Starting phenix.real_space_refine on Sat Feb 17 23:46:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjo_23880/02_2024/7mjo_23880_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjo_23880/02_2024/7mjo_23880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjo_23880/02_2024/7mjo_23880.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjo_23880/02_2024/7mjo_23880.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjo_23880/02_2024/7mjo_23880_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjo_23880/02_2024/7mjo_23880_neut_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 ------------------------------------------------------------------------------- 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= 1.000 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 28 5.49 5 S 76 5.16 5 Cl 1 4.86 5 C 12656 2.51 5 N 3556 2.21 5 O 3658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B ARG 352": "NH1" <-> "NH2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "C ARG 347": "NH1" <-> "NH2" Residue "C ARG 352": "NH1" <-> "NH2" Residue "D ARG 51": "NH1" <-> "NH2" Residue "D ARG 70": "NH1" <-> "NH2" Residue "D ARG 187": "NH1" <-> "NH2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "D ARG 226": "NH1" <-> "NH2" Residue "D ARG 310": "NH1" <-> "NH2" Residue "D ARG 347": "NH1" <-> "NH2" Residue "D ARG 352": "NH1" <-> "NH2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "E ARG 189": "NH1" <-> "NH2" Residue "E ARG 304": "NH1" <-> "NH2" Residue "E ARG 776": "NH1" <-> "NH2" Residue "E ARG 815": "NH1" <-> "NH2" Residue "E ARG 1091": "NH1" <-> "NH2" Residue "E ARG 1112": "NH1" <-> "NH2" Residue "E ARG 1316": "NH1" <-> "NH2" Residue "E ARG 1382": "NH1" <-> "NH2" Residue "E ARG 1450": "NH1" <-> "NH2" Residue "G ARG 97": "NH1" <-> "NH2" Residue "G ARG 189": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19977 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2448 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 11, 'TRANS': 333} Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 15, 'ARG:plan': 6, 'PHE:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 131 Chain: "B" Number of atoms: 2426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2426 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 10, 'TRANS': 326} Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 2407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2407 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 10, 'TRANS': 326} Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 128 Chain: "D" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2423 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 10, 'TRANS': 326} Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 176 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 13, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 108 Chain: "E" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1420, 8338 Classifications: {'peptide': 1420} Incomplete info: {'truncation_to_alanine': 861} Link IDs: {'PTRANS': 44, 'TRANS': 1375} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 3014 Unresolved non-hydrogen angles: 3849 Unresolved non-hydrogen dihedrals: 2447 Unresolved non-hydrogen chiralities: 346 Planarities with less than four sites: {'GLN:plan1': 37, 'ARG:plan': 44, 'TYR:plan': 21, 'ASN:plan1': 49, 'TRP:plan': 11, 'HIS:plan': 19, 'PHE:plan': 44, 'GLU:plan': 62, 'ASP:plan': 51} Unresolved non-hydrogen planarities: 1521 Chain: "G" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1261 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 9, 'TRANS': 195} Unresolved non-hydrogen bonds: 433 Unresolved non-hydrogen angles: 563 Unresolved non-hydrogen dihedrals: 369 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 4, 'ASP:plan': 2, 'PHE:plan': 8, 'GLU:plan': 4, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 227 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 161 Unusual residues: {' K': 2, 'ATP': 1, 'PTY': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 72 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {'ATP': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'ATP': 1, 'POV': 1, 'PTY': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'POV': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 160 Unusual residues: {'ATP': 1, 'GBM': 1, 'PTY': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 54 Time building chain proxies: 11.30, per 1000 atoms: 0.57 Number of scatterers: 19977 At special positions: 0 Unit cell: (110.751, 157.035, 148.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 Cl 1 17.00 S 76 16.00 P 28 15.00 O 3658 8.00 N 3556 7.00 C 12656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 152 " distance=1.84 Simple disulfide: pdb=" SG CYS C 120 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS D 120 " - pdb=" SG CYS D 152 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 24 " distance=2.03 Simple disulfide: pdb=" SG CYS E1407 " - pdb=" SG CYS E1409 " distance=2.04 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 24 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 F 1 " - " NAG F 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG F 1 " - " ASN G 9 " " NAG N 1 " - " ASN E 9 " Time building additional restraints: 9.37 Conformation dependent library (CDL) restraints added in 4.2 seconds 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5638 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 13 sheets defined 45.3% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.83 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.898A pdb=" N ASP A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 69 through 97 Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 127 through 138 Processing helix chain 'A' and resid 153 through 182 Processing helix chain 'A' and resid 283 through 287 removed outlier: 4.285A pdb=" N VAL A 286 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 354 through 357 No H-bonds generated for 'chain 'A' and resid 354 through 357' Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 69 through 97 removed outlier: 4.684A pdb=" N VAL B 74 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 104 No H-bonds generated for 'chain 'B' and resid 101 through 104' Processing helix chain 'B' and resid 112 through 115 No H-bonds generated for 'chain 'B' and resid 112 through 115' Processing helix chain 'B' and resid 127 through 138 Processing helix chain 'B' and resid 153 through 183 Processing helix chain 'B' and resid 282 through 285 No H-bonds generated for 'chain 'B' and resid 282 through 285' Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'C' and resid 57 through 65 Processing helix chain 'C' and resid 69 through 97 removed outlier: 3.994A pdb=" N LEU C 73 " --> pdb=" O TRP C 69 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N VAL C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 128 through 138 Processing helix chain 'C' and resid 153 through 183 removed outlier: 3.521A pdb=" N GLN C 183 " --> pdb=" O MET C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 279 removed outlier: 4.289A pdb=" N ASP C 279 " --> pdb=" O PRO C 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 276 through 279' Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 357 through 360 No H-bonds generated for 'chain 'C' and resid 357 through 360' Processing helix chain 'D' and resid 59 through 65 Processing helix chain 'D' and resid 69 through 72 No H-bonds generated for 'chain 'D' and resid 69 through 72' Processing helix chain 'D' and resid 75 through 98 removed outlier: 3.664A pdb=" N HIS D 98 " --> pdb=" O VAL D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 127 through 138 removed outlier: 3.929A pdb=" N GLU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 184 removed outlier: 4.851A pdb=" N ALA D 184 " --> pdb=" O LYS D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 279 removed outlier: 3.880A pdb=" N ASP D 279 " --> pdb=" O PRO D 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 276 through 279' Processing helix chain 'D' and resid 284 through 287 Processing helix chain 'D' and resid 315 through 317 No H-bonds generated for 'chain 'D' and resid 315 through 317' Processing helix chain 'D' and resid 339 through 341 No H-bonds generated for 'chain 'D' and resid 339 through 341' Processing helix chain 'D' and resid 355 through 358 No H-bonds generated for 'chain 'D' and resid 355 through 358' Processing helix chain 'D' and resid 362 through 365 No H-bonds generated for 'chain 'D' and resid 362 through 365' Processing helix chain 'E' and resid 23 through 47 Proline residue: E 33 - end of helix removed outlier: 4.581A pdb=" N ILE E 40 " --> pdb=" O PHE E 36 " (cutoff:3.500A) Proline residue: E 43 - end of helix Processing helix chain 'E' and resid 57 through 63 removed outlier: 4.325A pdb=" N THR E 62 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TRP E 63 " --> pdb=" O HIS E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 96 removed outlier: 3.693A pdb=" N GLN E 96 " --> pdb=" O VAL E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 104 No H-bonds generated for 'chain 'E' and resid 102 through 104' Processing helix chain 'E' and resid 106 through 127 removed outlier: 3.592A pdb=" N VAL E 113 " --> pdb=" O VAL E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 158 removed outlier: 3.843A pdb=" N LEU E 135 " --> pdb=" O LYS E 132 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA E 136 " --> pdb=" O LEU E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 195 removed outlier: 4.506A pdb=" N VAL E 190 " --> pdb=" O ASN E 186 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG E 191 " --> pdb=" O VAL E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 224 Processing helix chain 'E' and resid 229 through 236 removed outlier: 4.076A pdb=" N THR E 233 " --> pdb=" O TRP E 229 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LEU E 234 " --> pdb=" O TRP E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 255 No H-bonds generated for 'chain 'E' and resid 252 through 255' Processing helix chain 'E' and resid 258 through 275 removed outlier: 4.046A pdb=" N GLU E 266 " --> pdb=" O VAL E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 325 Proline residue: E 315 - end of helix removed outlier: 3.873A pdb=" N ARG E 324 " --> pdb=" O GLY E 320 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N VAL E 325 " --> pdb=" O ILE E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 393 removed outlier: 3.923A pdb=" N ASN E 379 " --> pdb=" O GLU E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 404 Processing helix chain 'E' and resid 408 through 412 Processing helix chain 'E' and resid 418 through 433 Proline residue: E 429 - end of helix Processing helix chain 'E' and resid 435 through 449 removed outlier: 4.064A pdb=" N MET E 440 " --> pdb=" O VAL E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 502 removed outlier: 4.416A pdb=" N VAL E 459 " --> pdb=" O VAL E 455 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE E 460 " --> pdb=" O GLY E 456 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL E 461 " --> pdb=" O ALA E 457 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU E 462 " --> pdb=" O ALA E 458 " (cutoff:3.500A) Proline residue: E 465 - end of helix removed outlier: 4.434A pdb=" N THR E 472 " --> pdb=" O TYR E 468 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS E 473 " --> pdb=" O PHE E 469 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY E 498 " --> pdb=" O GLU E 494 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE E 499 " --> pdb=" O ILE E 495 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LYS E 500 " --> pdb=" O LEU E 496 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU E 501 " --> pdb=" O LYS E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 557 removed outlier: 5.095A pdb=" N SER E 514 " --> pdb=" O PHE E 511 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA E 542 " --> pdb=" O MET E 539 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ILE E 543 " --> pdb=" O ASN E 540 " (cutoff:3.500A) Proline residue: E 544 - end of helix Processing helix chain 'E' and resid 565 through 578 removed outlier: 3.821A pdb=" N PHE E 569 " --> pdb=" O PRO E 565 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ALA E 570 " --> pdb=" O ALA E 566 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER E 571 " --> pdb=" O GLU E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 607 removed outlier: 4.177A pdb=" N LEU E 584 " --> pdb=" O THR E 580 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG E 590 " --> pdb=" O SER E 586 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL E 593 " --> pdb=" O VAL E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 707 through 714 Processing helix chain 'E' and resid 762 through 767 Processing helix chain 'E' and resid 774 through 784 removed outlier: 3.989A pdb=" N CYS E 784 " --> pdb=" O VAL E 780 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 792 Processing helix chain 'E' and resid 796 through 798 No H-bonds generated for 'chain 'E' and resid 796 through 798' Processing helix chain 'E' and resid 810 through 822 Processing helix chain 'E' and resid 844 through 854 Processing helix chain 'E' and resid 894 through 898 removed outlier: 3.520A pdb=" N LYS E 898 " --> pdb=" O ASP E 894 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 894 through 898' Processing helix chain 'E' and resid 901 through 909 removed outlier: 3.773A pdb=" N TRP E 906 " --> pdb=" O LEU E 902 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS E 907 " --> pdb=" O TYR E 903 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR E 908 " --> pdb=" O GLU E 904 " (cutoff:3.500A) Processing helix chain 'E' and resid 963 through 965 No H-bonds generated for 'chain 'E' and resid 963 through 965' Processing helix chain 'E' and resid 975 through 984 removed outlier: 3.547A pdb=" N SER E 984 " --> pdb=" O TRP E 980 " (cutoff:3.500A) Processing helix chain 'E' and resid 993 through 1014 Processing helix chain 'E' and resid 1030 through 1033 removed outlier: 4.081A pdb=" N ALA E1033 " --> pdb=" O PHE E1030 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1030 through 1033' Processing helix chain 'E' and resid 1036 through 1071 removed outlier: 4.376A pdb=" N GLY E1040 " --> pdb=" O ILE E1037 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU E1045 " --> pdb=" O GLY E1042 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N CYS E1046 " --> pdb=" O ILE E1043 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N VAL E1053 " --> pdb=" O SER E1050 " (cutoff:3.500A) Processing helix chain 'E' and resid 1077 through 1082 Processing helix chain 'E' and resid 1085 through 1101 removed outlier: 4.148A pdb=" N ASP E1095 " --> pdb=" O ARG E1091 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR E1096 " --> pdb=" O PHE E1092 " (cutoff:3.500A) Processing helix chain 'E' and resid 1103 through 1127 Processing helix chain 'E' and resid 1129 through 1134 removed outlier: 3.947A pdb=" N ILE E1133 " --> pdb=" O PRO E1129 " (cutoff:3.500A) Processing helix chain 'E' and resid 1137 through 1176 removed outlier: 3.518A pdb=" N PHE E1144 " --> pdb=" O VAL E1140 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER E1153 " --> pdb=" O PHE E1149 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LYS E1154 " --> pdb=" O ARG E1150 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN E1164 " --> pdb=" O ASP E1160 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N LEU E1165 " --> pdb=" O ASP E1161 " (cutoff:3.500A) Proline residue: E1166 - end of helix removed outlier: 3.811A pdb=" N CYS E1169 " --> pdb=" O LEU E1165 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE E1171 " --> pdb=" O LEU E1167 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA E1175 " --> pdb=" O PHE E1171 " (cutoff:3.500A) Processing helix chain 'E' and resid 1188 through 1237 removed outlier: 3.643A pdb=" N ARG E1193 " --> pdb=" O PHE E1190 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU E1195 " --> pdb=" O GLN E1192 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N THR E1198 " --> pdb=" O LEU E1195 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE E1203 " --> pdb=" O THR E1200 " (cutoff:3.500A) Processing helix chain 'E' and resid 1241 through 1279 removed outlier: 4.390A pdb=" N ASN E1256 " --> pdb=" O LEU E1252 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR E1257 " --> pdb=" O THR E1253 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU E1258 " --> pdb=" O ILE E1254 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASN E1259 " --> pdb=" O THR E1255 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TRP E1260 " --> pdb=" O ASN E1256 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS E1277 " --> pdb=" O GLY E1273 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL E1278 " --> pdb=" O ALA E1274 " (cutoff:3.500A) Processing helix chain 'E' and resid 1344 through 1353 removed outlier: 4.286A pdb=" N LYS E1348 " --> pdb=" O THR E1344 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N SER E1349 " --> pdb=" O GLY E1345 " (cutoff:3.500A) Processing helix chain 'E' and resid 1381 through 1384 Processing helix chain 'E' and resid 1424 through 1427 No H-bonds generated for 'chain 'E' and resid 1424 through 1427' Processing helix chain 'E' and resid 1454 through 1458 Processing helix chain 'E' and resid 1476 through 1490 Processing helix chain 'E' and resid 1503 through 1506 No H-bonds generated for 'chain 'E' and resid 1503 through 1506' Processing helix chain 'E' and resid 1527 through 1532 Processing helix chain 'E' and resid 1537 through 1540 No H-bonds generated for 'chain 'E' and resid 1537 through 1540' Processing helix chain 'G' and resid 23 through 46 removed outlier: 3.845A pdb=" N ASP G 27 " --> pdb=" O PRO G 23 " (cutoff:3.500A) Proline residue: G 33 - end of helix removed outlier: 4.354A pdb=" N PHE G 39 " --> pdb=" O VAL G 35 " (cutoff:3.500A) Proline residue: G 43 - end of helix Processing helix chain 'G' and resid 69 through 96 removed outlier: 4.076A pdb=" N TRP G 73 " --> pdb=" O HIS G 69 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER G 95 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLN G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 104 No H-bonds generated for 'chain 'G' and resid 102 through 104' Processing helix chain 'G' and resid 106 through 126 Processing helix chain 'G' and resid 131 through 158 removed outlier: 3.953A pdb=" N LEU G 135 " --> pdb=" O LYS G 132 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL G 153 " --> pdb=" O ILE G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 186 removed outlier: 4.151A pdb=" N VAL G 172 " --> pdb=" O CYS G 168 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N MET G 173 " --> pdb=" O ILE G 169 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL G 174 " --> pdb=" O THR G 170 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE G 175 " --> pdb=" O GLY G 171 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 191 through 193 Processing sheet with id= B, first strand: chain 'A' and resid 198 through 202 removed outlier: 3.678A pdb=" N VAL A 198 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 244 through 248 removed outlier: 4.594A pdb=" N ILE A 227 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 328 through 330 Processing sheet with id= E, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.611A pdb=" N ALA B 197 " --> pdb=" O GLN B 319 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE B 210 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 246 through 248 removed outlier: 3.545A pdb=" N VAL B 229 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE B 227 " --> pdb=" O ILE B 248 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 233 through 235 removed outlier: 3.501A pdb=" N THR B 233 " --> pdb=" O VAL B 241 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 210 through 212 Processing sheet with id= I, first strand: chain 'C' and resid 245 through 248 removed outlier: 4.496A pdb=" N ILE C 227 " --> pdb=" O ILE C 248 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 244 through 248 removed outlier: 4.285A pdb=" N ILE D 227 " --> pdb=" O ILE D 248 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 328 through 330 Processing sheet with id= L, first strand: chain 'E' and resid 748 through 750 removed outlier: 6.535A pdb=" N ILE E 828 " --> pdb=" O ALA E 749 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 1513 through 1516 removed outlier: 5.017A pdb=" N LYS E1516 " --> pdb=" O ILE E1520 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE E1520 " --> pdb=" O LYS E1516 " (cutoff:3.500A) 982 hydrogen bonds defined for protein. 2376 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: 6.07 Time building geometry restraints manager: 9.