: 0.8353 (ttt-90) REVERT: B 149 LEU cc_start: 0.6003 (tp) cc_final: 0.5783 (tp) REVERT: C 275 ARG cc_start: 0.6021 (mtp180) cc_final: 0.5531 (mtp180) REVERT: C 309 ILE cc_start: 0.7541 (tt) cc_final: 0.7293 (pt) REVERT: C 350 GLU cc_start: 0.5014 (mm-30) cc_final: 0.4744 (mm-30) REVERT: C 354 ILE cc_start: 0.7340 (mt) cc_final: 0.6976 (mt) REVERT: C 357 LEU cc_start: 0.6551 (mt) cc_final: 0.6179 (mt) REVERT: C 359 ARG cc_start: 0.5684 (ttp80) cc_final: 0.5468 (ptm-80) REVERT: C 362 GLN cc_start: 0.7156 (mt0) cc_final: 0.6642 (pt0) REVERT: C 391 ILE cc_start: 0.8692 (mt) cc_final: 0.8275 (tt) REVERT: C 402 LYS cc_start: 0.7712 (mttm) cc_final: 0.7476 (mmpt) REVERT: C 408 GLN cc_start: 0.6405 (mm-40) cc_final: 0.6074 (mm110) REVERT: C 412 LEU cc_start: 0.7284 (tp) cc_final: 0.7076 (tp) REVERT: C 415 GLN cc_start: 0.7971 (mt0) cc_final: 0.7324 (mm110) REVERT: E 14 PHE cc_start: 0.7537 (t80) cc_final: 0.7274 (m-10) REVERT: E 32 TRP cc_start: 0.7737 (m100) cc_final: 0.7416 (m100) REVERT: E 120 MET cc_start: 0.7503 (tpt) cc_final: 0.6967 (mmt) REVERT: E 131 LYS cc_start: 0.6823 (tptm) cc_final: 0.6038 (tmtt) REVERT: E 133 ARG cc_start: 0.6577 (ptp-170) cc_final: 0.5610 (ptp-170) REVERT: E 178 TYR cc_start: 0.7431 (m-10) cc_final: 0.7193 (m-80) REVERT: E 207 MET cc_start: 0.8211 (pmm) cc_final: 0.7924 (ptm) REVERT: F 45 ASP cc_start: 0.9081 (m-30) cc_final: 0.8802 (t0) REVERT: F 116 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.8011 (ttp80) REVERT: F 281 MET cc_start: 0.9255 (tpp) cc_final: 0.8928 (tpp) REVERT: F 302 ASP cc_start: 0.9384 (m-30) cc_final: 0.8828 (p0) REVERT: F 397 ASP cc_start: 0.9528 (t0) cc_final: 0.9204 (t0) REVERT: F 436 MET cc_start: 0.9262 (mtp) cc_final: 0.9056 (mtp) REVERT: F 490 MET cc_start: 0.9195 (mmt) cc_final: 0.8848 (mmt) REVERT: F 498 ASP cc_start: 0.9108 (m-30) cc_final: 0.8907 (t0) REVERT: F 514 TYR cc_start: 0.9122 (m-10) cc_final: 0.8781 (m-80) REVERT: F 536 VAL cc_start: 0.8409 (t) cc_final: 0.8159 (m) REVERT: F 562 ASP cc_start: 0.8676 (m-30) cc_final: 0.8427 (t0) REVERT: F 567 GLU cc_start: 0.9474 (mt-10) cc_final: 0.9247 (mm-30) REVERT: F 571 ASP cc_start: 0.9368 (m-30) cc_final: 0.9146 (t0) REVERT: F 572 ILE cc_start: 0.9254 (mt) cc_final: 0.8777 (tp) REVERT: F 576 ILE cc_start: 0.9313 (mm) cc_final: 0.9028 (mm) REVERT: F 603 ASP cc_start: 0.9294 (m-30) cc_final: 0.9026 (t70) REVERT: F 624 LEU cc_start: 0.9524 (tp) cc_final: 0.9310 (tt) REVERT: F 680 THR cc_start: 0.8915 (m) cc_final: 0.8415 (p) REVERT: F 688 GLU cc_start: 0.9172 (tt0) cc_final: 0.8848 (tp30) REVERT: F 707 ARG cc_start: 0.8880 (ttt90) cc_final: 0.8518 (tpt-90) REVERT: F 725 LYS cc_start: 0.9331 (mttt) cc_final: 0.8663 (tmtt) REVERT: F 758 ASN cc_start: 0.8949 (t0) cc_final: 0.6752 (t0) REVERT: F 763 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8621 (tm-30) REVERT: F 851 MET cc_start: 0.2144 (mtt) cc_final: 0.0823 (ttm) REVERT: F 871 THR cc_start: 0.9313 (p) cc_final: 0.9077 (t) REVERT: F 878 PHE cc_start: 0.9126 (t80) cc_final: 0.8913 (t80) REVERT: F 886 MET cc_start: 0.9144 (tpp) cc_final: 0.8881 (tpt) REVERT: F 990 SER cc_start: 0.8710 (m) cc_final: 0.8433 (p) REVERT: F 1013 ASN cc_start: 0.9365 (t0) cc_final: 0.9035 (t0) outliers start: 35 outliers final: 14 residues processed: 751 average time/residue: 0.1558 time to fit residues: 180.6785 Evaluate side-chains 476 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 461 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 542 TRP Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 656 PHE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1068 PHE Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 428 TYR Chi-restraints excluded: chain F residue 615 ASN Chi-restraints excluded: chain F residue 782 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 0.3980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN A 456 GLN A 464 GLN A 602 GLN ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 ASN A 996 HIS A 999 ASN ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1154 ASN A1183 ASN A1299 GLN A1303 ASN A1374 ASN A1383 ASN E 38 HIS F 43 GLN F 313 ASN F 316 ASN F 357 ASN F 379 ASN F 395 ASN B F 480 ASN F 644 GLN F 679 ASN F 685 ASN F 716 ASN F 756 GLN ** F 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.135808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.108454 restraints weight = 66165.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.108382 restraints weight = 34344.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.108933 restraints weight = 32371.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.109416 restraints weight = 22734.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.110570 restraints weight = 19734.017| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22073 Z= 0.187 Angle : 0.922 16.117 29970 Z= 0.472 Chirality : 0.052 0.519 3449 Planarity : 0.007 0.106 3745 Dihedral : 9.025 91.326 2925 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.95 % Allowed : 10.55 % Favored : 88.50 % Rotamer: Outliers : 2.79 % Allowed : 11.90 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 5.61 % Twisted General : 0.63 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.69 (0.14), residues: 2638 helix: -1.90 (0.11), residues: 1337 sheet: -1.30 (0.32), residues: 249 loop : -3.41 (0.17), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 95 TYR 0.031 0.002 TYR C 388 PHE 0.030 0.002 PHE F 783 TRP 0.029 0.002 TRP F 824 HIS 0.012 0.001 HIS A 996 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.19 (22035) covalent geometry : angle 0.89729 / 0.47 (29873) SS BOND : bond 0.01435 / 0.57 ( 11) SS BOND : angle 2.20242 / 1.38 ( 22) hydrogen bonds : bond 0.06043 / 3.92 ( 929) hydrogen bonds : angle 5.81867 / 3.95 ( 2748) Misc. bond : bond 0.00263 / 0.14 ( 2) link_BETA1-4 : bond 0.00438 / 0.19 ( 10) link_BETA1-4 : angle 2.36635 / 1.33 ( 30) link_NAG-ASN : bond 0.01209 / 0.83 ( 15) link_NAG-ASN : angle 5.05876 / 2.78 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 586 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.8332 (mmt) cc_final: 0.8089 (mpp) REVERT: A 295 THR cc_start: 0.8585 (p) cc_final: 0.8170 (t) REVERT: A 366 TYR cc_start: 0.7035 (m-10) cc_final: 0.6784 (m-10) REVERT: A 375 VAL cc_start: 0.6648 (m) cc_final: 0.6426 (p) REVERT: A 427 ASP cc_start: 0.6948 (t70) cc_final: 0.6102 (m-30) REVERT: A 434 PHE cc_start: 0.7874 (m-10) cc_final: 0.7546 (m-80) REVERT: A 444 LEU cc_start: 0.9182 (mt) cc_final: 0.8852 (tt) REVERT: A 470 VAL cc_start: 0.9117 (m) cc_final: 0.8819 (p) REVERT: A 483 MET cc_start: 0.6233 (tmm) cc_final: 0.6020 (tmm) REVERT: A 497 ASN cc_start: 0.8883 (m-40) cc_final: 0.8488 (t0) REVERT: A 598 ASP cc_start: 0.7499 (t0) cc_final: 0.7065 (t0) REVERT: A 615 ASP cc_start: 0.6902 (t0) cc_final: 0.6385 (t0) REVERT: A 686 MET cc_start: 0.4638 (ptp) cc_final: 0.4083 (ptm) REVERT: A 806 LEU cc_start: 0.8808 (mt) cc_final: 0.8598 (tt) REVERT: A 811 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8226 (mt) REVERT: A 828 ARG cc_start: 0.7671 (mtp85) cc_final: 0.7220 (mmt180) REVERT: A 906 ARG cc_start: 0.7505 (ptp-170) cc_final: 0.7144 (tpt-90) REVERT: A 941 MET cc_start: 0.8107 (mtt) cc_final: 0.7798 (mtt) REVERT: A 1086 ARG cc_start: 0.6903 (ttm-80) cc_final: 0.6686 (tpt90) REVERT: A 1087 GLN cc_start: 0.6822 (tt0) cc_final: 0.6215 (pp30) REVERT: A 1163 LEU cc_start: 0.9128 (mt) cc_final: 0.8712 (tt) REVERT: A 1165 MET cc_start: 0.8485 (tmm) cc_final: 0.8204 (tmm) REVERT: A 1166 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8726 (tt) REVERT: A 1381 MET cc_start: 0.7792 (mtt) cc_final: 0.7395 (mtp) REVERT: A 1401 GLU cc_start: 0.8283 (tt0) cc_final: 0.7498 (tp30) REVERT: A 1453 MET cc_start: 0.4704 (tmm) cc_final: 0.4422 (tmm) REVERT: B 165 LEU cc_start: 0.3178 (OUTLIER) cc_final: 