Starting phenix.real_space_refine on Fri Oct 11 19:29:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tms_26001/10_2024/7tms_26001.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tms_26001/10_2024/7tms_26001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tms_26001/10_2024/7tms_26001.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tms_26001/10_2024/7tms_26001.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tms_26001/10_2024/7tms_26001.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tms_26001/10_2024/7tms_26001.cif" } resolution = 3.8 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= 0.078 sd= 1.456 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 232 5.16 5 C 36713 2.51 5 N 9869 2.21 5 O 10836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 113 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 57652 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 4542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4542 Classifications: {'peptide': 593} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 562} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 3677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3677 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 448} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 2, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 4547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4547 Classifications: {'peptide': 593} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 562} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP%COO:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3694 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 448} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 4578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4578 Classifications: {'peptide': 593} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 562} Chain: "F" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3731 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 451} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1325 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PTRANS': 6, 'TRANS': 214} Unresolved non-hydrogen bonds: 440 Unresolved non-hydrogen angles: 545 Unresolved non-hydrogen dihedrals: 347 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 14, 'ASP:plan': 11, 'PHE:plan': 3, 'GLU:plan': 20, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 235 Chain: "H" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 556 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 155 Chain: "I" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1346 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'PTRANS': 6, 'TRANS': 214} Unresolved non-hydrogen bonds: 421 Unresolved non-hydrogen angles: 527 Unresolved non-hydrogen dihedrals: 324 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 14, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 24, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 248 Chain: "J" Number of atoms: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 562 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 1, 'TRANS': 109} Unresolved non-hydrogen bonds: 313 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 148 Chain: "K" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1263 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PTRANS': 6, 'TRANS': 217} Unresolved non-hydrogen bonds: 532 Unresolved non-hydrogen angles: 658 Unresolved non-hydrogen dihedrals: 415 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 1, 'ASN:plan1': 16, 'ASP:plan': 11, 'PHE:plan': 3, 'GLU:plan': 26, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 272 Chain: "L" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 556 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 1, 'TRANS': 109} Unresolved non-hydrogen bonds: 319 Unresolved non-hydrogen angles: 389 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 150 Chain: "M" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1463 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 3, 'TRANS': 219} Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 438 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 209 Chain: "N" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 587 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 109} Unresolved non-hydrogen bonds: 352 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 279 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 9, 'PHE:plan': 6, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 201 Chain: "O" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 1808 Classifications: {'peptide': 357} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 303} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 340} Chain breaks: 1 Unresolved non-hydrogen bonds: 1094 Unresolved non-hydrogen angles: 1400 Unresolved non-hydrogen dihedrals: 900 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 6, 'TYR:plan': 13, 'ASN:plan1': 22, 'TRP:plan': 3, 'ASP:plan': 18, 'PHE:plan': 20, 'GLU:plan': 27, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 600 Chain: "P" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 2229 Classifications: {'peptide': 440} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 394} Link IDs: {'PTRANS': 9, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 1367 Unresolved non-hydrogen angles: 1740 Unresolved non-hydrogen dihedrals: 1101 Unresolved non-hydrogen chiralities: 152 Planarities with less than four sites: {'GLN:plan1': 24, 'ASP:plan': 29, 'TYR:plan': 9, 'ASN:plan1': 23, 'TRP:plan': 4, 'HIS:plan': 10, 'PHE:plan': 16, 'GLU:plan': 32, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 695 Chain: "a" Number of atoms: 5362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5362 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PTRANS': 21, 'TRANS': 712} Chain breaks: 2 Unresolved non-hydrogen bonds: 611 Unresolved non-hydrogen angles: 763 Unresolved non-hydrogen dihedrals: 510 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 8, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 18, 'PHE:plan': 7, 'GLU:plan': 17, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 362 Chain: "b" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 400 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "c" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1464 