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3252 1.31 - 1.44: 5346 1.44 - 1.57: 11572 1.57 - 1.71: 54 1.71 - 1.84: 116 Bond restraints: 20340 Sorted by residual: bond pdb=" C29 POV B 503 " pdb="C210 POV B 503 " ideal model delta sigma weight residual 1.333 1.544 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C29 POV D 801 " pdb="C210 POV D 801 " ideal model delta sigma weight residual 1.333 1.544 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C29 POV C 504 " pdb="C210 POV C 504 " ideal model delta sigma weight residual 1.333 1.544 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" O5 GBM E1602 " pdb=" S2 GBM E1602 " ideal model delta sigma weight residual 1.448 1.650 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" O4 GBM E1602 " pdb=" S2 GBM E1602 " ideal model delta sigma weight residual 1.453 1.651 -0.198 2.00e-02 2.50e+03 9.83e+01 ... (remaining 20335 not shown) Histogram of bond angle deviations from ideal: 98.58 - 106.09: 449 106.09 - 113.59: 11766 113.59 - 121.10: 10056 121.10 - 128.61: 5498 128.61 - 136.11: 163 Bond angle restraints: 27932 Sorted by residual: angle pdb=" PB ATP E1601 " pdb=" O3B ATP E1601 " pdb=" PG ATP E1601 " ideal model delta sigma weight residual 139.87 118.66 21.21 1.00e+00 1.00e+00 4.50e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 118.76 21.11 1.00e+00 1.00e+00 4.45e+02 angle pdb=" PB ATP B 502 " pdb=" O3B ATP B 502 " pdb=" PG ATP B 502 " ideal model delta sigma weight residual 139.87 120.42 19.45 1.00e+00 1.00e+00 3.78e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 121.04 18.83 1.00e+00 1.00e+00 3.55e+02 angle pdb=" PA ATP B 501 " pdb=" O3A ATP B 501 " pdb=" PB ATP B 501 " ideal model delta sigma weight residual 136.83 118.05 18.78 1.00e+00 1.00e+00 3.53e+02 ... (remaining 27927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.78: 11737 34.78 - 69.57: 269 69.57 - 104.35: 35 104.35 - 139.13: 10 139.13 - 173.91: 3 Dihedral angle restraints: 12054 sinusoidal: 3396 harmonic: 8658 Sorted by residual: dihedral pdb=" CB CYS E1407 " pdb=" SG CYS E1407 " pdb=" SG CYS E1409 " pdb=" CB CYS E1409 " ideal model delta sinusoidal sigma weight residual -86.00 -139.09 53.09 1 1.00e+01 1.00e-02 3.83e+01 dihedral pdb=" N1 PTY A 504 " pdb=" C2 PTY A 504 " pdb=" C3 PTY A 504 " pdb=" O11 PTY A 504 " ideal model delta sinusoidal sigma weight residual 65.33 -120.76 -173.91 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA PHE A 56 " pdb=" C PHE A 56 " pdb=" N LEU A 57 " pdb=" CA LEU A 57 " ideal model delta harmonic sigma weight residual -180.00 -157.01 -22.99 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 12051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2942 0.070 - 0.141: 412 0.141 - 0.211: 25 0.211 - 0.281: 7 0.281 - 0.352: 4 Chirality restraints: 3390 Sorted by residual: chirality pdb=" CA TRP E 230 " pdb=" N TRP E 230 " pdb=" C TRP E 230 " pdb=" CB TRP E 230 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA LEU E 902 " pdb=" N LEU E 902 " pdb=" C LEU E 902 " pdb=" CB LEU E 902 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA TYR E 228 " pdb=" N TYR E 228 " pdb=" C TYR E 228 " pdb=" CB TYR E 228 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 3387 not shown) Planarity restraints: 3601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 145 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C PHE E 145 " -0.056 2.00e-02 2.50e+03 pdb=" O PHE E 145 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE E 146 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET E 143 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.17e+00 pdb=" C MET E 143 " 0.046 2.00e-02 2.50e+03 pdb=" O MET E 143 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA E 144 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E1061 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.65e+00 pdb=" C ALA E1061 " 0.045 2.00e-02 2.50e+03 pdb=" O ALA E1061 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS E1062 " -0.015 2.00e-02 2.50e+03 ... (remaining 3598 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.51: 117 2.51 - 3.17: 18134 3.17 - 3.83: 35696 3.83 - 4.48: 42307 4.48 - 5.14: 68104 Nonbonded interactions: 164358 Sorted by model distance: nonbonded pdb=" NE2 HIS D 196 " pdb=" OE1 GLN D 319 " model vdw 1.857 2.520 nonbonded pdb=" CB ALA B 34 " pdb=" O GLY C 333 " model vdw 2.046 3.460 nonbonded pdb=" CD2 HIS D 196 " pdb=" OE1 GLN D 319 " model vdw 2.128 3.260 nonbonded pdb=" O LEU G 37 " pdb=" OG1 THR G 41 " model vdw 2.131 2.440 nonbonded pdb=" NH1 ARG E1213 " pdb=" O5 GBM E1602 " model vdw 2.215 2.520 ... (remaining 164353 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 32 or (resid 33 through 35 and (name N or name \ CA or name C or name O or name CB )) or resid 36 through 44 or (resid 45 through \ 46 and (name N or name CA or name C or name O or name CB )) or resid 47 through \ 49 or (resid 50 and (name N or name CA or name C or name O or name CB )) or res \ id 51 through 54 or (resid 55 and (name N or name CA or name C or name O or name \ CB )) or resid 56 through 58 or (resid 59 and (name N or name CA or name C or n \ ame O or name CB )) or resid 60 through 65 or (resid 66 and (name N or name CA o \ r name C or name O or name CB )) or resid 67 through 74 or (resid 75 and (name N \ or name CA or name C or name O or name CB )) or resid 76 through 80 or (resid 8 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 82 through 9 \ 3 or (resid 94 through 95 and (name N or name CA or name C or name O or name CB \ )) or resid 96 through 100 or (resid 101 and (name N or name CA or name C or nam \ e O or name CB )) or resid 102 through 104 or (resid 105 through 107 and (name N \ or name CA or name C or name O or name CB )) or resid 108 through 124 or (resid \ 125 through 126 and (name N or name CA or name C or name O or name CB )) or res \ id 127 or (resid 128 through 130 and (name N or name CA or name C or name O or n \ ame CB )) or resid 131 or (resid 132 and (name N or name CA or name C or name O \ or name CB )) or resid 133 through 134 or (resid 135 through 137 and (name N or \ name CA or name C or name O or name CB )) or resid 138 or (resid 139 and (name N \ or name CA or name C or name O or name CB )) or resid 140 or (resid 141 and (na \ me N or name CA or name C or name O or name CB )) or resid 142 through 161 or (r \ esid 162 and (name N or name CA or name C or name O or name CB )) or resid 163 o \ r (resid 164 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 65 through 167 or (resid 168 through 169 and (name N or name CA or name C or nam \ e O or name CB )) or resid 170 through 180 or (resid 181 through 185 and (name N \ or name CA or name C or name O or name CB )) or resid 186 through 189 or (resid \ 190 and (name N or name CA or name C or name O or name CB )) or resid 191 or (r \ esid 192 and (name N or name CA or name C or name O or name CB )) or resid 193 t \ hrough 198 or (resid 199 through 200 and (name N or name CA or name C or name O \ or name CB )) or resid 201 through 204 or (resid 205 and (name N or name CA or n \ ame C or name O or name CB )) or resid 206 or (resid 207 through 208 and (name N \ or name CA or name C or name O or name CB )) or resid 209 through 210 or (resid \ 211 through 212 and (name N or name CA or name C or name O or name CB )) or res \ id 213 or (resid 214 and (name N or name CA or name C or name O or name CB )) or \ resid 215 through 216 or (resid 217 through 225 and (name N or name CA or name \ C or name O or name CB )) or resid 226 through 229 or (resid 230 and (name N or \ name CA or name C or name O or name CB )) or resid 231 through 250 or (resid 251 \ and (name N or name CA or name C or name O or name CB )) or resid 252 through 2 \ 54 or (resid 255 through 258 and (name N or name CA or name C or name O or name \ CB )) or resid 259 through 260 or (resid 261 through 263 and (name N or name CA \ or name C or name O or name CB )) or resid 264 or (resid 265 through 275 and (na \ me N or name CA or name C or name O or name CB )) or resid 276 or (resid 277 and \ (name N or name CA or name C or name O or name CB )) or resid 278 or (resid 279 \ through 290 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 91 or (resid 292 and (name N or name CA or name C or name O or name CB )) or res \ id 293 or (resid 294 through 295 and (name N or name CA or name C or name O or n \ ame CB )) or resid 296 or (resid 297 and (name N or name CA or name C or name O \ or name CB )) or resid 298 or (resid 299 and (name N or name CA or name C or nam \ e O or name CB )) or resid 300 or (resid 301 through 303 and (name N or name CA \ or name C or name O or name CB )) or resid 304 through 315 or (resid 316 through \ 317 and (name N or name CA or name C or name O or name CB )) or resid 318 throu \ gh 321 or (resid 322 and (name N or name CA or name C or name O or name CB )) or \ resid 323 through 324 or (resid 325 through 326 and (name N or name CA or name \ C or name O or name CB )) or resid 327 or (resid 328 through 332 and (name N or \ name CA or name C or name O or name CB )) or resid 333 through 336 or (resid 337 \ and (name N or name CA or name C or name O or name CB )) or resid 338 through 3 \ 39 or (resid 340 and (name N or name CA or name C or name O or name CB )) or res \ id 341 through 343 or (resid 344 and (name N or name CA or name C or name O or n \ ame CB )) or resid 345 through 366)) selection = (chain 'B' and (resid 31 through 34 or (resid 35 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 39 or (resid 40 and (name N or nam \ e CA or name C or name O or name CB )) or resid 41 through 47 or (resid 48 and ( \ name N or name CA or name C or name O or name CB )) or resid 49 through 51 or (r \ esid 52 through 53 and (name N or name CA or name C or name O or name CB )) or r \ esid 54 or (resid 55 and (name N or name CA or name C or name O or name CB )) or \ resid 56 through 57 or (resid 58 through 59 and (name N or name CA or name C or \ name O or name CB )) or resid 60 through 67 or (resid 68 and (name N or name CA \ or name C or name O or name CB )) or resid 69 or (resid 70 and (name N or name \ CA or name C or name O or name CB )) or resid 71 through 84 or (resid 85 and (na \ me N or name CA or name C or name O or name CB )) or resid 86 through 93 or (res \ id 94 through 95 and (name N or name CA or name C or name O or name CB )) or res \ id 96 through 104 or (resid 105 through 107 and (name N or name CA or name C or \ name O or name CB )) or (resid 108 through 119 and (name N or name CA or name C \ or name O or name CB )) or resid 120 through 121 or (resid 122 and (name N or na \ me CA or name C or name O or name CB )) or resid 123 through 124 or (resid 125 t \ hrough 126 and (name N or name CA or name C or name O or name CB )) or resid 127 \ or (resid 128 through 130 and (name N or name CA or name C or name O or name CB \ )) or resid 131 or (resid 132 and (name N or name CA or name C or name O or nam \ e CB )) or resid 133 or (resid 134 through 137 and (name N or name CA or name C \ or name O or name CB )) or resid 138 through 147 or (resid 148 through 151 and ( \ name N or name CA or name C or name O or name CB )) or resid 152 through 156 or \ (resid 157 and (name N or name CA or name C or name O or name CB )) or resid 158 \ through 163 or (resid 164 and (name N or name CA or name C or name O or name CB \ )) or resid 165 through 167 or (resid 168 through 169 and (name N or name CA or \ name C or name O or name CB )) or resid 170 through 171 or (resid 172 through 1 \ 73 and (name N or name CA or name C or name O or name CB )) or resid 174 through \ 176 or (resid 