0.2936 (tp) REVERT: C 362 GLN cc_start: 0.7328 (mt0) cc_final: 0.6931 (pt0) REVERT: C 364 VAL cc_start: 0.6961 (t) cc_final: 0.6622 (p) REVERT: C 391 ILE cc_start: 0.8370 (mt) cc_final: 0.8065 (tt) REVERT: C 440 GLU cc_start: 0.8373 (tp30) cc_final: 0.7823 (pm20) REVERT: E 1 MET cc_start: 0.4688 (ttt) cc_final: 0.3809 (mmm) REVERT: E 32 TRP cc_start: 0.6564 (m100) cc_final: 0.6138 (m100) REVERT: E 51 PHE cc_start: 0.7947 (m-80) cc_final: 0.7524 (m-80) REVERT: E 56 ILE cc_start: 0.6884 (mp) cc_final: 0.6273 (mt) REVERT: E 131 LYS cc_start: 0.6890 (tptm) cc_final: 0.6043 (tmtt) REVERT: E 133 ARG cc_start: 0.5648 (ptp-170) cc_final: 0.5123 (ptp-170) REVERT: E 152 PHE cc_start: 0.9014 (t80) cc_final: 0.8795 (t80) REVERT: E 209 GLN cc_start: 0.7645 (mm-40) cc_final: 0.6800 (mm-40) REVERT: F 71 THR cc_start: 0.7692 (m) cc_final: 0.7381 (p) REVERT: F 254 LYS cc_start: 0.8423 (mtmm) cc_final: 0.8201 (mtmt) REVERT: F 302 ASP cc_start: 0.7698 (m-30) cc_final: 0.7361 (p0) REVERT: F 345 GLN cc_start: 0.8309 (mm-40) cc_final: 0.8082 (mm-40) REVERT: F 490 MET cc_start: 0.8799 (mmt) cc_final: 0.8300 (mmt) REVERT: F 663 PHE cc_start: 0.8123 (m-80) cc_final: 0.7862 (m-10) REVERT: F 725 LYS cc_start: 0.8660 (mttt) cc_final: 0.8328 (tmtt) REVERT: F 758 ASN cc_start: 0.8633 (t0) cc_final: 0.5120 (t0) REVERT: F 851 MET cc_start: 0.1712 (mtt) cc_final: 0.0800 (ttm) REVERT: F 886 MET cc_start: 0.8016 (tpp) cc_final: 0.7464 (tpt) outliers start: 63 outliers final: 34 residues processed: 620 average time/residue: 0.1431 time to fit residues: 143.0378 Evaluate side-chains 486 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 449 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 266 PRO Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 542 TRP Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1031 MET Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1068 PHE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1284 ILE Chi-restraints excluded: chain A residue 1368 CYS Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 373 HIS Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 165 HIS Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain F residue 428 TYR Chi-restraints excluded: chain F residue 905 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 231 optimal weight: 0.9990 chunk 108 optimal weight: 0.4980 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 223 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 chunk 245 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 ASN A 993 ASN ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 GLN ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN F 348 ASN F 520 ASN F 773 ASN ** F 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.133500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.107050 restraints weight = 79477.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.107324 restraints weight = 48684.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.108076 restraints weight = 40539.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.108824 restraints weight = 26073.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.109792 restraints weight = 22453.292| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22073 Z= 0.175 Angle : 0.854 13.034 29970 Z= 0.436 Chirality : 0.050 0.482 3449 Planarity : 0.006 0.109 3745 Dihedral : 8.097 82.769 2910 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.87 % Allowed : 11.12 % Favored : 88.00 % Rotamer: Outliers : 3.54 % Allowed : 16.14 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 5.61 % Twisted General : 0.51 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.15), residues: 2638 helix: -0.96 (0.13), residues: 1354 sheet: -1.24 (0.32), residues: 262 loop : -3.31 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 887 TYR 0.029 0.002 TYR F 609 PHE 0.025 0.002 PHE F 783 TRP 0.026 0.002 TRP F 824 HIS 0.007 0.001 HIS C 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (22035) covalent geometry : angle 0.83409 / 0.43 (29873) SS BOND : bond 0.01648 / 0.82 ( 11) SS BOND : angle 1.65631 / 1.04 ( 22) hydrogen bonds : bond 0.05023 / 3.24 ( 929) hydrogen bonds : angle 5.24672 / 3.55 ( 2748) Misc. bond : bond 0.00070 / 0.03 ( 2) link_BETA1-4 : bond 0.00446 / 0.23 ( 10) link_BETA1-4 : angle 1.97265 / 1.14 ( 30) link_NAG-ASN : bond 0.00970 / 0.54 ( 15) link_NAG-ASN : angle 4.46432 / 2.46 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 489 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 THR cc_start: 0.8653 (p) cc_final: 0.8241 (t) REVERT: A 332 VAL cc_start: 0.8824 (OUTLIER) cc_final: 0.8438 (p) REVERT: A 341 ARG cc_start: 0.8443 (ptp90) cc_final: 0.7998 (ptp90) REVERT: A 366 TYR cc_start: 0.7021 (m-10) cc_final: 0.6718 (m-10) REVERT: A 427 ASP cc_start: 0.6849 (t70) cc_final: 0.6050 (m-30) REVERT: A 470 VAL cc_start: 0.9167 (m) cc_final: 0.8894 (p) REVERT: A 497 ASN cc_start: 0.8845 (m-40) cc_final: 0.8502 (t0) REVERT: A 527 LEU cc_start: 0.8526 (mp) cc_final: 0.8284 (mm) REVERT: A 598 ASP cc_start: 0.7436 (t0) cc_final: 0.7031 (t0) REVERT: A 615 ASP cc_start: 0.6733 (t0) cc_final: 0.6245 (t0) REVERT: A 657 LEU cc_start: 0.8795 (mt) cc_final: 0.7995 (mt) REVERT: A 686 MET cc_start: 0.4746 (ptp) cc_final: 0.4200 (ptm) REVERT: A 806 LEU cc_start: 0.8727 (mt) cc_final: 0.8402 (tt) REVERT: A 828 ARG cc_start: 0.7721 (mtp85) cc_final: 0.7426 (mmt180) REVERT: A 835 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.7496 (t80) REVERT: A 851 MET cc_start: 0.4524 (mmp) cc_final: 0.3125 (ttm) REVERT: A 941 MET cc_start: 0.8249 (mtt) cc_final: 0.7874 (mtt) REVERT: A 1165 MET cc_start: 0.8611 (tmm) cc_final: 0.8351 (tmm) REVERT: A 1166 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8633 (tt) REVERT: A 1401 GLU cc_start: 0.8486 (tt0) cc_final: 0.7468 (tp30) REVERT: A 1410 ASP cc_start: 0.8737 (m-30) cc_final: 0.8503 (m-30) REVERT: A 1453 MET cc_start: 0.4428 (tmm) cc_final: 0.4116 (tmm) REVERT: C 362 GLN cc_start: 0.7231 (mt0) cc_final: 0.6798 (pt0) REVERT: C 391 ILE cc_start: 0.8377 (mt) cc_final: 0.7997 (tt) REVERT: C 415 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.6727 (pp30) REVERT: C 440 GLU cc_start: 0.8600 (tp30) cc_final: 0.7974 (pm20) REVERT: E 1 MET cc_start: 0.4275 (ttt) cc_final: 0.3548 (mmm) REVERT: E 32 TRP cc_start: 0.6541 (m100) cc_final: 0.6161 (m100) REVERT: E 51 PHE cc_start: 0.7981 (m-80) cc_final: 0.7757 (m-80) REVERT: E 56 ILE cc_start: 0.6989 (mp) cc_final: 0.6445 (mt) REVERT: E 131 LYS cc_start: 0.6568 (tptm) cc_final: 0.5791 (tmtt) REVERT: E 133 ARG cc_start: 0.5473 (ptp-170) cc_final: 0.5077 (ptp-170) REVERT: F 71 THR cc_start: 0.7615 (m) cc_final: 0.7403 (p) REVERT: F 302 ASP cc_start: 0.7776 (m-30) cc_final: 0.7309 (p0) REVERT: F 345 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8350 (mm-40) REVERT: F 383 LYS cc_start: 0.8756 (mttt) cc_final: 0.8493 (mptt) REVERT: F 532 LYS cc_start: 0.8009 (mtmt) cc_final: 0.7648 (pttt) REVERT: F 725 LYS cc_start: 0.8754 (mttt) cc_final: 0.8280 (tmtt) REVERT: F 851 MET cc_start: 0.1585 (mtt) cc_final: 0.0277 (ttt) outliers start: 81 outliers final: 44 residues processed: 535 average time/residue: 0.1385 time to fit residues: 120.0430 Evaluate side-chains 466 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 418 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 266 PRO Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 542 TRP Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1031 MET Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1068 PHE Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 373 HIS Chi-restraints excluded: chain C residue 415 GLN Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain F residue 428 TYR Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 615 ASN Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 881 ILE Chi-restraints excluded: chain F residue 977 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 31 optimal weight: 6.9990 chunk 50 optimal weight: 0.0980 chunk 85 optimal weight: 0.7980 chunk 163 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 221 optimal weight: 0.0970 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 83 ASN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 HIS E 209 GLN E 210 ASN F 520 ASN ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 756 GLN F 888 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.135517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.108612 restraints weight = 85455.