Starting phenix.real_space_refine on Wed Mar 20 11:18:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4j_37266/03_2024/8w4j_37266.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4j_37266/03_2024/8w4j_37266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4j_37266/03_2024/8w4j_37266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4j_37266/03_2024/8w4j_37266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4j_37266/03_2024/8w4j_37266.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4j_37266/03_2024/8w4j_37266.pdb" } resolution = 3.06 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.046 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: 4 Type Number sf(0) Gaussians S 106 5.16 5 C 17054 2.51 5 N 4985 2.21 5 O 5020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 75": "OD1" <-> "OD2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 459": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27165 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3510 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 21, 'TRANS': 463} Chain breaks: 2 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 18, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 177 Chain: "B" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3549 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 21, 'TRANS': 462} Chain breaks: 2 Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 20, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 149 Chain: "C" Number of atoms: 3600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3600 Classifications: {'peptide': 487} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 21, 'TRANS': 465} Chain breaks: 2 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 120 Chain: "D" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3632 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 21, 'TRANS': 464} Chain breaks: 2 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 89 Chain: "E" Number of atoms: 3611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3611 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 21, 'TRANS': 464} Chain breaks: 2 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "F" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3619 Classifications: {'peptide': 487} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 21, 'TRANS': 465} Chain breaks: 1 Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 11, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 110 Chain: "I" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 2812 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 492} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 547} Chain breaks: 1 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1835 Unresolved non-hydrogen angles: 2381 Unresolved non-hydrogen dihedrals: 1540 Unresolved non-hydrogen chiralities: 158 Planarities with less than four sites: {'GLN:plan1': 26, 'ARG:plan': 37, 'TYR:plan': 30, 'ASN:plan1': 25, 'TRP:plan': 9, 'HIS:plan': 22, 'PHE:plan': 16, 'GLU:plan': 38, 'ASP:plan': 29} Unresolved non-hydrogen planarities: 1100 Chain: "J" Number of atoms: 2832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 2832 Classifications: {'peptide': 574} Incomplete info: {'truncation_to_alanine': 496} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 551} Chain breaks: 1 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1849 Unresolved non-hydrogen angles: 2399 Unresolved non-hydrogen dihedrals: 1552 Unresolved non-hydrogen chiralities: 159 Planarities with less than four sites: {'GLN:plan1': 26, 'ARG:plan': 37, 'TYR:plan': 30, 'ASN:plan1': 25, 'TRP:plan': 9, 'HIS:plan': 23, 'PHE:plan': 16, 'GLU:plan': 39, 'ASP:plan': 29} Unresolved non-hydrogen planarities: 1109 Time building chain proxies: 14.24, per 1000 atoms: 0.52 Number of scatterers: 27165 At special positions: 0 Unit cell: (133.45, 153.85, 212.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 106 16.00 O 5020 8.00 N 4985 7.00 C 17054 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 9.93 Conformation dependent library (CDL) restraints added in 5.0 seconds 8034 Ramachandran restraints generated. 4017 Oldfield, 0 Emsley, 4017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7406 Finding SS restraints... Secondary structure from input PDB file: 165 helices and 27 sheets defined 50.0% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'A' and resid 67 through 88 removed outlier: 4.675A pdb=" N ASP A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LYS A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 102 Processing helix chain 'A' and resid 103 through 110 removed outlier: 3.876A pdb=" N ARG A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 175 removed outlier: 3.573A pdb=" N TYR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 removed outlier: 3.710A pdb=" N ASN A 192 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 193 " --> pdb=" O PRO A 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 189 through 193' Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.726A pdb=" N LYS A 200 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 244 removed outlier: 3.887A pdb=" N MET A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 248 Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.240A pdb=" N VAL A 255 " --> pdb=" O HIS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.587A pdb=" N ARG A 274 " --> pdb=" O SER A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 344 through 355 removed outlier: 3.524A pdb=" N HIS A 355 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.726A pdb=" N GLU A 373 " --> pdb=" O SER A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 420 removed outlier: 3.681A pdb=" N ASP A 414 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 416 " --> pdb=" O GLU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.585A pdb=" N ASN A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 448 Processing helix chain 'A' and resid 455 through 478 Processing helix chain 'A' and resid 490 through 499 removed outlier: 3.631A pdb=" N ASP A 495 " --> pdb=" O ALA A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 528 removed outlier: 4.001A pdb=" N ILE A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 528 " --> pdb=" O THR A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 552 removed outlier: 3.843A pdb=" N ALA A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A 548 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR A 550 " --> pdb=" O VAL A 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 86 removed outlier: 3.976A pdb=" N ASP B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 110 removed outlier: 3.919A pdb=" N ARG B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 109 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 175 removed outlier: 3.761A pdb=" N LYS B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 163 " --> pdb=" O ASP B 159 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 174 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL B 175 " --> pdb=" O LYS B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 194 through 211 removed outlier: 3.755A pdb=" N GLU B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 244 removed outlier: 4.048A pdb=" N MET B 233 " --> pdb=" O GLY B 229 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 244 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 248 Processing helix chain 'B' and resid 250 through 255 removed outlier: 4.272A pdb=" N VAL B 255 " --> pdb=" O HIS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.849A pdb=" N ARG B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 283 " --> pdb=" O GLY B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 removed outlier: 3.726A pdb=" N ILE B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 322 Processing helix chain 'B' and resid 344 through 355 Processing helix chain 'B' and resid 410 through 420 removed outlier: 3.503A pdb=" N ASP B 414 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 431 removed outlier: 3.673A pdb=" N ASN B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 448 Processing helix chain 'B' and resid 455 through 475 Processing helix chain 'B' and resid 490 through 499 removed outlier: 3.606A pdb=" N ASP B 495 " --> pdb=" O ALA B 491 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 526 removed outlier: 3.977A pdb=" N ILE B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 554 removed outlier: 3.727A pdb=" N VAL B 549 " --> pdb=" O LYS B 545 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR B 550 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY B 554 " --> pdb=" O TYR B 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 87 removed outlier: 4.347A pdb=" N ASP C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 103 Processing helix chain 'C' and resid 105 through 110 removed outlier: 3.609A pdb=" N LYS C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 175 removed outlier: 3.563A pdb=" N THR C 169 " --> pdb=" O ALA C 165 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL C 175 " --> pdb=" O LYS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 193 removed outlier: 3.638A pdb=" N TYR C 193 " --> pdb=" O PRO C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 212 removed outlier: 3.659A pdb=" N LYS C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 243 removed outlier: 3.659A pdb=" N TRP C 235 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 248 removed outlier: 4.450A pdb=" N TYR C 247 " --> pdb=" O ILE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 4.226A pdb=" N VAL C 255 " --> pdb=" O HIS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.575A pdb=" N ARG C 274 " --> pdb=" O SER C 270 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE C 283 " --> pdb=" O GLY C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 294 Processing helix chain 'C' and resid 310 through 322 removed outlier: 3.504A pdb=" N