177 and (name N or name CA or name C or name O or name CB )) or r \ esid 178 through 179 or (resid 180 through 185 and (name N or name CA or name C \ or name O or name CB )) or resid 186 or (resid 187 through 190 and (name N or na \ me CA or name C or name O or name CB )) or resid 191 through 193 or (resid 194 a \ nd (name N or name CA or name C or name O or name CB )) or resid 195 through 198 \ or (resid 199 through 200 and (name N or name CA or name C or name O or name CB \ )) or resid 201 through 204 or (resid 205 and (name N or name CA or name C or n \ ame O or name CB )) or resid 206 or (resid 207 through 208 and (name N or name C \ A or name C or name O or name CB )) or resid 209 or (resid 210 through 212 and ( \ name N or name CA or name C or name O or name CB )) or resid 213 or (resid 214 a \ nd (name N or name CA or name C or name O or name CB )) or resid 215 through 221 \ or (resid 222 through 225 and (name N or name CA or name C or name O or name CB \ )) or resid 226 or (resid 227 and (name N or name CA or name C or name O or nam \ e CB )) or resid 228 through 236 or (resid 237 and (name N or name CA or name C \ or name O or name CB )) or resid 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 or (resid 241 and (name N or name CA or \ name C or name O or name CB )) or resid 242 through 254 or (resid 255 through 2 \ 58 and (name N or name CA or name C or name O or name CB )) or resid 259 through \ 260 or (resid 261 through 263 and (name N or name CA or name C or name O or nam \ e CB )) or resid 264 through 268 or (resid 269 through 275 and (name N or name C \ A or name C or name O or name CB )) or resid 276 or (resid 277 and (name N or na \ me CA or name C or name O or name CB )) or resid 278 or (resid 279 through 290 a \ nd (name N or name CA or name C or name O or name CB )) or resid 291 or (resid 2 \ 92 and (name N or name CA or name C or name O or name CB )) or resid 293 or (res \ id 294 through 295 and (name N or name CA or name C or name O or name CB )) or r \ esid 296 through 298 or (resid 299 and (name N or name CA or name C or name O or \ name CB )) or resid 300 or (resid 301 through 303 and (name N or name CA or nam \ e C or name O or name CB )) or resid 304 through 305 or (resid 306 and (name N o \ r name CA or name C or name O or name CB )) or resid 307 through 311 or (resid 3 \ 12 and (name N or name CA or name C or name O or name CB )) or resid 313 through \ 315 or (resid 316 through 317 and (name N or name CA or name C or name O or nam \ e CB )) or resid 318 through 327 or (resid 328 through 332 and (name N or name C \ A or name C or name O or name CB )) or resid 333 through 335 or (resid 336 throu \ gh 337 and (name N or name CA or name C or name O or name CB )) or resid 338 thr \ ough 339 or (resid 340 and (name N or name CA or name C or name O or name CB )) \ or resid 341 through 343 or (resid 344 and (name N or name CA or name C or name \ O or name CB )) or resid 345 through 347 or (resid 348 through 350 and (name N o \ r name CA or name C or name O or name CB )) or resid 351 through 352 or (resid 3 \ 53 through 361 and (name N or name CA or name C or name O or name CB )) or resid \ 362 through 366)) selection = (chain 'C' and (resid 31 through 32 or (resid 33 through 35 and (name N or name \ CA or name C or name O or name CB )) or resid 36 through 39 or (resid 40 and (na \ me N or name CA or name C or name O or name CB )) or resid 41 through 44 or (res \ id 45 through 46 and (name N or name CA or name C or name O or name CB )) or res \ id 47 or (resid 48 and (name N or name CA or name C or name O or name CB )) or r \ esid 49 through 57 or (resid 58 through 59 and (name N or name CA or name C or n \ ame O or name CB )) or resid 60 through 67 or (resid 68 and (name N or name CA o \ r name C or name O or name CB )) or resid 69 or (resid 70 and (name N or name CA \ or name C or name O or name CB )) or resid 71 through 80 or (resid 81 and (name \ N or name CA or name C or name O or name CB )) or resid 82 through 84 or (resid \ 85 and (name N or name CA or name C or name O or name CB )) or resid 86 through \ 93 or (resid 94 through 95 and (name N or name CA or name C or name O or name C \ B )) or resid 96 through 100 or (resid 101 and (name N or name CA or name C or n \ ame O or name CB )) or resid 102 through 121 or (resid 122 and (name N or name C \ A or name C or name O or name CB )) or resid 123 through 125 or (resid 126 and ( \ name N or name CA or name C or name O or name CB )) or resid 127 through 128 or \ (resid 129 through 130 and (name N or name CA or name C or name O or name CB )) \ or resid 131 through 133 or (resid 134 through 137 and (name N or name CA or nam \ e C or name O or name CB )) or resid 138 or (resid 139 and (name N or name CA or \ name C or name O or name CB )) or resid 140 or (resid 141 and (name N or name C \ A or name C or name O or name CB )) or resid 142 through 147 or (resid 148 throu \ gh 151 and (name N or name CA or name C or name O or name CB )) or resid 152 thr \ ough 156 or (resid 157 and (name N or name CA or name C or name O or name CB )) \ or resid 158 through 161 or (resid 162 and (name N or name CA or name C or name \ O or name CB )) or resid 163 through 167 or (resid 168 through 169 and (name N o \ r name CA or name C or name O or name CB )) or resid 170 through 171 or (resid 1 \ 72 through 173 and (name N or name CA or name C or name O or name CB )) or resid \ 174 through 179 or (resid 180 through 185 and (name N or name CA or name C or n \ ame O or name CB )) or resid 186 or (resid 187 through 190 and (name N or name C \ A or name C or name O or name CB )) or resid 191 or (resid 192 and (name N or na \ me CA or name C or name O or name CB )) or resid 193 or (resid 194 and (name N o \ r name CA or name C or name O or name CB )) or resid 195 through 198 or (resid 1 \ 99 through 200 and (name N or name CA or name C or name O or name CB )) or resid \ 201 through 206 or (resid 207 through 208 and (name N or name CA or name C or n \ ame O or name CB )) or resid 209 or (resid 210 through 212 and (name N or name C \ A or name C or name O or name CB )) or resid 213 through 217 or (resid 218 throu \ gh 225 and (name N or name CA or name C or name O or name CB )) or resid 226 or \ (resid 227 and (name N or name CA or name C or name O or name CB )) or resid 228 \ through 229 or (resid 230 and (name N or name CA or name C or name O or name CB \ )) or resid 231 through 236 or (resid 237 and (name N or name CA or name C or n \ ame O or name CB )) or resid 238 through 240 or (resid 241 and (name N or name C \ A or name C or name O or name CB )) or resid 242 through 249 or (resid 250 throu \ gh 251 and (name N or name CA or name C or name O or name CB )) or resid 252 thr \ ough 255 or (resid 256 through 258 and (name N or name CA or name C or name O or \ name CB )) or resid 259 through 261 or (resid 262 through 263 and (name N or na \ me CA or name C or name O or name CB )) or resid 264 through 265 or (resid 266 t \ hrough 275 and (name N or name CA or name C or name O or name CB )) or resid 276 \ or (resid 277 and (name N or name CA or name C or name O or name CB )) or resid \ 278 through 279 or (resid 280 through 290 and (name N or name CA or name C or n \ ame O or name CB )) or resid 291 through 293 or (resid 294 through 295 and (name \ N or name CA or name C or name O or name CB )) or resid 296 or (resid 297 and ( \ name N or name CA or name C or name O or name CB )) or resid 298 through 301 or \ (resid 302 through 303 and (name N or name CA or name C or name O or name CB )) \ or resid 304 through 305 or (resid 306 and (name N or name CA or name C or name \ O or name CB )) or resid 307 through 310 or (resid 311 through 312 and (name N o \ r name CA or name C or name O or name CB )) or resid 313 through 321 or (resid 3 \ 22 and (name N or name CA or name C or name O or name CB )) or resid 323 through \ 324 or (resid 325 through 326 and (name N or name CA or name C or name O or nam \ e CB )) or resid 327 or (resid 328 through 332 and (name N or name CA or name C \ or name O or name CB )) or resid 333 through 335 or (resid 336 through 337 and ( \ name N or name CA or name C or name O or name CB )) or resid 338 through 343 or \ (resid 344 and (name N or name CA or name C or name O or name CB )) or resid 345 \ through 347 or (resid 348 through 350 and (name N or name CA or name C or name \ O or name CB )) or resid 351 through 352 or (resid 353 through 361 and (name N o \ r name CA or name C or name O or name CB )) or resid 362 through 366)) selection = (chain 'D' and (resid 31 through 32 or (resid 33 through 35 and (name N or name \ CA or name C or name O or name CB )) or resid 36 through 39 or (resid 40 and (na \ me N or name CA or name C or name O or name CB )) or resid 41 through 44 or (res \ id 45 through 46 and (name N or name CA or name C or name O or name CB )) or res \ id 47 or (resid 48 and (name N or name CA or name C or name O or name CB )) or r \ esid 49 or (resid 50 and (name N or name CA or name C or name O or name CB )) or \ resid 51 through 52 or (resid 53 and (name N or name CA or name C or name O or \ name CB )) or resid 54 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 or (resid 70 and (name N or name CA or nam \ e C or name O or name CB )) or resid 71 through 74 or (resid 75 and (name N or n \ ame CA or name C or name O or name CB )) or resid 76 through 80 or (resid 81 and \ (name N or name CA or name C or name O or name CB )) or resid 82 through 84 or \ (resid 85 and (name N or name CA or name C or name O or name CB )) or resid 86 t \ hrough 88 or (resid 89 and (name N or name CA or name C or name O or name CB )) \ or resid 90 through 118 or (resid 119 and (name N or name CA or name C or name O \ or name CB )) or resid 120 through 121 or (resid 122 and (name N or name CA or \ name C or name O or name CB )) or resid 123 through 124 or (resid 125 through 12 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 127 or (resi \ d 128 through 130 and (name N or name CA or name C or name O or name CB )) or re \ sid 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) o \ r resid 133 or (resid 134 through 137 and (name N or name CA or name C or name O \ or name CB )) or resid 138 or (resid 139 and (name N or name CA or name C or na \ me O or name CB )) or resid 140 or (resid 141 and (name N or name CA or name C o \ r name O or name CB )) or resid 142 through 147 or (resid 148 through 151 and (n \ ame N or name CA or name C or name O or name CB )) or resid 152 through 156 or ( \ resid 157 and (name N or name CA or name C or name O or name CB )) or resid 158 \ through 163 or (resid 164 and (name N or name CA or name C or name O or name CB \ )) or resid 165 through 171 or (resid 172 through 173 and (name N or name CA or \ name C or name O or