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 195} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2769 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 333} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "e" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 510 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 60} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "f" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 467 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 60} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "g" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1128 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "h" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "i" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "j" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "k" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1129 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "l" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1131 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "m" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "n" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1130 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1123 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 151} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 25.00, per 1000 atoms: 0.43 Number of scatterers: 57652 At special positions: 0 Unit cell: (142.998, 188.662, 261.963, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 232 16.00 P 2 15.00 O 10836 8.00 N 9869 7.00 C 36713 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.86 Conformation dependent library (CDL) restraints added in 6.3 seconds 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15206 Finding SS restraints... Secondary structure from input PDB file: 299 helices and 38 sheets defined 63.5% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.59 Creating SS restraints... Processing helix chain 'A' and resid 111 through 120 Processing helix chain 'A' and resid 237 through 243 Processing helix chain 'A' and resid 261 through 273 removed outlier: 3.704A pdb=" N ILE A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 297 removed outlier: 3.507A pdb=" N PHE A 297 " --> pdb=" O VAL A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 345 removed outlier: 4.547A pdb=" N ILE A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 372 removed outlier: 3.565A pdb=" N TRP A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 394 removed outlier: 3.542A pdb=" N ARG A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 442 through 448 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 477 through 503 removed outlier: 4.304A pdb=" N GLN A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 507 Processing helix chain 'A' and resid 508 through 525 Processing helix chain 'A' and resid 539 through 563 Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 574 through 585 removed outlier: 4.064A pdb=" N LYS A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 587 No H-bonds generated for 'chain 'A' and resid 586 through 587' Processing helix chain 'A' and resid 588 through 591 Processing helix chain 'A' and resid 592 through 615 Processing helix chain 'B' and resid 105 through 109 removed outlier: 4.285A pdb=" N LEU B 109 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 179 through 191 Processing helix chain 'B' and resid 218 through 232 Processing helix chain 'B' and resid 233 through 236 removed outlier: 3.691A pdb=" N GLU B 236 " --> pdb=" O GLY B 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 233 through 236' Processing helix chain 'B' and resid 248 through 270 Proline residue: B 256 - end of helix Processing helix chain 'B' and resid 280 through 295 Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 307 through 317 removed outlier: 3.600A pdb=" N ASP B 311 " --> pdb=" O TYR B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 354 Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 382 through 386 Processing helix chain 'B' and resid 395 through 418 removed outlier: 4.061A pdb=" N ALA B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 443 removed outlier: 3.712A pdb=" N GLU B 434 " --> pdb=" O LYS B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 466 Processing helix chain 'B' and resid 477 through 485 Processing helix chain 'C' and resid 111 through 119 Processing helix chain 'C' and resid 237 through 244 Processing helix chain 'C' and resid 260 through 272 removed outlier: 4.590A pdb=" N SER C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 294 removed outlier: 3.506A pdb=" N VAL C 293 " --> pdb=" O GLU C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 299 Processing helix chain 'C' and resid 325 through 345 removed outlier: 4.227A pdb=" N ILE C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR C 334 " --> pdb=" O GLU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 372 Processing helix chain 'C' and resid 383 through 393 Processing helix chain 'C' and resid 425 through 433 removed outlier: 3.766A pdb=" N GLY C 433 " --> pdb=" O THR C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 448 removed outlier: 3.531A pdb=" N ARG C 448 " --> pdb=" O LYS C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 475 Processing helix chain 'C' and resid 477 through 503 removed outlier: 4.116A pdb=" N LEU C 501 " --> pdb=" O GLN C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 525 Processing helix chain 'C' and resid 539 through 563 Processing helix chain 'C' and resid 566 through 574 Processing helix chain 'C' and resid 574 through 584 Processing helix chain 'C' and resid 585 through 587 No H-bonds generated for 'chain 'C' and resid 585 through 587' Processing helix chain 'C' and resid 588 through 591 Processing helix chain 'C' and resid 592 through 615 Processing helix chain 'D' and resid 105 through 109 Processing helix chain 'D' and resid 140 through 142 No H-bonds generated for 'chain 'D' and resid 140 through 142' Processing helix chain 'D' and resid 155 through 160 Processing helix chain 'D' and resid 179 through 190 Processing helix chain 'D' and resid 218 through 232 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 249 through 252 Processing helix chain 'D' and resid 253 through 269 removed outlier: 4.337A pdb=" N ARG D 257 " --> pdb=" O ILE