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.109935 restraints weight = 48712.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.110391 restraints weight = 38824.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.111151 restraints weight = 24555.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.112511 restraints weight = 21013.897| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22073 Z= 0.140 Angle : 0.805 14.448 29970 Z= 0.405 Chirality : 0.049 0.409 3449 Planarity : 0.005 0.103 3745 Dihedral : 7.545 80.007 2910 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.68 % Allowed : 10.59 % Favored : 88.72 % Rotamer: Outliers : 3.05 % Allowed : 17.82 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 5.61 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.16), residues: 2638 helix: -0.45 (0.13), residues: 1365 sheet: -1.20 (0.32), residues: 263 loop : -3.21 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F1032 TYR 0.027 0.001 TYR C 388 PHE 0.026 0.002 PHE F 783 TRP 0.025 0.001 TRP A 50 HIS 0.006 0.001 HIS A 992 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (22035) covalent geometry : angle 0.78782 / 0.40 (29873) SS BOND : bond 0.00149 / 0.08 ( 11) SS BOND : angle 1.19210 / 0.77 ( 22) hydrogen bonds : bond 0.04268 / 2.72 ( 929) hydrogen bonds : angle 4.80680 / 3.26 ( 2748) Misc. bond : bond 0.00056 / 0.03 ( 2) link_BETA1-4 : bond 0.00473 / 0.22 ( 10) link_BETA1-4 : angle 1.77781 / 1.02 ( 30) link_NAG-ASN : bond 0.00884 / 0.52 ( 15) link_NAG-ASN : angle 4.08635 / 2.24 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 504 time to evaluate : 0.780 Fit side-chains revert: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 274 HIS cc_start: 0.7254 (OUTLIER) cc_final: 0.6596 (m-70) REVERT: A 292 GLU cc_start: 0.7648 (tp30) cc_final: 0.7406 (tp30) REVERT: A 295 THR cc_start: 0.8650 (p) cc_final: 0.8148 (t) REVERT: A 327 ASN cc_start: 0.8541 (t0) cc_final: 0.8261 (t0) REVERT: A 366 TYR cc_start: 0.7049 (m-10) cc_final: 0.6721 (m-10) REVERT: A 427 ASP cc_start: 0.6744 (t70) cc_final: 0.6000 (m-30) REVERT: A 470 VAL cc_start: 0.9144 (m) cc_final: 0.8835 (p) REVERT: A 497 ASN cc_start: 0.8794 (m-40) cc_final: 0.8453 (t0) REVERT: A 598 ASP cc_start: 0.7244 (t0) cc_final: 0.6928 (t0) REVERT: A 615 ASP cc_start: 0.6527 (t0) cc_final: 0.5928 (t0) REVERT: A 806 LEU cc_start: 0.8691 (mt) cc_final: 0.8411 (tt) REVERT: A 811 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8126 (mt) REVERT: A 828 ARG cc_start: 0.7754 (mtp85) cc_final: 0.7291 (mmt180) REVERT: A 835 PHE cc_start: 0.7795 (OUTLIER) cc_final: 0.7482 (t80) REVERT: A 906 ARG cc_start: 0.7536 (ptp-170) cc_final: 0.6927 (tpp80) REVERT: A 941 MET cc_start: 0.8194 (mtt) cc_final: 0.7878 (mtt) REVERT: A 1069 GLN cc_start: 0.7135 (mm110) cc_final: 0.6635 (mm-40) REVERT: A 1087 GLN cc_start: 0.6945 (tt0) cc_final: 0.6535 (pp30) REVERT: A 1125 PHE cc_start: 0.7679 (m-80) cc_final: 0.7318 (m-80) REVERT: A 1165 MET cc_start: 0.8699 (tmm) cc_final: 0.8357 (tmm) REVERT: A 1166 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8575 (tt) REVERT: A 1187 PHE cc_start: 0.8883 (t80) cc_final: 0.8565 (t80) REVERT: A 1381 MET cc_start: 0.7481 (mtt) cc_final: 0.7247 (mtp) REVERT: A 1401 GLU cc_start: 0.8330 (tt0) cc_final: 0.7602 (tp30) REVERT: A 1453 MET cc_start: 0.4749 (tmm) cc_final: 0.4436 (tmm) REVERT: C 308 ARG cc_start: 0.5778 (mtm180) cc_final: 0.5345 (mtm180) REVERT: C 362 GLN cc_start: 0.7182 (mt0) cc_final: 0.6797 (pt0) REVERT: C 391 ILE cc_start: 0.8488 (mt) cc_final: 0.8051 (tt) REVERT: C 440 GLU cc_start: 0.8566 (tp30) cc_final: 0.7896 (pm20) REVERT: E 1 MET cc_start: 0.4258 (ttt) cc_final: 0.3569 (mmm) REVERT: E 56 ILE cc_start: 0.7378 (mp) cc_final: 0.7124 (mt) REVERT: E 131 LYS cc_start: 0.6419 (tptm) cc_final: 0.5614 (tmtt) REVERT: E 133 ARG cc_start: 0.5305 (ptp-170) cc_final: 0.4936 (ptp-170) REVERT: E 182 PHE cc_start: 0.7882 (t80) cc_final: 0.7572 (t80) REVERT: F 302 ASP cc_start: 0.7745 (m-30) cc_final: 0.7302 (p0) REVERT: F 345 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8341 (mm-40) REVERT: F 411 TYR cc_start: 0.8291 (t80) cc_final: 0.8077 (t80) REVERT: F 449 THR cc_start: 0.9211 (m) cc_final: 0.8779 (p) REVERT: F 508 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8028 (pt) REVERT: F 663 PHE cc_start: 0.8093 (m-80) cc_final: 0.7754 (m-10) REVERT: F 725 LYS cc_start: 0.8712 (mttt) cc_final: 0.8223 (tmtt) REVERT: F 775 ASN cc_start: 0.8724 (p0) cc_final: 0.8496 (p0) REVERT: F 851 MET cc_start: 0.1560 (mtt) cc_final: 0.0517 (ttt) REVERT: F 891 ASN cc_start: 0.7954 (OUTLIER) cc_final: 0.7708 (t0) REVERT: F 1020 MET cc_start: 0.7229 (ppp) cc_final: 0.6999 (ppp) outliers start: 70 outliers final: 38 residues processed: 538 average time/residue: 0.1365 time to fit residues: 119.3465 Evaluate side-chains 488 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 444 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 266 PRO Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 542 TRP Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1068 PHE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1319 CYS Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 373 HIS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 428 TYR Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 891 ASN Chi-restraints excluded: chain F residue 905 SER Chi-restraints excluded: chain F residue 977 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 14 optimal weight: 0.3980 chunk 114 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 236 optimal weight: 0.8980 chunk 211 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 39 optimal weight: 0.0060 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 ASN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 GLN ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 520 ASN ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.135941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.109422 restraints weight = 83495.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.110460 restraints weight = 48035.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.110982 restraints weight = 37639.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.111736 restraints weight = 23866.