ARG C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR C 319 " --> pdb=" O HIS C 315 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS C 321 " --> pdb=" O MET C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 355 removed outlier: 3.594A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP C 350 " --> pdb=" O LYS C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'C' and resid 410 through 420 removed outlier: 3.762A pdb=" N LYS C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 416 " --> pdb=" O GLU C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 431 removed outlier: 4.311A pdb=" N ASN C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 448 Processing helix chain 'C' and resid 455 through 479 removed outlier: 3.680A pdb=" N VAL C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN C 471 " --> pdb=" O LEU C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 499 Processing helix chain 'C' and resid 501 through 528 removed outlier: 3.992A pdb=" N ILE C 505 " --> pdb=" O SER C 501 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG C 519 " --> pdb=" O GLU C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 552 removed outlier: 3.669A pdb=" N ALA C 537 " --> pdb=" O ASP C 533 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL C 549 " --> pdb=" O LYS C 545 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR C 550 " --> pdb=" O VAL C 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 89 removed outlier: 3.591A pdb=" N MET D 69 " --> pdb=" O ASN D 65 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE D 73 " --> pdb=" O MET D 69 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE D 74 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS D 84 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 102 No H-bonds generated for 'chain 'D' and resid 100 through 102' Processing helix chain 'D' and resid 103 through 110 removed outlier: 3.858A pdb=" N ARG D 107 " --> pdb=" O ARG D 103 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 175 removed outlier: 3.750A pdb=" N TYR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL D 175 " --> pdb=" O LYS D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 193 Processing helix chain 'D' and resid 194 through 213 removed outlier: 3.650A pdb=" N LYS D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 241 removed outlier: 3.652A pdb=" N MET D 233 " --> pdb=" O GLY D 229 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.508A pdb=" N GLN D 262 " --> pdb=" O PRO D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 285 removed outlier: 3.509A pdb=" N PHE D 283 " --> pdb=" O GLY D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 291 Processing helix chain 'D' and resid 310 through 323 Processing helix chain 'D' and resid 344 through 355 Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 392 through 396 removed outlier: 3.664A pdb=" N VAL D 396 " --> pdb=" O ALA D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 420 removed outlier: 3.618A pdb=" N LYS D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE D 416 " --> pdb=" O GLU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 431 removed outlier: 3.844A pdb=" N ASN D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 448 Processing helix chain 'D' and resid 455 through 478 removed outlier: 3.670A pdb=" N LYS D 477 " --> pdb=" O SER D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 499 Processing helix chain 'D' and resid 501 through 528 removed outlier: 4.003A pdb=" N ILE D 505 " --> pdb=" O SER D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 552 removed outlier: 3.549A pdb=" N ALA D 537 " --> pdb=" O ASP D 533 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU D 552 " --> pdb=" O LYS D 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 86 removed outlier: 4.113A pdb=" N ASP E 83 " --> pdb=" O SER E 79 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LYS E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 110 removed outlier: 3.976A pdb=" N ARG E 107 " --> pdb=" O ARG E 103 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 175 removed outlier: 3.548A pdb=" N TYR E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 193 removed outlier: 3.530A pdb=" N TYR E 193 " --> pdb=" O PRO E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 211 removed outlier: 3.671A pdb=" N GLU E 199 " --> pdb=" O ASP E 195 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS E 200 " --> pdb=" O ASN E 196 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS E 211 " --> pdb=" O MET E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 removed outlier: 3.703A pdb=" N MET E 233 " --> pdb=" O GLY E 229 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR E 239 " --> pdb=" O TRP E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 255 removed outlier: 4.324A pdb=" N VAL E 255 " --> pdb=" O HIS E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 285 removed outlier: 3.520A pdb=" N PHE E 283 " --> pdb=" O GLY E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 294 Processing helix chain 'E' and resid 310 through 323 removed outlier: 3.895A pdb=" N TYR E 319 " --> pdb=" O HIS E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 355 removed outlier: 3.535A pdb=" N HIS E 355 " --> pdb=" O PHE E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 374 removed outlier: 3.574A pdb=" N GLU E 373 " --> pdb=" O SER E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 396 removed outlier: 3.723A pdb=" N VAL E 396 " --> pdb=" O ALA E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 420 removed outlier: 3.812A pdb=" N LYS E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE E 416 " --> pdb=" O GLU E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 431 removed outlier: 3.829A pdb=" N ASN E 431 " --> pdb=" O ASP E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 448 Processing helix chain 'E' and resid 455 through 478 removed outlier: 3.626A pdb=" N LYS E 477 " --> pdb=" O SER E 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 490 through 499 Processing helix chain 'E' and resid 501 through 528 removed outlier: 3.764A pdb=" N ILE E 505 " --> pdb=" O SER E 501 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG E 519 " --> pdb=" O GLU E 515 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR E 524 " --> pdb=" O GLN E 520 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA E 525 " --> pdb=" O ILE E 521 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET E 526 " --> pdb=" O MET E 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 554 removed outlier: 3.688A pdb=" N ALA E 537 " --> pdb=" O ASP E 533 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY E 554 " --> pdb=" O TYR E 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 89 removed outlier: 3.887A pdb=" N VAL F 70 " --> pdb=" O PHE F 66 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU F 71 " --> pdb=" O PHE F 67 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER F 79 " --> pdb=" O ASP F 75 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE F 80 " --> pdb=" O ARG F 76 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL F 81 " --> pdb=" O GLY F 77 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP F 83 " --> pdb=" O SER F 79 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS F 84 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU F 87 " --> pdb=" O ASP F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 102 Processing helix chain 'F' and resid 103 through 110 removed outlier: 4.125A pdb=" N ARG F 107 " --> pdb=" O ARG F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 175 removed outlier: 3.901A pdb=" N TYR F 170 " --> pdb=" O SER F 166 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL F 175 " --> pdb=" O LYS F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 193 removed outlier: 3.742A pdb=" N TYR F 193 " --> pdb=" O PRO F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 212 removed outlier: 3.746A pdb=" N LYS F 212 " --> pdb=" O GLU F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 241 removed outlier: 3.759A pdb=" N MET F 233 " --> pdb=" O GLY F 229 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP F 235 " --> pdb=" O ARG F 231 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA F 237 " --> pdb=" O MET F 233 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP F 238 " --> pdb=" O SER F 234 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR F 239 " --> pdb=" O TRP F 235 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR F 240 " --> pdb=" O ILE F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 255 removed outlier: 4.150A pdb=" N VAL F 255 " --> pdb=" O HIS F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 263 Processing helix chain 'F' and resid 270 through 285 removed outlier: 3.647A pdb=" N PHE F 283 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 293 removed outlier: 3.742A pdb=" N ILE F 292 " --> pdb=" O SER F 288 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU F 293 " --> pdb=" O TYR F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 323 removed outlier: 3.867A pdb=" N PHE F 323 " --> pdb=" O TYR F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 355 removed outlier: 3.503A pdb=" N HIS F 355 " --> pdb=" O PHE F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 420 removed outlier: 3.872A pdb=" N LYS F 415 " --> pdb=" O PRO F 411 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE F 416 " --> pdb=" O GLU F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 431 removed outlier: 4.085A pdb=" N ASN F 431 " --> pdb=" O ASP F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 448 Processing helix chain 'F' and resid 455 through 476 Processing helix chain 'F' and resid 490 through 499 Processing helix chain 'F' and resid 501 through 528 removed outlier: 3.827A pdb=" N ILE F 505 " --> pdb=" O SER F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 552 removed outlier: 3.740A pdb=" N ALA F 537 " --> pdb=" O ASP F 533 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU F 552 " --> pdb=" O LYS F 548 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 47 removed outlier: 3.787A pdb=" N GLY I 47 " --> pdb=" O LEU I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 72 removed outlier: 3.736A pdb=" N CYS I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 80 removed outlier: 4.003A pdb=" N GLY I 77 " --> pdb=" O ASP I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 88 removed outlier: 3.703A pdb=" N GLN I 88 " --> pdb=" O GLU I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 111 Processing helix chain 'I' and resid 120 through 129 removed outlier: 4.435A pdb=" N GLN I 129 " --> pdb=" O VAL I 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 146 Processing helix chain 'I' and resid 148 through 150 No H-bonds generated for 'chain 'I' and resid 148 through 150' Processing helix chain 'I' and resid 151 through 163 Processing helix chain 'I' and resid 167 through 178 Processing helix chain 'I' and resid 178 through 183 Processing helix chain 'I' and resid 186 through 191 removed outlier: 3.658A pdb=" N GLN I 190 " --> pdb=" O ASP I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 193 through 202 Processing helix chain 'I' and resid 211 through 222 Processing helix chain 'I' and resid 223 through 228 Processing helix chain 'I' and resid 238 through 243 removed outlier: 3.927A pdb=" N GLU I 242 " --> pdb=" O PRO I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 261 removed outlier: 3.978A pdb=" N LEU I 254 " --> pdb=" O GLU I 250 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ARG I 256 " --> pdb=" O GLU I 252 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU I 257 " --> pdb=" O VAL I 253 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS I 260 " --> pdb=" O ARG I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 266 through 276 removed outlier: 4.430A pdb=" N VAL I 270 " --> pdb=" O LEU I 266 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET I 275 " --> pdb=" O ALA I 271 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR I 276 " --> pdb=" O SER I 272 " (cutoff:3.500A) Processing helix chain 'I' and resid 277 through 279 No H-bonds generated for 'chain 'I' and resid 277 through 279' Processing helix chain 'I' and resid 594 through 600 Processing helix chain 'J' and resid 31 through 46 Processing helix chain 'J' and resid 64 through 70 removed outlier: 3.684A pdb=" N LEU J 68 " --> pdb=" O HIS J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 80 removed outlier: 3.904A pdb=" N ARG J 76 " --> pdb=" O CYS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 88 removed outlier: 3.760A pdb=" N GLN J 88 " --> pdb=" O GLU J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 111 Processing helix chain 'J' and resid 119 through 130 Processing helix chain 'J' and resid 132 through 146 Processing helix chain 'J' and resid 148 through 151 Processing helix chain 'J' and resid 152 through 163 removed outlier: 3.746A pdb=" N TYR J 156 " --> pdb=" O ILE J 152 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG J 157 " --> pdb=" O LEU J 153 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU J 158 " --> pdb=" O ASP J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 185 removed outlier: 5.920A pdb=" N VAL J 180 " --> pdb=" O LEU J 176 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ALA J 181 " --> pdb=" O LYS J 177 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG J 184 " --> pdb=" O VAL J 180 " (cutoff:3.500A) Processing helix chain 'J' and resid 186 through 191 Processing helix chain 'J' and resid 192 through 202 Processing helix chain 'J' and resid 209 through 222 Processing helix chain 'J' and resid 223 through 228 Processing helix chain 'J' and resid 238 through 244 Processing helix chain 'J' and resid 250 through 260 removed outlier: 3.685A pdb=" N LYS J 260 " --> pdb=" O ARG J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 279 Processing helix chain 'J' and resid 280 through 287 Proline residue: J 284 - end of helix removed outlier: 3.862A pdb=" N GLN J 287 " --> pdb=" O PRO J 284 " (cutoff:3.500A) Processing helix chain 'J' and resid 502 through 506 removed outlier: 3.615A pdb=" N ALA J 505 " --> pdb=" O ASN J 502 " (cutoff:3.500A) Processing helix chain 'J' and resid 594 through 599 removed outlier: 4.254A pdb=" N LEU J 598 " --> pdb=" O PRO J 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.277A pdb=" N ARG A 151 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS A 147 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ALA A 184 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N CYS A 146 " --> pdb=" O VAL A 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.277A pdb=" N ARG A 151 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL E 115 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N LYS E 147 " --> pdb=" O ALA E 182 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ALA E 184 " --> pdb=" O LYS E 147 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY E 149 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL E 186 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG E 151 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N CYS E 146 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA E 223 " --> pdb=" O CYS E 146 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY E 148 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 337 through 338 removed outlier: 7.780A pdb=" N VAL A 306 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL A 330 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR A 303 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ILE A 380 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL A 305 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU A 379 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE A 401 " --> pdb=" O ILE A 425 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 221 through 223 removed outlier: 6.131A pdb=" N GLY B 148 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LYS B 147 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ALA B 184 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLY B 149 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL B 186 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG B 151 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 115 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU D 130 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU D 133 " --> pdb=" O LYS D 187 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LYS D 147 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ALA D 184 " --> pdb=" O LYS D 147 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLY D 149 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N VAL D 186 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG D 151 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N CYS D 146 " --> pdb=" O VAL D 221 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 365 through 367 removed outlier: 4.310A pdb=" N SER B 336 " --> pdb=" O TYR B 367 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N PHE B 304 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N GLY B 331 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL B 306 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR B 303 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N ILE B 380 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL B 305 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU B 379 " --> pdb=" O ALA B 402 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 150 through 153 removed outlier: 6.600A pdb=" N ARG C 151 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLU C 133 " --> pdb=" O LYS C 187 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLU F 133 " --> pdb=" O LYS F 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 150 through 153 removed outlier: 6.600A pdb=" N ARG C 151 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLU C 133 " --> pdb=" O LYS C 187 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLU F 133 " --> pdb=" O LYS F 187 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LYS F 147 " --> pdb=" O ALA F 182 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ALA F 184 " --> pdb=" O LYS F 147 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY F 149 " --> pdb=" O ALA F 184 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL F 186 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS F 146 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ALA F 223 " --> pdb=" O CYS F 146 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY F 148 " --> pdb=" O ALA F 223 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 146 through 147 removed outlier: 5.983A pdb=" N CYS C 146 " --> pdb=" O VAL C 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 303 through 306 removed outlier: 6.617A pdb=" N PHE C 304 " --> pdb=" O CYS C 327 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA C 329 " --> pdb=" O PHE C 304 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 400 through 402 removed outlier: 7.168A pdb=" N ILE C 401 " --> pdb=" O ILE C 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 337 through 338 removed outlier: 3.588A pdb=" N VAL D 330 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N PHE D 304 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N GLY D 331 " --> pdb=" O PHE D 304 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL D 306 " --> pdb=" O GLY D 331 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU D 379 " --> pdb=" O ALA D 402 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE D 401 " --> pdb=" O ILE D 425 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 337 through 338 removed outlier: 7.337A pdb=" N PHE E 304 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N GLY E 331 " --> pdb=" O PHE E 304 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL E 306 " --> pdb=" O