Starting phenix.real_space_refine on Sun Sep 13 19:25:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y76_33653/09_2026/7y76_33653.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y76_33653/09_2026/7y76_33653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y76_33653/09_2026/7y76_33653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y76_33653/09_2026/7y76_33653.map" model { file = "/net/cci-nas-00/data/ceres_data/7y76_33653/09_2026/7y76_33653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y76_33653/09_2026/7y76_33653.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7y76_33653/09_2026/7y76_33653.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y76_33653/09_2026/7y76_33653.cif" } resolution = 3.2 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 6 5.49 5 S 146 5.16 5 C 16340 2.51 5 N 4006 2.21 5 O 4680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25180 Number of models: 1 Model: "" Number of chains: 26 Chain: "B" Number of atoms: 4499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4499 Classifications: {'peptide': 573} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 552} Chain: "A" Number of atoms: 6102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 6102 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 35, 'TRANS': 714} Chain: "E" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1578 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 4499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4499 Classifications: {'peptide': 573} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 552} Chain: "C" Number of atoms: 6102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 6102 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 35, 'TRANS': 714} Chain: "F" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1578 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 172 Unusual residues: {'3PH': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 172 Unusual residues: {'3PH': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.41, per 1000 atoms: 0.21 Number of scatterers: 25180 At special positions: 0 Unit cell: (159.789, 144.571, 216.313, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 146 16.00 P 6 15.00 O 4680 8.00 N 4006 7.00 C 16340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 309 " - pdb=" SG CYS B 358 " distance=2.04 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.05 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.04 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 139 " distance=2.03 Simple disulfide: pdb=" SG CYS D 309 " - pdb=" SG CYS D 358 " distance=2.04 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.05 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.04 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A 901 " - " ASN A 322 " " NAG B1001 " - " ASN B 131 " " NAG B1002 " - " ASN B 332 " " NAG C 901 " - " ASN C 322 " " NAG D1001 " - " ASN D 131 " " NAG D1002 " - " ASN D 332 " " NAG G 1 " - " ASN B 357 " " NAG H 1 " - " ASN A 53 " " NAG I 1 " - " ASN A 90 " " NAG J 1 " - " ASN A 103 " " NAG K 1 " - " ASN A 432 " " NAG L 1 " - " ASN A 546 " " NAG M 1 " - " ASN A 690 " " NAG N 1 " - " ASN E 343 " " NAG O 1 " - " ASN D 357 " " NAG P 1 " - " ASN C 53 " " NAG Q 1 " - " ASN C 90 " " NAG R 1 " - " ASN C 103 " " NAG S 1 " - " ASN C 432 " " NAG T 1 " - " ASN C 546 " " NAG U 1 " - " ASN C 690 " " NAG V 1 " - " ASN F 343 " Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 378 " pdb=" ZN C 902 " pdb="ZN ZN C 902 " - pdb=" NE2 HIS C 374 " pdb="ZN ZN C 902 " - pdb=" NE2 HIS C 378 " 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5704 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 16 sheets defined 62.1% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 29 through 38 removed outlier: 3.749A pdb=" N TYR B 33 " --> pdb=" O TRP B 29 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 55 removed outlier: 3.848A pdb=" N VAL B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 55 through 70 removed outlier: 3.690A pdb=" N LEU B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 removed outlier: 3.578A pdb=" N SER B 81 " --> pdb=" O TRP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 85 through 115 removed outlier: 4.530A pdb=" N VAL B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N MET B 100 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL B 104 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE B 105 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 125 removed outlier: 4.000A pdb=" N VAL B 125 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 142 removed outlier: 3.672A pdb=" N ALA B 142 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'B' and resid 168 through 187 Processing helix chain 'B' and resid 195 through 216 Proline residue: B 203 - end of helix Processing helix chain 'B' and resid 220 through 229 removed outlier: 3.648A pdb=" N LEU B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 252 removed outlier: 3.846A pdb=" N TRP B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 263 removed outlier: 3.507A pdb=" N ALA B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 321 removed outlier: 4.001A pdb=" N HIS B 275 " --> pdb=" O ASN B 271 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 340 Processing helix chain 'B' and resid 344 through 349 Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.834A pdb=" N THR B 366 " --> pdb=" O SER B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 388 through 420 removed outlier: 3.774A pdb=" N ALA B 413 " --> pdb=" O GLY B 409 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Proline residue: B 417 - end of helix removed outlier: 3.672A pdb=" N ASP B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.803A pdb=" N SER B 426 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N HIS B 427 " --> pdb=" O ILE B 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 423 through 427' Processing helix chain 'B' and resid 429 through 446 removed outlier: 3.644A pdb=" N ILE B 433 " --> pdb=" O PRO B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 450 Processing helix chain 'B' and resid 452 through 483 removed outlier: 4.035A pdb=" N TRP B 456 " --> pdb=" O ALA B 452 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASP B 462 " --> pdb=" O ASP B 458 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 498 Processing helix chain 'B' and resid 502 through 509 Processing helix chain 'B' and resid 512 through 528 removed outlier: 3.677A pdb=" N VAL B 518 " --> pdb=" O PRO B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 568 removed outlier: 4.450A pdb=" N LEU B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 580 Processing helix chain 'A' and resid 21 through 53 removed outlier: 3.517A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 81 Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.674A pdb=" N ILE A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.822A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 removed outlier: 3.566A pdb=" N ASN A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.668A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.668A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 