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.112398 restraints weight = 20596.982| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3596 r_free = 0.3596 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3596 r_free = 0.3596 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22073 Z= 0.137 Angle : 0.802 15.309 29970 Z= 0.399 Chirality : 0.048 0.448 3449 Planarity : 0.005 0.102 3745 Dihedral : 7.224 75.289 2907 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.57 % Allowed : 10.71 % Favored : 88.72 % Rotamer: Outliers : 2.83 % Allowed : 19.81 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 5.61 % 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 are not related in a simple way. whole: -1.92 (0.16), residues: 2638 helix: -0.05 (0.14), residues: 1372 sheet: -0.97 (0.32), residues: 255 loop : -3.13 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F1032 TYR 0.026 0.001 TYR C 388 PHE 0.042 0.002 PHE F 783 TRP 0.026 0.001 TRP F 824 HIS 0.011 0.001 HIS C 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (22035) covalent geometry : angle 0.78683 / 0.40 (29873) SS BOND : bond 0.00992 / 0.44 ( 11) SS BOND : angle 1.15229 / 0.71 ( 22) hydrogen bonds : bond 0.03980 / 2.54 ( 929) hydrogen bonds : angle 4.65144 / 3.17 ( 2748) Misc. bond : bond 0.00335 / 0.18 ( 2) link_BETA1-4 : bond 0.00394 / 0.19 ( 10) link_BETA1-4 : angle 1.61230 / 0.93 ( 30) link_NAG-ASN : bond 0.00738 / 0.44 ( 15) link_NAG-ASN : angle 3.80734 / 2.10 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 494 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 HIS cc_start: 0.7357 (OUTLIER) cc_final: 0.6544 (m-70) REVERT: A 295 THR cc_start: 0.8582 (p) cc_final: 0.8282 (t) REVERT: A 327 ASN cc_start: 0.8558 (t0) cc_final: 0.8316 (t0) REVERT: A 366 TYR cc_start: 0.6996 (m-10) cc_final: 0.6685 (m-10) REVERT: A 427 ASP cc_start: 0.6732 (t70) cc_final: 0.6003 (m-30) REVERT: A 470 VAL cc_start: 0.9122 (m) cc_final: 0.8808 (p) REVERT: A 497 ASN cc_start: 0.8766 (m-40) cc_final: 0.8373 (t0) REVERT: A 500 ASP cc_start: 0.8514 (t0) cc_final: 0.8212 (t0) REVERT: A 527 LEU cc_start: 0.8480 (mm) cc_final: 0.7960 (mt) REVERT: A 598 ASP cc_start: 0.7317 (t0) cc_final: 0.6988 (t0) REVERT: A 615 ASP cc_start: 0.6565 (t0) cc_final: 0.6082 (t0) REVERT: A 656 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.7422 (t80) REVERT: A 828 ARG cc_start: 0.7870 (mtp85) cc_final: 0.7359 (mmt180) REVERT: A 835 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.7442 (t80) REVERT: A 843 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.6783 (t80) REVERT: A 851 MET cc_start: 0.4308 (mmp) cc_final: 0.2931 (mtm) REVERT: A 941 MET cc_start: 0.8205 (mtt) cc_final: 0.7887 (mtt) REVERT: A 948 GLN cc_start: 0.8433 (tp40) cc_final: 0.8004 (tp-100) REVERT: A 1056 MET cc_start: 0.8041 (mmm) cc_final: 0.7018 (tmm) REVERT: A 1057 MET cc_start: 0.6513 (mtt) cc_final: 0.6148 (mtt) REVERT: A 1069 GLN cc_start: 0.7052 (mm110) cc_final: 0.6572 (mm-40) REVERT: A 1125 PHE cc_start: 0.7674 (m-80) cc_final: 0.7332 (m-80) REVERT: A 1159 ILE cc_start: 0.9342 (tp) cc_final: 0.9127 (pt) REVERT: A 1165 MET cc_start: 0.8768 (tmm) cc_final: 0.8514 (tmm) REVERT: A 1166 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8738 (tt) REVERT: A 1292 ILE cc_start: 0.8269 (mm) cc_final: 0.8051 (mm) REVERT: A 1359 TYR cc_start: 0.6532 (m-80) cc_final: 0.6157 (m-80) REVERT: A 1381 MET cc_start: 0.7309 (mtt) cc_final: 0.7060 (mtp) REVERT: A 1401 GLU cc_start: 0.8456 (tt0) cc_final: 0.7762 (tp30) REVERT: A 1453 MET cc_start: 0.4778 (tmm) cc_final: 0.4472 (tmm) REVERT: C 308 ARG cc_start: 0.5614 (mtm180) cc_final: 0.5347 (mtm110) REVERT: C 353 ARG cc_start: 0.8196 (tpt-90) cc_final: 0.7437 (tmm-80) REVERT: C 391 ILE cc_start: 0.8496 (mt) cc_final: 0.8023 (tt) REVERT: C 415 GLN cc_start: 0.7080 (pt0) cc_final: 0.6739 (pp30) REVERT: C 440 GLU cc_start: 0.8564 (tp30) cc_final: 0.7905 (pm20) REVERT: E 1 MET cc_start: 0.4346 (ttt) cc_final: 0.3521 (mmm) REVERT: E 24 MET cc_start: 0.6087 (ptt) cc_final: 0.5886 (ppp) REVERT: E 56 ILE cc_start: 0.7291 (mp) cc_final: 0.6813 (mt) REVERT: E 131 LYS cc_start: 0.6518 (tptm) cc_final: 0.5601 (tmtt) REVERT: E 133 ARG cc_start: 0.5058 (ptp-170) cc_final: 0.4483 (ptp-170) REVERT: E 165 MET cc_start: 0.6231 (pmm) cc_final: 0.4763 (tpt) REVERT: E 182 PHE cc_start: 0.7938 (t80) cc_final: 0.7642 (t80) REVERT: F 102 LEU cc_start: 0.9228 (mt) cc_final: 0.8905 (mt) REVERT: F 411 TYR cc_start: 0.8330 (t80) cc_final: 0.8093 (t80) REVERT: F 490 MET cc_start: 0.8645 (mtp) cc_final: 0.8097 (mtp) REVERT: F 534 ILE cc_start: 0.8787 (pt) cc_final: 0.8514 (pt) REVERT: F 663 PHE cc_start: 0.8178 (m-80) cc_final: 0.7838 (m-10) REVERT: F 725 LYS cc_start: 0.8811 (mttt) cc_final: 0.8318 (tmtt) REVERT: F 775 ASN cc_start: 0.8578 (p0) cc_final: 0.8372 (p0) REVERT: F 824 TRP cc_start: 0.8761 (t60) cc_final: 0.8325 (t60) REVERT: F 851 MET cc_start: 0.0958 (mtt) cc_final: 0.0124 (ttt) REVERT: F 891 ASN cc_start: 0.7824 (OUTLIER) cc_final: 0.7603 (t0) outliers start: 65 outliers final: 41 residues processed: 528 average time/residue: 0.1364 time to fit residues: 117.6722 Evaluate side-chains 484 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 437 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 266 PRO Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 542 TRP Chi-restraints excluded: chain A residue 656 PHE Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 843 PHE Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1068 PHE Chi-restraints excluded: chain A residue 1076 TYR Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1319 CYS Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1368 CYS Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1394 LEU Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 373 HIS Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 176 TYR Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 615 ASN Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 891 ASN Chi-restraints excluded: chain F residue 905 SER Chi-restraints excluded: chain F residue 977 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 181 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 127 optimal weight: 30.0000 chunk 183 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 160 optimal weight: 8.9990 chunk 147 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 ASN ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 HIS F 169 HIS F 520 ASN F 773 ASN F 888 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.132040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.105288 restraints weight = 81750.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.105932 restraints weight = 47555.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.106364 restraints weight = 41950.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.107159 restraints weight = 26108.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.108498 restraints weight = 22289.724| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22073 Z= 0.212 Angle : 0.841 13.057 29970 Z= 0.422 Chirality : 0.049 0.368 3449 Planarity : 0.006 0.101 3745 Dihedral : 7.105 73.014 2905 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.61 % Allowed : 11.66 % Favored : 87.74 % Rotamer: Outliers : 3.89 % Allowed : 20.08 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 4.67 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.16), residues: 2638 helix: 0.11 (0.14), residues: 1360 sheet: -1.01 (0.33), residues: 258 loop : -3.08 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F1032 TYR 0.026 0.002 TYR C 388 PHE 0.030 0.002 PHE F 783 TRP 0.016 0.002 TRP E 32 HIS 0.007 0.001 HIS C 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 (22035) covalent geometry : angle 0.82790 / 0.42 (29873) SS BOND : bond 0.00606 / 0.29 ( 11) SS BOND : angle 1.42286 / 0.83 ( 22) hydrogen bonds : bond 0.04079 / 2.60 ( 929) hydrogen bonds : angle 4.79199 / 3.25 ( 2748) Misc. bond : bond 0.00074 / 0.04 ( 2) link_BETA1-4 : bond 0.00368 / 0.17 ( 10) link_BETA1-4 : angle 1.75979 / 1.07 ( 30) link_NAG-ASN : bond 0.00620 / 0.36 ( 15) link_NAG-ASN : angle 3.63363 / 2.03 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 435 time to evaluate : 0.889 Fit side-chains revert: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 274 HIS cc_start: 0.7584 (OUTLIER) cc_final: 0.6741 (m-70) REVERT: A 295 THR cc_start: 0.8840 (p) cc_final: 0.8577 (t) REVERT: A 327 ASN cc_start: 0.8687 (t0) cc_final: 0.8402 (t0) REVERT: A 366 TYR cc_start: 0.7203 (m-10) cc_final: 0.6745 (m-10) REVERT: A 427 ASP cc_start: 0.6915 (t70) cc_final: 0.6009 (m-30) REVERT: A 470 VAL cc_start: 0.9174 (m) cc_final: 