GLY E 331 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU E 379 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE E 401 " --> pdb=" O ILE E 425 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 337 through 338 removed outlier: 7.823A pdb=" N VAL F 306 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL F 330 " --> pdb=" O VAL F 306 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU F 379 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE F 401 " --> pdb=" O ILE F 425 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 417 through 418 removed outlier: 3.596A pdb=" N ARG I 418 " --> pdb=" O ALA I 427 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ALA I 427 " --> pdb=" O ARG I 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'I' and resid 442 through 444 removed outlier: 4.168A pdb=" N ALA I 442 " --> pdb=" O TYR I 449 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR I 449 " --> pdb=" O ALA I 442 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 488 through 491 removed outlier: 3.845A pdb=" N ALA I 489 " --> pdb=" O TYR I 496 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR I 496 " --> pdb=" O ALA I 489 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 552 through 553 removed outlier: 3.532A pdb=" N SER I 558 " --> pdb=" O SER I 553 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 565 through 567 removed outlier: 4.815A pdb=" N ILE I 565 " --> pdb=" O GLU I 574 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU I 574 " --> pdb=" O ILE I 565 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASP I 567 " --> pdb=" O CYS I 572 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N CYS I 572 " --> pdb=" O ASP I 567 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'J' and resid 55 through 56 removed outlier: 3.508A pdb=" N VAL J 56 " --> pdb=" O ARG J 59 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 313 through 314 removed outlier: 4.546A pdb=" N VAL J 313 " --> pdb=" O HIS J 307 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N HIS J 307 " --> pdb=" O VAL J 313 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 319 through 322 removed outlier: 3.752A pdb=" N GLU J 327 " --> pdb=" O ASN J 322 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 343 through 347 removed outlier: 3.606A pdb=" N GLY J 343 " --> pdb=" O ILE J 354 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL J 351 " --> pdb=" O TYR J 372 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 394 through 397 removed outlier: 3.701A pdb=" N TYR J 400 " --> pdb=" O VAL J 397 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 442 through 443 removed outlier: 3.672A pdb=" N ALA J 442 " --> pdb=" O TYR J 449 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 454 through 455 Processing sheet with id=AC8, first strand: chain 'J' and resid 538 through 542 removed outlier: 3.854A pdb=" N GLY J 538 " --> pdb=" O LEU J 549 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU J 549 " --> pdb=" O GLY J 538 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR J 566 " --> pdb=" O ILE J 546 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL J 548 " --> pdb=" O HIS J 564 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N HIS J 564 " --> pdb=" O VAL J 548 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 552 through 553 removed outlier: 3.553A pdb=" N SER J 558 " --> pdb=" O SER J 553 " (cutoff:3.500A) 1405 hydrogen bonds defined for protein. 3987 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: 9.87 Time building geometry restraints manager: 10.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9435 1.34 - 1.46: 5575 1.46 - 1.58: 12445 1.58 - 1.70: 0 1.70 - 1.81: 176 Bond restraints: 27631 Sorted by residual: bond pdb=" C THR F 144 " pdb=" N PRO F 145 " ideal model delta sigma weight residual 1.333 1.349 -0.015 1.01e-02 9.80e+03 2.21e+00 bond pdb=" C THR F 296 " pdb=" N PRO F 297 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.84e+00 bond pdb=" C GLU J 536 " pdb=" O GLU J 536 " ideal model delta sigma weight residual 1.235 1.230 0.005 4.70e-03 4.53e+04 1.16e+00 bond pdb=" N CYS J 299 " pdb=" CA CYS J 299 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.15e+00 bond pdb=" CB PRO D 297 " pdb=" CG PRO D 297 " ideal model delta sigma weight residual 1.492 1.542 -0.050 5.00e-02 4.00e+02 1.00e+00 ... (remaining 27626 not shown) Histogram of bond angle deviations from ideal: 96.79 - 104.23: 398 104.23 - 111.66: 12991 111.66 - 119.10: 8829 119.10 - 126.54: 15173 126.54 - 133.97: 291 Bond angle restraints: 37682 Sorted by residual: angle pdb=" N VAL E 102 " pdb=" CA VAL E 102 " pdb=" C VAL E 102 " ideal model delta sigma weight residual 112.29 108.03 4.26 9.40e-01 1.13e+00 2.06e+01 angle pdb=" CA MET B 233 " pdb=" CB MET B 233 " pdb=" CG MET B 233 " ideal model delta sigma weight residual 114.10 108.05 6.05 2.00e+00 2.50e-01 9.15e+00 angle pdb=" CB MET B 290 " pdb=" CG MET B 290 " pdb=" SD MET B 290 " ideal model delta sigma weight residual 112.70 121.69 -8.99 3.00e+00 1.11e-01 8.99e+00 angle pdb=" CA LYS C 191 " pdb=" CB LYS C 191 " pdb=" CG LYS C 191 " ideal model delta sigma weight residual 114.10 119.98 -5.88 2.00e+00 2.50e-01 8.63e+00 angle pdb=" CA PRO F 297 " pdb=" N PRO F 297 " pdb=" CD PRO F 297 " ideal model delta sigma weight residual 112.00 107.92 4.08 1.40e+00 5.10e-01 8.50e+00 ... (remaining 37677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 15118 17.55 - 35.10: 962 35.10 - 52.65: 135 52.65 - 70.21: 19 70.21 - 87.76: 7 Dihedral angle restraints: 16241 sinusoidal: 4689 harmonic: 11552 Sorted by residual: dihedral pdb=" CA THR F 296 " pdb=" C THR F 296 " pdb=" N PRO F 297 " pdb=" CA PRO F 297 " ideal model delta harmonic sigma weight residual -180.00 -147.23 -32.77 0 5.00e+00 4.00e-02 4.30e+01 dihedral pdb=" CA GLN E 97 " pdb=" C GLN E 97 " pdb=" N LYS E 98 " pdb=" CA LYS E 98 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA MET C 233 " pdb=" C MET C 233 " pdb=" N SER C 234 " pdb=" CA SER C 234 " ideal model delta harmonic sigma weight residual 180.00 160.60 19.40 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 16238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2839 0.034 - 0.068: 1121 0.068 - 0.103: 302 0.103 - 0.137: 143 0.137 - 0.171: 7 Chirality restraints: 4412 Sorted by residual: chirality pdb=" CA THR E 144 " pdb=" N THR E 144 " pdb=" C THR E 144 " pdb=" CB THR E 144 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CA THR D 144 " pdb=" N THR D 144 " pdb=" C THR D 144 " pdb=" CB THR D 144 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CB ILE B 485 " pdb=" CA ILE B 485 " pdb=" CG1 ILE B 485 " pdb=" CG2 ILE B 485 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 4409 not shown) Planarity restraints: 5017 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 296 " 0.075 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO F 297 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO F 297 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO F 297 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 144 " 0.042 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO F 145 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO F 145 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 145 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 485 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO E 486 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 486 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 486 " 0.030 5.00e-02 4.00e+02 ... (remaining 5014 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 515 2.70 - 3.25: 26826 3.25 - 3.80: 41045 3.80 - 4.35: 48313 4.35 - 4.90: 84535 Nonbonded interactions: 201234 Sorted by model distance: nonbonded pdb=" OG1 THR D 194 " pdb=" OE1 GLU D 197 " model vdw 2.155 2.440 nonbonded pdb=" OD2 ASP D 533 " pdb=" OG1 THR D 536 " model vdw 2.220 2.440 nonbonded pdb=" OG SER F 153 " pdb=" OD1 ASP F 155 " model vdw 2.238 2.440 nonbonded pdb=" OG SER C 153 " pdb=" OD1 ASP C 155 " model vdw 2.256 2.440 nonbonded pdb=" OG SER A 261 " pdb=" OE2 GLU F 552 " model vdw 2.264 2.440 ... (remaining 201229 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 65 through 74 or (resid 75 through 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 89 or (resid 90 through \ 99 and (name N or name CA or name C or name O or name CB )) or resid 100 throug \ h 132 or (resid 133 and (name N or name CA or name C or name O or name CB )) or \ resid 134 through 152 or (resid 153 and (name N or name CA or name C or name O o \ r name CB )) or resid 154 through 194 or (resid 195 and (name N or name CA or na \ me C or name O or name CB )) or resid 196 through 207 or (resid 208 and (name N \ or name CA or name C or name O or name CB )) or resid 209 through 224 or (resid \ 225 through 226 and (name N or name CA or name C or name O or name CB )) or resi \ d 227 through 280 or (resid 281 and (name N or name CA or name C or name O or na \ me CB )) or resid 282 through 292 or (resid 293 and (name N or name CA or name C \ or name O or name CB )) or resid 294 or (resid 295 through 296 and (name N or n \ ame CA or name C or name O or name CB )) or resid 297 through 298 or (resid 299 \ and (name N or name CA or name C or name O or name CB )) or resid 300 through 33 \ 6 or (resid 337 and (name N or name CA or name C or name O or name CB )) or resi \ d 338 through 385 or (resid 386 through 387 and (name N or name CA or name C or \ name O or name CB )) or resid 388 through 389 or (resid 390 and (name N or name \ CA or name C or name O or name CB )) or resid 391 through 414 or (resid 415 and \ (name N or name CA or name C or name O or name CB )) or resid 416 through 430 or \ (resid 431 through 432 and (name N or name CA or name C or name O or name CB )) \ or resid 433 through 456 or (resid 457 and (name N or name CA or name C or name \ O or name CB )) or resid 458 through 479 or resid 484 through 491 or (resid 492 \ and (name N or