name CB )) or resid 174 through 179 or (resid 180 through 18 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 186 or (resi \ d 187 through 190 and (name N or name CA or name C or name O or name CB )) or re \ sid 191 or (resid 192 and (name N or name CA or name C or name O or name CB )) o \ r resid 193 or (resid 194 and (name N or name CA or name C or name O or name CB \ )) or resid 195 through 197 or (resid 198 through 200 and (name N or name CA or \ name C or name O or name CB )) or resid 201 through 204 or (resid 205 and (name \ N or name CA or name C or name O or name CB )) or resid 206 through 207 or (resi \ d 208 and (name N or name CA or name C or name O or name CB )) or resid 209 or ( \ resid 210 through 212 and (name N or name CA or name C or name O or name CB )) o \ r resid 213 or (resid 214 and (name N or name CA or name C or name O or name CB \ )) or resid 215 through 217 or (resid 218 through 225 and (name N or name CA or \ name C or name O or name CB )) or resid 226 or (resid 227 and (name N or name CA \ or name C or name O or name CB )) or resid 228 through 229 or (resid 230 and (n \ ame N or name CA or name C or name O or name CB )) or resid 231 through 236 or ( \ resid 237 and (name N or name CA or name C or name O or name CB )) or resid 238 \ through 247 or (resid 248 and (name N or name CA or name C or name O or name CB \ )) or resid 249 or (resid 250 through 251 and (name N or name CA or name C or na \ me O or name CB )) or resid 252 through 254 or (resid 255 through 258 and (name \ N or name CA or name C or name O or name CB )) or resid 259 through 260 or (resi \ d 261 through 263 and (name N or name CA or name C or name O or name CB )) or re \ sid 264 through 265 or (resid 266 through 275 and (name N or name CA or name C o \ r name O or name CB )) or resid 276 through 282 or (resid 283 through 290 and (n \ ame N or name CA or name C or name O or name CB )) or resid 291 or (resid 292 an \ d (name N or name CA or name C or name O or name CB )) or resid 293 through 294 \ or (resid 295 and (name N or name CA or name C or name O or name CB )) or resid \ 296 or (resid 297 and (name N or name CA or name C or name O or name CB )) or re \ sid 298 or (resid 299 and (name N or name CA or name C or name O or name CB )) o \ r resid 300 or (resid 301 through 303 and (name N or name CA or name C or name O \ or name CB )) or resid 304 through 310 or (resid 311 through 312 and (name N or \ name CA or name C or name O or name CB )) or resid 313 through 316 or (resid 31 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 318 through \ 321 or (resid 322 and (name N or name CA or name C or name O or name CB )) or re \ sid 323 through 324 or (resid 325 through 326 and (name N or name CA or name C o \ r name O or name CB )) or resid 327 through 328 or (resid 329 through 332 and (n \ ame N or name CA or name C or name O or name CB )) or resid 333 through 335 or ( \ resid 336 through 337 and (name N or name CA or name C or name O or name CB )) o \ r resid 338 through 352 or (resid 353 through 361 and (name N or name CA or name \ C or name O or name CB )) or resid 362 through 366)) } ncs_group { reference = chain 'F' selection = chain 'N' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.500 Check model and map are aligned: 0.300 Set scattering table: 0.200 Process input model: 56.030 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 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 : 0.008 0.211 20340 Z= 0.539 Angle : 1.063 21.207 27932 Z= 0.640 Chirality : 0.050 0.352 3390 Planarity : 0.005 0.046 3599 Dihedral : 16.267 173.913 6395 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 16.41 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.16), residues: 2959 helix: 0.78 (0.15), residues: 1298 sheet: -1.31 (0.36), residues: 219 loop : -2.45 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 92 HIS 0.013 0.001 HIS D 98 PHE 0.039 0.002 PHE B 178 TYR 0.035 0.002 TYR E 370 ARG 0.005 0.001 ARG C 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 577 time to evaluate : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7366 (ttm) cc_final: 0.6972 (tpp) REVERT: A 102 TYR cc_start: 0.8871 (t80) cc_final: 0.8247 (t80) REVERT: A 121 VAL cc_start: 0.9264 (t) cc_final: 0.8921 (t) REVERT: A 124 VAL cc_start: 0.9331 (t) cc_final: 0.9004 (p) REVERT: A 214 ASP cc_start: 0.8677 (t0) cc_final: 0.8283 (t0) REVERT: A 220 ILE cc_start: 0.8911 (mm) cc_final: 0.8251 (mm) REVERT: A 256 SER cc_start: 0.9206 (t) cc_final: 0.8947 (t) REVERT: A 257 ASN cc_start: 0.8211 (p0) cc_final: 0.7579 (p0) REVERT: A 320 TRP cc_start: 0.9120 (t-100) cc_final: 0.8730 (t-100) REVERT: A 341 LYS cc_start: 0.8859 (mtpm) cc_final: 0.8626 (mtmt) REVERT: B 48 LYS cc_start: 0.9095 (mttm) cc_final: 0.8879 (mttt) REVERT: B 58 GLN cc_start: 0.9197 (tp40) cc_final: 0.8744 (tp40) REVERT: B 64 LEU cc_start: 0.9176 (tp) cc_final: 0.8834 (tp) REVERT: B 186 ARG cc_start: 0.6688 (ptp-170) cc_final: 0.6428 (ptp90) REVERT: B 232 LYS cc_start: 0.9229 (ttpp) cc_final: 0.9019 (tttt) REVERT: B 320 TRP cc_start: 0.8508 (t-100) cc_final: 0.8098 (t60) REVERT: B 336 SER cc_start: 0.9450 (t) cc_final: 0.9233 (t) REVERT: B 347 ARG cc_start: 0.8192 (ttm170) cc_final: 0.7944 (mtp85) REVERT: C 36 PHE cc_start: 0.9002 (t80) cc_final: 0.8788 (t80) REVERT: C 44 ASN cc_start: 0.8817 (p0) cc_final: 0.8543 (p0) REVERT: C 48 LYS cc_start: 0.8620 (tppt) cc_final: 0.8330 (ttmm) REVERT: C 92 TRP cc_start: 0.9220 (t60) cc_final: 0.9013 (t60) REVERT: C 161 LEU cc_start: 0.9331 (tp) cc_final: 0.9030 (tp) REVERT: C 183 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7566 (mt0) REVERT: C 209 MET cc_start: 0.8758 (mtt) cc_final: 0.8472 (mtt) REVERT: C 231 LYS cc_start: 0.8972 (ptmm) cc_final: 0.8722 (ptmm) REVERT: D 178 PHE cc_start: 0.6500 (t80) cc_final: 0.5661 (t80) REVERT: D 244 HIS cc_start: 0.8535 (t-90) cc_final: 0.8200 (t70) REVERT: D 255 GLU cc_start: 0.8438 (mp0) cc_final: 0.8167 (mm-30) REVERT: D 284 ASP cc_start: 0.8902 (m-30) cc_final: 0.8612 (t70) REVERT: D 288 GLN cc_start: 0.8634 (tp40) cc_final: 0.7826 (tp40) REVERT: E 856 GLN cc_start: 0.4897 (tp40) cc_final: 0.4605 (mm-40) REVERT: E 1126 TYR cc_start: 0.7522 (t80) cc_final: 0.7269 (t80) REVERT: E 1250 TYR cc_start: 0.7260 (m-80) cc_final: 0.7052 (m-80) REVERT: E 1260 TRP cc_start: 0.8205 (m100) cc_final: 0.7768 (m100) REVERT: E 1263 ARG cc_start: 0.8668 (tpp80) cc_final: 0.8030 (tpp80) REVERT: G 1 MET cc_start: 0.4804 (mtp) cc_final: 0.4598 (mtm) REVERT: G 189 ARG cc_start: 0.6646 (ttp-170) cc_final: 0.5681 (mtm110) outliers start: 0 outliers final: 0 residues processed: 577 average time/residue: 0.3063 time to fit residues: 274.6098 Evaluate side-chains 503 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 503 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 50.0000 chunk 223 optimal weight: 0.0470 chunk 124 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 231 optimal weight: 0.0020 chunk 89 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 172 optimal weight: 50.0000 chunk 267 optimal weight: 50.0000 overall best weight: 1.3688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 287 ASN ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 20340 Z= 0.166 Angle : 0.579 9.544 27932 Z= 0.303 Chirality : 0.045 0.204 3390 Planarity : 0.005 0.047 3599 Dihedral : 14.528 162.513 3699 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.51 % Allowed : 20.84 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.16), residues: 2959 helix: 1.19 (0.15), residues: 1280 sheet: -0.88 (0.38), residues: 203 loop : -2.12 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 69 HIS 0.004 0.001 HIS D 98 PHE 0.042 0.002 PHE D 178 TYR 0.027 0.001 TYR E 370 ARG 0.004 0.000 ARG C 352 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 530 time to evaluate : 2.357 Fit side-chains revert: symmetry clash REVERT: A 84 TRP cc_start: 0.9107 (m-10) cc_final: 0.8696 (m-10) REVERT: A 102 TYR cc_start: 0.8897 (t80) cc_final: 0.8363 (t80) REVERT: A 147 MET cc_start: 0.8644 (ptp) cc_final: 0.8321 (ptp) REVERT: A 168 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.9007 (mm) REVERT: A 214 ASP cc_start: 0.8600 (t0) cc_final: 0.8251 (t0) REVERT: A 256 SER cc_start: 0.9104 (t) cc_final: 0.8764 (t) REVERT: A 257 ASN cc_start: 0.7956 (p0) cc_final: 0.7473 (p0) REVERT: A 296 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8797 (pt) REVERT: A 319 GLN cc_start: 0.8982 (pt0) cc_final: 0.8355 (pt0) REVERT: A 320 TRP cc_start: 0.9023 (t-100) cc_final: 0.8775 (t-100) REVERT: A 322 HIS cc_start: 0.8635 (m90) cc_final: 0.8275 (m170) REVERT: B 58 GLN cc_start: 0.8967 (tp40) cc_final: 0.8389 (tp40) REVERT: B 64 LEU cc_start: 0.8941 (tp) cc_final: 0.8568 (tp) REVERT: B 179 MET cc_start: 0.8241 (tpt) cc_final: 0.7702 (tpp) REVERT: B 186 ARG cc_start: 0.6795 (ptp-170) cc_final: 0.6545 (ptp90) REVERT: B 232 LYS cc_start: 0.9164 (ttpp) cc_final: 0.8945 (tttp) REVERT: B 320 TRP cc_start: 0.8339 (t-100) cc_final: 0.7936 (t60) REVERT: C 44 ASN cc_start: 0.8663 (p0) cc_final: 0.8425 (p0) REVERT: C 48 LYS cc_start: 0.8754 (tppt) cc_final: 0.8521 (ttmm) REVERT: C 57 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8070 (tt) REVERT: C 78 MET cc_start: 0.7362 (ttp) cc_final: 0.7131 (ttp) REVERT: C 92 TRP cc_start: 0.9202 (t60) cc_final: 0.9000 (t60) REVERT: C 183 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7488 (mt0) REVERT: C 209 MET cc_start: 0.8724 (mtt) cc_final: 0.8385 (mtt) REVERT: D 178 PHE cc_start: 0.5858 (t80) cc_final: 0.5531 (t80) REVERT: D 244 HIS cc_start: 0.8486 (t-90) cc_final: 0.8083 (t-90) REVERT: D 247 ASP cc_start: 0.8598 (m-30) cc_final: 0.8296 (m-30) REVERT: D 255 GLU cc_start: 0.8460 (mp0) cc_final: 0.8126 (mm-30) REVERT: D 284 ASP cc_start: 0.8870 (m-30) cc_final: 0.8594 (t70) REVERT: E 173 MET cc_start: 0.7609 (tpp) cc_final: 0.7399 (tpp) REVERT: E 229 TRP cc_start: 0.5754 (OUTLIER) cc_final: 0.5111 (m-10) REVERT: E 507 TRP cc_start: 0.5888 (m100) cc_final: 0.5662 (m100) REVERT: E 1250 TYR cc_start: 0.7250 (m-80) cc_final: 0.7044 (m-80) REVERT: E 1260 TRP cc_start: 0.8156 (m100) cc_final: 0.7716 (m100) REVERT: E 1263 ARG cc_start: 0.8646 (tpp80) cc_final: 0.8053 (tpp80) REVERT: G 189 ARG cc_start: 0.5974 (ttp-170) cc_final: 0.5111 (mtm110) outliers start: 46 outliers final: 25 residues processed: 547 average time/residue: 0.2910 time to fit residues: 248.5217 Evaluate side-chains 543 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 514 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 274 ARG Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 229 TRP Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 766 ILE Chi-restraints excluded: chain E residue 1083 THR Chi-restraints excluded: chain E residue 1225 CYS Chi-restraints excluded: chain E residue 1371 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 148 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 222 optimal weight: 20.0000 chunk 182 optimal weight: 30.0000 chunk 73 optimal weight: 10.0000 chunk 268 optimal weight: 1.9990 chunk 289 optimal weight: 10.0000 chunk 239 optimal weight: 7.9990 chunk 266 optimal weight: 30.0000 chunk 91 optimal weight: 3.9990 chunk 215 optimal weight: 40.