193 removed outlier: 3.513A pdb=" N LEU A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.768A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.962A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 removed outlier: 3.880A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.647A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.797A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 366 through 383 removed outlier: 3.966A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.292A pdb=" N ALA A 387 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.661A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.549A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 3.708A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 444 removed outlier: 3.985A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.635A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.756A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 526 " --> pdb=" O GLN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.577A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.761A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 623 through 629 removed outlier: 3.557A pdb=" N ALA A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 658 removed outlier: 3.717A pdb=" N MET A 640 " --> pdb=" O ASN A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 715 removed outlier: 3.722A pdb=" N SER A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N SER A 709 " --> pdb=" O ARG A 705 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ARG A 710 " --> pdb=" O MET A 706 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 715 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 767 removed outlier: 3.536A pdb=" N VAL A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 342 Processing helix chain 'E' and resid 403 through 410 removed outlier: 3.757A pdb=" N GLU E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.568A pdb=" N ASN E 422 " --> pdb=" O ILE E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'D' and resid 12 through 23 Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.748A pdb=" N TYR D 33 " --> pdb=" O TRP D 29 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR D 38 " --> pdb=" O LEU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 55 removed outlier: 3.848A pdb=" N VAL D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 55 through 70 removed outlier: 3.691A pdb=" N LEU D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 81 removed outlier: 3.578A pdb=" N SER D 81 " --> pdb=" O TRP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 85 through 115 removed outlier: 4.530A pdb=" N VAL D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET D 100 " --> pdb=" O PHE D 96 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL D 104 " --> pdb=" O MET D 100 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE D 105 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASN D 106 " --> pdb=" O TYR D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 125 removed outlier: 4.002A pdb=" N VAL D 125 " --> pdb=" O PRO D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 142 removed outlier: 3.672A pdb=" N ALA D 142 " --> pdb=" O GLU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'D' and resid 168 through 187 Processing helix chain 'D' and resid 195 through 216 Proline residue: D 203 - end of helix Processing helix chain 'D' and resid 220 through 229 removed outlier: 3.649A pdb=" N LEU D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 252 removed outlier: 3.847A pdb=" N TRP D 241 " --> pdb=" O ASN D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 263 removed outlier: 3.507A pdb=" N ALA D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 321 removed outlier: 4.000A pdb=" N HIS D 275 " --> pdb=" O ASN D 271 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE D 292 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL D 293 " --> pdb=" O PHE D 289 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR D 294 " --> pdb=" O ALA D 290 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE D 321 " --> pdb=" O LEU D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 340 Processing helix chain 'D' and resid 344 through 349 Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.835A pdb=" N THR D 366 " --> pdb=" O SER D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 383 Processing helix chain 'D' and resid 388 through 420 removed outlier: 3.774A pdb=" N ALA D 413 " --> pdb=" O GLY D 409 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE D 414 " --> pdb=" O ASN D 410 " (cutoff:3.500A) Proline residue: D 417 - end of helix removed outlier: 3.672A pdb=" N ASP D 420 " --> pdb=" O THR D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 427 removed outlier: 3.804A pdb=" N SER D 426 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N HIS D 427 " --> pdb=" O ILE D 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 423 through 427' Processing helix chain 'D' and resid 429 through 446 removed outlier: 3.644A pdb=" N ILE D 433 " --> pdb=" O PRO D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 450 Processing helix chain 'D' and resid 452 through 483 removed outlier: 4.035A pdb=" N TRP D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP D 462 " --> pdb=" O ASP D 458 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER D 468 " --> pdb=" O ALA D 464 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 498 Processing helix chain 'D' and resid 502 through 509 Processing helix chain 'D' and resid 512 through 528 removed outlier: 3.679A pdb=" N VAL D 518 " --> pdb=" O PRO D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 568 removed outlier: 4.451A pdb=" N LEU D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA D 557 " --> pdb=" O ALA D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 580 Processing helix chain 'C' and resid 21 through 53 removed outlier: 3.517A pdb=" N GLU C 37 " --> pdb=" O ASN C 33 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASP C 38 " --> pdb=" O HIS C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 81 Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.675A pdb=" N ILE C 88 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 102 removed outlier: 3.822A pdb=" N GLN C 102 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 130 removed outlier: 3.566A pdb=" N ASN C 121 " --> pdb=" O ASN C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 155 removed outlier: 3.668A pdb=" N ILE C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA C 153 " --> pdb=" O ASN C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 172 removed outlier: 3.668A pdb=" N ARG C 169 " --> pdb=" O TRP C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 193 removed outlier: 3.513A pdb=" N LEU C 176 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C 177 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Proline residue: C 178 - end of helix removed outlier: 3.768A pdb=" N GLU C 182 " --> pdb=" O PRO C 178 