name CA or name C or name O or name CB )) or resid 493 through 4 \ 97 or (resid 498 and (name N or name CA or name C or name O or name CB )) or res \ id 499 through 525 or (resid 526 and (name N or name CA or name C or name O or n \ ame CB )) or resid 527 through 551 or (resid 552 through 553 and (name N or name \ CA or name C or name O or name CB )) or resid 554)) selection = (chain 'B' and (resid 65 or (resid 66 through 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 74 or (resid 75 through 76 and (na \ me N or name CA or name C or name O or name CB )) or resid 77 through 89 or (res \ id 90 through 99 and (name N or name CA or name C or name O or name CB )) or res \ id 100 through 158 or (resid 159 through 160 and (name N or name CA or name C or \ name O or name CB )) or resid 161 through 175 or (resid 176 and (name N or name \ CA or name C or name O or name CB )) or resid 177 through 194 or (resid 195 and \ (name N or name CA or name C or name O or name CB )) or resid 196 through 224 o \ r (resid 225 through 226 and (name N or name CA or name C or name O or name CB ) \ ) or resid 227 through 230 or (resid 231 and (name N or name CA or name C or nam \ e O or name CB )) or resid 232 through 237 or (resid 238 and (name N or name CA \ or name C or name O or name CB )) or resid 239 through 247 or (resid 248 and (na \ me N or name CA or name C or name O or name CB )) or resid 249 through 285 or (r \ esid 286 through 287 and (name N or name CA or name C or name O or name CB )) or \ resid 288 through 290 or (resid 291 through 293 and (name N or name CA or name \ C or name O or name CB )) or resid 294 or (resid 295 through 296 and (name N or \ name CA or name C or name O or name CB )) or resid 297 through 298 or (resid 299 \ and (name N or name CA or name C or name O or name CB )) or resid 300 through 3 \ 21 or (resid 322 and (name N or name CA or name C or name O or name CB )) or res \ id 323 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 or (resid 352 through 354 and (name N or name \ CA or name C or name O or name CB )) or resid 355 through 357 or (resid 358 thr \ ough 359 and (name N or name CA or name C or name O or name CB )) or resid 360 t \ hrough 386 or (resid 387 and (name N or name CA or name C or name O or name CB ) \ ) or resid 388 through 456 or (resid 457 and (name N or name CA or name C or nam \ e O or name CB )) or resid 458 through 476 or (resid 477 and (name N or name CA \ or name C or name O or name CB )) or resid 478 through 479 or resid 484 through \ 486 or (resid 487 and (name N or name CA or name C or name O or name CB )) or re \ sid 488 through 491 or (resid 492 and (name N or name CA or name C or name O or \ name CB )) or resid 493 through 494 or (resid 495 and (name N or name CA or name \ C or name O or name CB )) or resid 496 through 497 or (resid 498 and (name N or \ name CA or name C or name O or name CB )) or resid 499 through 502 or (resid 50 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 504 through \ 514 or (resid 515 and (name N or name CA or name C or name O or name CB )) or re \ sid 516 through 543 or (resid 544 and (name N or name CA or name C or name O or \ name CB )) or resid 545 through 554)) selection = (chain 'C' and (resid 65 or (resid 66 through 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 90 or (resid 91 through 99 and (na \ me N or name CA or name C or name O or name CB )) or resid 100 through 129 or (r \ esid 130 and (name N or name CA or name C or name O or name CB )) or resid 131 t \ hrough 132 or (resid 133 and (name N or name CA or name C or name O or name CB ) \ ) or resid 134 through 143 or (resid 144 and (name N or name CA or name C or nam \ e O or name CB )) or resid 145 through 152 or (resid 153 and (name N or name CA \ or name C or name O or name CB )) or resid 154 or (resid 155 and (name N or name \ CA or name C or name O or name CB )) or resid 156 through 158 or (resid 159 thr \ ough 160 and (name N or name CA or name C or name O or name CB )) or resid 161 t \ hrough 175 or (resid 176 and (name N or name CA or name C or name O or name CB ) \ ) or resid 177 through 190 or (resid 191 and (name N or name CA or name C or nam \ e O or name CB )) or resid 192 through 194 or (resid 195 and (name N or name CA \ or name C or name O or name CB )) or resid 196 through 207 or (resid 208 and (na \ me N or name CA or name C or name O or name CB )) or resid 209 through 219 or (r \ esid 220 and (name N or name CA or name C or name O or name CB )) or resid 221 t \ hrough 230 or (resid 231 and (name N or name CA or name C or name O or name CB ) \ ) or resid 232 through 237 or (resid 238 and (name N or name CA or name C or nam \ e O or name CB )) or resid 239 through 247 or (resid 248 and (name N or name CA \ or name C or name O or name CB )) or resid 249 through 285 or (resid 286 through \ 287 and (name N or name CA or name C or name O or name CB )) or resid 288 throu \ gh 291 or (resid 292 through 293 and (name N or name CA or name C or name O or n \ ame CB )) or resid 294 or (resid 295 through 296 and (name N or name CA or name \ C or name O or name CB )) or resid 297 through 298 or (resid 299 and (name N or \ name CA or name C or name O or name CB )) or resid 300 through 343 or (resid 344 \ and (name N or name CA or name C or name O or name CB )) or resid 345 through 3 \ 47 or (resid 348 through 350 and (name N or name CA or name C or name O or name \ CB )) or resid 351 or (resid 352 through 354 and (name N or name CA or name C or \ name O or name CB )) or resid 355 through 356 or (resid 357 through 359 and (na \ me N or name CA or name C or name O or name CB )) or resid 360 through 374 or (r \ esid 375 and (name N or name CA or name C or name O or name CB )) or resid 376 t \ hrough 384 or (resid 385 through 387 and (name N or name CA or name C or name O \ or name CB )) or resid 388 or (resid 389 through 390 and (name N or name CA or n \ ame C or name O or name CB )) or resid 391 through 411 or (resid 412 through 415 \ and (name N or name CA or name C or name O or name CB )) or resid 416 through 4 \ 30 or (resid 431 through 432 and (name N or name CA or name C or name O or name \ CB )) or resid 433 through 456 or (resid 457 and (name N or name CA or name C or \ name O or name CB )) or resid 458 through 476 or (resid 477 and (name N or name \ CA or name C or name O or name CB )) or resid 478 through 479 or resid 484 thro \ ugh 491 or (resid 492 and (name N or name CA or name C or name O or name CB )) o \ r resid 493 through 494 or (resid 495 and (name N or name CA or name C or name O \ or name CB )) or resid 496 through 497 or (resid 498 and (name N or name CA or \ name C or name O or name CB )) or resid 499 through 502 or (resid 503 and (name \ N or name CA or name C or name O or name CB )) or resid 504 through 514 or (resi \ d 515 and (name N or name CA or name C or name O or name CB )) or resid 516 thro \ ugh 518 or (resid 519 and (name N or name CA or name C or name O or name CB )) o \ r resid 520 through 525 or (resid 526 and (name N or name CA or name C or name O \ or name CB )) or resid 527 through 543 or (resid 544 and (name N or name CA or \ name C or name O or name CB )) or resid 545 through 551 or (resid 552 through 55 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 554)) selection = (chain 'D' and (resid 65 or (resid 66 through 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 70 or (resid 71 and (name N or nam \ e CA or name C or name O or name CB )) or resid 72 through 74 or (resid 75 throu \ gh 76 and (name N or name CA or name C or name O or name CB )) or resid 77 throu \ gh 81 or (resid 82 through 84 and (name N or name CA or name C or name O or name \ CB )) or resid 85 through 86 or (resid 87 through 99 and (name N or name CA or \ name C or name O or name CB )) or resid 100 through 132 or (resid 133 and (name \ N or name CA or name C or name O or name CB )) or resid 134 through 143 or (resi \ d 144 and (name N or name CA or name C or name O or name CB )) or resid 145 thro \ ugh 152 or (resid 153 and (name N or name CA or name C or name O or name CB )) o \ r resid 154 or (resid 155 and (name N or name CA or name C or name O or name CB \ )) or resid 156 through 158 or (resid 159 through 160 and (name N or name CA or \ name C or name O or name CB )) or resid 161 through 175 or (resid 176 and (name \ N or name CA or name C or name O or name CB )) or resid 177 through 194 or (resi \ d 195 and (name N or name CA or name C or name O or name CB )) or resid 196 thro \ ugh 219 or (resid 220 and (name N or name CA or name C or name O or name CB )) o \ r resid 221 through 224 or (resid 225 through 226 and (name N or name CA or name \ C or name O or name CB )) or resid 227 through 230 or (resid 231 and (name N or \ name CA or name C or name O or name CB )) or resid 232 through 237 or (resid 23 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 239 through \ 247 or (resid 248 and (name N or name CA or name C or name O or name CB )) or re \ sid 249 through 280 or (resid 281 and (name N or name CA or name C or name O or \ name CB )) or resid 282 through 285 or (resid 286 through 287 and (name N or nam \ e CA or name C or name O or name CB )) or resid 288 through 291 or (resid 292 th \ rough 293 and (name N or name CA or name C or name O or name CB )) or (resid 294 \ through 296 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 97 through 321 or (resid 322 and (name N or name CA or name C or name O or name \ CB )) or resid 323 through 325 or (resid 326 and (name N or name CA or name C or \ name O or name CB )) or resid 327 through 331 or (resid 332 through 334 and (na \ me N or name CA or name C or name O or name CB )) or resid 335 or (resid 336 thr \ ough 337 and (name N or name CA or name C or name O or name CB )) or resid 338 t \ hrough 340 or (resid 341 and (name N or name CA or name C or name O or name CB ) \ ) or resid 342 through 347 or (resid 348 through 350 and (name N