0.8857 (p) REVERT: A 497 ASN cc_start: 0.8849 (m-40) cc_final: 0.8541 (t0) REVERT: A 527 LEU cc_start: 0.8264 (mm) cc_final: 0.7841 (mt) REVERT: A 598 ASP cc_start: 0.7425 (t0) cc_final: 0.6975 (t0) REVERT: A 615 ASP cc_start: 0.6986 (t0) cc_final: 0.6228 (t0) REVERT: A 656 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7467 (t80) REVERT: A 806 LEU cc_start: 0.8814 (mt) cc_final: 0.8414 (tt) REVERT: A 828 ARG cc_start: 0.7989 (mtp85) cc_final: 0.7356 (mmt180) REVERT: A 835 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.7525 (t80) REVERT: A 843 PHE cc_start: 0.7529 (OUTLIER) cc_final: 0.6848 (t80) REVERT: A 906 ARG cc_start: 0.7605 (ptp-170) cc_final: 0.7067 (tpt-90) REVERT: A 941 MET cc_start: 0.8305 (mtt) cc_final: 0.7964 (mtt) REVERT: A 948 GLN cc_start: 0.8476 (tp40) cc_final: 0.8082 (tp-100) REVERT: A 1031 MET cc_start: 0.8312 (mtt) cc_final: 0.7912 (mtt) REVERT: A 1069 GLN cc_start: 0.7101 (mm110) cc_final: 0.6635 (mm-40) REVERT: A 1110 GLN cc_start: 0.8402 (mt0) cc_final: 0.6729 (tp-100) REVERT: A 1125 PHE cc_start: 0.7679 (m-80) cc_final: 0.7336 (m-80) REVERT: A 1166 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8777 (tt) REVERT: A 1189 ILE cc_start: 0.9299 (tp) cc_final: 0.9063 (tt) REVERT: A 1401 GLU cc_start: 0.8403 (tt0) cc_final: 0.7665 (tp30) REVERT: A 1452 ASN cc_start: 0.7547 (p0) cc_final: 0.6547 (p0) REVERT: C 353 ARG cc_start: 0.8199 (tpt-90) cc_final: 0.7345 (tmm-80) REVERT: C 415 GLN cc_start: 0.7163 (pt0) cc_final: 0.6893 (pp30) REVERT: C 440 GLU cc_start: 0.8605 (tp30) cc_final: 0.7933 (pm20) REVERT: E 1 MET cc_start: 0.4389 (ttt) cc_final: 0.3548 (mmm) REVERT: E 56 ILE cc_start: 0.7405 (mp) cc_final: 0.7000 (mt) REVERT: E 131 LYS cc_start: 0.6582 (tptm) cc_final: 0.5627 (tmtt) REVERT: E 133 ARG cc_start: 0.5041 (ptp-170) cc_final: 0.4497 (ptp-170) REVERT: E 165 MET cc_start: 0.6397 (pmm) cc_final: 0.4966 (tpt) REVERT: E 193 PHE cc_start: 0.8174 (t80) cc_final: 0.7815 (t80) REVERT: F 102 LEU cc_start: 0.9274 (mt) cc_final: 0.8801 (mt) REVERT: F 489 VAL cc_start: 0.9606 (p) cc_final: 0.9219 (m) REVERT: F 490 MET cc_start: 0.8729 (mtp) cc_final: 0.7921 (mtp) REVERT: F 508 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8108 (pt) REVERT: F 663 PHE cc_start: 0.8229 (m-80) cc_final: 0.7816 (m-80) REVERT: F 725 LYS cc_start: 0.8857 (mttt) cc_final: 0.8330 (tmtt) REVERT: F 824 TRP cc_start: 0.8726 (t60) cc_final: 0.8323 (t60) REVERT: F 851 MET cc_start: 0.1086 (mtt) cc_final: 0.0176 (ttt) REVERT: F 891 ASN cc_start: 0.7804 (OUTLIER) cc_final: 0.7493 (t0) outliers start: 88 outliers final: 56 residues processed: 482 average time/residue: 0.1379 time to fit residues: 108.6206 Evaluate side-chains 472 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 409 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 266 PRO Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 542 TRP Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 656 PHE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 843 PHE Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1037 ASN Chi-restraints excluded: chain A residue 1076 TYR Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1313 VAL Chi-restraints excluded: chain A residue 1319 CYS Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1368 CYS Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 373 HIS Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 176 TYR Chi-restraints excluded: chain F residue 165 HIS Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 615 ASN Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 891 ASN Chi-restraints excluded: chain F residue 905 SER Chi-restraints excluded: chain F residue 977 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 128 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 200 optimal weight: 0.1980 chunk 31 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 123 optimal weight: 20.0000 chunk 133 optimal weight: 0.4980 chunk 169 optimal weight: 7.9990 chunk 249 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 ASN A1071 GLN ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1303 ASN ** A1398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 HIS F 520 ASN F1007 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.135693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.103905 restraints weight = 94007.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.106158 restraints weight = 43100.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.106611 restraints weight = 27128.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.107047 restraints weight = 24542.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.107457 restraints weight = 20498.421| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 22073 Z= 0.146 Angle : 0.822 15.332 29970 Z= 0.406 Chirality : 0.048 0.397 3449 Planarity : 0.005 0.098 3745 Dihedral : 6.926 69.761 2903 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.53 % Allowed : 11.16 % Favored : 88.31 % Rotamer: Outliers : 3.14 % Allowed : 21.72 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 5.61 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.16), residues: 2638 helix: 0.25 (0.14), residues: 1365 sheet: -1.00 (0.33), residues: 255 loop : -3.04 (0.18), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F1032 TYR 0.028 0.001 TYR C 388 PHE 0.032 0.001 PHE F 783 TRP 0.018 0.001 TRP F 824 HIS 0.007 0.001 HIS C 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (22035) covalent geometry : angle 0.80822 / 0.40 (29873) SS BOND : bond 0.00315 / 0.14 ( 11) SS BOND : angle 2.04680 / 1.22 ( 22) hydrogen bonds : bond 0.03862 / 2.45 ( 929) hydrogen bonds : angle 4.67730 / 3.18 ( 2748) Misc. bond : bond 0.00036 / 0.02 ( 2) link_BETA1-4 : bond 0.00412 / 0.20 ( 10) link_BETA1-4 : angle 1.66624 / 0.99 ( 30) link_NAG-ASN : bond 0.00753 / 0.48 ( 15) link_NAG-ASN : angle 3.59605 / 1.99 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 439 time to evaluate : 0.835 Fit side-chains revert: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 274 HIS cc_start: 0.7337 (OUTLIER) cc_final: 0.6604 (m-70) REVERT: A 295 THR cc_start: 0.8849 (p) cc_final: 0.8513 (t) REVERT: A 366 TYR cc_start: 0.7232 (m-10) cc_final: 0.6776 (m-10) REVERT: A 427 ASP cc_start: 0.6961 (t70) cc_final: 0.6022 (m-30) REVERT: A 470 VAL cc_start: 0.9173 (m) cc_final: 0.8839 (p) REVERT: A 497 ASN cc_start: 0.8773 (m-40) cc_final: 0.8470 (t0) REVERT: A 598 ASP cc_start: 0.7054 (t0) cc_final: 0.6715 (t0) REVERT: A 615 ASP cc_start: 0.6712 (t0) cc_final: 0.6069 (t0) REVERT: A 656 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.7419 (t80) REVERT: A 806 LEU cc_start: 0.8610 (mt) cc_final: 0.8319 (tt) REVERT: A 820 ASP cc_start: 0.6345 (OUTLIER) cc_final: 0.5840 (t70) REVERT: A 828 ARG cc_start: 0.8052 (mtp85) cc_final: 0.7288 (mmt180) REVERT: A 835 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.7450 (t80) REVERT: A 906 ARG cc_start: 0.7575 (ptp-170) cc_final: 0.6985 (tpt-90) REVERT: A 941 MET cc_start: 0.8236 (mtt) cc_final: 0.7929 (mtt) REVERT: A 948 GLN cc_start: 0.8278 (tp40) cc_final: 0.7954 (tp-100) REVERT: A 1056 MET cc_start: 0.7863 (mmm) cc_final: 0.7106 (tmm) REVERT: A 1069 GLN cc_start: 0.7011 (mm110) cc_final: 0.6769 (mm-40) REVERT: A 1110 GLN cc_start: 0.8449 (mt0) cc_final: 0.6735 (tp-100) REVERT: A 1125 PHE cc_start: 0.7815 (m-80) cc_final: 0.7430 (m-80) REVERT: A 1166 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8927 (tt) REVERT: A 1189 ILE cc_start: 0.9290 (tp) cc_final: 0.9032 (tt) REVERT: A 1359 TYR cc_start: 0.6555 (m-80) cc_final: 0.6179 (m-80) REVERT: A 1401 GLU cc_start: 0.8370 (tt0) cc_final: 0.7596 (tp30) REVERT: A 1452 ASN cc_start: 0.7668 (p0) cc_final: 0.6818 (p0) REVERT: C 350 GLU cc_start: 0.5429 (mm-30) cc_final: 0.5134 (mm-30) REVERT: C 353 ARG