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 HIS A 287 ASN ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN E 83 HIS E 555 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20340 Z= 0.238 Angle : 0.584 9.795 27932 Z= 0.305 Chirality : 0.045 0.241 3390 Planarity : 0.004 0.047 3599 Dihedral : 13.627 161.402 3699 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 4.43 % Allowed : 22.82 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.16), residues: 2959 helix: 1.08 (0.15), residues: 1301 sheet: -0.77 (0.38), residues: 197 loop : -2.12 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 91 HIS 0.010 0.001 HIS E 555 PHE 0.044 0.002 PHE D 178 TYR 0.028 0.001 TYR E 370 ARG 0.008 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 509 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 TRP cc_start: 0.9096 (m-10) cc_final: 0.8684 (m-10) REVERT: A 102 TYR cc_start: 0.8683 (t80) cc_final: 0.8263 (t80) REVERT: A 121 VAL cc_start: 0.9226 (t) cc_final: 0.8935 (t) REVERT: A 190 THR cc_start: 0.8165 (p) cc_final: 0.7845 (t) REVERT: A 256 SER cc_start: 0.9232 (t) cc_final: 0.8984 (t) REVERT: A 257 ASN cc_start: 0.8030 (p0) cc_final: 0.7473 (p0) REVERT: A 296 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8878 (pt) REVERT: A 320 TRP cc_start: 0.9121 (t-100) cc_final: 0.8682 (t-100) REVERT: B 58 GLN cc_start: 0.9154 (tp40) cc_final: 0.8624 (tp40) REVERT: B 64 LEU cc_start: 0.9028 (tp) cc_final: 0.8566 (tp) REVERT: B 179 MET cc_start: 0.8423 (tpt) cc_final: 0.7988 (tpp) REVERT: B 287 ASN cc_start: 0.8087 (t0) cc_final: 0.7604 (t0) REVERT: B 320 TRP cc_start: 0.8425 (t-100) cc_final: 0.8080 (t60) REVERT: C 44 ASN cc_start: 0.8620 (p0) cc_final: 0.8391 (p0) REVERT: C 48 LYS cc_start: 0.8710 (tppt) cc_final: 0.8483 (ttmm) REVERT: C 161 LEU cc_start: 0.9307 (tp) cc_final: 0.9100 (tt) REVERT: C 183 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7428 (mt0) REVERT: D 178 PHE cc_start: 0.6068 (t80) cc_final: 0.5477 (t80) REVERT: D 244 HIS cc_start: 0.8546 (t-90) cc_final: 0.8222 (t-90) REVERT: D 255 GLU cc_start: 0.8456 (mp0) cc_final: 0.8142 (mm-30) REVERT: D 284 ASP cc_start: 0.8956 (m-30) cc_final: 0.8611 (t70) REVERT: E 112 PHE cc_start: 0.8032 (t80) cc_final: 0.7742 (t80) REVERT: E 494 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7555 (tt0) REVERT: E 1250 TYR cc_start: 0.7290 (m-80) cc_final: 0.7080 (m-80) REVERT: E 1260 TRP cc_start: 0.8214 (m100) cc_final: 0.7772 (m100) REVERT: E 1263 ARG cc_start: 0.8590 (tpp80) cc_final: 0.8038 (tpp80) outliers start: 58 outliers final: 42 residues processed: 535 average time/residue: 0.2973 time to fit residues: 250.1951 Evaluate side-chains 545 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 502 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 1083 THR Chi-restraints excluded: chain E residue 1225 CYS Chi-restraints excluded: chain E residue 1258 LEU Chi-restraints excluded: chain E residue 1371 ILE Chi-restraints excluded: chain E residue 1439 THR Chi-restraints excluded: chain G residue 172 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 265 optimal weight: 40.0000 chunk 201 optimal weight: 0.4980 chunk 139 optimal weight: 50.0000 chunk 29 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 180 optimal weight: 9.9990 chunk 269 optimal weight: 9.9990 chunk 285 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 255 optimal weight: 50.0000 chunk 76 optimal weight: 9.9990 overall best weight: 7.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 20340 Z= 0.320 Angle : 0.630 9.121 27932 Z= 0.330 Chirality : 0.046 0.267 3390 Planarity : 0.005 0.047 3599 Dihedral : 13.252 158.450 3699 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 5.88 % Allowed : 23.21 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.16), residues: 2959 helix: 0.91 (0.15), residues: 1291 sheet: -0.87 (0.39), residues: 199 loop : -2.10 (0.16), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 91 HIS 0.011 0.001 HIS B 269 PHE 0.046 0.002 PHE D 178 TYR 0.025 0.002 TYR E 370 ARG 0.004 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 518 time to evaluate : 2.303 Fit side-chains revert: symmetry clash REVERT: A 84 TRP cc_start: 0.9104 (m-10) cc_final: 0.8582 (m-10) REVERT: A 102 TYR cc_start: 0.8739 (t80) cc_final: 0.8274 (t80) REVERT: A 256 SER cc_start: 0.9352 (t) cc_final: 0.9126 (t) REVERT: A 269 HIS cc_start: 0.8951 (OUTLIER) cc_final: 0.7863 (t70) REVERT: A 285 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.8903 (tp) REVERT: A 296 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8912 (pt) REVERT: A 320 TRP cc_start: 0.9157 (t-100) cc_final: 0.8733 (t-100) REVERT: B 64 LEU cc_start: 0.9080 (tp) cc_final: 0.8696 (tp) REVERT: B 147 MET cc_start: 0.8794 (ttm) cc_final: 0.8532 (ttm) REVERT: B 179 MET cc_start: 0.8593 (tpt) cc_final: 0.8162 (tpp) REVERT: B 232 LYS cc_start: 0.9004 (ttpp) cc_final: 0.8726 (tttp) REVERT: B 287 ASN cc_start: 0.8286 (t0) cc_final: 0.7836 (t0) REVERT: B 320 TRP cc_start: 0.8440 (t-100) cc_final: 0.8105 (t60) REVERT: C 44 ASN cc_start: 0.8676 (p0) cc_final: 0.8429 (p0) REVERT: C 48 LYS cc_start: 0.8743 (tppt) cc_final: 0.8519 (ttmm) REVERT: C 183 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7496 (mt0) REVERT: D 178 PHE cc_start: 0.6137 (t80) cc_final: 0.5589 (t80) REVERT: D 244 HIS cc_start: 0.8535 (t-90) cc_final: 0.8266 (t70) REVERT: D 255 GLU cc_start: 0.8459 (mp0) cc_final: 0.8129 (mm-30) REVERT: D 284 ASP cc_start: 0.9031 (m-30) cc_final: 0.8625 (t70) REVERT: E 112 PHE cc_start: 0.8090 (t80) cc_final: 0.7744 (t80) REVERT: E 494 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7611 (tt0) REVERT: E 1250 TYR cc_start: 0.7323 (m-80) cc_final: 0.7084 (m-80) REVERT: E 1260 TRP cc_start: 0.8238 (m100) cc_final: 0.7745 (m100) REVERT: E 1263 ARG cc_start: 0.8651 (tpp80) cc_final: 0.8121 (tpp80) REVERT: G 189 ARG cc_start: 0.6233 (ttp-170) cc_final: 0.5495 (mtm110) outliers start: 77 outliers final: 58 residues processed: 550 average time/residue: 0.2989 time to fit residues: 257.8589 Evaluate side-chains 570 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 509 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 866 THR Chi-restraints excluded: chain E residue 1083 THR Chi-restraints excluded: chain E residue 1225 CYS Chi-restraints excluded: chain E residue 1258 LEU Chi-restraints excluded: chain E residue 1371 ILE Chi-restraints excluded: chain E residue 1439 THR Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain G residue 172 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 237 optimal weight: 9.9990 chunk 161 optimal weight: 40.0000 chunk 4 optimal weight: 10.0000 chunk 212 optimal weight: 50.0000 chunk 117 optimal weight: 8.9990 chunk 243 optimal weight: 4.9990 chunk 197 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 145 optimal weight: 0.0070 chunk 255 optimal weight: 40.0000 chunk 71 optimal weight: 6.9990 overall best weight: 6.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 HIS D 228 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20340 Z= 0.276 Angle : 0.604 9.056 27932 Z= 0.315 Chirality : 0.045 0.253 3390 Planarity : 0.004 0.046 3599 Dihedral : 12.817 159.264 3699 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 6.11 % Allowed : 24.66 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.16), residues: 2959 helix: 0.98 (0.15), residues: 1284 sheet: -0.77 (0.39), residues: 202 loop : -2.08 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 91 HIS 0.009 0.001 HIS B 269 PHE 0.042 0.002 PHE D 178 TYR 0.024 0.001 TYR E 370 ARG 0.005 0.000 ARG C 195 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 518 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.9464 (t80) cc_final: 0.9261 (t80) REVERT: A 84 TRP cc_start: 0.9124 (m-10) cc_final: 0.8554 (m-10) REVERT: A 102 TYR cc_start: 0.8712 (t80) cc_final: 0.8276 (t80) REVERT: A 256 SER cc_start: 0.9225 (t) cc_final: 0.9019 (t) REVERT: A 257 ASN cc_start: 0.8120 (p0) cc_final: 0.7709 (p0) REVERT: A 269 HIS cc_start: 0.8861 (OUTLIER) cc_final: 0.7799 (t70) REVERT: A 285 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.8896 (tp) REVERT: A 296 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8883 (pt) REVERT: A 320 TRP cc_start: 0.9095 (t-100) cc_final: 0.8734 (t-100) REVERT: B 64 LEU cc_start: 0.9087 (tp) cc_final: 0.8662 (tp) REVERT: B 147 MET cc_start: 0.8877 (ttm) cc_final: 0.8670 (ttm) REVERT: B 232 LYS cc_start: 0.9086 (ttpp) cc_final: 0.8876 (tttp) REVERT: B 287 ASN cc_start: 0.8272 (t0) cc_final: 0.7806 (t0) REVERT: B 320 TRP cc_start: 0.8431 (t-100) cc_final: 0.8088 (t60) REVERT: B 324 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7725 (t80) REVERT: C 44 ASN cc_start: 0.8653 (p0) cc_final: 0.8421 (p0) REVERT: C 48 LYS cc_start: 0.8765 (tppt) cc_final: 0.8542 (ttmm) REVERT: C 179 MET cc_start: 0.7988 (tpt) cc_final: 0.7646 (tpp) REVERT: C 183 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7388 (mt0) REVERT: D 178 PHE cc_start: 0.6331 (t80) cc_final: 0.5774 (t80) REVERT: D 244 HIS cc_start: 0.8519 (t-90) cc_final: 0.8264 (t70) REVERT: D 255 GLU cc_start: 0.8475 (mp0) cc_final: 0.8144 (mm-30) REVERT: D 284 ASP cc_start: 0.9023 (m-30) cc_final: 0.8593 (t70) REVERT: E 112 PHE cc_start: 0.8062 (t80) cc_final: 0.7739 (t80) REVERT: E 494 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7586 (tt0) REVERT: E 507 TRP cc_start: 0.5834 (m100) cc_final: 0.5509 (m100) REVERT: E 1250 TYR cc_start: 0.7280 (m-80) cc_final: 0.7054 (m-80) REVERT: E 1260 TRP cc_start: 0.8064 (m100) cc_final: 0.7759 (m100) REVERT: E 1263 ARG cc_start: 0.8621 (tpp80) cc_final: 0.8089 (tpp80) REVERT: G 189 ARG cc_start: 0.6189 (ttp-170) cc_final: 0.5506 (mtm110) outliers start: 80 outliers final: 62 residues processed: 556 average time/residue: 0.2906 time to fit residues: 252.5551 Evaluate side-chains 576 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 510 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 1083 THR Chi-restraints excluded: chain E residue 1163 THR Chi-restraints excluded: chain E residue 1225 CYS Chi-restraints excluded: chain E residue 1235 ILE Chi-restraints excluded: chain E residue 1258 LEU Chi-restraints excluded: chain E residue 1371 ILE Chi-restraints excluded: chain E residue 1439 THR Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 172 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 95 optimal weight: 10.0000 chunk 256 optimal weight: 50.0000 chunk 56 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 285 