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 186 " --> pdb=" O GLU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 220 through 230 removed outlier: 3.962A pdb=" N GLU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 249 removed outlier: 3.880A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 293 through 300 removed outlier: 3.647A pdb=" N VAL C 298 " --> pdb=" O THR C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 318 removed outlier: 3.797A pdb=" N VAL C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 331 Processing helix chain 'C' and resid 366 through 383 removed outlier: 3.966A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.291A pdb=" N ALA C 387 " --> pdb=" O ALA C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 393 removed outlier: 3.661A pdb=" N ARG C 393 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 412 removed outlier: 3.550A pdb=" N ALA C 403 " --> pdb=" O GLY C 399 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER C 409 " --> pdb=" O GLY C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 422 removed outlier: 3.709A pdb=" N SER C 420 " --> pdb=" O LYS C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 444 removed outlier: 3.984A pdb=" N ILE C 436 " --> pdb=" O ASN C 432 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS C 441 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 448 No H-bonds generated for 'chain 'C' and resid 446 through 448' Processing helix chain 'C' and resid 449 through 466 Processing helix chain 'C' and resid 472 through 484 removed outlier: 3.635A pdb=" N ARG C 482 " --> pdb=" O TRP C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 513 through 533 removed outlier: 3.756A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE C 523 " --> pdb=" O THR C 519 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN C 526 " --> pdb=" O GLN C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 Processing helix chain 'C' and resid 547 through 559 removed outlier: 3.577A pdb=" N GLY C 551 " --> pdb=" O SER C 547 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 574 removed outlier: 3.762A pdb=" N VAL C 573 " --> pdb=" O ALA C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 588 through 599 Processing helix chain 'C' and resid 623 through 629 removed outlier: 3.558A pdb=" N ALA C 627 " --> pdb=" O SER C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 658 removed outlier: 3.718A pdb=" N MET C 640 " --> pdb=" O ASN C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 715 removed outlier: 3.722A pdb=" N SER C 707 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N SER C 709 " --> pdb=" O ARG C 705 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ARG C 710 " --> pdb=" O MET C 706 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP C 713 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE C 715 " --> pdb=" O ILE C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 767 removed outlier: 3.536A pdb=" N VAL C 745 " --> pdb=" O ILE C 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 342 Processing helix chain 'F' and resid 403 through 410 removed outlier: 3.757A pdb=" N GLU F 406 " --> pdb=" O ARG F 403 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER F 408 " --> pdb=" O ASN F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 422 removed outlier: 3.567A pdb=" N ASN F 422 " --> pdb=" O ILE F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.098A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.641A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 670 through 676 removed outlier: 4.463A pdb=" N LEU A 675 " --> pdb=" O SER A 680 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N SER A 680 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS A 619 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.634A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL E 433 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS E 378 " --> pdb=" O VAL E 433 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 391 through 392 removed outlier: 3.549A pdb=" N PHE E 392 " --> pdb=" O VAL E 524 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL E 524 " --> pdb=" O PHE E 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 452 through 453 Processing sheet with id=AA8, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'C' and resid 131 through 133 Processing sheet with id=AB1, first strand: chain 'C' and resid 262 through 263 removed outlier: 6.098A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 347 through 352 removed outlier: 6.641A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 670 through 676 removed outlier: 4.463A pdb=" N LEU C 675 " --> pdb=" O SER C 680 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER C 680 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS C 619 " --> pdb=" O LEU C 725 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 354 through 358 removed outlier: 3.636A pdb=" N VAL F 395 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL F 433 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS F 378 " --> pdb=" O VAL F 433 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 391 through 392 removed outlier: 3.549A pdb=" N PHE F 392 " --> pdb=" O VAL F 524 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL F 524 " --> pdb=" O PHE F 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 452 through 453 Processing sheet with id=AB7, first strand: chain 'F' and resid 473 through 474 1236 hydrogen bonds defined for protein. 3588 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.75 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7742 1.34 - 1.47: 6946 1.47 - 1.60: 10912 1.60 - 1.72: 6 1.72 - 1.85: 232 Bond restraints: 25838 Sorted by residual: bond pdb=" C31 3PH D1003 " pdb=" O31 3PH D1003 " ideal model delta sigma weight residual 1.325 1.456 -0.131 2.00e-02 2.50e+03 4.28e+01 bond pdb=" C31 3PH B1003 " pdb=" O31 3PH B1003 " ideal model delta sigma weight residual 1.325 1.455 -0.130 2.00e-02 2.50e+03 4.24e+01 bond pdb=" C31 3PH D1005 " pdb=" O31 3PH D1005 " ideal model delta sigma weight residual 1.325 1.455 -0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" C21 3PH D1003 " pdb=" O21 3PH D1003 " ideal model delta sigma weight residual 1.328 1.457 -0.129 2.00e-02 2.50e+03 4.16e+01 bond pdb=" C21 3PH B1003 " pdb=" O21 3PH B1003 " ideal model delta sigma weight residual 1.328 1.457 -0.129 2.00e-02 2.50e+03 4.16e+01 ... (remaining 25833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 34475 2.72 - 5.45: 523 5.45 - 8.17: 53 8.17 - 10.89: 16 10.89 - 13.61: 1 Bond angle restraints: 35068 Sorted by residual: angle pdb=" N VAL E 367 " pdb=" CA VAL E 367 " pdb=" C VAL E 367 " ideal model delta sigma weight residual 113.71 107.40 6.31 9.50e-01 1.11e+00 4.41e+01 angle pdb=" N VAL F 367 " pdb=" CA VAL F 367 " pdb=" C VAL F 367 " ideal model delta sigma weight residual 113.71 107.44 6.27 9.50e-01 1.11e+00 4.36e+01 angle pdb=" C LEU A 267 " pdb=" N GLY A 268 " pdb=" CA GLY A 268 " ideal model delta sigma weight residual 123.30 117.60 5.70 1.06e+00 8.90e-01 2.89e+01 angle pdb=" C LEU C 267 " pdb=" N GLY