Starting phenix.real_space_refine on Fri Sep 19 01:19:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5gjw_9515/09_2025/5gjw_9515.cif Found real_map, /net/cci-nas-00/data/ceres_data/5gjw_9515/09_2025/5gjw_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 { model { file = "/net/cci-nas-00/data/ceres_data/5gjw_9515/09_2025/5gjw_9515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5gjw_9515/09_2025/5gjw_9515.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5gjw_9515/09_2025/5gjw_9515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5gjw_9515/09_2025/5gjw_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 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 dihedrals: 3 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 dihedrals: 21 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: 6.49, per 1000 atoms: 0.30 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: 1.97 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.84 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: 4.22 Time building geometry restraints manager: 2.52 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: 12966 23.12 - 46.24: 386 46.24 - 69.37: 71 69.37 - 92.49: 19 92.49 - 115.61: 10 Dihedral angle restraints: 13452 sinusoidal: 5611 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 13449 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.710 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 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 : 12.600 115.611 8347 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 aren 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 covalent geometry : bond 0.01158 (22035) covalent geometry : angle 1.51360 (29873) SS BOND : bond 0.02403 ( 11) SS BOND : angle 14.36723 ( 22) hydrogen bonds : bond 0.30440 ( 929) hydrogen bonds : angle 10.36651 ( 2748) Misc. bond : bond 0.29398 ( 2) link_BETA1-4 : bond 0.00994 ( 10) link_BETA1-4 : angle 3.84674 ( 30) link_NAG-ASN : bond 0.00998 ( 15) link_NAG-ASN : angle 7.02614 ( 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 : 0.814 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: 0.9029 (t) REVERT: A 327 ASN cc_start: 0.9125 (m-40) cc_final: 0.8919 (m-40) REVERT: A 343 LYS cc_start: 0.7642 (mttm) cc_final: 0.7291 (tptt) REVERT: A 423 TRP cc_start: 0.7502 (t-100) cc_final: 0.7298 (t-100) REVERT: A 427 ASP cc_start: 0.8156 (t70) cc_final: 0.7177 (m-30) REVERT: A 436 TRP cc_start: 0.7606 (m100) cc_final: 0.7048 (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: 0.8949 (t0) REVERT: A 632 TYR cc_start: 0.8093 (t80) cc_final: 0.7892 (t80) REVERT: A 641 PHE cc_start: 0.8962 (m-10) cc_final: 0.8617 (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: 0.8470 (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: 0.7602 (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: 0.8426 (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: 0.8456 (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: 0.8361 (tp30) REVERT: A 1405 ILE cc_start: 0.8195 (mp) cc_final: 0.7829 (mt) REVERT: A 1428 ARG cc_start: 0.8559 (ttt90) cc_final: 0.8294 (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: 0.5532 (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: 0.8368 (tp) 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: 0.7075 (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: 0.7194 (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: 0.8829 (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: 0.8430 (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: 0.9147 (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: 0.9018 (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: 0.8622 (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: 0.8912 (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: 0.1608 time to fit residues: 185.6087 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 : 0.834 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1183 ASN A1299 GLN A1374 ASN A1383 ASN E 38 HIS F 43 GLN 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 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.135736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.108480 restraints weight = 66336.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.108406 restraints weight = 34437.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.109103 restraints weight = 31519.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.109486 restraints weight = 22662.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.110539 restraints weight = 19880.793| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 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 = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22073 Z= 0.186 Angle : 0.926 15.853 29970 Z= 0.474 Chirality : 0.052 0.552 3449 Planarity : 0.007 0.107 3745 Dihedral : 10.869 91.824 3446 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.95 % Allowed : 10.59 % Favored : 88.46 % Rotamer: Outliers : 2.92 % Allowed : 11.76 % 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 aren not related in a simple way. whole: -3.68 (0.14), residues: 2638 helix: -1.89 (0.11), residues: 1333 sheet: -1.30 (0.32), residues: 249 loop : -3.40 (0.17), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 95 TYR 0.029 0.002 TYR F 609 PHE 0.030 0.002 PHE F 783 TRP 0.029 0.002 TRP F 824 HIS 0.013 0.002 HIS A 996 Details of bonding type rmsd covalent geometry : bond 0.00392 (22035) covalent geometry : angle 0.89908 (29873) SS BOND : bond 0.00587 ( 11) SS BOND : angle 2.07945 ( 22) hydrogen bonds : bond 0.06115 ( 929) hydrogen bonds : angle 5.84473 ( 2748) Misc. bond : bond 0.00051 ( 2) link_BETA1-4 : bond 0.00730 ( 10) link_BETA1-4 : angle 2.62290 ( 30) link_NAG-ASN : bond 0.01141 ( 15) link_NAG-ASN : angle 5.22595 ( 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 651 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 584 time to evaluate : 0.867 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: symmetry clash REVERT: A 222 MET cc_start: 0.8317 (mmt) cc_final: 0.8076 (mpp) REVERT: A 295 THR cc_start: 0.8638 (p) cc_final: 0.8193 (t) REVERT: A 375 VAL cc_start: 0.6708 (m) cc_final: 0.6492 (p) REVERT: A 427 ASP cc_start: 0.6955 (t70) cc_final: 0.6107 (m-30) REVERT: A 434 PHE cc_start: 0.7865 (m-10) cc_final: 0.7566 (m-80) REVERT: A 444 LEU cc_start: 0.9180 (mt) cc_final: 0.8852 (tt) REVERT: A 470 VAL cc_start: 0.9125 (m) cc_final: 0.8821 (p) REVERT: A 483 MET cc_start: 0.6236 (tmm) cc_final: 0.6028 (tmm) REVERT: A 497 ASN cc_start: 0.8869 (m-40) cc_final: 0.8461 (t0) REVERT: A 598 ASP cc_start: 0.7532 (t0) cc_final: 0.7076 (t0) REVERT: A 615 ASP cc_start: 0.6811 (t0) cc_final: 0.6343 (t0) REVERT: A 686 MET cc_start: 0.4851 (ptp) cc_final: 0.4497 (ptm) REVERT: A 806 LEU cc_start: 0.8812 (mt) cc_final: 0.8606 (tt) REVERT: A 811 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8229 (mt) REVERT: A 828 ARG cc_start: 0.7675 (mtp85) cc_final: 0.7223 (mmt180) REVERT: A 906 ARG cc_start: 0.7515 (ptp-170) cc_final: 0.7141 (tpt-90) REVERT: A 941 MET cc_start: 0.8123 (mtt) cc_final: 0.7812 (mtt) REVERT: A 1086 ARG cc_start: 0.6911 (ttm-80) cc_final: 0.6699 (tpt90) REVERT: A 1087 GLN cc_start: 0.6828 (tt0) cc_final: 0.6223 (pp30) REVERT: A 1163 LEU cc_start: 0.9134 (mt) cc_final: 0.8760 (tt) REVERT: A 1165 