cc_start: 0.8210 (tpt-90) cc_final: 0.7441 (tmm-80) REVERT: C 415 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7109 (pp30) REVERT: C 440 GLU cc_start: 0.8623 (tp30) cc_final: 0.7971 (pm20) REVERT: E 56 ILE cc_start: 0.7298 (mp) cc_final: 0.6862 (mt) REVERT: E 131 LYS cc_start: 0.6671 (tptm) cc_final: 0.5692 (tmtt) REVERT: E 133 ARG cc_start: 0.5047 (ptp-170) cc_final: 0.4416 (ptp-170) REVERT: E 165 MET cc_start: 0.6346 (pmm) cc_final: 0.4966 (tpt) REVERT: F 102 LEU cc_start: 0.9227 (mt) cc_final: 0.8909 (mt) REVERT: F 449 THR cc_start: 0.9148 (m) cc_final: 0.8859 (p) REVERT: F 489 VAL cc_start: 0.9651 (p) cc_final: 0.9336 (m) REVERT: F 490 MET cc_start: 0.8778 (mtp) cc_final: 0.8178 (mtm) REVERT: F 508 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8168 (pt) REVERT: F 663 PHE cc_start: 0.8217 (m-80) cc_final: 0.7870 (m-10) REVERT: F 725 LYS cc_start: 0.8921 (mttt) cc_final: 0.8371 (tmtt) REVERT: F 824 TRP cc_start: 0.8757 (t60) cc_final: 0.8342 (t60) REVERT: F 851 MET cc_start: 0.0905 (mtt) cc_final: 0.0002 (ttt) REVERT: F 891 ASN cc_start: 0.7621 (OUTLIER) cc_final: 0.7384 (t160) outliers start: 71 outliers final: 51 residues processed: 480 average time/residue: 0.1349 time to fit residues: 106.5561 Evaluate side-chains 472 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 413 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 266 PRO Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 542 TRP Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 656 PHE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1068 PHE Chi-restraints excluded: chain A residue 1076 TYR Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1319 CYS Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1338 CYS Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 373 HIS Chi-restraints excluded: chain C residue 415 GLN Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 176 TYR Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 520 ASN Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 615 ASN Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 777 VAL Chi-restraints excluded: chain F residue 891 ASN Chi-restraints excluded: chain F residue 905 SER Chi-restraints excluded: chain F residue 977 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 184 optimal weight: 0.9990 chunk 146 optimal weight: 8.9990 chunk 226 optimal weight: 0.9990 chunk 173 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 264 optimal weight: 7.9990 chunk 245 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 ASN ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 HIS C 445 HIS ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 379 ASN F 520 ASN ** F 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.134733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.107709 restraints weight = 64494.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.107316 restraints weight = 33194.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.108009 restraints weight = 31738.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.108257 restraints weight = 22759.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.108786 restraints weight = 20174.170| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 22073 Z= 0.171 Angle : 0.827 13.241 29970 Z= 0.412 Chirality : 0.049 0.380 3449 Planarity : 0.005 0.101 3745 Dihedral : 6.849 68.396 2903 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.49 % Allowed : 11.69 % Favored : 87.81 % Rotamer: Outliers : 3.63 % Allowed : 21.36 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 4.67 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.16), residues: 2638 helix: 0.31 (0.14), residues: 1370 sheet: -1.08 (0.32), residues: 272 loop : -3.05 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 308 TYR 0.029 0.002 TYR A 650 PHE 0.039 0.002 PHE F 296 TRP 0.018 0.002 TRP A1406 HIS 0.006 0.001 HIS C 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (22035) covalent geometry : angle 0.81340 / 0.41 (29873) SS BOND : bond 0.00313 / 0.14 ( 11) SS BOND : angle 2.32532 / 1.38 ( 22) hydrogen bonds : bond 0.03825 / 2.43 ( 929) hydrogen bonds : angle 4.63480 / 3.15 ( 2748) Misc. bond : bond 0.00032 / 0.02 ( 2) link_BETA1-4 : bond 0.00368 / 0.18 ( 10) link_BETA1-4 : angle 1.67122 / 1.01 ( 30) link_NAG-ASN : bond 0.00667 / 0.41 ( 15) link_NAG-ASN : angle 3.46232 / 1.91 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 434 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 HIS cc_start: 0.7325 (OUTLIER) cc_final: 0.6522 (m-70) REVERT: A 295 THR cc_start: 0.8815 (p) cc_final: 0.8458 (t) REVERT: A 366 TYR cc_start: 0.7114 (m-10) cc_final: 0.6711 (m-10) REVERT: A 427 ASP cc_start: 0.6969 (t70) cc_final: 0.6014 (m-30) REVERT: A 470 VAL cc_start: 0.9198 (m) cc_final: 0.8883 (p) REVERT: A 497 ASN cc_start: 0.8813 (m-40) cc_final: 0.8525 (t0) REVERT: A 536 PHE cc_start: 0.8528 (m-10) cc_final: 0.8318 (m-80) REVERT: A 598 ASP cc_start: 0.6866 (t0) cc_final: 0.6530 (t0) REVERT: A 615 ASP cc_start: 0.6825 (t0) cc_final: 0.6099 (t0) REVERT: A 656 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.7320 (t80) REVERT: A 806 LEU cc_start: 0.8629 (mt) cc_final: 0.8341 (tt) REVERT: A 820 ASP cc_start: 0.6162 (OUTLIER) cc_final: 0.5776 (t70) REVERT: A 822 ILE cc_start: 0.7264 (mm) cc_final: 0.6946 (tp) REVERT: A 828 ARG cc_start: 0.8064 (mtp85) cc_final: 0.7411 (mmt180) REVERT: A 835 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7574 (t80) REVERT: A 843 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.7057 (t80) REVERT: A 906 ARG cc_start: 0.7560 (ptp-170) cc_final: 0.7108 (tpt-90) REVERT: A 948 GLN cc_start: 0.8324 (tp40) cc_final: 0.8031 (tp-100) REVERT: A 1056 MET cc_start: 0.7819 (mmm) cc_final: 0.7120 (tmm) REVERT: A 1069 GLN cc_start: 0.7003 (mm110) cc_final: 0.6782 (mm-40) REVERT: A 1189 ILE cc_start: 0.9240 (tp) cc_final: 0.8962 (tt) REVERT: A 1292 ILE cc_start: 0.8246 (mm) cc_final: 0.8025 (mm) REVERT: A 1295 VAL cc_start: 0.9181 (OUTLIER) cc_final: 0.8942 (p) REVERT: A 1359 TYR cc_start: 0.6536 (m-80) cc_final: 0.6049 (m-80) REVERT: A 1401 GLU cc_start: 0.8366 (tt0) cc_final: 0.7510 (tp30) REVERT: A 1452 ASN cc_start: 0.7902 (p0) cc_final: 0.7174 (p0) REVERT: C 350 GLU cc_start: 0.5331 (mm-30) cc_final: 0.5118 (mm-30) REVERT: C 353 ARG cc_start: 0.8183 (tpt-90) cc_final: 0.7503 (tmm-80) REVERT: C 415 GLN cc_start: 0.6973 (OUTLIER) cc_final: 0.6722 (pp30) REVERT: C 440 GLU cc_start: 0.8579 (tp30) cc_final: 0.7928 (pm20) REVERT: E 10 ARG cc_start: 0.7865 (mpp80) cc_final: 0.6996 (mtt90) REVERT: E 56 ILE cc_start: 0.7348 (mp) cc_final: 0.6909 (mt) REVERT: E 131 LYS cc_start: 0.6511 (tptm) cc_final: 0.5566 (tmtt) REVERT: E 133 ARG cc_start: 0.5014 (ptp-170) cc_final: 0.4358 (ptp-170) REVERT: E 165 MET cc_start: 0.6352 (pmm) cc_final: 0.4997 (tpt) REVERT: F 102 LEU cc_start: 0.9280 (mt) cc_final: 0.8927 (mt) REVERT: F 489 VAL cc_start: 0.9604 (p) cc_final: 0.9227 (m) REVERT: F 490 MET cc_start: 0.8798 (mtp) cc_final: 0.8278 (mtm) REVERT: F 508 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8114 (pt) REVERT: F 663 PHE cc_start: 0.8155 (m-80) cc_final: 0.7824 (m-80) REVERT: F 725 LYS cc_start: 0.8837 (mttt) cc_final: 0.8354 (tmtt) REVERT: F 824 TRP cc_start: 0.8653 (t60) cc_final: 0.8383 (t60) REVERT: F 851 MET cc_start: 0.0889 (mtt) cc_final: 0.0181 (ttt) outliers start: 82 outliers final: 62 residues processed: 478 average time/residue: 0.1407 time to fit residues: 109.8426 Evaluate side-chains 487 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 417 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 266 PRO Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 542 TRP Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 656 PHE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 843 