C 268 " pdb=" CA GLY C 268 " ideal model delta sigma weight residual 123.30 117.61 5.69 1.06e+00 8.90e-01 2.88e+01 angle pdb=" N PRO E 373 " pdb=" CA PRO E 373 " pdb=" C PRO E 373 " ideal model delta sigma weight residual 113.47 106.03 7.44 1.43e+00 4.89e-01 2.71e+01 ... (remaining 35063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 12807 17.14 - 34.27: 1545 34.27 - 51.41: 425 51.41 - 68.55: 101 68.55 - 85.68: 22 Dihedral angle restraints: 14900 sinusoidal: 5996 harmonic: 8904 Sorted by residual: dihedral pdb=" CB CYS F 379 " pdb=" SG CYS F 379 " pdb=" SG CYS F 432 " pdb=" CB CYS F 432 " ideal model delta sinusoidal sigma weight residual 93.00 40.25 52.75 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual 93.00 40.28 52.72 1 1.00e+01 1.00e-02 3.78e+01 dihedral pdb=" CB CYS E 391 " pdb=" SG CYS E 391 " pdb=" SG CYS E 525 " pdb=" CB CYS E 525 " ideal model delta sinusoidal sigma weight residual 93.00 48.73 44.27 1 1.00e+01 1.00e-02 2.73e+01 ... (remaining 14897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 3554 0.085 - 0.169: 318 0.169 - 0.254: 24 0.254 - 0.338: 4 0.338 - 0.423: 2 Chirality restraints: 3902 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN C 90 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CA PHE E 374 " pdb=" N PHE E 374 " pdb=" C PHE E 374 " pdb=" CB PHE E 374 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 3899 not shown) Planarity restraints: 4390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 687 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO A 688 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 688 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 688 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 687 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO C 688 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 688 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 688 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 234 " 0.028 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO C 235 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 235 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 235 " 0.023 5.00e-02 4.00e+02 ... (remaining 4387 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 291 2.58 - 3.16: 22246 3.16 - 3.74: 37992 3.74 - 4.32: 51845 4.32 - 4.90: 86132 Nonbonded interactions: 198506 Sorted by model distance: nonbonded pdb=" OE1 GLU C 402 " pdb="ZN ZN C 902 " model vdw 1.996 2.230 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 902 " model vdw 1.996 2.230 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 902 " model vdw 2.087 2.230 nonbonded pdb=" OE2 GLU C 402 " pdb="ZN ZN C 902 " model vdw 2.089 2.230 nonbonded pdb=" O ASN E 439 " pdb=" OG SER E 443 " model vdw 2.203 3.040 ... (remaining 198501 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.450 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 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 : 0.010 0.301 25896 Z= 0.443 Angle : 0.868 13.613 35214 Z= 0.448 Chirality : 0.052 0.423 3902 Planarity : 0.004 0.049 4368 Dihedral : 16.497 85.684 9148 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.84 % Favored : 90.83 % Rotamer: Outliers : 5.15 % Allowed : 16.06 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.40 (0.13), residues: 3030 helix: -1.66 (0.11), residues: 1662 sheet: -1.29 (0.45), residues: 116 loop : -3.15 (0.15), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 559 TYR 0.025 0.002 TYR C 183 PHE 0.019 0.002 PHE B 295 TRP 0.014 0.002 TRP C 459 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00954 / 0.43 (25838) covalent geometry : angle 0.84414 / 0.44 (35068) SS BOND : bond 0.00851 / 0.50 ( 16) SS BOND : angle 2.00432 / 1.24 ( 32) hydrogen bonds : bond 0.15869 / 10.18 ( 1236) hydrogen bonds : angle 6.45196 / 4.58 ( 3588) metal coordination : bond 0.21369 / 10.96 ( 4) link_BETA1-4 : bond 0.00646 / 0.45 ( 16) link_BETA1-4 : angle 2.31834 / 1.39 ( 48) link_NAG-ASN : bond 0.00823 / 0.47 ( 22) link_NAG-ASN : angle 4.16249 / 2.89 ( 66) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 209 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 225 MET cc_start: 0.7887 (mtt) cc_final: 0.7587 (mtt) REVERT: A 323 MET cc_start: 0.8921 (mmp) cc_final: 0.8693 (mmp) REVERT: A 736 GLN cc_start: 0.3725 (OUTLIER) cc_final: 0.3177 (tm-30) REVERT: E 357 ARG cc_start: 0.7917 (tmm-80) cc_final: 0.7634 (tmm-80) REVERT: E 471 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7978 (tm-30) REVERT: E 472 ILE cc_start: 0.8965 (mm) cc_final: 0.8743 (mt) REVERT: D 77 TRP cc_start: 0.6830 (m100) cc_final: 0.6123 (m100) REVERT: D 225 MET cc_start: 0.7890 (mtt) cc_final: 0.7593 (mtt) REVERT: C 406 GLU cc_start: 0.8022 (tp30) cc_final: 0.7803 (mm-30) REVERT: C 736 GLN cc_start: 0.3573 (OUTLIER) cc_final: 0.3315 (tt0) REVERT: F 472 ILE cc_start: 0.9021 (mm) cc_final: 0.8805 (mt) outliers start: 136 outliers final: 82 residues processed: 330 average time/residue: 0.1459 time to fit residues: 79.7887 Evaluate side-chains 254 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 170 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 385 TYR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain C residue 759 ILE Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain F residue 524 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 9.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN B 461 ASN ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 42 GLN A 51 ASN A 139 GLN A 159 ASN A 210 ASN A 239 HIS A 378 HIS A 472 GLN A 493 HIS A 505 HIS A 599 ASN E 417 ASN E 422 ASN ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 ASN D 461 ASN ** D 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN C 51 ASN C 102 GLN C 159 ASN C 210 ASN C 239 HIS C 378 HIS C 472 GLN C 493 HIS C 505 HIS C 599 ASN F 422 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.124035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.075833 restraints weight = 58876.696| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.17 r_work: 0.2838 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.482 25896 Z= 0.202 Angle : 0.665 12.560 35214 Z= 0.326 Chirality : 0.043 0.271 3902 Planarity : 0.004 0.056 4368 Dihedral : 10.466 59.930 3634 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.37 % Favored : 93.47 % Rotamer: Outliers : 3.41 % Allowed : 17.27 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.15), residues: 3030 helix: -0.13 (0.12), residues: 1692 sheet: -1.20 (0.51), residues: 92 loop : -2.64 (0.16), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 70 TYR 0.030 0.001 TYR D 504 PHE 0.015 0.001 PHE C 746 TRP 0.022 0.001 TRP B 77 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (25838) covalent geometry : angle 0.64111 / 0.32 (35068) SS BOND : bond 0.00896 / 0.55 ( 16) SS BOND : angle 2.18578 / 1.38 ( 32) hydrogen bonds : bond 0.05271 / 3.45 ( 1236) hydrogen bonds : angle 4.53838 / 3.23 ( 3588) metal coordination : bond 0.34028 / 16.62 ( 4) link_BETA1-4 : bond 0.00428 / 0.24 ( 16) link_BETA1-4 : angle 1.80626 / 1.04 ( 48) link_NAG-ASN : bond 0.00678 / 0.35 ( 22) link_NAG-ASN : angle 3.58679 / 2.44 ( 66) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 195 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 252 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8274 (mm) REVERT: B 349 SER cc_start: 0.9166 (OUTLIER) cc_final: 0.8927 (p) REVERT: B 446 MET cc_start: 0.7688 (tpp) cc_final: 0.7481 (tpp) REVERT: E 406 GLU cc_start: 0.8457 (mp0) cc_final: 0.8192 (mp0) REVERT: E 458 LYS cc_start: 0.8968 (mmmt) cc_final: 0.8723 (mmmt) REVERT: E 471 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7994 (tm-30) REVERT: E 472 ILE cc_start: 0.8959 (mm) cc_final: 0.8654 (mt) REVERT: D 100 MET cc_start: 0.8490 (mtt) cc_final: 0.7785 (mpp) REVERT: D 349 SER cc_start: 0.9111 (OUTLIER) cc_final: 0.8897 (p) REVERT: D 384 ASN cc_start: 0.7787 (OUTLIER) cc_final: 0.7551 (t0) REVERT: C 102 GLN cc_start: 0.9118 (pt0) cc_final: 0.8633 (pm20) REVERT: C 123 MET cc_start: 0.9318 (mtp) cc_final: 0.9001 (mtm) REVERT: F 406 GLU cc_start: 0.8453 (mp0) cc_final: 0.8219 (mp0) REVERT: F 458 LYS cc_start: 0.8945 (mmmt) cc_final: 0.8679 (mmmt) REVERT: F 472 ILE cc_start: 0.9100 (mm) cc_final: 0.8881 (mt) outliers start: 90 outliers final: 50 residues processed: 274 average time/residue: 0.1391 time to fit residues: 63.9549 Evaluate side-chains 234 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 180 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 384 ASN Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 759 ILE Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 148 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 25 optimal weight: 0.0010 chunk 39 optimal weight: 20.0000 chunk 279 optimal weight: 0.0370 chunk 188 optimal weight: 9.9990 chunk 191 optimal weight: 0.9980 chunk 69 optimal weight: 0.3980 chunk 75 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 165 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 64.5648 > 50:) overall best weight: 0.6866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 ASN B 275 HIS ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN A 139 GLN ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.125160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.073840 restraints weight = 58971.081| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.84 r_work: 0.2889 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 25896 Z= 0.117 Angle : 0.620 12.455 35214 Z= 0.302 Chirality : 0.042 0.282 3902 Planarity : 0.004 0.043 4368 Dihedral : 9.086 59.860 3560 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.80 % Favored : 93.04 % Rotamer: Outliers : 3.33 % Allowed : 17.95 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.15), residues: 3030 helix: 0.45 (0.13), residues: 1690 sheet: -0.85 (0.52), residues: 92 loop : -2.30 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 245 TYR 0.033 0.001 TYR B 504 PHE 0.015 0.001 PHE C 746 TRP 0.028 0.001 TRP B 505 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (25838) covalent geometry : angle 0.59377 / 0.30 (35068) SS BOND : bond 0.00928 / 0.55 ( 16) SS BOND : angle 2.61500 / 1.60 ( 32) hydrogen bonds : bond 0.04579 / 2.99 ( 1236) hydrogen bonds : angle 4.29447 / 3.07 ( 3588) metal coordination : bond 0.02012 / 1.02 ( 4) link_BETA1-4 : bond 0.00461 / 0.26 ( 16) link_BETA1-4 : angle 1.80521 / 1.06 ( 48) link_NAG-ASN : bond 0.00683 / 0.35 ( 22) link_NAG-ASN : angle 3.47553 / 2.35 ( 66) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 191 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 MET cc_start: 0.8402 (mtt) cc_final: 0.7838 (mpp) REVERT: B 198 PHE cc_start: 0.6950 (m-80) cc_final: 0.6499 (m-10) REVERT: B 446 MET cc_start: 0.7739 (tpp) cc_final: 0.7458 (tpp) REVERT: B 450 MET cc_start: 0.8829 (tpp) cc_final: 0.8456 (tpp) REVERT: E 406 GLU cc_start: 0.8622 (mp0) cc_final: 0.8342 (mp0) REVERT: E 458 LYS cc_start: 0.9003 (mmmt) cc_final: 0.8794 (mmmt) REVERT: E 471 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8104 (tm-30) REVERT: D 450 MET cc_start: 0.8600 (tpp) cc_final: 0.8236 (tpp) REVERT: C 102 GLN cc_start: 0.9249 (pt0) cc_final: 0.8850 (pm20) REVERT: C 123 MET cc_start: 0.9400 (mtp) cc_final: 0.9105 (mtm) REVERT: F 406 GLU cc_start: 0.8565 (mp0) cc_final: 0.8298 (mp0) outliers start: 88 outliers final: 45 residues processed: 263 average time/residue: 0.1382 time to fit residues: 61.4468 Evaluate side-chains 224 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 179 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 516 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 74 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 186 optimal weight: 8.9990 chunk 246 optimal weight: 3.9990 chunk 265 optimal weight: 0.9990 chunk 285 optimal weight: 20.0000 chunk 280 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 ASN ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.124154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.076296 restraints weight = 58544.098| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.25 r_work: 0.2833 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25896 Z= 0.161 Angle : 0.629 12.340 35214 Z= 0.304 Chirality : 0.043 0.278 3902 Planarity : 0.004 0.042 4368 Dihedral : 8.488 59.880 3547 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.63 % Favored : 93.20 % Rotamer: Outliers : 3.41 % Allowed : 18.79 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.15), residues: 3030 helix: 0.65 (0.13), residues: 1704 sheet: -0.66 (0.52), residues: 90 loop : -2.13 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 357 TYR 0.019 0.001 TYR D 378 PHE 0.016 0.001 PHE C 315 TRP 0.021 0.001 TRP D 77 HIS 0.006 0.001 HIS C 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (25838) covalent geometry : angle 0.60542 / 0.30 (35068) SS BOND : bond 0.00715 / 0.45 ( 16) SS BOND : angle 2.09637 / 1.33 ( 32) hydrogen bonds : bond 0.04692 / 3.06 ( 1236) hydrogen bonds : angle 4.21445 / 3.02 ( 3588) metal coordination : bond 0.00558 / 0.28 ( 4) link_BETA1-4 : bond 0.00422 / 0.24 ( 16) link_BETA1-4 : angle 1.76668 / 1.05 ( 48) link_NAG-ASN : bond 0.00632 / 0.32 ( 22) link_NAG-ASN : angle 3.47464 / 2.34 ( 66) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 192 time to evaluate : 0.937 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: B 198 PHE cc_start: 0.6972 (m-80) cc_final: 0.6596 (m-10) REVERT: B 446 MET cc_start: 0.7711 (tpp) cc_final: 0.7440 (tpp) REVERT: A 256 ILE cc_start: 0.9669 (OUTLIER) cc_final: 0.9384 (mm) REVERT: A 428 PHE cc_start: 0.8153 (t80) cc_final: 0.7594 (t80) REVERT: E 406 GLU cc_start: 0.8564 (mp0) cc_final: 0.8247 (mp0) REVERT: E 471 GLU cc_start: 0.8283 (tm-30) cc_final: 0.8019 (tm-30) REVERT: D 83 TYR cc_start: 0.4999 (OUTLIER) cc_final: 0.4552 (m-10) REVERT: D 450 MET cc_start: 0.8626 (tpp) cc_final: 0.8294 (tpp) REVERT: C 102 GLN cc_start: 0.9156 (pt0) cc_final: 0.8688 (pm20) REVERT: C 256 ILE cc_start: 0.9675 (OUTLIER) cc_final: 0.9420 (mm) REVERT: C 736 GLN cc_start: 0.3080 (OUTLIER) cc_final: 0.2608 (tm-30) REVERT: F 406 GLU cc_start: 0.8564 (mp0) cc_final: 0.8261 (mp0) outliers start: 90 outliers final: 53 residues processed: 269 average time/residue: 0.1392 