or name CA or n \ ame C or name O or name CB )) or resid 351 or (resid 352 through 354 and (name N \ or name CA or name C or name O or name CB )) or resid 355 through 357 or (resid \ 358 through 359 and (name N or name CA or name C or name O or name CB )) or res \ id 360 through 374 or (resid 375 and (name N or name CA or name C or name O or n \ ame CB )) or resid 376 or (resid 377 and (name N or name CA or name C or name O \ or name CB )) or resid 378 through 384 or (resid 385 through 387 and (name N or \ name CA or name C or name O or name CB )) or resid 388 or (resid 389 through 390 \ and (name N or name CA or name C or name O or name CB )) or resid 391 through 3 \ 98 or (resid 399 and (name N or name CA or name C or name O or name CB )) or res \ id 400 through 413 or (resid 414 through 415 and (name N or name CA or name C or \ name O or name CB )) or resid 416 through 426 or (resid 427 and (name N or name \ CA or name C or name O or name CB )) or resid 428 through 430 or (resid 431 thr \ ough 432 and (name N or name CA or name C or name O or name CB )) or resid 433 t \ hrough 456 or (resid 457 and (name N or name CA or name C or name O or name CB ) \ ) or resid 458 or (resid 459 and (name N or name CA or name C or name O or name \ CB )) or resid 460 through 476 or (resid 477 and (name N or name CA or name C or \ name O or name CB )) or resid 478 through 479 or resid 484 through 514 or (resi \ d 515 and (name N or name CA or name C or name O or name CB )) or resid 516 thro \ ugh 525 or (resid 526 and (name N or name CA or name C or name O or name CB )) o \ r resid 527 through 551 or (resid 552 through 553 and (name N or name CA or name \ C or name O or name CB )) or resid 554)) selection = (chain 'E' and (resid 65 or (resid 66 through 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 74 or (resid 75 through 76 and (na \ me N or name CA or name C or name O or name CB )) or resid 77 through 81 or (res \ id 82 through 84 and (name N or name CA or name C or name O or name CB )) or res \ id 85 through 89 or (resid 90 through 99 and (name N or name CA or name C or nam \ e O or name CB )) or resid 100 through 129 or (resid 130 and (name N or name CA \ or name C or name O or name CB )) or resid 131 through 132 or (resid 133 and (na \ me N or name CA or name C or name O or name CB )) or resid 134 through 143 or (r \ esid 144 and (name N or name CA or name C or name O or name CB )) or resid 145 t \ hrough 152 or (resid 153 and (name N or name CA or name C or name O or name CB ) \ ) or resid 154 through 158 or (resid 159 through 160 and (name N or name CA or n \ ame C or name O or name CB )) or resid 161 through 175 or (resid 176 and (name N \ or name CA or name C or name O or name CB )) or resid 177 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 194 or (resid 195 and (name N or name CA or name C or name O or name CB )) or \ resid 196 through 207 or (resid 208 and (name N or name CA or name C or name O \ or name CB )) or resid 209 through 219 or (resid 220 and (name N or name CA or n \ ame C or name O or name CB )) or resid 221 through 224 or (resid 225 through 226 \ and (name N or name CA or name C or name O or name CB )) or resid 227 through 2 \ 30 or (resid 231 and (name N or name CA or name C or name O or name CB )) or res \ id 232 through 237 or (resid 238 and (name N or name CA or name C or name O or n \ ame CB )) or resid 239 through 247 or (resid 248 and (name N or name CA or name \ C or name O or name CB )) or resid 249 through 280 or (resid 281 and (name N or \ name CA or name C or name O or name CB )) or resid 282 through 290 or (resid 291 \ through 293 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 94 or (resid 295 through 296 and (name N or name CA or name C or name O or name \ CB )) or resid 297 through 298 or (resid 299 and (name N or name CA or name C or \ name O or name CB )) or resid 300 through 321 or (resid 322 and (name N or name \ CA or name C or name O or name CB )) or resid 323 through 336 or (resid 337 and \ (name N or name CA or name C or name O or name CB )) or resid 338 through 347 o \ r (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 354 and (name N or name CA or n \ ame C or name O or name CB )) or resid 355 through 357 or (resid 358 through 359 \ and (name N or name CA or name C or name O or name CB )) or resid 360 through 3 \ 76 or (resid 377 and (name N or name CA or name C or name O or name CB )) or res \ id 378 through 386 or (resid 387 and (name N or name CA or name C or name O or n \ ame CB )) or resid 388 or (resid 389 through 390 and (name N or name CA or name \ C or name O or name CB )) or resid 391 through 426 or (resid 427 and (name N or \ name CA or name C or name O or name CB )) or resid 428 through 430 or (resid 431 \ through 432 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 33 through 471 or (resid 472 and (name N or name CA or name C or name O or name \ CB )) or resid 473 through 476 or (resid 477 and (name N or name CA or name C or \ name O or name CB )) or resid 478 through 479 or resid 484 through 497 or (resi \ d 498 and (name N or name CA or name C or name O or name CB )) or resid 499 thro \ ugh 502 or (resid 503 and (name N or name CA or name C or name O or name CB )) o \ r resid 504 through 514 or (resid 515 and (name N or name CA or name C or name O \ or name CB )) or resid 516 through 518 or (resid 519 and (name N or name CA or \ name C or name O or name CB )) or resid 520 through 525 or (resid 526 and (name \ N or name CA or name C or name O or name CB )) or resid 527 through 551 or (resi \ d 552 through 553 and (name N or name CA or name C or name O or name CB )) or re \ sid 554)) selection = (chain 'F' and (resid 65 or (resid 66 through 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 74 or (resid 75 through 76 and (na \ me N or name CA or name C or name O or name CB )) or resid 77 through 81 or (res \ id 82 through 84 and (name N or name CA or name C or name O or name CB )) or res \ id 85 through 89 or (resid 90 through 99 and (name N or name CA or name C or nam \ e O or name CB )) or resid 100 through 129 or (resid 130 and (name N or name CA \ or name C or name O or name CB )) or resid 131 through 132 or (resid 133 and (na \ me N or name CA or name C or name O or name CB )) or resid 134 through 152 or (r \ esid 153 and (name N or name CA or name C or name O or name CB )) or resid 154 o \ r (resid 155 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 56 through 158 or (resid 159 through 160 and (name N or name CA or name C or nam \ e O or name CB )) or resid 161 through 190 or (resid 191 and (name N or name CA \ or name C or name O or name CB )) or resid 192 through 207 or (resid 208 and (na \ me N or name CA or name C or name O or name CB )) or resid 209 through 219 or (r \ esid 220 and (name N or name CA or name C or name O or name CB )) or resid 221 t \ hrough 224 or (resid 225 through 226 and (name N or name CA or name C or name O \ or name CB )) or resid 227 through 230 or (resid 231 and (name N or name CA or n \ ame C or name O or name CB )) or resid 232 through 237 or (resid 238 and (name N \ or name CA or name C or name O or name CB )) or resid 239 through 247 or (resid \ 248 and (name N or name CA or name C or name O or name CB )) or resid 249 throu \ gh 280 or (resid 281 and (name N or name CA or name C or name O or name CB )) or \ resid 282 through 285 or (resid 286 through 287 and (name N or name CA or name \ C or name O or name CB )) or resid 288 through 290 or (resid 291 through 293 and \ (name N or name CA or name C or name O or name CB )) or resid 294 or (resid 295 \ through 296 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 97 through 298 or (resid 299 and (name N or name CA or name C or name O or name \ CB )) or resid 300 through 321 or (resid 322 and (name N or name CA or name C or \ name O or name CB )) or resid 323 through 325 or (resid 326 and (name N or name \ CA or name C or name O or name CB )) or resid 327 through 332 or (resid 333 thr \ ough 334 and (name N or name CA or name C or name O or name CB )) or (resid 335 \ through 337 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 8 or (resid 339 and (name N or name CA or name C or name O or name CB )) or resi \ d 340 through 343 or (resid 344 and (name N or name CA or name C or name O or na \ me 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 or (resid 352 through 354 and \ (name N or name CA or name C or name O or name CB )) or resid 355 through 356 or \ (resid 357 through 359 and (name N or name CA or name C or name O or name CB )) \ or resid 360 through 376 or (resid 377 and (name N or name CA or name C or name \ O or name CB )) or resid 378 through 386 or (resid 387 and (name N or name CA o \ r name C or name O or name CB )) or resid 388 through 430 or (resid 431 through \ 432 and (name N or name CA or name C or name O or name CB )) or resid 433 throug \ h 456 or (resid 457 and (name N or name CA or name C or name O or name CB )) or \ resid 458 or (resid 459 and (name N or name CA or name C or name O or name CB )) \ or resid 460 through 471 or (resid 472 and (name N or name CA or name C or name \ O or name CB )) or resid 473 through 476 or (resid 477 and (name N or name CA o \ r name C or name O or name CB )) or resid 478 through 479 or resid 484 through 4 \ 97 or (resid 498 and (name N or name CA or name C or name O or name CB )) or res \ id 499 through 502 or (resid 503 and (name N or name CA or name C or name O or n \ ame CB )) or resid 504 through 514 or (resid 515 and (name N or name CA or name \ C or name O or name CB )) or resid 516 through 518 or (resid 519 and (name N or \ name CA or name C or name O or name CB )) or resid 520 through 525 or (resid 526 \ and (name N or name CA or name C or name O or name CB )) or resid 527 through 5 \ 43 or (resid 544 and (name N or name CA or name C or name O or name CB )) or res \ id 545 through 551 or (resid 552 through 553 and (name N or name CA or name C or \ name O or name CB )) or resid 554)) } ncs_group { reference = chain 'I' selection = (chain 'J' and (resid 23 through 228 or resid 237 through 600)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.250 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: 23.980 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 69.820 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.130 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 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 : 0.003 0.050 27631 Z= 0.174 Angle : 0.483 8.994 37682 Z= 0.268 Chirality : 0.042 0.171 4412 Planarity : 0.004 0.114 5017 Dihedral : 11.807 87.758 8835 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.08 % Favored : 95.82 % Rotamer: Outliers : 0.05 % Allowed : 0.14 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: 0.64 (0.14), residues: 4017 helix: 1.88 (0.13), residues: 1730 sheet: -0.15 (0.29), residues: 352 loop : -0.83 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 338 HIS 0.006 0.001 HIS D 315 PHE 0.010 0.001 PHE B 214 TYR 0.021 0.001 TYR E 550 ARG 0.006 0.000 ARG E 476 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8034 Ramachandran restraints generated. 