PHE Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 993 ASN Chi-restraints excluded: chain A residue 1037 ASN Chi-restraints excluded: chain A residue 1076 TYR Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1319 CYS Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1338 CYS Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 373 HIS Chi-restraints excluded: chain C residue 415 GLN Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 176 TYR Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 520 ASN Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 615 ASN Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 777 VAL Chi-restraints excluded: chain F residue 891 ASN Chi-restraints excluded: chain F residue 905 SER Chi-restraints excluded: chain F residue 977 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 113 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 176 optimal weight: 0.0870 chunk 60 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 193 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 228 optimal weight: 0.0470 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 GLN C 445 HIS ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 520 ASN ** F 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.136613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.110187 restraints weight = 79084.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.111164 restraints weight = 45368.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.111790 restraints weight = 35441.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.112279 restraints weight = 23478.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.113057 restraints weight = 20795.157| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 22073 Z= 0.139 Angle : 0.836 15.577 29970 Z= 0.413 Chirality : 0.049 0.365 3449 Planarity : 0.005 0.099 3745 Dihedral : 6.757 67.023 2903 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.49 % Allowed : 11.05 % Favored : 88.46 % Rotamer: Outliers : 3.05 % Allowed : 22.29 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 3.74 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.16), residues: 2638 helix: 0.43 (0.14), residues: 1365 sheet: -0.93 (0.32), residues: 266 loop : -2.92 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 308 TYR 0.031 0.001 TYR A 650 PHE 0.038 0.002 PHE E 146 TRP 0.016 0.001 TRP F 824 HIS 0.013 0.001 HIS A 992 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (22035) covalent geometry : angle 0.82351 / 0.41 (29873) SS BOND : bond 0.00237 / 0.11 ( 11) SS BOND : angle 2.09501 / 1.26 ( 22) hydrogen bonds : bond 0.03817 / 2.44 ( 929) hydrogen bonds : angle 4.59039 / 3.12 ( 2748) Misc. bond : bond 0.00024 / 0.01 ( 2) link_BETA1-4 : bond 0.00393 / 0.19 ( 10) link_BETA1-4 : angle 1.58314 / 0.94 ( 30) link_NAG-ASN : bond 0.00691 / 0.43 ( 15) link_NAG-ASN : angle 3.35864 / 1.84 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 456 time to evaluate : 0.825 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 HIS cc_start: 0.7047 (OUTLIER) cc_final: 0.6569 (m-70) REVERT: A 366 TYR cc_start: 0.6890 (m-10) cc_final: 0.6565 (m-10) REVERT: A 427 ASP cc_start: 0.6866 (t70) cc_final: 0.5966 (m-30) REVERT: A 470 VAL cc_start: 0.9164 (m) cc_final: 0.8835 (p) REVERT: A 497 ASN cc_start: 0.8834 (m-40) cc_final: 0.8527 (t0) REVERT: A 598 ASP cc_start: 0.6807 (t0) cc_final: 0.6457 (t0) REVERT: A 615 ASP cc_start: 0.6712 (t0) cc_final: 0.6145 (t0) REVERT: A 656 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.7215 (t80) REVERT: A 806 LEU cc_start: 0.8627 (mt) cc_final: 0.8365 (tt) REVERT: A 820 ASP cc_start: 0.6167 (OUTLIER) cc_final: 0.5816 (t70) REVERT: A 822 ILE cc_start: 0.7266 (mm) cc_final: 0.6950 (tp) REVERT: A 828 ARG cc_start: 0.8018 (mtp85) cc_final: 0.7387 (mmt180) REVERT: A 843 PHE cc_start: 0.7429 (OUTLIER) cc_final: 0.6898 (t80) REVERT: A 899 LEU cc_start: 0.9338 (mm) cc_final: 0.9006 (mm) REVERT: A 906 ARG cc_start: 0.7482 (ptp-170) cc_final: 0.7076 (tpt-90) REVERT: A 948 GLN cc_start: 0.8408 (tp40) cc_final: 0.8089 (tp-100) REVERT: A 1056 MET cc_start: 0.7732 (mmm) cc_final: 0.7142 (tmm) REVERT: A 1058 ASN cc_start: 0.8456 (m-40) cc_final: 0.8157 (m110) REVERT: A 1189 ILE cc_start: 0.9202 (tp) cc_final: 0.8925 (tt) REVERT: A 1254 ARG cc_start: 0.8999 (ttp80) cc_final: 0.8719 (ttp80) REVERT: A 1292 ILE cc_start: 0.8023 (mm) cc_final: 0.7803 (mm) REVERT: A 1359 TYR cc_start: 0.6413 (m-80) cc_final: 0.5966 (m-80) REVERT: A 1401 GLU cc_start: 0.8270 (tt0) cc_final: 0.7462 (tp30) REVERT: A 1452 ASN cc_start: 0.7965 (p0) cc_final: 0.7318 (p0) REVERT: C 350 GLU cc_start: 0.5211 (mm-30) cc_final: 0.4782 (mm-30) REVERT: C 353 ARG cc_start: 0.8188 (tpt-90) cc_final: 0.7392 (tmm-80) REVERT: C 440 GLU cc_start: 0.8517 (tp30) cc_final: 0.7860 (pm20) REVERT: E 56 ILE cc_start: 0.7317 (mp) cc_final: 0.6858 (mt) REVERT: E 131 LYS cc_start: 0.6414 (tptm) cc_final: 0.5549 (tmtt) REVERT: E 133 ARG cc_start: 0.4942 (ptp-170) cc_final: 0.4212 (ptp-170) REVERT: E 165 MET cc_start: 0.6536 (pmm) cc_final: 0.5140 (tpt) REVERT: E 182 PHE cc_start: 0.8124 (t80) cc_final: 0.7915 (t80) REVERT: F 102 LEU cc_start: 0.9319 (mt) cc_final: 0.8973 (mt) REVERT: F 449 THR cc_start: 0.9179 (m) cc_final: 0.8780 (p) REVERT: F 489 VAL cc_start: 0.9556 (p) cc_final: 0.9179 (m) REVERT: F 490 MET cc_start: 0.8692 (mtp) cc_final: 0.8228 (mtm) REVERT: F 508 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8012 (pt) REVERT: F 536 VAL cc_start: 0.6887 (OUTLIER) cc_final: 0.6580 (m) REVERT: F 663 PHE cc_start: 0.8108 (m-80) cc_final: 0.7856 (m-10) REVERT: F 725 LYS cc_start: 0.8724 (mttt) cc_final: 0.8338 (tmtt) REVERT: F 775 ASN cc_start: 0.8440 (p0) cc_final: 0.8237 (p0) REVERT: F 824 TRP cc_start: 0.8686 (t60) cc_final: 0.8466 (t60) REVERT: F 851 MET cc_start: 0.0744 (mtt) cc_final: 0.0097 (ttt) outliers start: 69 outliers final: 52 residues processed: 490 average time/residue: 0.1335 time to fit residues: 107.3400 Evaluate side-chains 486 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 428 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 266 PRO Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 542 TRP Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 656 PHE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 843 PHE Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1037 ASN Chi-restraints excluded: chain A residue 1076 TYR Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1306 PHE Chi-restraints excluded: chain A residue 1319 CYS Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1338 CYS Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 373 HIS Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 176 TYR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 417 SER Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 615 ASN Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 777 VAL Chi-restraints excluded: chain F residue 891 ASN Chi-restraints excluded: chain F residue 905 SER Chi-restraints excluded: chain F residue 977 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 183 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 181 optimal weight: 0.4980 chunk 81 optimal weight: 0.6980 chunk 146 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 106 optimal weight: 0.0570 chunk 33 optimal weight: 0.9980 chunk 147 optimal weight: 40.0000 chunk 217 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 ASN A1069 GLN ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 HIS ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 ASN F 520 ASN F 655 ASN ** F 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.137568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.111301 restraints weight = 76403.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.111890 restraints weight = 41075.