time to fit residues: 62.8982 Evaluate side-chains 234 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 177 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 204 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 269 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 41 optimal weight: 30.0000 chunk 197 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 189 optimal weight: 0.9990 chunk 216 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 ASN ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 ASN B 283 ASN B 537 GLN A 338 ASN D 27 ASN ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 ASN D 384 ASN ** D 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.122329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.074620 restraints weight = 58124.045| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.89 r_work: 0.2796 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 25896 Z= 0.274 Angle : 0.691 12.364 35214 Z= 0.339 Chirality : 0.046 0.273 3902 Planarity : 0.004 0.041 4368 Dihedral : 8.320 59.721 3542 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.06 % Favored : 92.84 % Rotamer: Outliers : 3.37 % Allowed : 19.58 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.15), residues: 3030 helix: 0.63 (0.13), residues: 1714 sheet: -0.45 (0.53), residues: 86 loop : -2.05 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 357 TYR 0.025 0.002 TYR A 183 PHE 0.016 0.002 PHE C 315 TRP 0.012 0.002 TRP D 77 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00649 / 0.27 (25838) covalent geometry : angle 0.66684 / 0.33 (35068) SS BOND : bond 0.00965 / 0.58 ( 16) SS BOND : angle 2.61756 / 1.52 ( 32) hydrogen bonds : bond 0.05285 / 3.48 ( 1236) hydrogen bonds : angle 4.31663 / 3.09 ( 3588) metal coordination : bond 0.00955 / 0.48 ( 4) link_BETA1-4 : bond 0.00451 / 0.26 ( 16) link_BETA1-4 : angle 1.86475 / 1.12 ( 48) link_NAG-ASN : bond 0.00653 / 0.35 ( 22) link_NAG-ASN : angle 3.56450 / 2.41 ( 66) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 187 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 TYR cc_start: 0.4836 (OUTLIER) cc_final: 0.4278 (m-10) REVERT: B 198 PHE cc_start: 0.6955 (m-80) cc_final: 0.6567 (m-10) REVERT: B 225 MET cc_start: 0.7838 (mtt) cc_final: 0.7637 (mtm) REVERT: B 450 MET cc_start: 0.8404 (tpp) cc_final: 0.8005 (tpp) REVERT: A 256 ILE cc_start: 0.9686 (OUTLIER) cc_final: 0.9442 (mm) REVERT: A 428 PHE cc_start: 0.8216 (t80) cc_final: 0.7937 (t80) REVERT: A 736 GLN cc_start: 0.3196 (OUTLIER) cc_final: 0.2801 (tm-30) REVERT: E 406 GLU cc_start: 0.8492 (mp0) cc_final: 0.8156 (mp0) REVERT: E 471 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7945 (tm-30) REVERT: D 83 TYR cc_start: 0.5231 (OUTLIER) cc_final: 0.4580 (m-10) REVERT: D 225 MET cc_start: 0.7848 (mtt) cc_final: 0.7647 (mtm) REVERT: D 384 ASN cc_start: 0.7749 (OUTLIER) cc_final: 0.7502 (t0) REVERT: C 102 GLN cc_start: 0.9123 (pt0) cc_final: 0.8629 (pm20) REVERT: C 256 ILE cc_start: 0.9690 (OUTLIER) cc_final: 0.9451 (mm) REVERT: C 736 GLN cc_start: 0.3067 (OUTLIER) cc_final: 0.2666 (tm-30) REVERT: F 406 GLU cc_start: 0.8552 (mp0) cc_final: 0.8258 (mp0) outliers start: 89 outliers final: 53 residues processed: 264 average time/residue: 0.1425 time to fit residues: 63.0595 Evaluate side-chains 235 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 175 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 384 ASN Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 282 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 299 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 262 optimal weight: 0.6980 chunk 172 optimal weight: 6.9990 chunk 274 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN A 345 HIS ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.124181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.072355 restraints weight = 58162.684| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.79 r_work: 0.2863 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 25896 Z= 0.135 Angle : 0.640 13.034 35214 Z= 0.308 Chirality : 0.043 0.290 3902 Planarity : 0.004 0.041 4368 Dihedral : 7.974 59.209 3539 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.27 % Favored : 93.63 % Rotamer: Outliers : 2.99 % Allowed : 20.23 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.16), residues: 3030 helix: 0.81 (0.13), residues: 1710 sheet: -0.14 (0.61), residues: 66 loop : -1.92 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 346 TYR 0.018 0.001 TYR D 378 PHE 0.018 0.001 PHE D 489 TRP 0.012 0.001 TRP D 77 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (25838) covalent geometry : angle 0.60929 / 0.30 (35068) SS BOND : bond 0.01211 / 0.77 ( 16) SS BOND : angle 3.75977 / 2.16 ( 32) hydrogen bonds : bond 0.04467 / 2.93 ( 1236) hydrogen bonds : angle 4.15821 / 2.98 ( 3588) metal coordination : bond 0.00295 / 0.15 ( 4) link_BETA1-4 : bond 0.00410 / 0.23 ( 16) link_BETA1-4 : angle 1.81299 / 1.06 ( 48) link_NAG-ASN : bond 0.00651 / 0.33 ( 22) link_NAG-ASN : angle 3.45041 / 2.32 ( 66) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 186 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 TYR cc_start: 0.4928 (OUTLIER) cc_final: 0.4248 (m-10) REVERT: B 198 PHE cc_start: 0.7013 (m-80) cc_final: 0.6614 (m-10) REVERT: B 225 MET cc_start: 0.7921 (mtt) cc_final: 0.7713 (mtm) REVERT: B 450 MET cc_start: 0.8537 (tpp) cc_final: 0.8220 (tpp) REVERT: A 102 GLN cc_start: 0.9355 (pt0) cc_final: 0.8862 (pm20) REVERT: A 256 ILE cc_start: 0.9698 (OUTLIER) cc_final: 0.9423 (mm) REVERT: A 428 PHE cc_start: 0.8171 (t80) cc_final: 0.7542 (t80) REVERT: A 736 GLN cc_start: 0.3381 (OUTLIER) cc_final: 0.2927 (tm-30) REVERT: E 406 GLU cc_start: 0.8717 (mp0) cc_final: 0.8374 (mp0) REVERT: E 452 ARG cc_start: 0.8605 (mtm110) cc_final: 0.8389 (mtm110) REVERT: E 471 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8046 (tm-30) REVERT: E 488 CYS cc_start: 0.8228 (m) cc_final: 0.7952 (p) REVERT: D 83 TYR cc_start: 0.5343 (OUTLIER) cc_final: 0.4623 (m-10) REVERT: D 225 MET cc_start: 0.7934 (mtt) cc_final: 0.7721 (mtm) REVERT: D 450 MET cc_start: 0.8436 (tpp) cc_final: 0.8068 (tpp) REVERT: C 102 GLN cc_start: 0.9315 (pt0) cc_final: 0.8841 (pm20) REVERT: C 256 ILE cc_start: 0.9700 (OUTLIER) cc_final: 0.9430 (mm) REVERT: C 428 PHE cc_start: 0.8134 (t80) cc_final: 0.7553 (t80) REVERT: C 736 GLN cc_start: 0.3136 (OUTLIER) cc_final: 0.2605 (tm-30) REVERT: F 406 GLU cc_start: 0.8720 (mp0) cc_final: 0.8355 (mp0) REVERT: F 488 CYS cc_start: 0.8279 (m) cc_final: 0.7995 (p) outliers start: 79 outliers final: 46 residues processed: 255 average time/residue: 0.1454 time to fit residues: 62.1110 Evaluate side-chains 228 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 176 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 48 TRP Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 251 optimal weight: 0.9980 chunk 41 optimal weight: 40.0000 chunk 159 optimal weight: 5.9990 chunk 203 optimal weight: 0.7980 chunk 199 optimal weight: 8.9990 chunk 241 optimal weight: 7.9990 chunk 188 optimal weight: 1.9990 chunk 172 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 