MET cc_start: 0.8484 (tmm) cc_final: 0.8212 (tmm) REVERT: A 1381 MET cc_start: 0.7783 (mtt) cc_final: 0.7386 (mtp) REVERT: A 1401 GLU cc_start: 0.8282 (tt0) cc_final: 0.7498 (tp30) REVERT: A 1453 MET cc_start: 0.4699 (tmm) cc_final: 0.4420 (tmm) REVERT: B 165 LEU cc_start: 0.3551 (OUTLIER) cc_final: 0.3264 (tp) REVERT: C 362 GLN cc_start: 0.7331 (mt0) cc_final: 0.6931 (pt0) REVERT: C 364 VAL cc_start: 0.6981 (t) cc_final: 0.6635 (p) REVERT: C 391 ILE cc_start: 0.8279 (mt) cc_final: 0.8059 (tt) REVERT: C 411 HIS cc_start: 0.6475 (m-70) cc_final: 0.5970 (m-70) REVERT: C 440 GLU cc_start: 0.8378 (tp30) cc_final: 0.7825 (pm20) REVERT: E 1 MET cc_start: 0.4693 (ttt) cc_final: 0.3811 (mmm) REVERT: E 32 TRP cc_start: 0.6570 (m100) cc_final: 0.6137 (m100) REVERT: E 51 PHE cc_start: 0.7952 (m-80) cc_final: 0.7521 (m-80) REVERT: E 56 ILE cc_start: 0.6905 (mp) cc_final: 0.6288 (mt) REVERT: E 131 LYS cc_start: 0.6896 (tptm) cc_final: 0.6052 (tmtt) REVERT: E 133 ARG cc_start: 0.5639 (ptp-170) cc_final: 0.5118 (ptp-170) REVERT: E 152 PHE cc_start: 0.9019 (t80) cc_final: 0.8806 (t80) REVERT: E 209 GLN cc_start: 0.7645 (mm-40) cc_final: 0.6805 (mm-40) REVERT: F 71 THR cc_start: 0.7696 (m) cc_final: 0.7385 (p) REVERT: F 302 ASP cc_start: 0.7712 (m-30) cc_final: 0.7212 (p0) REVERT: F 345 GLN cc_start: 0.8309 (mm-40) cc_final: 0.8086 (mm-40) REVERT: F 490 MET cc_start: 0.8784 (mmt) cc_final: 0.8281 (mmt) REVERT: F 725 LYS cc_start: 0.8670 (mttt) cc_final: 0.8332 (tmtt) REVERT: F 758 ASN cc_start: 0.8706 (t0) cc_final: 0.5145 (t0) REVERT: F 851 MET cc_start: 0.1719 (mtt) cc_final: 0.0797 (ttm) REVERT: F 886 MET cc_start: 0.8021 (tpp) cc_final: 0.7464 (tpt) outliers start: 67 outliers final: 33 residues processed: 621 average time/residue: 0.1413 time to fit residues: 139.9711 Evaluate side-chains 485 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 450 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 108 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 223 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 252 optimal weight: 2.9990 chunk 245 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A1303 ASN ** 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 313 ASN F 316 ASN F 348 ASN F 520 ASN F 756 GLN F 773 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.132982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.106170 restraints weight = 79901.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.106285 restraints weight = 48282.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.107058 restraints weight = 41020.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.107995 restraints weight = 26233.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.108878 restraints weight = 22363.490| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 22073 Z= 0.182 Angle : 0.873 14.836 29970 Z= 0.443 Chirality : 0.052 0.521 3449 Planarity : 0.006 0.109 3745 Dihedral : 9.633 83.221 3431 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.87 % Allowed : 11.09 % Favored : 88.04 % Rotamer: Outliers : 3.76 % Allowed : 15.79 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 5.61 % Twisted General : 0.55 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.85 (0.15), residues: 2638 helix: -0.98 (0.13), residues: 1353 sheet: -1.31 (0.32), residues: 267 loop : -3.29 (0.18), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 165 TYR 0.028 0.002 TYR F 609 PHE 0.024 0.002 PHE F 783 TRP 0.026 0.002 TRP F 824 HIS 0.005 0.001 HIS C 373 Details of bonding type rmsd covalent geometry : bond 0.00391 (22035) covalent geometry : angle 0.85108 (29873) SS BOND : bond 0.02771 ( 11) SS BOND : angle 1.64585 ( 22) hydrogen bonds : bond 0.05092 ( 929) hydrogen bonds : angle 5.31034 ( 2748) Misc. bond : bond 0.00012 ( 2) link_BETA1-4 : bond 0.00457 ( 10) link_BETA1-4 : angle 2.49135 ( 30) link_NAG-ASN : bond 0.00856 ( 15) link_NAG-ASN : angle 4.64233 ( 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: 86 poor density : 484 time to evaluate : 0.843 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 295 THR cc_start: 0.8667 (p) cc_final: 0.8244 (t) REVERT: A 341 ARG cc_start: 0.8492 (ptp90) cc_final: 0.8065 (ptp90) REVERT: A 366 TYR cc_start: 0.6780 (m-80) cc_final: 0.6308 (m-80) REVERT: A 427 ASP cc_start: 0.6897 (t70) cc_final: 0.6051 (m-30) REVERT: A 444 LEU cc_start: 0.9170 (mt) cc_final: 0.8869 (tt) REVERT: A 470 VAL cc_start: 0.9186 (m) cc_final: 0.8909 (p) REVERT: A 497 ASN cc_start: 0.8952 (m-40) cc_final: 0.8625 (t0) REVERT: A 598 ASP cc_start: 0.7491 (t0) cc_final: 0.7077 (t0) REVERT: A 615 ASP cc_start: 0.6724 (t0) cc_final: 0.6307 (t0) REVERT: A 686 MET cc_start: 0.4850 (ptp) cc_final: 0.4634 (ptm) REVERT: A 806 LEU cc_start: 0.8699 (mt) cc_final: 0.8418 (tt) REVERT: A 828 ARG cc_start: 0.7759 (mtp85) cc_final: 0.7427 (mmt180) REVERT: A 835 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.7485 (t80) REVERT: A 851 MET cc_start: 0.4706 (mmp) cc_final: 0.3364 (ttm) REVERT: A 906 ARG cc_start: 0.7901 (ptp-170) cc_final: 0.7164 (tpt-90) REVERT: A 941 MET cc_start: 0.8297 (mtt) cc_final: 0.7921 (mtt) REVERT: A 1086 ARG cc_start: 0.6956 (ttm-80) cc_final: 0.6746 (tpt90) REVERT: A 1166 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8679 (tt) REVERT: A 1305 ASN cc_start: 0.7935 (t0) cc_final: 0.7135 (t0) REVERT: A 1381 MET cc_start: 0.7585 (mtt) cc_final: 0.7273 (mtp) REVERT: A 1401 GLU cc_start: 0.8513 (tt0) cc_final: 0.7478 (tp30) REVERT: A 1453 MET cc_start: 0.4409 (tmm) cc_final: 0.4094 (tmm) REVERT: C 292 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.6829 (ttm) REVERT: C 362 GLN cc_start: 0.7252 (mt0) cc_final: 0.6904 (pt0) REVERT: C 387 VAL cc_start: 0.7703 (p) cc_final: 0.7461 (m) REVERT: C 391 ILE cc_start: 0.8357 (mt) cc_final: 0.8002 (tt) REVERT: C 402 LYS cc_start: 0.5357 (OUTLIER) cc_final: 0.5022 (mmpt) REVERT: C 415 GLN cc_start: 0.7140 (pt0) cc_final: 0.6855 (pp30) REVERT: C 440 GLU cc_start: 0.8539 (tp30) cc_final: 0.7955 (pm20) REVERT: E 1 MET cc_start: 0.4349 (ttt) cc_final: 0.3606 (mmm) REVERT: E 32 TRP cc_start: 0.6566 (m100) cc_final: 0.6167 (m100) REVERT: E 51 PHE cc_start: 0.8020 (m-80) cc_final: 0.7766 (m-80) REVERT: E 56 ILE cc_start: 0.7018 (mp) cc_final: 0.6449 (mt) REVERT: E 131 LYS cc_start: 0.6602 (tptm) cc_final: 0.5812 (tmtt) REVERT: E 133 ARG cc_start: 0.5514 (ptp-170) cc_final: 0.5112 (ptp-170) REVERT: E 152 PHE cc_start: 0.8923 (t80) cc_final: 0.8722 (t80) REVERT: F 71 THR cc_start: 0.7674 (m) cc_final: 0.7447 (p) REVERT: F 254 LYS cc_start: 0.8514 (mtmm) cc_final: 0.8192 (mttp) REVERT: F 345 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8340 (mm-40) REVERT: F 725 LYS cc_start: 0.8812 (mttt) cc_final: 0.8266 (tmtt) REVERT: F 758 ASN cc_start: 0.8670 (t0) cc_final: 0.8410 (t0) REVERT: F 851 MET cc_start: 0.1566 (mtt) cc_final: 0.0248 (ttt) outliers start: 86 outliers final: 50 residues processed: 529 average time/residue: 0.1439 time to fit residues: 122.5541 Evaluate side-chains 475 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 421 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 175 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 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 472 LEU Chi-restraints excluded: chain A residue 526 VAL 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 580 LEU Chi-restraints excluded: chain A residue 790 VAL 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 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 1197 VAL Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1371 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 A residue 1433 LEU Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 373 HIS Chi-restraints excluded: chain C residue 402 LYS 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 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 771 LEU Chi-restraints excluded: chain F residue 905 SER Chi-restraints excluded: chain F residue 977 CYS Chi-restraints excluded: chain F residue 990 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 0.0170 chunk 85 optimal weight: 0.9990 chunk 163 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 221 optimal weight: 8.