4017 Oldfield, 0 Emsley, 4017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8034 Ramachandran restraints generated. 4017 Oldfield, 0 Emsley, 4017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 3.641 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.3348 time to fit residues: 68.0964 Evaluate side-chains 106 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 3.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 339 optimal weight: 0.6980 chunk 304 optimal weight: 40.0000 chunk 169 optimal weight: 0.8980 chunk 104 optimal weight: 0.0670 chunk 205 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 315 optimal weight: 30.0000 chunk 121 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 234 optimal weight: 0.8980 chunk 365 optimal weight: 10.0000 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN E 421 ASN F 246 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.0716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 27631 Z= 0.146 Angle : 0.443 7.863 37682 Z= 0.238 Chirality : 0.042 0.167 4412 Planarity : 0.004 0.114 5017 Dihedral : 3.432 32.929 4297 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.63 % Favored : 96.32 % Rotamer: Outliers : 0.34 % Allowed : 5.26 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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 (0.14), residues: 4017 helix: 2.13 (0.13), residues: 1738 sheet: -0.13 (0.28), residues: 368 loop : -0.75 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 235 HIS 0.003 0.001 HIS C 114 PHE 0.012 0.001 PHE E 417 TYR 0.012 0.001 TYR D 550 ARG 0.004 0.000 ARG E 476 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8034 Ramachandran restraints generated. 4017 Oldfield, 0 Emsley, 4017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8034 Ramachandran restraints generated. 4017 Oldfield, 0 Emsley, 4017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 110 time to evaluate : 3.347 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 114 average time/residue: 0.3054 time to fit residues: 63.5521 Evaluate side-chains 112 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 3.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain F residue 338 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 202 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 303 optimal weight: 50.0000 chunk 248 optimal weight: 0.0170 chunk 100 optimal weight: 1.9990 chunk 365 optimal weight: 20.0000 chunk 395 optimal weight: 50.0000 chunk 325 optimal weight: 3.9990 chunk 362 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 293 optimal weight: 0.9990 overall best weight: 0.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN B 445 ASN E 285 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 27631 Z= 0.152 Angle : 0.432 8.175 37682 Z= 0.230 Chirality : 0.042 0.168 4412 Planarity : 0.003 0.113 5017 Dihedral : 3.316 33.601 4297 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.66 % Favored : 96.29 % Rotamer: Outliers : 0.48 % Allowed : 6.99 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: 1.04 (0.14), residues: 4017 helix: 2.31 (0.13), residues: 1743 sheet: 0.02 (0.29), residues: 343 loop : -0.73 (0.14), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 442 HIS 0.003 0.001 HIS A 315 PHE 0.008 0.001 PHE A 493 TYR 0.010 0.001 TYR D 539 ARG 0.003 0.000 ARG E 476 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8034 Ramachandran restraints generated. 4017 Oldfield, 0 Emsley, 4017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8034 Ramachandran restraints generated. 4017 Oldfield, 0 Emsley, 4017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 3.364 Fit side-chains REVERT: D 71 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7295 (tm-30) outliers start: 10 outliers final: 3 residues processed: 118 average time/residue: 0.3259 time to fit residues: 69.7161 Evaluate side-chains 112 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 3.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain F residue 338 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 361 optimal weight: 0.0570 chunk 274 optimal weight: 0.8980 chunk 189 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 174 optimal weight: 9.9990 chunk 245 optimal weight: 5.9990 chunk 367 optimal weight: 9.9990 chunk 388 optimal weight: 50.0000 chunk 191 optimal weight: 0.7980 chunk 347 optimal weight: 50.0000 chunk 104 optimal weight: 0.8980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN F 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 27631 Z= 0.139 Angle : 0.421 8.529 37682 Z= 0.223 Chirality : 0.041 0.159 4412 Planarity : 0.003 0.112 5017 Dihedral : 3.266 33.839 4297 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.61 % Favored : 96.34 % Rotamer: Outliers : 0.82 % Allowed : 8.49 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: 1.15 (0.14), residues: 4017 helix: 2.41 (0.13), residues: 1738 sheet: 0.09 (0.29), residues: 353 loop : -0.69 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 442 HIS 0.003 0.001 HIS A 315 PHE 0.009 0.001 PHE D 351 TYR 0.007 0.001 TYR D 539 ARG 0.002 0.000 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8034 Ramachandran restraints generated. 4017 Oldfield, 0 Emsley, 4017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8034 Ramachandran restraints generated. 4017 Oldfield, 0 Emsley, 4017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 3.116 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 129 average time/residue: 0.3106 time to fit residues: 72.2381 Evaluate side-chains 116 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain F residue 338 TRP Chi-restraints excluded: chain F residue 530 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 323 optimal weight: 50.0000 chunk 220 optimal weight: 0.9980 chunk 5 optimal weight: 0.0470 chunk 289 optimal weight: 110.0000 chunk 160 optimal weight: 4.9990 chunk 331 optimal weight: 30.0000 chunk 268 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 198 optimal weight: 0.7980 chunk 348 optimal weight: 5.9990 chunk 98 optimal weight: 0.0470 overall best weight: 1.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN A 114 HIS A 141 GLN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN E 447 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27631 Z= 0.205 Angle : 0.452 8.427 37682 Z= 0.240 Chirality : 0.042 0.160 4412 Planarity : 0.003 0.113 5017 Dihedral : 3.359 33.108 4297 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.16 % Favored : 95.79 % Rotamer: Outliers : 1.16 % Allowed : 9.93 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: 1.08 (0.14), residues: 4017 helix: 2.31 (0.13), residues: 1766 sheet: -0.06 (0.28), residues: 367 loop : -0.70 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 442 HIS 0.003 0.001 HIS A 315 PHE 0.011 0.001 PHE A 493 TYR 0.011 0.001 TYR A 152 ARG 0.002 0.000 ARG C 203 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8034 Ramachandran restraints generated. 4017 Oldfield, 0 Emsley, 4017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8034 Ramachandran restraints generated. 4017 Oldfield, 0 Emsley, 4017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 2.641 Fit side-chains REVERT: F 550 TYR cc_start: 0.9082 (OUTLIER) cc_final: 0.7998 (t80) outliers start: 24 outliers final: 13 residues processed: 129 average time/residue: 0.3408 time to fit residues: 79.2711 Evaluate side-chains 121 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 3.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 550 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 130 optimal weight: 0.9990 chunk 349 optimal weight: 50.0000 chunk 76 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 388 optimal weight: 50.0000 chunk 322 optimal weight: 30.0000 chunk 180 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 128 optimal weight: 0.0570 chunk 204 optimal weight: 4.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 ASN B 114 HIS B 445 ASN D 421 ASN D 445 ASN D 463 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 27631 Z= 0.320 Angle : 0.507 9.682 37682 Z= 0.269 Chirality : 0.044 0.177 4412 Planarity : 0.004 0.114 5017 Dihedral : 3.648 32.619 4297 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.56 % Favored : 95.39 % Rotamer: Outliers : 1.25 % Allowed : 10.51 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: 1.01 (0.14), residues: 4017 helix: 2.27 (0.13), residues: 1761 sheet: -0.24 (0.27), residues: 402 loop : -0.71 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 442 HIS 0.004 0.001 HIS A 139 PHE 0.013 0.001 PHE A 493 TYR 0.015 0.001 TYR A 152 ARG 0.004 0.000 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8034 Ramachandran restraints generated. 