246 optimal weight: 0.7980 chunk 263 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 ASN A 345 HIS ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.125077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.077097 restraints weight = 58173.587| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.22 r_work: 0.2865 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 25896 Z= 0.117 Angle : 0.629 12.656 35214 Z= 0.300 Chirality : 0.042 0.295 3902 Planarity : 0.003 0.042 4368 Dihedral : 7.729 59.920 3537 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.34 % Favored : 93.60 % Rotamer: Outliers : 2.61 % Allowed : 20.38 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.16), residues: 3030 helix: 0.88 (0.13), residues: 1716 sheet: -0.34 (0.60), residues: 70 loop : -1.88 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 452 TYR 0.016 0.001 TYR D 378 PHE 0.016 0.001 PHE C 315 TRP 0.017 0.001 TRP D 509 HIS 0.026 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (25838) covalent geometry : angle 0.60263 / 0.29 (35068) SS BOND : bond 0.00766 / 0.48 ( 16) SS BOND : angle 2.97605 / 1.77 ( 32) hydrogen bonds : bond 0.04172 / 2.73 ( 1236) hydrogen bonds : angle 4.08136 / 2.93 ( 3588) metal coordination : bond 0.00209 / 0.11 ( 4) link_BETA1-4 : bond 0.00415 / 0.23 ( 16) link_BETA1-4 : angle 1.79303 / 1.06 ( 48) link_NAG-ASN : bond 0.00646 / 0.33 ( 22) link_NAG-ASN : angle 3.38982 / 2.27 ( 66) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 184 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 TYR cc_start: 0.4888 (OUTLIER) cc_final: 0.4255 (m-10) REVERT: B 198 PHE cc_start: 0.6985 (m-80) cc_final: 0.6560 (m-10) REVERT: B 450 MET cc_start: 0.8511 (tpp) cc_final: 0.8092 (tpp) REVERT: A 102 GLN cc_start: 0.9186 (pt0) cc_final: 0.8702 (pm20) REVERT: A 256 ILE cc_start: 0.9673 (OUTLIER) cc_final: 0.9382 (mm) REVERT: A 428 PHE cc_start: 0.8096 (t80) cc_final: 0.7533 (t80) REVERT: E 406 GLU cc_start: 0.8644 (mp0) cc_final: 0.8286 (mp0) REVERT: E 452 ARG cc_start: 0.8530 (mtm110) cc_final: 0.8207 (mtm110) REVERT: D 83 TYR cc_start: 0.5361 (OUTLIER) cc_final: 0.4714 (m-10) REVERT: D 100 MET cc_start: 0.8548 (mtt) cc_final: 0.7863 (mpp) REVERT: D 450 MET cc_start: 0.8515 (tpp) cc_final: 0.8112 (tpp) REVERT: C 102 GLN cc_start: 0.9139 (pt0) cc_final: 0.8676 (pm20) REVERT: C 256 ILE cc_start: 0.9673 (OUTLIER) cc_final: 0.9401 (mm) REVERT: C 428 PHE cc_start: 0.8075 (t80) cc_final: 0.7452 (t80) REVERT: F 406 GLU cc_start: 0.8652 (mp0) cc_final: 0.8253 (mp0) outliers start: 69 outliers final: 45 residues processed: 245 average time/residue: 0.1457 time to fit residues: 59.9096 Evaluate side-chains 224 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 175 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 275 optimal weight: 0.7980 chunk 149 optimal weight: 0.0170 chunk 71 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 210 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 overall best weight: 1.3420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.125037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.073618 restraints weight = 58378.241| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.82 r_work: 0.2882 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25896 Z= 0.125 Angle : 0.626 12.137 35214 Z= 0.299 Chirality : 0.042 0.287 3902 Planarity : 0.004 0.082 4368 Dihedral : 7.567 59.498 3535 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.40 % Favored : 93.53 % Rotamer: Outliers : 2.84 % Allowed : 20.23 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.16), residues: 3030 helix: 0.97 (0.13), residues: 1714 sheet: 0.17 (0.63), residues: 66 loop : -1.82 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 346 TYR 0.017 0.001 TYR D 378 PHE 0.014 0.001 PHE C 315 TRP 0.018 0.001 TRP B 509 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (25838) covalent geometry : angle 0.59973 / 0.29 (35068) SS BOND : bond 0.00848 / 0.48 ( 16) SS BOND : angle 2.97971 / 1.89 ( 32) hydrogen bonds : bond 0.04127 / 2.70 ( 1236) hydrogen bonds : angle 4.06762 / 2.92 ( 3588) metal coordination : bond 0.00292 / 0.15 ( 4) link_BETA1-4 : bond 0.00426 / 0.24 ( 16) link_BETA1-4 : angle 1.76816 / 1.05 ( 48) link_NAG-ASN : bond 0.00627 / 0.32 ( 22) link_NAG-ASN : angle 3.35117 / 2.24 ( 66) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 192 time to evaluate : 0.863 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: B 83 TYR cc_start: 0.4952 (OUTLIER) cc_final: 0.4211 (m-10) REVERT: B 198 PHE cc_start: 0.6964 (m-80) cc_final: 0.6570 (m-10) REVERT: B 225 MET cc_start: 0.8240 (mtm) cc_final: 0.7810 (ppp) REVERT: B 450 MET cc_start: 0.8545 (tpp) cc_final: 0.8170 (tpp) REVERT: B 508 MET cc_start: 0.7925 (mmm) cc_final: 0.7378 (mmm) REVERT: A 256 ILE cc_start: 0.9681 (OUTLIER) cc_final: 0.9391 (mm) REVERT: A 428 PHE cc_start: 0.8140 (t80) cc_final: 0.7797 (t80) REVERT: A 736 GLN cc_start: 0.3426 (OUTLIER) cc_final: 0.3018 (tm-30) REVERT: E 406 GLU cc_start: 0.8724 (mp0) cc_final: 0.8318 (mp0) REVERT: E 452 ARG cc_start: 0.8631 (mtm110) cc_final: 0.8337 (mtm110) REVERT: E 472 ILE cc_start: 0.8925 (mm) cc_final: 0.8713 (mt) REVERT: D 83 TYR cc_start: 0.5582 (OUTLIER) cc_final: 0.4874 (m-10) REVERT: D 96 PHE cc_start: 0.7212 (t80) cc_final: 0.6802 (t80) REVERT: D 100 MET cc_start: 0.8466 (mtt) cc_final: 0.7836 (mpp) REVERT: D 225 MET cc_start: 0.8230 (mtm) cc_final: 0.7808 (ppp) REVERT: D 450 MET cc_start: 0.8681 (tpp) cc_final: 0.8347 (tpp) REVERT: C 102 GLN cc_start: 0.9274 (pt0) cc_final: 0.8826 (pm20) REVERT: C 256 ILE cc_start: 0.9678 (OUTLIER) cc_final: 0.9388 (mm) REVERT: C 428 PHE cc_start: 0.8026 (t80) cc_final: 0.7566 (t80) outliers start: 75 outliers final: 51 residues processed: 260 average time/residue: 0.1489 time to fit residues: 63.5904 Evaluate side-chains 239 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 183 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 74 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 156 optimal weight: 30.0000 chunk 289 optimal weight: 6.9990 chunk 130 optimal weight: 30.0000 chunk 20 optimal weight: 0.0980 chunk 134 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 ASN A 345 HIS ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 537 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.124382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.076111 restraints weight = 58613.124| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.25 r_work: 0.2830 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 25896 Z= 0.164 Angle : 0.649 12.061 35214 Z= 0.311 Chirality : 0.043 0.281 3902 Planarity : 0.004 0.156 4368 Dihedral : 7.535 59.187 3535 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.47 % Favored : 93.47 % Rotamer: Outliers : 2.46 % Allowed : 20.57 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.16), residues: 3030 helix: 0.95 (0.13), residues: 1714 sheet: 0.59 (0.66), residues: 62 loop : -1.80 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 357 TYR 0.018 0.001 TYR D 378 PHE 0.040 0.001 PHE D 489 TRP 0.021 0.001 TRP D 509 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (25838) covalent