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** 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 411 HIS E 209 GLN E 210 ASN F 311 GLN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.134963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.107978 restraints weight = 85456.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.109298 restraints weight = 48675.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.109594 restraints weight = 40703.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.110827 restraints weight = 25099.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.111262 restraints weight = 20832.247| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22073 Z= 0.144 Angle : 0.814 14.457 29970 Z= 0.410 Chirality : 0.050 0.461 3449 Planarity : 0.006 0.104 3745 Dihedral : 8.576 80.126 3431 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.68 % Allowed : 10.86 % Favored : 88.46 % Rotamer: Outliers : 3.41 % Allowed : 17.38 % Favored : 79.21 % 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 aren not related in a simple way. whole: -2.33 (0.16), residues: 2638 helix: -0.46 (0.13), residues: 1357 sheet: -1.23 (0.32), residues: 262 loop : -3.14 (0.18), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 646 TYR 0.027 0.002 TYR C 388 PHE 0.025 0.002 PHE F 783 TRP 0.025 0.002 TRP F 824 HIS 0.006 0.001 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.00306 (22035) covalent geometry : angle 0.79483 (29873) SS BOND : bond 0.00418 ( 11) SS BOND : angle 1.40964 ( 22) hydrogen bonds : bond 0.04356 ( 929) hydrogen bonds : angle 4.87351 ( 2748) Misc. bond : bond 0.00027 ( 2) link_BETA1-4 : bond 0.00325 ( 10) link_BETA1-4 : angle 2.18747 ( 30) link_NAG-ASN : bond 0.00894 ( 15) link_NAG-ASN : angle 4.24663 ( 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 560 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 482 time to evaluate : 0.783 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: A 274 HIS cc_start: 0.7339 (OUTLIER) cc_final: 0.6792 (m-70) REVERT: A 295 THR cc_start: 0.8658 (p) cc_final: 0.8236 (t) REVERT: A 327 ASN cc_start: 0.8582 (t0) cc_final: 0.8300 (t0) REVERT: A 366 TYR cc_start: 0.6839 (m-80) cc_final: 0.6611 (m-10) REVERT: A 427 ASP cc_start: 0.6787 (t70) cc_final: 0.6010 (m-30) REVERT: A 470 VAL cc_start: 0.9149 (m) cc_final: 0.8853 (p) REVERT: A 497 ASN cc_start: 0.8827 (m-40) cc_final: 0.8485 (t0) REVERT: A 598 ASP cc_start: 0.7271 (t0) cc_final: 0.6935 (t0) REVERT: A 615 ASP cc_start: 0.6631 (t0) cc_final: 0.5955 (t0) REVERT: A 811 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8128 (mt) REVERT: A 828 ARG cc_start: 0.7822 (mtp85) cc_final: 0.7363 (mmt180) REVERT: A 835 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.7476 (t80) REVERT: A 906 ARG cc_start: 0.7567 (ptp-170) cc_final: 0.6930 (tpp80) REVERT: A 941 MET cc_start: 0.8202 (mtt) cc_final: 0.7890 (mtt) REVERT: A 1069 GLN cc_start: 0.7346 (mm110) cc_final: 0.6728 (mm-40) REVERT: A 1087 GLN cc_start: 0.6951 (tt0) cc_final: 0.6477 (pp30) REVERT: A 1381 MET cc_start: 0.7443 (mtt) cc_final: 0.7241 (mtm) REVERT: A 1401 GLU cc_start: 0.8351 (tt0) cc_final: 0.7580 (tp30) REVERT: A 1453 MET cc_start: 0.4735 (tmm) cc_final: 0.4426 (tmm) REVERT: C 292 MET cc_start: 0.7233 (mtm) cc_final: 0.6915 (ttm) REVERT: C 353 ARG cc_start: 0.8283 (tpt-90) cc_final: 0.7354 (tmm-80) REVERT: C 362 GLN cc_start: 0.7191 (mt0) cc_final: 0.6796 (pt0) REVERT: C 387 VAL cc_start: 0.7759 (p) cc_final: 0.7496 (m) REVERT: C 391 ILE cc_start: 0.8459 (mt) cc_final: 0.8094 (tt) REVERT: C 412 LEU cc_start: 0.7197 (pt) cc_final: 0.6897 (pp) REVERT: C 440 GLU cc_start: 0.8598 (tp30) cc_final: 0.7961 (pm20) REVERT: E 1 MET cc_start: 0.4287 (ttt) cc_final: 0.3520 (mmm) REVERT: E 56 ILE cc_start: 0.7388 (mp) cc_final: 0.7133 (mt) REVERT: E 131 LYS cc_start: 0.6430 (tptm) cc_final: 0.5622 (tmtt) REVERT: E 133 ARG cc_start: 0.5340 (ptp-170) cc_final: 0.4971 (ptp-170) REVERT: F 411 TYR cc_start: 0.8343 (t80) cc_final: 0.8128 (t80) REVERT: F 508 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8049 (pt) REVERT: F 663 PHE cc_start: 0.8178 (m-80) cc_final: 0.7745 (m-80) REVERT: F 725 LYS cc_start: 0.8763 (mttt) cc_final: 0.8245 (tmtt) REVERT: F 775 ASN cc_start: 0.8739 (p0) cc_final: 0.8522 (p0) REVERT: F 851 MET cc_start: 0.1569 (mtt) cc_final: 0.0511 (ttt) REVERT: F 891 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7662 (t0) outliers start: 78 outliers final: 46 residues processed: 519 average time/residue: 0.1393 time to fit residues: 116.3306 Evaluate side-chains 480 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 429 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 66 VAL 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 572 ILE Chi-restraints excluded: chain A residue 578 MET 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 1076 TYR Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1188 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 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 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 176 TYR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 14 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 chunk 141 optimal weight: 0.0270 chunk 236 optimal weight: 0.9990 chunk 211 optimal weight: 4.9990 chunk 164 optimal weight: 0.0000 chunk 212 optimal weight: 0.8980 chunk 186 optimal weight: 0.1980 chunk 39 optimal weight: 6.9990 overall best weight: 0.4244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 HIS 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** B 135 HIS F 520 ASN ** F 549 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 = 0.3990 r_free = 0.3990 target = 0.136276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.109608 restraints weight = 87673.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.110602 restraints weight = 50468.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.111039 restraints weight = 42178.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.112284 restraints weight = 25996.