4017 Oldfield, 0 Emsley, 4017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8034 Ramachandran restraints generated. 4017 Oldfield, 0 Emsley, 4017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 3.131 Fit side-chains REVERT: E 290 MET cc_start: 0.9031 (mmm) cc_final: 0.8586 (mmm) REVERT: E 552 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: F 550 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.8033 (t80) outliers start: 26 outliers final: 14 residues processed: 129 average time/residue: 0.3059 time to fit residues: 71.1235 Evaluate side-chains 122 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 2.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 552 GLU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 550 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 374 optimal weight: 50.0000 chunk 43 optimal weight: 0.9990 chunk 221 optimal weight: 7.9990 chunk 284 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 327 optimal weight: 50.0000 chunk 217 optimal weight: 3.9990 chunk 387 optimal weight: 50.0000 chunk 242 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 178 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN E 494 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 27631 Z= 0.367 Angle : 0.541 11.063 37682 Z= 0.288 Chirality : 0.045 0.217 4412 Planarity : 0.004 0.114 5017 Dihedral : 3.915 31.774 4297 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.75 % Favored : 95.20 % Rotamer: Outliers : 1.49 % Allowed : 10.80 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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 (0.14), residues: 4017 helix: 2.11 (0.13), residues: 1774 sheet: -0.22 (0.27), residues: 385 loop : -0.77 (0.14), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 338 HIS 0.006 0.001 HIS B 114 PHE 0.015 0.002 PHE C 283 TYR 0.016 0.001 TYR A 152 ARG 0.005 0.000 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8034 Ramachandran restraints generated. 4017 Oldfield, 0 Emsley, 4017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8034 Ramachandran restraints generated. 4017 Oldfield, 0 Emsley, 4017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 105 time to evaluate : 3.188 Fit side-chains REVERT: E 290 MET cc_start: 0.9044 (mmm) cc_final: 0.8553 (mmm) REVERT: E 552 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: F 290 MET cc_start: 0.8949 (mmm) cc_final: 0.8614 (tpp) REVERT: F 550 TYR cc_start: 0.9076 (OUTLIER) cc_final: 0.8133 (t80) outliers start: 31 outliers final: 18 residues processed: 130 average time/residue: 0.3203 time to fit residues: 74.9107 Evaluate side-chains 123 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 2.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 550 TYR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 552 GLU Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 550 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 239 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 246 optimal weight: 2.9990 chunk 263 optimal weight: 0.0980 chunk 191 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 304 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 ASN B 445 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 27631 Z= 0.134 Angle : 0.448 10.736 37682 Z= 0.236 Chirality : 0.042 0.161 4412 Planarity : 0.003 0.110 5017 Dihedral : 3.581 35.103 4297 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.19 % Rotamer: Outliers : 0.96 % Allowed : 11.43 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: 1.09 (0.14), residues: 4017 helix: 2.36 (0.13), residues: 1770 sheet: -0.22 (0.27), residues: 371 loop : -0.71 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 338 HIS 0.004 0.001 HIS A 315 PHE 0.011 0.001 PHE D 351 TYR 0.008 0.001 TYR E 528 ARG 0.003 0.000 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8034 Ramachandran restraints generated. 4017 Oldfield, 0 Emsley, 4017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8034 Ramachandran restraints generated. 4017 Oldfield, 0 Emsley, 4017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 4.155 Fit side-chains REVERT: A 299 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8454 (t80) REVERT: E 290 MET cc_start: 0.9017 (mmm) cc_final: 0.8663 (mmm) REVERT: F 550 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.8226 (t80) outliers start: 20 outliers final: 12 residues processed: 126 average time/residue: 0.3304 time to fit residues: 76.1042 Evaluate side-chains 121 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 3.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 550 TYR Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 550 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 352 optimal weight: 50.0000 chunk 371 optimal weight: 50.0000 chunk 338 optimal weight: 10.0000 chunk 361 optimal weight: 20.0000 chunk 217 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 283 optimal weight: 1.9990 chunk 110 optimal weight: 0.0970 chunk 326 optimal weight: 20.0000 chunk 341 optimal weight: 50.0000 chunk 359 optimal weight: 9.9990 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 541 ASN B 445 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 27631 Z= 0.382 Angle : 0.544 11.619 37682 Z= 0.288 Chirality : 0.045 0.211 4412 Planarity : 0.004 0.112 5017 Dihedral : 3.824 31.622 4297 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.90 % Favored : 95.05 % Rotamer: Outliers : 1.11 % Allowed : 11.86 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: 0.96 (0.14), residues: 4017 helix: 2.23 (0.13), residues: 1767 sheet: -0.38 (0.26), residues: 404 loop : -0.71 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 338 HIS 0.005 0.001 HIS B 114 PHE 0.013 0.001 PHE A 493 TYR 0.016 0.001 TYR A 152 ARG 0.005 0.000 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8034 Ramachandran restraints generated. 4017 Oldfield, 0 Emsley, 4017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8034 Ramachandran restraints generated. 4017 Oldfield, 0 Emsley, 4017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 3.369 Fit side-chains REVERT: A 299 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8653 (t80) REVERT: E 290 MET cc_start: 0.9059 (mmm) cc_final: 0.8663 (mmm) REVERT: E 552 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: F 550 TYR cc_start: 0.9059 (OUTLIER) cc_final: 0.8180 (t80) outliers start: 23 outliers final: 12 residues processed: 126 average time/residue: 0.3501 time to fit residues: 79.7583 Evaluate side-chains 120 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 3.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 550 TYR Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 552 GLU Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 550 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 237 optimal weight: 0.8980 chunk 381 optimal weight: 30.0000 chunk 233 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 265 optimal weight: 0.2980 chunk 400 optimal weight: 4.9990 chunk 368 optimal weight: 8.9990 chunk 318 optimal weight: 40.0000 chunk 33 optimal weight: 5.9990 chunk 246 optimal weight: 2.9990 chunk 195 optimal weight: 0.0060 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 ASN B 445 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27631 Z= 0.176 Angle : 0.465 12.490 37682 Z= 0.245 Chirality : 0.042 0.166 4412 Planarity : 0.004 0.111 5017 Dihedral : 3.629 32.415 4297 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.96 % Favored : 95.99 % Rotamer: Outliers : 0.72 % Allowed : 12.10 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: 1.07 (0.14), residues: 4017 helix: 2.34 (0.13), residues: 1776 sheet: -0.31 (0.27), residues: 386 loop : -0.70 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 442 HIS 0.004 0.001 HIS A 315 PHE 0.011 0.001 PHE D 351 TYR 0.008 0.001 TYR D 439 ARG 0.003 0.000 ARG C 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8034 Ramachandran restraints generated. 4017 Oldfield, 0 Emsley, 4017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8034 Ramachandran restraints generated. 4017 Oldfield, 0 Emsley, 4017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 2.858 Fit side-chains REVERT: A 299 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8538 (t80) REVERT: E 290 MET cc_start: 0.9038 (mmm) cc_final: 0.8716 (mmm) REVERT: F 550 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.8241 (t80) outliers start: 15 outliers final: 11 residues processed: 119 average time/residue: 0.3072 time to fit residues: 66.0244 Evaluate side-chains 121 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 550 TYR Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 550 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 253 optimal weight: 1.9990 chunk 339 optimal weight: 0.0170 chunk 97 optimal weight: 0.9980 chunk 294 optimal weight: 20.0000 chunk 47 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 319 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 327 optimal weight: 50.0000 chunk 40 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 445 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.085060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.054248 restraints weight = 92977.012| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.82 r_work: 0.2777 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 27631 Z= 0.148 Angle : 0.450 12.835 37682 Z= 0.235 Chirality : 0.042 0.168 4412 Planarity : 0.003 0.109 5017 Dihedral : 3.465 33.447 4297 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.93 % Favored : 96.02 % Rotamer: Outliers : 0.72 % Allowed : 12.20 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: 1.17 (0.14), residues: 4017 helix: 2.43 (0.13), residues: 1772 sheet: -0.23 (0.27), residues: 375 loop : -0.66 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 442 HIS 0.003 0.001 HIS B 114 PHE 0.010 0.001 PHE D 351 TYR 0.007 0.001 TYR E 528 ARG 0.003 0.000 ARG C 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5351.40 seconds wall clock time: 97 minutes 34.05 seconds (5854.05 seconds total)