optimal weight: 9.9990 chunk 236 optimal weight: 50.0000 chunk 132 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 149 optimal weight: 30.0000 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 287 ASN ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20340 Z= 0.292 Angle : 0.608 8.769 27932 Z= 0.319 Chirality : 0.045 0.261 3390 Planarity : 0.005 0.047 3599 Dihedral : 12.640 158.974 3699 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 6.11 % Allowed : 25.65 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.16), residues: 2959 helix: 0.92 (0.15), residues: 1297 sheet: -0.79 (0.38), residues: 202 loop : -2.10 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 91 HIS 0.010 0.001 HIS B 269 PHE 0.044 0.002 PHE D 178 TYR 0.022 0.001 TYR E 370 ARG 0.007 0.000 ARG B 274 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 511 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 TRP cc_start: 0.9151 (m-10) cc_final: 0.8550 (m-10) REVERT: A 102 TYR cc_start: 0.8715 (t80) cc_final: 0.8276 (t80) REVERT: A 138 GLN cc_start: 0.9081 (tt0) cc_final: 0.8751 (tp40) REVERT: A 256 SER cc_start: 0.9267 (t) cc_final: 0.9063 (t) REVERT: A 257 ASN cc_start: 0.8129 (p0) cc_final: 0.7730 (p0) REVERT: A 269 HIS cc_start: 0.8867 (OUTLIER) cc_final: 0.7823 (t70) REVERT: A 285 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.8906 (tp) REVERT: A 296 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8877 (pt) REVERT: A 320 TRP cc_start: 0.9106 (t-100) cc_final: 0.8741 (t-100) REVERT: B 39 LYS cc_start: 0.8810 (mmmt) cc_final: 0.8198 (tptm) REVERT: B 58 GLN cc_start: 0.9211 (tp40) cc_final: 0.8721 (tp40) REVERT: B 64 LEU cc_start: 0.9101 (tp) cc_final: 0.8703 (tp) REVERT: B 147 MET cc_start: 0.8954 (ttm) cc_final: 0.8747 (ttm) REVERT: B 179 MET cc_start: 0.8614 (tpt) cc_final: 0.8168 (tpp) REVERT: B 232 LYS cc_start: 0.9081 (ttpp) cc_final: 0.8875 (tttp) REVERT: B 287 ASN cc_start: 0.8275 (t0) cc_final: 0.7810 (t0) REVERT: B 320 TRP cc_start: 0.8439 (t-100) cc_final: 0.8099 (t60) REVERT: B 324 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7730 (t80) REVERT: C 44 ASN cc_start: 0.8654 (p0) cc_final: 0.8414 (p0) REVERT: C 48 LYS cc_start: 0.8782 (tppt) cc_final: 0.8553 (ttmm) REVERT: C 87 PHE cc_start: 0.8841 (m-80) cc_final: 0.8556 (m-80) REVERT: C 96 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.7858 (t80) REVERT: C 161 LEU cc_start: 0.9163 (tt) cc_final: 0.8915 (tt) REVERT: C 167 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8510 (mm) REVERT: C 183 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7541 (mt0) REVERT: D 244 HIS cc_start: 0.8514 (t-90) cc_final: 0.8262 (t70) REVERT: D 255 GLU cc_start: 0.8387 (mp0) cc_final: 0.8033 (mm-30) REVERT: D 258 ASN cc_start: 0.9492 (OUTLIER) cc_final: 0.8917 (m-40) REVERT: D 284 ASP cc_start: 0.9099 (m-30) cc_final: 0.8638 (t70) REVERT: E 112 PHE cc_start: 0.8074 (t80) cc_final: 0.7739 (t80) REVERT: E 494 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7589 (tt0) REVERT: E 507 TRP cc_start: 0.5851 (m100) cc_final: 0.5551 (m100) REVERT: E 1250 TYR cc_start: 0.7268 (m-80) cc_final: 0.7004 (m-80) REVERT: E 1260 TRP cc_start: 0.8091 (m100) cc_final: 0.7773 (m100) REVERT: E 1263 ARG cc_start: 0.8743 (tpp80) cc_final: 0.8278 (tpp80) REVERT: G 189 ARG cc_start: 0.6203 (ttp-170) cc_final: 0.5524 (mtm110) outliers start: 80 outliers final: 65 residues processed: 549 average time/residue: 0.3051 time to fit residues: 261.9923 Evaluate side-chains 575 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 503 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 196 HIS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 96 PHE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 258 ASN Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 490 LYS Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 866 THR Chi-restraints excluded: chain E residue 1083 THR Chi-restraints excluded: chain E residue 1163 THR Chi-restraints excluded: chain E residue 1225 CYS Chi-restraints excluded: chain E residue 1235 ILE Chi-restraints excluded: chain E residue 1258 LEU Chi-restraints excluded: chain E residue 1371 ILE Chi-restraints excluded: chain E residue 1439 THR Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain G residue 172 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 275 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 162 optimal weight: 20.0000 chunk 208 optimal weight: 0.0030 chunk 161 optimal weight: 30.0000 chunk 240 optimal weight: 6.9990 chunk 159 optimal weight: 40.0000 chunk 284 optimal weight: 50.0000 chunk 177 optimal weight: 50.0000 chunk 173 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 overall best weight: 6.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 287 ASN ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20340 Z= 0.285 Angle : 0.603 8.493 27932 Z= 0.316 Chirality : 0.045 0.260 3390 Planarity : 0.004 0.045 3599 Dihedral : 12.435 158.544 3699 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 6.34 % Allowed : 26.79 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.16), residues: 2959 helix: 0.89 (0.15), residues: 1302 sheet: -0.57 (0.39), residues: 192 loop : -2.16 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 92 HIS 0.010 0.001 HIS B 269 PHE 0.044 0.002 PHE D 178 TYR 0.022 0.001 TYR E 370 ARG 0.006 0.000 ARG B 274 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 508 time to evaluate : 2.440 Fit side-chains revert: symmetry clash REVERT: A 84 TRP cc_start: 0.9159 (m-10) cc_final: 0.8551 (m-10) REVERT: A 102 TYR cc_start: 0.8713 (t80) cc_final: 0.8280 (t80) REVERT: A 138 GLN cc_start: 0.9075 (tt0) cc_final: 0.8726 (tp40) REVERT: A 256 SER cc_start: 0.9260 (t) cc_final: 0.9042 (t) REVERT: A 257 ASN cc_start: 0.8120 (p0) cc_final: 0.7654 (p0) REVERT: A 269 HIS cc_start: 0.8862 (OUTLIER) cc_final: 0.7897 (t70) REVERT: A 285 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.8898 (tp) REVERT: A 296 LEU cc_start: 0.9162 (pt) cc_final: 0.8839 (pt) REVERT: A 320 TRP cc_start: 0.9075 (t-100) cc_final: 0.8719 (t-100) REVERT: B 58 GLN cc_start: 0.9080 (tp40) cc_final: 0.8607 (tp40) REVERT: B 64 LEU cc_start: 0.9122 (tp) cc_final: 0.8715 (tp) REVERT: B 147 MET cc_start: 0.8935 (ttm) cc_final: 0.8734 (ttm) REVERT: B 148 MET cc_start: 0.8378 (ttp) cc_final: 0.8171 (ptm) REVERT: B 179 MET cc_start: 0.8686 (tpt) cc_final: 0.8177 (tpp) REVERT: B 287 ASN cc_start: 0.8278 (t0) cc_final: 0.7814 (t0) REVERT: B 320 TRP cc_start: 0.8468 (t-100) cc_final: 0.8121 (t60) REVERT: B 324 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7766 (t80) REVERT: C 44 ASN cc_start: 0.8627 (p0) cc_final: 0.8386 (p0) REVERT: C 48 LYS cc_start: 0.8798 (tppt) cc_final: 0.8579 (ttmm) REVERT: C 87 PHE cc_start: 0.8817 (m-80) cc_final: 0.8504 (m-80) REVERT: C 96 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.7899 (t80) REVERT: C 161 LEU cc_start: 0.9146 (tt) cc_final: 0.8917 (tt) REVERT: C 167 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8486 (mm) REVERT: C 183 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7504 (mt0) REVERT: D 244 HIS cc_start: 0.8504 (t-90) cc_final: 0.8260 (t70) REVERT: D 255 GLU cc_start: 0.8389 (mp0) cc_final: 0.8032 (mm-30) REVERT: D 258 ASN cc_start: 0.9489 (OUTLIER) cc_final: 0.8898 (m-40) REVERT: D 284 ASP cc_start: 0.9101 (m-30) cc_final: 0.8626 (t70) REVERT: E 112 PHE cc_start: 0.8077 (t80) cc_final: 0.7738 (t80) REVERT: E 494 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7592 (tt0) REVERT: E 1250 TYR cc_start: 0.7259 (m-80) cc_final: 0.6989 (m-80) REVERT: E 1260 TRP cc_start: 0.8122 (m100) cc_final: 0.7661 (m100) REVERT: E 1263 ARG cc_start: 0.8747 (tpp80) cc_final: 0.8305 (tpp80) REVERT: G 189 ARG cc_start: 0.6205 (ttp-170) cc_final: 0.5529 (mtm110) outliers start: 83 outliers final: 70 residues processed: 548 average time/residue: 0.2940 time to fit residues: 252.4525 Evaluate side-chains 580 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 504 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 196 HIS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 96 PHE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 258 ASN Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 173 MET Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 490 LYS Chi-restraints excluded: chain E residue 1083 THR Chi-restraints excluded: chain E residue 1163 THR Chi-restraints excluded: chain E residue 1225 CYS Chi-restraints excluded: chain E residue 1235 ILE Chi-restraints excluded: chain E residue 1258 LEU Chi-restraints excluded: chain E residue 1371 ILE Chi-restraints excluded: chain E residue 1439 THR Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 172 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 175 optimal weight: 30.0000 chunk 113 optimal weight: 1.9990 chunk 169 optimal weight: 40.0000 chunk 85 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 chunk 193 optimal weight: 50.0000 chunk 140 optimal weight: 9.9990 chunk 26 optimal weight: 0.0980 chunk 223 optimal weight: 50.0000 chunk 258 optimal weight: 30.0000 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN D 228 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20340 Z= 0.245 Angle : 0.585 8.802 27932 Z= 0.305 Chirality : 0.045 0.245 3390 Planarity : 0.004 0.046 3599 Dihedral : 12.152 158.180 3699 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 5.80 % Allowed : 27.25 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.16), residues: 2959 helix: 0.96 (0.15), residues: 1305 sheet: -0.50 (0.39), residues: 192 loop : -2.09 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 230 HIS 0.008 0.001 HIS B 269 PHE 0.040 0.002 PHE D 178 TYR 0.022 0.001 TYR E 370 ARG 0.007 0.000 ARG E1213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 507 time to evaluate : 2.257 Fit side-chains revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8717 (t80) cc_final: 0.8290 (t80) REVERT: A 256 SER cc_start: 0.9227 (t) cc_final: 0.9006 (t) REVERT: A 257 ASN cc_start: 0.8226 (p0) cc_final: 0.7786 (p0) REVERT: A 269 HIS cc_start: 0.8833 (OUTLIER) cc_final: 0.7944 (t-90) REVERT: A 285 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.8877 (tp) REVERT: A 296 LEU cc_start: 0.9155 (pt) cc_final: 0.8812 (pt) REVERT: A 320 TRP cc_start: 0.9043 (t-100) cc_final: 0.8725 (t-100) REVERT: B 39 LYS cc_start: 0.8878 (mmmt) cc_final: 0.8658 (mmtt) REVERT: B 58 GLN cc_start: 0.9094 (tp40) cc_final: 0.8642 (tp40) REVERT: B 64 LEU cc_start: 0.9109 (tp) cc_final: 0.8698 (tp) REVERT: B 92 TRP cc_start: 0.9041 (t60) cc_final: 0.8792 (t60) REVERT: B 148 MET cc_start: 0.8356 (ttp) cc_final: 0.8044 (ptm) REVERT: B 179 MET cc_start: 0.8603 (tpt) cc_final: 0.8086 (tpp) REVERT: B 287 ASN cc_start: 0.8283 (t0) cc_final: 0.7791 (t0) REVERT: B 320 TRP cc_start: 0.8434 (t-100) cc_final: 0.8084 (t60) REVERT: B 324 