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.112816 restraints weight = 21601.454| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22073 Z= 0.137 Angle : 0.803 15.136 29970 Z= 0.399 Chirality : 0.049 0.441 3449 Planarity : 0.005 0.100 3745 Dihedral : 7.937 75.308 3426 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.57 % Allowed : 10.78 % Favored : 88.65 % Rotamer: Outliers : 2.57 % Allowed : 19.55 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 5.61 % 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 aren not related in a simple way. whole: -1.95 (0.16), residues: 2638 helix: -0.12 (0.14), residues: 1374 sheet: -0.93 (0.33), residues: 255 loop : -3.09 (0.18), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 646 TYR 0.026 0.001 TYR C 388 PHE 0.042 0.001 PHE F 783 TRP 0.019 0.001 TRP F 824 HIS 0.006 0.001 HIS C 411 Details of bonding type rmsd covalent geometry : bond 0.00291 (22035) covalent geometry : angle 0.78565 (29873) SS BOND : bond 0.00401 ( 11) SS BOND : angle 1.30835 ( 22) hydrogen bonds : bond 0.03991 ( 929) hydrogen bonds : angle 4.67246 ( 2748) Misc. bond : bond 0.00013 ( 2) link_BETA1-4 : bond 0.00430 ( 10) link_BETA1-4 : angle 1.89004 ( 30) link_NAG-ASN : bond 0.00885 ( 15) link_NAG-ASN : angle 4.00846 ( 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 550 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 491 time to evaluate : 0.879 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: A 274 HIS cc_start: 0.7236 (OUTLIER) cc_final: 0.6387 (m-70) REVERT: A 295 THR cc_start: 0.8618 (p) cc_final: 0.8202 (t) REVERT: A 366 TYR cc_start: 0.6740 (m-80) cc_final: 0.6504 (m-10) REVERT: A 427 ASP cc_start: 0.6732 (t70) cc_final: 0.5992 (m-30) REVERT: A 470 VAL cc_start: 0.9113 (m) cc_final: 0.8790 (p) REVERT: A 497 ASN cc_start: 0.8780 (m-40) cc_final: 0.8453 (t0) REVERT: A 598 ASP cc_start: 0.7280 (t0) cc_final: 0.6949 (t0) REVERT: A 615 ASP cc_start: 0.6484 (t0) cc_final: 0.5971 (t0) REVERT: A 656 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.7375 (t80) REVERT: A 828 ARG cc_start: 0.7861 (mtp85) cc_final: 0.7405 (mmt180) REVERT: A 835 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7470 (t80) REVERT: A 843 PHE cc_start: 0.7606 (OUTLIER) cc_final: 0.6937 (t80) REVERT: A 941 MET cc_start: 0.8190 (mtt) cc_final: 0.7863 (mtt) REVERT: A 948 GLN cc_start: 0.8396 (tp40) cc_final: 0.7964 (tp-100) REVERT: A 1056 MET cc_start: 0.8023 (mmm) cc_final: 0.7000 (tmm) REVERT: A 1057 MET cc_start: 0.6649 (mtt) cc_final: 0.6233 (mtm) REVERT: A 1069 GLN cc_start: 0.7235 (mm110) cc_final: 0.6762 (mm110) REVERT: A 1159 ILE cc_start: 0.9377 (tp) cc_final: 0.9166 (pt) REVERT: A 1165 MET cc_start: 0.8662 (tmm) cc_final: 0.8428 (tmm) REVERT: A 1292 ILE cc_start: 0.8031 (mm) cc_final: 0.7787 (mm) REVERT: A 1401 GLU cc_start: 0.8413 (tt0) cc_final: 0.7643 (tp30) REVERT: A 1453 MET cc_start: 0.4715 (tmm) cc_final: 0.4382 (tmm) REVERT: C 292 MET cc_start: 0.7210 (mtm) cc_final: 0.6786 (ttm) REVERT: C 350 GLU cc_start: 0.5351 (mm-30) cc_final: 0.5084 (mm-30) REVERT: C 353 ARG cc_start: 0.8263 (tpt-90) cc_final: 0.7434 (tmm-80) REVERT: C 362 GLN cc_start: 0.7184 (mt0) cc_final: 0.6868 (pt0) REVERT: C 391 ILE cc_start: 0.8484 (mt) cc_final: 0.8061 (tt) REVERT: C 412 LEU cc_start: 0.7360 (pt) cc_final: 0.6919 (pp) REVERT: C 440 GLU cc_start: 0.8567 (tp30) cc_final: 0.7905 (pm20) REVERT: E 1 MET cc_start: 0.4282 (ttt) cc_final: 0.3539 (mmm) REVERT: E 56 ILE cc_start: 0.7310 (mp) cc_final: 0.6877 (mt) REVERT: E 131 LYS cc_start: 0.6516 (tptm) cc_final: 0.5578 (tmtt) REVERT: E 133 ARG cc_start: 0.5074 (ptp-170) cc_final: 0.4496 (ptp-170) REVERT: E 182 PHE cc_start: 0.7922 (t80) cc_final: 0.7625 (t80) REVERT: F 256 MET cc_start: 0.7678 (ttm) cc_final: 0.7219 (mtm) REVERT: F 393 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7905 (mm-40) REVERT: F 411 TYR cc_start: 0.8346 (t80) cc_final: 0.8077 (t80) REVERT: F 663 PHE cc_start: 0.8178 (m-80) cc_final: 0.7774 (m-10) REVERT: F 725 LYS cc_start: 0.8783 (mttt) cc_final: 0.8303 (tmtt) REVERT: F 775 ASN cc_start: 0.8687 (p0) cc_final: 0.8444 (p0) REVERT: F 851 MET cc_start: 0.0972 (mtt) cc_final: 0.0114 (ttt) REVERT: F 891 ASN cc_start: 0.7807 (OUTLIER) cc_final: 0.7557 (t0) outliers start: 59 outliers final: 40 residues processed: 520 average time/residue: 0.1416 time to fit residues: 119.0164 Evaluate side-chains 467 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 422 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 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 325 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 441 ILE 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 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 1277 LEU Chi-restraints excluded: chain A residue 1319 CYS Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1384 PHE 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 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 502 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 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: 2.9990 chunk 100 optimal weight: 10.0000 chunk 127 optimal weight: 30.0000 chunk 183 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 160 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 257 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 ASN A 993 ASN A1142 GLN ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 HIS F 520 ASN F 773 ASN F 888 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.135856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.109361 restraints weight = 83740.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.109812 restraints weight = 49652.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.110430 restraints weight = 42662.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.111158 restraints weight = 27523.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.112211 restraints weight = 23711.995| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 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 = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22073 Z= 0.170 Angle : 0.813 13.438 29970 Z= 0.407 Chirality : 0.049 0.425 3449 Planarity : 0.005 0.103 3745 Dihedral : 7.794 72.998 3426 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.57 % Allowed : 11.01 % Favored : 88.42 % Rotamer: Outliers : 3.72 % Allowed : 19.64 % Favored : 76.65 % 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 aren not related in a simple way. whole: -1.71 (0.16), residues: 2638 helix: 0.15 (0.14), residues: 1370 sheet: -0.94 (0.33), residues: 260 loop : -3.07 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 600 TYR 0.037 0.002 TYR F 220 PHE 0.032 0.002 PHE F 783 TRP 0.050 0.002 TRP A1406 HIS 0.005 0.001 HIS A 453 Details of bonding type rmsd covalent geometry : bond 0.00379 (22035) covalent geometry : angle 0.79755 (29873) SS BOND : bond 0.00336 ( 11) SS BOND : angle 1.28158 ( 22) hydrogen bonds : bond 0.03952 ( 929) hydrogen bonds : angle 4.67761 ( 2748) Misc. bond : bond 0.00079 ( 2) link_BETA1-4 : bond 0.00404 ( 10) link_BETA1-4 : angle 1.85851 ( 30) link_NAG-ASN : bond 0.00727 ( 15) link_NAG-ASN : angle 3.82182 ( 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 516 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 432 time to evaluate : 0.812 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: A 274 HIS cc_start: 0.7330 (OUTLIER) cc_final: 0.6571 (m-70) REVERT: A 295 THR cc_start: 0.8703 (p) cc_final: 0.8269 (t) REVERT: A 366 TYR cc_start: 0.6970 (m-10) cc_final: 0.6579 (m-10) REVERT: A 427 ASP cc_start: 0.6804 (t70) cc_final: 0.5961 (m-30) REVERT: A 470 VAL cc_start: 0.9152 (m) cc_final: 0.8838 (p) REVERT: A 497 ASN cc_start: 0.8789 (m-40) cc_final: 