geometry : angle 0.62383 / 0.30 (35068) SS BOND : bond 0.01088 / 0.69 ( 16) SS BOND : angle 3.02282 / 1.87 ( 32) hydrogen bonds : bond 0.04365 / 2.86 ( 1236) hydrogen bonds : angle 4.08360 / 2.94 ( 3588) metal coordination : bond 0.00512 / 0.26 ( 4) link_BETA1-4 : bond 0.00428 / 0.24 ( 16) link_BETA1-4 : angle 1.77509 / 1.05 ( 48) link_NAG-ASN : bond 0.00606 / 0.31 ( 22) link_NAG-ASN : angle 3.34901 / 2.24 ( 66) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 188 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 TYR cc_start: 0.4900 (OUTLIER) cc_final: 0.4198 (m-10) REVERT: B 198 PHE cc_start: 0.6921 (m-80) cc_final: 0.6513 (m-10) REVERT: B 225 MET cc_start: 0.8127 (mtm) cc_final: 0.7735 (ppp) REVERT: B 450 MET cc_start: 0.8559 (tpp) cc_final: 0.8244 (tpp) REVERT: B 508 MET cc_start: 0.7918 (mmm) cc_final: 0.7248 (mmm) REVERT: A 102 GLN cc_start: 0.9121 (pt0) cc_final: 0.8709 (pm20) REVERT: A 256 ILE cc_start: 0.9675 (OUTLIER) cc_final: 0.9415 (mm) REVERT: A 428 PHE cc_start: 0.8148 (t80) cc_final: 0.7817 (t80) REVERT: A 736 GLN cc_start: 0.3254 (OUTLIER) cc_final: 0.2877 (tm-30) REVERT: E 406 GLU cc_start: 0.8697 (mp0) cc_final: 0.8237 (mp0) REVERT: E 452 ARG cc_start: 0.8539 (mtm110) cc_final: 0.8216 (mtm110) REVERT: D 83 TYR cc_start: 0.5497 (OUTLIER) cc_final: 0.4812 (m-10) REVERT: D 96 PHE cc_start: 0.7193 (t80) cc_final: 0.6810 (t80) REVERT: D 100 MET cc_start: 0.8384 (mtt) cc_final: 0.7771 (mpp) REVERT: D 225 MET cc_start: 0.8122 (mtm) cc_final: 0.7737 (ppp) REVERT: D 450 MET cc_start: 0.8564 (tpp) cc_final: 0.8249 (tpp) REVERT: C 256 ILE cc_start: 0.9676 (OUTLIER) cc_final: 0.9413 (mm) REVERT: C 428 PHE cc_start: 0.8085 (t80) cc_final: 0.7689 (t80) REVERT: C 736 GLN cc_start: 0.3074 (OUTLIER) cc_final: 0.2617 (tm-30) outliers start: 65 outliers final: 54 residues processed: 247 average time/residue: 0.1494 time to fit residues: 60.9954 Evaluate side-chains 241 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 181 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 91 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 191 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 251 optimal weight: 0.5980 chunk 264 optimal weight: 0.9990 chunk 223 optimal weight: 2.9990 chunk 56 optimal weight: 20.0000 chunk 187 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 ASN A 345 HIS ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 537 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.125227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.073813 restraints weight = 58236.946| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.80 r_work: 0.2887 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 25896 Z= 0.123 Angle : 0.634 12.016 35214 Z= 0.304 Chirality : 0.042 0.290 3902 Planarity : 0.004 0.141 4368 Dihedral : 7.434 59.622 3535 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.47 % Favored : 93.47 % Rotamer: Outliers : 2.42 % Allowed : 20.49 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.16), residues: 3030 helix: 1.01 (0.13), residues: 1714 sheet: 0.71 (0.66), residues: 62 loop : -1.75 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 357 TYR 0.016 0.001 TYR D 378 PHE 0.014 0.001 PHE C 315 TRP 0.071 0.001 TRP D 505 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (25838) covalent geometry : angle 0.60920 / 0.30 (35068) SS BOND : bond 0.01026 / 0.65 ( 16) SS BOND : angle 2.94422 / 1.80 ( 32) hydrogen bonds : bond 0.04087 / 2.67 ( 1236) hydrogen bonds : angle 4.04639 / 2.91 ( 3588) metal coordination : bond 0.00263 / 0.13 ( 4) link_BETA1-4 : bond 0.00418 / 0.23 ( 16) link_BETA1-4 : angle 1.77402 / 1.05 ( 48) link_NAG-ASN : bond 0.00625 / 0.32 ( 22) link_NAG-ASN : angle 3.29807 / 2.20 ( 66) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 185 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 TYR cc_start: 0.5055 (OUTLIER) cc_final: 0.4281 (m-10) REVERT: B 198 PHE cc_start: 0.6921 (m-80) cc_final: 0.6500 (m-10) REVERT: B 225 MET cc_start: 0.8197 (mtm) cc_final: 0.7769 (ppp) REVERT: B 450 MET cc_start: 0.8679 (tpp) cc_final: 0.8438 (tpp) REVERT: B 508 MET cc_start: 0.8008 (mmm) cc_final: 0.7352 (mmm) REVERT: A 102 GLN cc_start: 0.9213 (pt0) cc_final: 0.8837 (pm20) REVERT: A 256 ILE cc_start: 0.9671 (OUTLIER) cc_final: 0.9372 (mm) REVERT: A 428 PHE cc_start: 0.8150 (t80) cc_final: 0.7796 (t80) REVERT: A 736 GLN cc_start: 0.3317 (OUTLIER) cc_final: 0.2907 (tm-30) REVERT: E 452 ARG cc_start: 0.8652 (mtm110) cc_final: 0.8398 (mtm110) REVERT: D 96 PHE cc_start: 0.7224 (t80) cc_final: 0.6821 (t80) REVERT: D 100 MET cc_start: 0.8435 (mtt) cc_final: 0.7833 (mpp) REVERT: D 225 MET cc_start: 0.8187 (mtm) cc_final: 0.7768 (ppp) REVERT: D 450 MET cc_start: 0.8580 (tpp) cc_final: 0.8259 (tpp) REVERT: D 508 MET cc_start: 0.7924 (mmm) cc_final: 0.7362 (mmm) REVERT: C 102 GLN cc_start: 0.9221 (pt0) cc_final: 0.8842 (pm20) REVERT: C 256 ILE cc_start: 0.9670 (OUTLIER) cc_final: 0.9392 (mm) REVERT: C 428 PHE cc_start: 0.8024 (t80) cc_final: 0.7563 (t80) REVERT: C 736 GLN cc_start: 0.3128 (OUTLIER) cc_final: 0.2634 (tm-30) outliers start: 64 outliers final: 56 residues processed: 242 average time/residue: 0.1435 time to fit residues: 57.5645 Evaluate side-chains 246 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 185 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 433 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 185 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 242 optimal weight: 6.9990 chunk 277 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 151 optimal weight: 30.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN A 345 HIS ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.124360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.076662 restraints weight = 58196.126| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.00 r_work: 0.2850 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 25896 Z= 0.151 Angle : 0.647 11.923 35214 Z= 0.310 Chirality : 0.043 0.283 3902 Planarity : 0.004 0.127 4368 Dihedral : 7.409 59.950 3535 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.63 % Favored : 93.30 % Rotamer: Outliers : 2.54 % Allowed : 20.49 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.16), residues: 3030 helix: 1.01 (0.13), residues: 1716 sheet: 0.64 (0.64), residues: 62 loop : -1.73 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 357 TYR 0.019 0.001 TYR D 504 PHE 0.013 0.001 PHE C 315 TRP 0.052 0.001 TRP D 505 HIS 0.004 0.001 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (25838) covalent geometry : angle 0.62222 / 0.30 (35068) SS BOND : bond 0.01008 / 0.64 ( 16) SS BOND : angle 3.00489 / 1.81 ( 32) hydrogen bonds : bond 0.04233 / 2.79 ( 1236) hydrogen bonds : angle 4.06426 / 2.93 ( 3588) metal coordination : bond 0.00410 / 0.21 ( 4) link_BETA1-4 : bond 0.00439 / 0.25 ( 16) link_BETA1-4 : angle 1.75677 / 1.04 ( 48) link_NAG-ASN : bond 0.00602 / 0.31 ( 22) link_NAG-ASN : angle 3.29129 / 2.19 ( 66) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7919.31 seconds wall clock time: 135 minutes 39.39 seconds (8139.39 seconds total)