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7728 (t80) REVERT: C 44 ASN cc_start: 0.8599 (p0) cc_final: 0.8380 (p0) REVERT: C 48 LYS cc_start: 0.8901 (tppt) cc_final: 0.8670 (ttmm) REVERT: C 87 PHE cc_start: 0.8787 (m-80) cc_final: 0.8502 (m-80) REVERT: C 96 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.7831 (t80) REVERT: C 167 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8503 (mm) REVERT: C 183 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7457 (mt0) REVERT: D 173 MET cc_start: 0.7628 (tpt) cc_final: 0.7193 (tmm) REVERT: D 244 HIS cc_start: 0.8467 (t-90) cc_final: 0.8236 (t70) REVERT: D 255 GLU cc_start: 0.8391 (mp0) cc_final: 0.8048 (mm-30) REVERT: D 284 ASP cc_start: 0.9094 (m-30) cc_final: 0.8632 (t70) REVERT: E 494 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7548 (tt0) REVERT: E 507 TRP cc_start: 0.5950 (m100) cc_final: 0.5683 (m100) REVERT: E 1250 TYR cc_start: 0.6937 (m-80) cc_final: 0.6614 (m-80) REVERT: E 1260 TRP cc_start: 0.8104 (m100) cc_final: 0.7647 (m100) REVERT: E 1263 ARG cc_start: 0.8717 (tpp80) cc_final: 0.8292 (tpp80) REVERT: G 189 ARG cc_start: 0.6048 (ttp-170) cc_final: 0.5511 (mtm110) outliers start: 76 outliers final: 66 residues processed: 547 average time/residue: 0.3005 time to fit residues: 257.5901 Evaluate side-chains 570 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 499 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 196 HIS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 96 PHE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 490 LYS Chi-restraints excluded: chain E residue 866 THR Chi-restraints excluded: chain E residue 1083 THR Chi-restraints excluded: chain E residue 1163 THR Chi-restraints excluded: chain E residue 1225 CYS Chi-restraints excluded: chain E residue 1235 ILE Chi-restraints excluded: chain E residue 1258 LEU Chi-restraints excluded: chain E residue 1371 ILE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 172 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 272 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 264 optimal weight: 8.9990 chunk 159 optimal weight: 0.1980 chunk 115 optimal weight: 20.0000 chunk 208 optimal weight: 30.0000 chunk 81 optimal weight: 5.9990 chunk 239 optimal weight: 10.0000 chunk 250 optimal weight: 9.9990 chunk 173 optimal weight: 20.0000 chunk 280 optimal weight: 9.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20340 Z= 0.223 Angle : 0.586 8.933 27932 Z= 0.302 Chirality : 0.044 0.275 3390 Planarity : 0.004 0.046 3599 Dihedral : 11.962 157.969 3699 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 5.88 % Allowed : 27.48 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.16), residues: 2959 helix: 1.05 (0.15), residues: 1297 sheet: -0.72 (0.38), residues: 205 loop : -2.03 (0.17), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 230 HIS 0.008 0.001 HIS A 322 PHE 0.036 0.002 PHE D 178 TYR 0.023 0.001 TYR E 370 ARG 0.005 0.000 ARG B 274 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 504 time to evaluate : 2.308 Fit side-chains revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8702 (t80) cc_final: 0.8288 (t80) REVERT: A 179 MET cc_start: 0.8507 (tpp) cc_final: 0.8268 (tpp) REVERT: A 256 SER cc_start: 0.9202 (t) cc_final: 0.8993 (t) REVERT: A 257 ASN cc_start: 0.8227 (p0) cc_final: 0.7806 (p0) REVERT: A 285 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8866 (tp) REVERT: A 320 TRP cc_start: 0.9091 (t-100) cc_final: 0.8741 (t-100) REVERT: B 39 LYS cc_start: 0.8857 (mmmt) cc_final: 0.8641 (mmtt) REVERT: B 58 GLN cc_start: 0.9055 (tp40) cc_final: 0.8638 (tp40) REVERT: B 64 LEU cc_start: 0.9094 (tp) cc_final: 0.8686 (tp) REVERT: B 179 MET cc_start: 0.8591 (tpt) cc_final: 0.7963 (tpp) REVERT: B 287 ASN cc_start: 0.8110 (t0) cc_final: 0.7584 (t0) REVERT: B 320 TRP cc_start: 0.8425 (t-100) cc_final: 0.8095 (t60) REVERT: B 324 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7782 (t80) REVERT: C 44 ASN cc_start: 0.8578 (p0) cc_final: 0.8354 (p0) REVERT: C 48 LYS cc_start: 0.8894 (tppt) cc_final: 0.8669 (ttmm) REVERT: C 87 PHE cc_start: 0.8773 (m-80) cc_final: 0.8507 (m-80) REVERT: C 96 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.7877 (t80) REVERT: C 167 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8463 (mm) REVERT: C 183 GLN cc_start: 0.7875 (mm-40) cc_final: 0.7481 (mt0) REVERT: D 255 GLU cc_start: 0.8392 (mp0) cc_final: 0.8027 (mm-30) REVERT: D 258 ASN cc_start: 0.9462 (OUTLIER) cc_final: 0.8855 (m-40) REVERT: D 284 ASP cc_start: 0.9088 (m-30) cc_final: 0.8642 (t70) REVERT: E 494 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7550 (tt0) REVERT: E 507 TRP cc_start: 0.5947 (m100) cc_final: 0.5697 (m100) REVERT: E 1250 TYR cc_start: 0.6910 (m-80) cc_final: 0.6576 (m-80) REVERT: E 1260 TRP cc_start: 0.8092 (m100) cc_final: 0.7627 (m100) REVERT: E 1263 ARG cc_start: 0.8697 (tpp80) cc_final: 0.8269 (tpp80) REVERT: G 189 ARG cc_start: 0.6045 (ttp-170) cc_final: 0.5510 (mtm110) outliers start: 77 outliers final: 65 residues processed: 546 average time/residue: 0.3108 time to fit residues: 266.7409 Evaluate side-chains 561 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 491 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 196 HIS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 96 PHE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 258 ASN Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 173 MET Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 866 THR Chi-restraints excluded: chain E residue 1083 THR Chi-restraints excluded: chain E residue 1163 THR Chi-restraints excluded: chain E residue 1225 CYS Chi-restraints excluded: chain E residue 1235 ILE Chi-restraints excluded: chain E residue 1258 LEU Chi-restraints excluded: chain E residue 1371 ILE Chi-restraints excluded: chain E residue 1439 THR Chi-restraints excluded: chain G residue 80 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 171 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 chunk 194 optimal weight: 50.0000 chunk 293 optimal weight: 50.0000 chunk 270 optimal weight: 50.0000 chunk 234 optimal weight: 0.6980 chunk 24 optimal weight: 9.9990 chunk 180 optimal weight: 8.9990 chunk 143 optimal weight: 20.0000 chunk 185 optimal weight: 0.7980 chunk 249 optimal weight: 50.0000 overall best weight: 2.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN E 83 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20340 Z= 0.172 Angle : 0.566 9.158 27932 Z= 0.291 Chirality : 0.044 0.200 3390 Planarity : 0.004 0.046 3599 Dihedral : 11.619 157.336 3699 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.82 % Allowed : 29.69 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.16), residues: 2959 helix: 1.12 (0.15), residues: 1305 sheet: -0.66 (0.38), residues: 205 loop : -1.89 (0.17), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 84 HIS 0.009 0.001 HIS A 322 PHE 0.031 0.002 PHE D 76 TYR 0.025 0.001 TYR E 370 ARG 0.005 0.000 ARG B 274 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 501 time to evaluate : 3.212 Fit side-chains revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8670 (t80) cc_final: 0.8265 (t80) REVERT: A 257 ASN cc_start: 0.8176 (p0) cc_final: 0.7772 (p0) REVERT: A 285 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.8859 (tp) REVERT: A 320 TRP cc_start: 0.9063 (t-100) cc_final: 0.8715 (t-100) REVERT: B 58 GLN cc_start: 0.8973 (tp40) cc_final: 0.8561 (tp40) REVERT: B 64 LEU cc_start: 0.8984 (tp) cc_final: 0.8605 (tp) REVERT: B 92 TRP cc_start: 0.8935 (t60) cc_final: 0.8687 (t60) REVERT: B 105 MET cc_start: 0.6899 (ttp) cc_final: 0.6698 (ttt) REVERT: B 147 MET cc_start: 0.7330 (ttm) cc_final: 0.6972 (ttm) REVERT: B 179 MET cc_start: 0.8507 (tpt) cc_final: 0.7898 (tpp) REVERT: B 287 ASN cc_start: 0.8219 (t0) cc_final: 0.7646 (t0) REVERT: B 320 TRP cc_start: 0.8409 (t-100) cc_final: 0.8067 (t60) REVERT: B 324 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7745 (t80) REVERT: C 44 ASN cc_start: 0.8543 (p0) cc_final: 0.8331 (p0) REVERT: C 67 LEU cc_start: 0.7997 (mt) cc_final: 0.7772 (mt) REVERT: C 183 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7417 (mt0) REVERT: D 173 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.6797 (tpt) REVERT: D 255 GLU cc_start: 0.8463 (mp0) cc_final: 0.8107 (mm-30) REVERT: D 284 ASP cc_start: 0.9078 (m-30) cc_final: 0.8640 (t70) REVERT: E 91 ILE cc_start: 0.9169 (mm) cc_final: 0.8968 (mm) REVERT: E 494 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7548 (tt0) REVERT: E 507 TRP cc_start: 0.5875 (m100) cc_final: 0.5638 (m100) REVERT: E 1250 TYR cc_start: 0.6825 (m-80) cc_final: 0.6513 (m-80) REVERT: E 1260 TRP cc_start: 0.8056 (m100) cc_final: 0.7499 (m100) REVERT: G 189 ARG cc_start: 0.6069 (ttp-170) cc_final: 0.5644 (mtm110) outliers start: 50 outliers final: 43 residues processed: 527 average time/residue: 0.2955 time to fit residues: 246.2163 Evaluate side-chains 539 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 493 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 173 MET Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 424 PHE Chi-restraints excluded: chain E residue 1083 THR Chi-restraints excluded: chain E residue 1163 THR Chi-restraints excluded: chain E residue 1225 CYS Chi-restraints excluded: chain E residue 1371 ILE Chi-restraints excluded: chain E residue 1439 THR Chi-restraints excluded: chain G residue 80 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 71 optimal weight: 5.9990 chunk 215 optimal weight: 0.0050 chunk 34 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 234 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 240 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS A 287 ASN ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN E 83 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.195497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.164000 restraints weight = 27059.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.163445 restraints weight = 29667.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.164492 restraints weight = 27143.762| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20340 Z= 0.174 Angle : 0.555 8.995 27932 Z= 0.284 Chirality : 0.044 0.192 3390 Planarity : 0.004 0.047 3599 Dihedral : 11.277 156.763 3699 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.36 % Allowed : 30.38 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.16), residues: 2959 helix: 1.22 (0.15), residues: 1304 sheet: -0.62 (0.37), residues: 205 loop : -1.81 (0.17), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 69 HIS 0.007 0.001 HIS A 322 PHE 0.035 0.002 PHE D 178 TYR 0.024 0.001 TYR E 370 ARG 0.005 0.000 ARG B 274 =============================================================================== Job complete usr+sys time: 4572.55 seconds wall clock time: 82 minutes 46.54 seconds (4966.54 seconds total)