0.8466 (t0) REVERT: A 598 ASP cc_start: 0.7204 (t0) cc_final: 0.6841 (t0) REVERT: A 615 ASP cc_start: 0.6794 (t0) cc_final: 0.6130 (t0) REVERT: A 656 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7469 (t80) REVERT: A 806 LEU cc_start: 0.8801 (mt) cc_final: 0.8401 (tt) REVERT: A 828 ARG cc_start: 0.7897 (mtp85) cc_final: 0.7382 (mmt180) REVERT: A 835 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7471 (t80) REVERT: A 941 MET cc_start: 0.8230 (mtt) cc_final: 0.7907 (mtt) REVERT: A 948 GLN cc_start: 0.8364 (tp40) cc_final: 0.7998 (tp-100) REVERT: A 1048 TYR cc_start: 0.9466 (t80) cc_final: 0.9251 (t80) REVERT: A 1069 GLN cc_start: 0.7099 (mm110) cc_final: 0.6734 (mm-40) REVERT: A 1359 TYR cc_start: 0.6480 (m-10) cc_final: 0.6143 (m-80) REVERT: A 1401 GLU cc_start: 0.8372 (tt0) cc_final: 0.7596 (tp30) REVERT: C 292 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6785 (ttm) REVERT: C 350 GLU cc_start: 0.5356 (mm-30) cc_final: 0.5153 (mm-30) REVERT: C 353 ARG cc_start: 0.8159 (tpt-90) cc_final: 0.7491 (tmm-80) REVERT: C 362 GLN cc_start: 0.7264 (mt0) cc_final: 0.7002 (pt0) REVERT: C 440 GLU cc_start: 0.8605 (tp30) cc_final: 0.7935 (pm20) REVERT: E 1 MET cc_start: 0.4368 (ttt) cc_final: 0.3540 (mmm) REVERT: E 56 ILE cc_start: 0.7341 (mp) cc_final: 0.6925 (mt) REVERT: E 131 LYS cc_start: 0.6497 (tptm) cc_final: 0.5540 (tmtt) REVERT: E 133 ARG cc_start: 0.4959 (ptp-170) cc_final: 0.4428 (ptp-170) REVERT: E 165 MET cc_start: 0.6167 (pmm) cc_final: 0.4476 (tpt) REVERT: F 411 TYR cc_start: 0.8350 (t80) cc_final: 0.8108 (t80) REVERT: F 489 VAL cc_start: 0.9544 (p) cc_final: 0.9125 (m) REVERT: F 508 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.7997 (pt) REVERT: F 663 PHE cc_start: 0.8142 (m-80) cc_final: 0.7812 (m-80) REVERT: F 725 LYS cc_start: 0.8786 (mttt) cc_final: 0.8307 (tmtt) REVERT: F 824 TRP cc_start: 0.8776 (t60) cc_final: 0.8441 (t60) REVERT: F 851 MET cc_start: 0.0987 (mtt) cc_final: 0.0209 (ttt) REVERT: F 891 ASN cc_start: 0.7629 (OUTLIER) cc_final: 0.7299 (t0) outliers start: 84 outliers final: 52 residues processed: 478 average time/residue: 0.1276 time to fit residues: 98.6419 Evaluate side-chains 458 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 400 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 105 ILE 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 325 ILE Chi-restraints excluded: chain A residue 328 LEU 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 656 PHE 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 993 ASN 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 1153 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 1330 LEU 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 A residue 1467 LEU Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 292 MET 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 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 176 TYR Chi-restraints excluded: chain F residue 165 HIS 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 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: 8.9990 chunk 132 optimal weight: 5.9990 chunk 200 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 133 optimal weight: 0.5980 chunk 169 optimal weight: 0.9990 chunk 249 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN ** A1131 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 445 HIS ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 520 ASN F1007 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.135330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.103842 restraints weight = 93870.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.105957 restraints weight = 43781.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.108272 restraints weight = 27139.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.108239 restraints weight = 23148.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.108144 restraints weight = 17977.294| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 22073 Z= 0.168 Angle : 0.819 13.145 29970 Z= 0.408 Chirality : 0.049 0.464 3449 Planarity : 0.005 0.103 3745 Dihedral : 7.691 70.032 3426 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.57 % Allowed : 11.24 % Favored : 88.19 % Rotamer: Outliers : 3.89 % Allowed : 20.88 % Favored : 75.23 % Cbeta Deviations : 0.04 % 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 aren not related in a simple way. whole: -1.59 (0.16), residues: 2638 helix: 0.26 (0.14), residues: 1364 sheet: -0.97 (0.32), residues: 260 loop : -2.97 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 308 TYR 0.029 0.002 TYR F 220 PHE 0.031 0.002 PHE F 783 TRP 0.063 0.002 TRP A1406 HIS 0.005 0.001 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.00378 (22035) covalent geometry : angle 0.80183 (29873) SS BOND : bond 0.00325 ( 11) SS BOND : angle 2.34682 ( 22) hydrogen bonds : bond 0.03904 ( 929) hydrogen bonds : angle 4.67070 ( 2748) Misc. bond : bond 0.00032 ( 2) link_BETA1-4 : bond 0.00395 ( 10) link_BETA1-4 : angle 1.85864 ( 30) link_NAG-ASN : bond 0.00777 ( 15) link_NAG-ASN : angle 3.79444 ( 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: 88 poor density : 422 time to evaluate : 0.859 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: A 274 HIS cc_start: 0.7402 (OUTLIER) cc_final: 0.6593 (m-70) REVERT: A 295 THR cc_start: 0.8784 (p) cc_final: 0.8558 (t) REVERT: A 337 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.7414 (m-10) REVERT: A 366 TYR cc_start: 0.7138 (m-10) cc_final: 0.6719 (m-10) REVERT: A 376 MET cc_start: 0.6482 (tpt) cc_final: 0.6097 (tpp) REVERT: A 427 ASP cc_start: 0.6900 (t70) cc_final: 0.5996 (m-30) REVERT: A 470 VAL cc_start: 0.9181 (m) cc_final: 0.8864 (p) REVERT: A 497 ASN cc_start: 0.8845 (m-40) cc_final: 0.8554 (t0) REVERT: A 598 ASP cc_start: 0.7048 (t0) cc_final: 0.6688 (t0) REVERT: A 615 ASP cc_start: 0.6791 (t0) cc_final: 0.6178 (t0) REVERT: A 656 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7686 (t80) REVERT: A 806 LEU cc_start: 0.8616 (mt) cc_final: 0.8329 (tt) REVERT: A 828 ARG cc_start: 0.8061 (mtp85) cc_final: 0.7347 (mmt180) REVERT: A 835 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.7424 (t80) REVERT: A 843 PHE cc_start: 0.7621 (OUTLIER) cc_final: 0.7156 (t80) REVERT: A 906 ARG cc_start: 0.7607 (ptp-170) cc_final: 0.7194 (tpt-90) REVERT: A 941 MET cc_start: 0.8258 (mtt) cc_final: 0.7862 (mtt) REVERT: A 948 GLN cc_start: 0.8254 (tp40) cc_final: 0.7927 (tp-100) REVERT: A 1056 MET cc_start: 0.7903 (mmm) cc_final: 0.7130 (tmm) REVERT: A 1069 GLN cc_start: 0.7124 (mm110) cc_final: 0.6809 (mm-40) REVERT: A 1189 ILE cc_start: 0.9351 (tp) cc_final: 0.9049 (tt) REVERT: A 1292 ILE cc_start: 0.8114 (mm) cc_final: 0.7896 (mm) REVERT: A 1359 TYR cc_start: 0.6585 (m-10) cc_final: 0.6149 (m-80) REVERT: A 1401 GLU cc_start: 0.8346 (tt0) cc_final: 0.7545 (tp30) REVERT: C 292 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.6863 (ttm) REVERT: C 350 GLU cc_start: 0.5372 (mm-30) cc_final: 0.5153 (mm-30) REVERT: C 353 ARG cc_start: 0.8162 (tpt-90) cc_final: 0.7497 (tmm-80) REVERT: C 362 GLN cc_start: 0.7327 (mt0) cc_final: 0.6959 (pt0) REVERT: C 440 GLU cc_start: 0.8606 (tp30) cc_final: 0.7949 (pm20) REVERT: E 1 MET cc_start: 0.4393 (ttt) cc_final: 0.3531 (mmm) REVERT: E 56 ILE cc_start: 0.7314 (mp) cc_final: 0.6859 (mt) REVERT: E 131 LYS cc_start: 0.6618 (tptm) cc_final: 0.5652 (tmtt) REVERT: E 133 ARG cc_start: 0.5043 (ptp-170) cc_final: 0.4431 (ptp-170) REVERT: E 165 MET cc_start: 0.6308 (pmm) cc_final: 0.4994 (tpt) REVERT: F 508 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8078 (pt) REVERT: F 536 VAL cc_start: 0.7061 (OUTLIER) cc_final: 0.6738 (m) REVERT: F 663 PHE cc_start: 0.8275 (m-80) cc_final: 0.7850 (m-80) REVERT: F 725 LYS cc_start: 0.8794 (mttt) cc_final: 0.8309 (tmtt) REVERT: F 824 TRP cc_start: 0.8778 (t60) cc_final: 0.8341 (t60) REVERT: F 851 MET cc_start: 0.1171 (mtt) cc_final: 0.0339 (ttt) REVERT: F 891 ASN cc_start: 0.7655 (OUTLIER) cc_final: 0.7345 (t0) outliers start: 88 outliers final: 62 residues processed: 471 average time/residue: 0.1358 time to fit residues: 104.8623 Evaluate side-chains 479 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 408 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 129 ILE 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 337 PHE 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 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 993 ASN Chi-restraints excluded: chain A residue 1037 ASN 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 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 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 1371 LEU Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain A residue 1405 ILE Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 292 MET 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 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 150 CYS 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 E residue 184 CYS Chi-restraints excluded: chain F residue 46 LEU 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 429 LEU 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 777 VAL Chi-restraints excluded: chain F residue 891 ASN 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: 2.9990 chunk 146 optimal weight: 8.9990 chunk 226 optimal weight: 0.0670 chunk 173 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 264 optimal weight: 2.9990 chunk 245 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 257 optimal weight: 3.9990 chunk 121 optimal weight: 20.0000 chunk 192 optimal weight: 0.8980 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** 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** C 294 GLN C 445 HIS ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 379 ASN F 520 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.136454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.109868 restraints weight = 64298.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.108606 restraints weight = 32625.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.109841 restraints weight = 30234.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.109873 restraints weight = 23040.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.110782 restraints weight = 20500.465| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 22073 Z= 0.142 Angle : 0.807 12.782 29970 Z= 0.401 Chirality : 0.049 0.413 3449 Planarity : 0.005 0.102 3745 Dihedral : 7.505 67.823 3426 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.24 % Favored : 88.34 % Rotamer: Outliers : 3.01 % Allowed : 21.89 % Favored : 75.10 % 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 aren not related in a simple way. whole: -1.46 (0.16), residues: 2638 helix: 0.38 (0.14), residues: 1370 sheet: -0.92 (0.32), residues: 265 loop : -2.95 (0.18), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 174 TYR 0.028 0.001 TYR C 388 PHE 0.030 0.001 PHE F 783 TRP 0.039 0.001 TRP A1406 HIS 0.006 0.001 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.00316 (22035) covalent geometry : angle 0.79166 (29873) SS BOND : bond 0.00283 ( 11) SS BOND : angle 2.14837 ( 22) hydrogen bonds : bond 0.03768 ( 929) hydrogen bonds : angle 4.56399 ( 2748) Misc. bond : bond 0.00013 ( 2) link_BETA1-4 : bond 0.00404 ( 10) link_BETA1-4 : angle 1.77210 ( 30) link_NAG-ASN : bond 0.00764 ( 15) link_NAG-ASN : angle 3.62427 ( 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 508 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 440 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 HIS cc_start: 0.7182 (OUTLIER) cc_final: 0.6641 (m-70) REVERT: A 295 THR cc_start: 0.8790 (p) cc_final: 0.8463 (t) REVERT: A 337 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.7444 (m-10) REVERT: A 366 TYR cc_start: 0.7010 (m-10) cc_final: 0.6624 (m-10) REVERT: A 376 MET cc_start: 0.6494 (tpt) cc_final: 0.6114 (tpp) REVERT: A 427 ASP cc_start: 0.6882 (t70) cc_final: 0.5997 (m-30) REVERT: A 470 VAL cc_start: 0.9182 (m) cc_final: 0.8848 (p) REVERT: A 493 MET cc_start: 0.6225 (mtm) cc_final: 0.5393 (mmt) REVERT: A 497 ASN cc_start: 0.8766 (m-40) cc_final: 0.8435 (t0) REVERT: A 598 ASP cc_start: 0.6785 (t0) cc_final: 0.6470 (t0) REVERT: A 615 ASP cc_start: 0.6744 (t0) cc_final: 0.6209 (t0) REVERT: A 806 LEU cc_start: 0.8612 (mt) cc_final: 0.8325 (tt) REVERT: A 828 ARG cc_start: 0.8065 (mtp85) cc_final: 0.7456 (mmt180) REVERT: A 843 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.7132 (t80) REVERT: A 906 ARG cc_start: 0.7545 (ptp-170) cc_final: 0.7072 (tpt-90) REVERT: A 941 MET cc_start: 0.8020 (mtt) cc_final: 0.7692 (mtt) REVERT: A 948 GLN cc_start: 0.8211 (tp40) cc_final: 0.7955 (tp-100) REVERT: A 1056 MET cc_start: 0.7708 (mmm) cc_final: 0.6982 (tmm) REVERT: A 1058 ASN cc_start: 0.8455 (m-40) cc_final: 0.8195 (m110) REVERT: A 1069 GLN cc_start: 0.6837 (mm110) cc_final: 0.6538 (mm-40) REVERT: A 1292 ILE cc_start: 0.7924 (mm) cc_final: 0.7668 (mm) REVERT: A 1359 TYR cc_start: 0.6550 (m-10) cc_final: 0.6015 (m-80) REVERT: C 308 ARG cc_start: 0.5313 (mtp-110) cc_final: 0.4528 (mtm110) REVERT: C 350 GLU cc_start: 0.5289 (mm-30) cc_final: 0.4846 (mm-30) REVERT: C 353 ARG cc_start: 0.8173 (tpt-90) cc_final: 0.7396 (tmm-80) REVERT: C 440 GLU cc_start: 0.8574 (tp30) cc_final: 0.7914 (pm20) REVERT: E 56 ILE cc_start: 0.7317 (mp) cc_final: 0.6857 (mt) REVERT: E 131 LYS cc_start: 0.6499 (tptm) cc_final: 0.5516 (tmtt) REVERT: E 133 ARG cc_start: 0.4985 (ptp-170) cc_final: 0.4327 (ptp-170) REVERT: E 165 MET cc_start: 0.6340 (pmm) cc_final: 0.4937 (tpt) REVERT: F 508 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8001 (pt) REVERT: F 536 VAL cc_start: 0.6902 (OUTLIER) cc_final: 0.6588 (m) REVERT: F 663 PHE cc_start: 0.8204 (m-80) cc_final: 0.7888 (m-10) REVERT: F 725 LYS cc_start: 0.8792 (mttt) cc_final: 0.8345 (tmtt) REVERT: F 824 TRP cc_start: 0.8706 (t60) cc_final: 0.8414 (t60) REVERT: F 851 MET cc_start: 0.1056 (mtt) cc_final: 0.0374 (ttt) outliers start: 68 outliers final: 54 residues processed: 479 average time/residue: 0.1369 time to fit residues: 106.0057 Evaluate side-chains 479 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 420 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 105 ILE 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 337 PHE 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 572 ILE Chi-restraints excluded: chain A residue 580 LEU 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 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 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 1368 CYS Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1467 LEU 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 E residue 34 VAL Chi-restraints excluded: chain E residue 176 TYR Chi-restraints excluded: chain E residue 184 CYS Chi-restraints excluded: chain F residue 46 LEU 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 561 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 113 optimal weight: 0.2980 chunk 78 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 176 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 193 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 173 optimal weight: 7.9990 chunk 228 optimal weight: 2.