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.112543 restraints weight = 34942.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.112834 restraints weight = 23319.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.113756 restraints weight = 20771.943| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.6041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22073 Z= 0.136 Angle : 0.821 15.190 29970 Z= 0.407 Chirality : 0.049 0.452 3449 Planarity : 0.005 0.104 3745 Dihedral : 6.608 67.349 2903 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.20 % Favored : 88.38 % Rotamer: Outliers : 2.61 % Allowed : 23.35 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 2.80 % 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 are not related in a simple way. whole: -1.24 (0.17), residues: 2638 helix: 0.51 (0.14), residues: 1357 sheet: -0.70 (0.32), residues: 259 loop : -2.76 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 347 TYR 0.026 0.001 TYR C 388 PHE 0.038 0.001 PHE F 296 TRP 0.035 0.002 TRP A1406 HIS 0.006 0.001 HIS A 992 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (22035) covalent geometry : angle 0.81034 / 0.40 (29873) SS BOND : bond 0.00223 / 0.10 ( 11) SS BOND : angle 1.91694 / 1.15 ( 22) hydrogen bonds : bond 0.03723 / 2.39 ( 929) hydrogen bonds : angle 4.50741 / 3.08 ( 2748) Misc. bond : bond 0.00034 / 0.02 ( 2) link_BETA1-4 : bond 0.00361 / 0.18 ( 10) link_BETA1-4 : angle 1.48661 / 0.88 ( 30) link_NAG-ASN : bond 0.00666 / 0.42 ( 15) link_NAG-ASN : angle 3.16269 / 1.72 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 447 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 HIS cc_start: 0.7135 (OUTLIER) cc_final: 0.6265 (m-70) REVERT: A 366 TYR cc_start: 0.7019 (m-10) cc_final: 0.6671 (m-10) REVERT: A 427 ASP cc_start: 0.6857 (t70) cc_final: 0.5990 (m-30) REVERT: A 470 VAL cc_start: 0.9185 (m) cc_final: 0.8859 (p) REVERT: A 497 ASN cc_start: 0.8726 (m-40) cc_final: 0.8376 (t0) REVERT: A 615 ASP cc_start: 0.6638 (t0) cc_final: 0.6129 (t0) REVERT: A 656 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7163 (t80) REVERT: A 806 LEU cc_start: 0.8619 (mt) cc_final: 0.8268 (tt) REVERT: A 820 ASP cc_start: 0.6114 (OUTLIER) cc_final: 0.5761 (t70) REVERT: A 822 ILE cc_start: 0.7158 (mm) cc_final: 0.6869 (tp) REVERT: A 828 ARG cc_start: 0.8018 (mtp85) cc_final: 0.7365 (mmt180) REVERT: A 843 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.6644 (t80) REVERT: A 899 LEU cc_start: 0.9331 (mm) cc_final: 0.9023 (mm) REVERT: A 906 ARG cc_start: 0.7500 (ptp-170) cc_final: 0.7061 (tpt-90) REVERT: A 948 GLN cc_start: 0.8361 (tp40) cc_final: 0.8129 (tp-100) REVERT: A 1004 MET cc_start: 0.8182 (mmm) cc_final: 0.7712 (tmm) REVERT: A 1056 MET cc_start: 0.7632 (mmm) cc_final: 0.7027 (tmm) REVERT: A 1069 GLN cc_start: 0.7137 (mm110) cc_final: 0.6646 (mm-40) REVERT: A 1158 THR cc_start: 0.9419 (m) cc_final: 0.9216 (p) REVERT: A 1292 ILE cc_start: 0.7862 (mm) cc_final: 0.7645 (mm) REVERT: A 1294 LEU cc_start: 0.8416 (mt) cc_final: 0.7908 (mp) REVERT: A 1359 TYR cc_start: 0.6349 (m-80) cc_final: 0.5936 (m-80) REVERT: A 1401 GLU cc_start: 0.8271 (tt0) cc_final: 0.7518 (tp30) REVERT: A 1452 ASN cc_start: 0.8030 (p0) cc_final: 0.7390 (p0) REVERT: C 350 GLU cc_start: 0.5325 (mm-30) cc_final: 0.4918 (mm-30) REVERT: C 353 ARG cc_start: 0.8161 (tpt-90) cc_final: 0.7357 (tmm-80) REVERT: C 440 GLU cc_start: 0.8545 (tp30) cc_final: 0.7876 (pm20) REVERT: E 131 LYS cc_start: 0.6496 (tptm) cc_final: 0.5519 (tmtt) REVERT: E 133 ARG cc_start: 0.4661 (ptp-170) cc_final: 0.3835 (ptp-170) REVERT: E 165 MET cc_start: 0.6497 (pmm) cc_final: 0.5167 (tpt) REVERT: E 182 PHE cc_start: 0.8069 (t80) cc_final: 0.7770 (t80) REVERT: F 102 LEU cc_start: 0.9267 (mt) cc_final: 0.8954 (mt) REVERT: F 411 TYR cc_start: 0.8398 (t80) cc_final: 0.8113 (t80) REVERT: F 449 THR cc_start: 0.9145 (m) cc_final: 0.8729 (p) REVERT: F 489 VAL cc_start: 0.9584 (p) cc_final: 0.9222 (m) REVERT: F 490 MET cc_start: 0.8745 (mtp) cc_final: 0.8015 (mtp) REVERT: F 508 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8004 (pt) REVERT: F 536 VAL cc_start: 0.6766 (OUTLIER) cc_final: 0.6501 (m) REVERT: F 663 PHE cc_start: 0.8082 (m-80) cc_final: 0.7819 (m-10) REVERT: F 725 LYS cc_start: 0.8720 (mttt) cc_final: 0.8326 (tmtt) REVERT: F 775 ASN cc_start: 0.8533 (p0) cc_final: 0.8328 (p0) REVERT: F 851 MET cc_start: 0.0999 (mtt) cc_final: 0.0469 (ttt) outliers start: 59 outliers final: 48 residues processed: 477 average time/residue: 0.1333 time to fit residues: 105.4003 Evaluate side-chains 481 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 427 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 656 PHE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 843 PHE Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1037 ASN Chi-restraints excluded: chain A residue 1076 TYR Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1306 PHE Chi-restraints excluded: chain A residue 1319 CYS Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1338 CYS Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1418 LYS Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 373 HIS Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 176 TYR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 417 SER Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 520 ASN Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 615 ASN Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 777 VAL Chi-restraints excluded: chain F residue 891 ASN Chi-restraints excluded: chain F residue 977 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 112 optimal weight: 9.9990 chunk 194 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 147 optimal weight: 20.0000 chunk 86 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 HIS ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 520 ASN ** F 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 866 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.134570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.103884 restraints weight = 103673.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.105271 restraints weight = 45213.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.107334 restraints weight = 31601.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.107186 restraints weight = 27347.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.107160 restraints weight = 21247.328| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.5984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 22073 Z= 0.202 Angle : 0.859 14.655 29970 Z= 0.430 Chirality : 0.050 0.362 3449 Planarity : 0.006 0.107 3745 Dihedral : 6.614 66.944 2901 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.46 % Allowed : 11.81 % Favored : 87.74 % Rotamer: Outliers : 2.83 % Allowed : 23.88 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 2.80 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.16), residues: 2638 helix: 0.45 (0.14), residues: 1362 sheet: -0.90 (0.32), residues: 274 loop : -2.90 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 308 TYR 0.032 0.002 TYR F 522 PHE 0.040 0.002 PHE A 839 TRP 0.059 0.002 TRP F 824 HIS 0.005 0.001 HIS F 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (22035) covalent geometry : angle 0.84852 / 0.43 (29873) SS BOND : bond 0.00305 / 0.13 ( 11) SS BOND : angle 2.01585 / 1.21 ( 22) hydrogen bonds : bond 0.03931 / 2.55 ( 929) hydrogen bonds : angle 4.70733 / 3.22 ( 2748) Misc. bond : bond 0.00035 / 0.02 ( 2) link_BETA1-4 : bond 0.00336 / 0.17 ( 10) link_BETA1-4 : angle 1.58894 / 0.97 ( 30) link_NAG-ASN : bond 0.00557 / 0.33 ( 15) link_NAG-ASN : angle 3.14070 / 1.73 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4490.62 seconds wall clock time: 78 minutes 15.69 seconds (4695.69 seconds total)