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 HIS ** A1154 ASN ** 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 520 ASN ** F 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.135237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.109214 restraints weight = 72080.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.109812 restraints weight = 39067.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.110418 restraints weight = 32490.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.110477 restraints weight = 23002.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.111425 restraints weight = 20045.895| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3596 r_free = 0.3596 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3596 r_free = 0.3596 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22073 Z= 0.171 Angle : 0.833 16.063 29970 Z= 0.415 Chirality : 0.049 0.415 3449 Planarity : 0.005 0.104 3745 Dihedral : 7.450 67.182 3424 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.53 % Allowed : 11.01 % Favored : 88.46 % Rotamer: Outliers : 3.05 % Allowed : 22.38 % Favored : 74.57 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 4.67 % 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 aren not related in a simple way. whole: -1.47 (0.16), residues: 2638 helix: 0.38 (0.14), residues: 1374 sheet: -1.04 (0.31), residues: 274 loop : -2.96 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1447 TYR 0.026 0.002 TYR A 313 PHE 0.029 0.002 PHE F 783 TRP 0.037 0.002 TRP A1406 HIS 0.013 0.001 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.00387 (22035) covalent geometry : angle 0.81852 (29873) SS BOND : bond 0.00271 ( 11) SS BOND : angle 2.05806 ( 22) hydrogen bonds : bond 0.03808 ( 929) hydrogen bonds : angle 4.61917 ( 2748) Misc. bond : bond 0.00039 ( 2) link_BETA1-4 : bond 0.00397 ( 10) link_BETA1-4 : angle 1.77218 ( 30) link_NAG-ASN : bond 0.00684 ( 15) link_NAG-ASN : angle 3.55809 ( 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 489 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 420 time to evaluate : 0.859 Fit side-chains 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: 0.7229 (OUTLIER) cc_final: 0.6427 (m-70) REVERT: A 295 THR cc_start: 0.8764 (p) cc_final: 0.8419 (t) REVERT: A 337 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7384 (m-10) REVERT: A 366 TYR cc_start: 0.6920 (m-10) cc_final: 0.6562 (m-10) REVERT: A 376 MET cc_start: 0.6444 (tpt) cc_final: 0.5955 (tpp) REVERT: A 427 ASP cc_start: 0.6887 (t70) cc_final: 0.5969 (m-30) REVERT: A 470 VAL cc_start: 0.9177 (m) cc_final: 0.8862 (p) REVERT: A 493 MET cc_start: 0.6165 (mtm) cc_final: 0.5385 (mmt) REVERT: A 497 ASN cc_start: 0.8888 (m-40) cc_final: 0.8543 (t0) REVERT: A 598 ASP cc_start: 0.6887 (t0) cc_final: 0.6573 (t0) REVERT: A 615 ASP cc_start: 0.6785 (t0) cc_final: 0.6171 (t0) REVERT: A 656 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7659 (t80) REVERT: A 806 LEU cc_start: 0.8590 (mt) cc_final: 0.8308 (tt) REVERT: A 822 ILE cc_start: 0.7211 (mm) cc_final: 0.6887 (tp) REVERT: A 828 ARG cc_start: 0.8046 (mtp85) cc_final: 0.7416 (mmt180) REVERT: A 843 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.7047 (t80) REVERT: A 906 ARG cc_start: 0.7468 (ptp-170) cc_final: 0.7077 (tpt-90) REVERT: A 941 MET cc_start: 0.8093 (mtt) cc_final: 0.7749 (mtt) REVERT: A 948 GLN cc_start: 0.8302 (tp40) cc_final: 0.8032 (tp-100) REVERT: A 1056 MET cc_start: 0.7843 (mmm) cc_final: 0.7228 (tmm) REVERT: A 1069 GLN cc_start: 0.6792 (mm110) cc_final: 0.6549 (mm-40) REVERT: A 1292 ILE cc_start: 0.8001 (mm) cc_final: 0.7788 (mm) REVERT: A 1323 GLU cc_start: 0.8151 (tp30) cc_final: 0.7936 (tp30) REVERT: A 1359 TYR cc_start: 0.6584 (m-10) cc_final: 0.6072 (m-80) REVERT: A 1427 ARG cc_start: 0.7540 (tmt-80) cc_final: 0.7005 (ppt170) REVERT: C 292 MET cc_start: 0.7869 (tpp) cc_final: 0.7084 (tpp) REVERT: C 295 LYS cc_start: 0.8696 (mttm) cc_final: 0.8375 (mttm) REVERT: C 308 ARG cc_start: 0.5285 (mtp-110) cc_final: 0.4494 (mtm110) REVERT: C 353 ARG cc_start: 0.8196 (tpt-90) cc_final: 0.7497 (tmm-80) REVERT: C 362 GLN cc_start: 0.5210 (pt0) cc_final: 0.4782 (pt0) REVERT: C 440 GLU cc_start: 0.8550 (tp30) cc_final: 0.7897 (pm20) REVERT: E 131 LYS cc_start: 0.6443 (tptm) cc_final: 0.5559 (tmtt) REVERT: E 133 ARG cc_start: 0.4978 (ptp-170) cc_final: 0.4254 (ptp-170) REVERT: E 165 MET cc_start: 0.6394 (pmm) cc_final: 0.4871 (tpt) REVERT: F 490 MET cc_start: 0.8854 (ttp) cc_final: 0.8513 (ptm) REVERT: F 508 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8038 (pt) REVERT: F 536 VAL cc_start: 0.6955 (OUTLIER) cc_final: 0.6652 (m) REVERT: F 663 PHE cc_start: 0.8153 (m-80) cc_final: 0.7853 (m-80) REVERT: F 725 LYS cc_start: 0.8750 (mttt) cc_final: 0.8327 (tmtt) REVERT: F 824 TRP cc_start: 0.8632 (t60) cc_final: 0.8359 (t60) REVERT: F 851 MET cc_start: 0.1162 (mtt) cc_final: 0.0456 (ttt) outliers start: 69 outliers final: 61 residues processed: 455 average time/residue: 0.1326 time to fit residues: 97.9235 Evaluate side-chains 475 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 408 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 129 ILE 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 337 PHE 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 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 947 VAL Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1037 ASN Chi-restraints excluded: chain A residue 1059 ILE 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 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 1319 CYS Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1338 CYS 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 1394 LEU Chi-restraints excluded: chain A residue 1467 LEU 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 E residue 34 VAL Chi-restraints excluded: chain E residue 150 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 46 LEU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 429 LEU 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 561 LEU 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 183 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 181 optimal weight: 0.1980 chunk 81 optimal weight: 0.6980 chunk 146 optimal weight: 8.9990 chunk 261 optimal weight: 20.0000 chunk 106 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 217 optimal weight: 0.2980 chunk 72 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 HIS A1154 ASN B 135 HIS C 445 HIS ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 520 ASN F 655 ASN F 866 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 = 0.4021 r_free = 0.4021 target = 0.137742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.111821 restraints weight = 76245.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.111458 restraints weight = 41660.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.112207 restraints weight = 38375.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.112805 restraints weight = 25083.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.113675 restraints weight = 21883.260| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.6005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22073 Z= 0.136 Angle : 0.822 15.046 29970 Z= 0.406 Chirality : 0.049 0.406 3449 Planarity : 0.005 0.101 3745 Dihedral : 7.269 66.185 3424 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.44 % Favored : 89.14 % Rotamer: Outliers : 2.65 % Allowed : 23.18 % Favored : 74.17 % 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 aren not related in a simple way. whole: -1.28 (0.16), residues: 2638 helix: 0.50 (0.14), residues: 1357 sheet: -0.85 (0.31), residues: 269 loop : -2.79 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1447 TYR 0.035 0.001 TYR A 650 PHE 0.042 0.001 PHE A 839 TRP 0.065 0.002 TRP A1406 HIS 0.010 0.001 HIS A 916 Details of bonding type rmsd covalent geometry : bond 0.00297 (22035) covalent geometry : angle 0.80850 (29873) SS BOND : bond 0.00233 ( 11) SS BOND : angle 1.85496 ( 22) hydrogen bonds : bond 0.03715 ( 929) hydrogen bonds : angle 4.50567 ( 2748) Misc. bond : bond 0.00006 ( 2) link_BETA1-4 : bond 0.00466 ( 10) link_BETA1-4 : angle 1.72893 ( 30) link_NAG-ASN : bond 0.00776 ( 15) link_NAG-ASN : angle 3.44453 ( 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 504 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 444 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 HIS cc_start: 0.7093 (OUTLIER) cc_final: 0.6250 (m-70) REVERT: A 295 THR cc_start: 0.8580 (p) cc_final: 0.8232 (t) REVERT: A 337 PHE cc_start: 0.7588 (OUTLIER) cc_final: 0.7362 (m-10) REVERT: A 366 TYR cc_start: 0.6905 (m-10) cc_final: 0.6609 (m-10) REVERT: A 376 MET cc_start: 0.6563 (tpt) cc_final: 0.6162 (tpp) REVERT: A 427 ASP cc_start: 0.6847 (t70) cc_final: 0.5981 (m-30) REVERT: A 470 VAL cc_start: 0.9172 (m) cc_final: 0.8841 (p) REVERT: A 493 MET cc_start: 0.6106 (mtm) cc_final: 0.5346 (mmt) REVERT: A 497 ASN cc_start: 0.8805 (m-40) cc_final: 0.8450 (t0) REVERT: A 598 ASP cc_start: 0.6627 (t0) cc_final: 0.6388 (t0) REVERT: A 615 ASP cc_start: 0.6586 (t0) cc_final: 0.6092 (t0) REVERT: A 806 LEU cc_start: 0.8575 (mt) cc_final: 0.8218 (tt) REVERT: A 820 ASP cc_start: 0.5892 (OUTLIER) cc_final: 0.5654 (t70) REVERT: A 822 ILE cc_start: 0.7105 (mm) cc_final: 0.6798 (tp) REVERT: A 828 ARG cc_start: 0.8017 (mtp85) cc_final: 0.7366 (mmt180) REVERT: A 906 ARG cc_start: 0.7640 (ptp-170) cc_final: 0.7069 (tpt-90) REVERT: A 948 GLN cc_start: 0.8320 (tp40) cc_final: 0.8046 (tp-100) REVERT: A 1056 MET cc_start: 0.7631 (mmm) cc_final: 0.7163 (tmm) REVERT: A 1069 GLN cc_start: 0.6667 (mm110) cc_final: 0.6434 (mm-40) REVERT: A 1359 TYR cc_start: 0.6483 (m-10) cc_final: 0.6008 (m-80) REVERT: A 1427 ARG cc_start: 0.7448 (tmt-80) cc_final: 0.6961 (ppt170) REVERT: C 292 MET cc_start: 0.7965 (tpp) cc_final: 0.7458 (tpp) REVERT: C 295 LYS cc_start: 0.8609 (mttm) cc_final: 0.8345 (mttm) REVERT: C 350 GLU cc_start: 0.5450 (mm-30) cc_final: 0.5047 (mm-30) REVERT: C 353 ARG cc_start: 0.8123 (tpt-90) cc_final: 0.7296 (tmm-80) REVERT: C 362 GLN cc_start: 0.5395 (pt0) cc_final: 0.5028 (pt0) REVERT: C 440 GLU cc_start: 0.8554 (tp30) cc_final: 0.7891 (pm20) REVERT: E 10 ARG cc_start: 0.7802 (mpp80) cc_final: 0.6544 (mtp180) REVERT: E 131 LYS cc_start: 0.6536 (tptm) cc_final: 0.5562 (tmtt) REVERT: E 133 ARG cc_start: 0.4664 (ptp-170) cc_final: 0.3795 (ptp-170) REVERT: E 165 MET cc_start: 0.6332 (pmm) cc_final: 0.4976 (tpt) REVERT: F 411 TYR cc_start: 0.8400 (t80) cc_final: 0.8115 (t80) REVERT: F 449 THR cc_start: 0.9157 (m) cc_final: 0.8739 (p) REVERT: F 490 MET cc_start: 0.8743 (ttp) cc_final: 0.8477 (ptm) REVERT: F 508 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7876 (pt) REVERT: F 536 VAL cc_start: 0.6711 (OUTLIER) cc_final: 0.6474 (m) REVERT: F 663 PHE cc_start: 0.8028 (m-80) cc_final: 0.7775 (m-10) REVERT: F 725 LYS cc_start: 0.8723 (mttt) cc_final: 0.8354 (tmtt) REVERT: F 824 TRP cc_start: 0.8642 (t60) cc_final: 0.8432 (t60) REVERT: F 851 MET cc_start: 0.0773 (mtt) cc_final: 0.0173 (ttt) outliers start: 60 outliers final: 46 residues processed: 478 average time/residue: 0.1284 time to fit residues: 100.1513 Evaluate side-chains 471 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 420 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 105 ILE 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 337 PHE Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 925 ILE 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 1059 ILE 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 1191 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 1368 CYS Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 150 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 46 LEU 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 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 977 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 112 optimal weight: 6.9990 chunk 194 optimal weight: 0.0070 chunk 93 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 overall best weight: 1.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** 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 520 ASN ** F 983 GLN ** 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 = 0.4002 r_free = 0.4002 target = 0.136339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.105671 restraints weight = 102308.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.107366 restraints weight = 43683.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.108339 restraints weight = 28051.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.108744 restraints weight = 24655.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.109327 restraints weight = 20320.078| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.6026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22073 Z= 0.152 Angle : 0.817 14.199 29970 Z= 0.406 Chirality : 0.049 0.408 3449 Planarity : 0.005 0.105 3745 Dihedral : 7.169 66.761 3422 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.12 % Favored : 88.46 % Rotamer: Outliers : 2.65 % Allowed : 23.53 % Favored : 73.82 % 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 aren not related in a simple way. whole: -1.32 (0.16), residues: 2638 helix: 0.50 (0.14), residues: 1358 sheet: -0.86 (0.31), residues: 274 loop : -2.86 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1447 TYR 0.039 0.001 TYR A 650 PHE 0.026 0.002 PHE A 839 TRP 0.051 0.002 TRP A1406 HIS 0.005 0.001 HIS A1398 Details of bonding type rmsd covalent geometry : bond 0.00344 (22035) covalent geometry : angle 0.80485 (29873) SS BOND : bond 0.00244 ( 11) SS BOND : angle 1.89753 ( 22) hydrogen bonds : bond 0.03739 ( 929) hydrogen bonds : angle 4.51418 ( 2748) Misc. bond : bond 0.00011 ( 2) link_BETA1-4 : bond 0.00369 ( 10) link_BETA1-4 : angle 1.68531 ( 30) link_NAG-ASN : bond 0.00634 ( 15) link_NAG-ASN : angle 3.36089 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4387.85 seconds wall clock time: 76 minutes 12.39 seconds (4572.39 seconds total)