D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 295 Processing helix chain 'D' and resid 300 through 304 removed outlier: 3.629A pdb=" N GLY D 303 " --> pdb=" O GLY D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 306 No H-bonds generated for 'chain 'D' and resid 305 through 306' Processing helix chain 'D' and resid 307 through 317 Processing helix chain 'D' and resid 344 through 354 removed outlier: 3.694A pdb=" N ILE D 353 " --> pdb=" O LEU D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 367 Processing helix chain 'D' and resid 382 through 386 removed outlier: 3.704A pdb=" N SER D 385 " --> pdb=" O LEU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 421 Processing helix chain 'D' and resid 426 through 443 Processing helix chain 'D' and resid 453 through 466 Processing helix chain 'D' and resid 467 through 468 No H-bonds generated for 'chain 'D' and resid 467 through 468' Processing helix chain 'D' and resid 469 through 473 Processing helix chain 'D' and resid 477 through 485 Processing helix chain 'E' and resid 111 through 119 Processing helix chain 'E' and resid 237 through 243 Processing helix chain 'E' and resid 261 through 273 Processing helix chain 'E' and resid 286 through 297 removed outlier: 4.059A pdb=" N MET E 290 " --> pdb=" O ARG E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 345 removed outlier: 3.710A pdb=" N GLU E 330 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 372 removed outlier: 3.787A pdb=" N TRP E 360 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 393 Processing helix chain 'E' and resid 418 through 422 removed outlier: 3.735A pdb=" N ASP E 422 " --> pdb=" O ALA E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 433 removed outlier: 3.539A pdb=" N GLY E 433 " --> pdb=" O THR E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 448 Processing helix chain 'E' and resid 467 through 475 removed outlier: 3.516A pdb=" N SER E 473 " --> pdb=" O LYS E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 503 Processing helix chain 'E' and resid 508 through 525 Processing helix chain 'E' and resid 539 through 563 Processing helix chain 'E' and resid 566 through 574 removed outlier: 3.763A pdb=" N ASP E 572 " --> pdb=" O SER E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 584 removed outlier: 3.732A pdb=" N LYS E 578 " --> pdb=" O THR E 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 587 No H-bonds generated for 'chain 'E' and resid 585 through 587' Processing helix chain 'E' and resid 588 through 591 Processing helix chain 'E' and resid 592 through 615 removed outlier: 3.623A pdb=" N THR E 615 " --> pdb=" O PHE E 611 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 16 Processing helix chain 'F' and resid 105 through 109 Processing helix chain 'F' and resid 155 through 160 Processing helix chain 'F' and resid 179 through 191 Processing helix chain 'F' and resid 218 through 232 Processing helix chain 'F' and resid 233 through 237 removed outlier: 3.933A pdb=" N GLU F 236 " --> pdb=" O GLY F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 252 Processing helix chain 'F' and resid 253 through 269 removed outlier: 4.062A pdb=" N ARG F 257 " --> pdb=" O ILE F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 296 Processing helix chain 'F' and resid 307 through 317 Processing helix chain 'F' and resid 344 through 354 Processing helix chain 'F' and resid 361 through 367 Processing helix chain 'F' and resid 382 through 387 removed outlier: 3.610A pdb=" N ALA F 386 " --> pdb=" O LEU F 382 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE F 387 " --> pdb=" O MET F 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 382 through 387' Processing helix chain 'F' and resid 395 through 421 removed outlier: 3.725A pdb=" N VAL F 419 " --> pdb=" O ALA F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 443 Processing helix chain 'F' and resid 453 through 466 Processing helix chain 'F' and resid 467 through 468 No H-bonds generated for 'chain 'F' and resid 467 through 468' Processing helix chain 'F' and resid 469 through 473 Processing helix chain 'F' and resid 477 through 485 removed outlier: 3.592A pdb=" N GLU F 483 " --> pdb=" O LYS F 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 16 Processing helix chain 'G' and resid 18 through 113 Processing helix chain 'G' and resid 113 through 133 Proline residue: G 119 - end of helix Processing helix chain 'G' and resid 145 through 164 removed outlier: 4.902A pdb=" N ASP G 154 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ASP G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA G 164 " --> pdb=" O TYR G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 214 Processing helix chain 'G' and resid 214 through 224 Processing helix chain 'H' and resid 3 through 104 removed outlier: 3.662A pdb=" N LYS H 70 " --> pdb=" O GLY H 66 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASP H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASP H 93 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 113 Processing helix chain 'I' and resid 113 through 133 Proline residue: I 119 - end of helix Processing helix chain 'I' and resid 145 through 152 Processing helix chain 'I' and resid 152 through 164 Processing helix chain 'I' and resid 203 through 214 Processing helix chain 'I' and resid 214 through 223 Processing helix chain 'J' and resid 3 through 103 removed outlier: 4.306A pdb=" N GLY J 66 " --> pdb=" O ALA J 62 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU J 67 " --> pdb=" O GLY J 63 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASP J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ASP J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 67 removed outlier: 4.332A pdb=" N LYS K 26 " --> pdb=" O ALA K 22 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU K 27 " --> pdb=" O PHE K 23 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER K 64 " --> pdb=" O GLY K 60 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LYS K 65 " --> pdb=" O ASN K 61 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS K 67 " --> pdb=" O LYS K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 113 removed outlier: 4.244A pdb=" N GLN K 73 " --> pdb=" O ALA K 69 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN K 74 " --> pdb=" O MET K 70 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE K 75 " --> pdb=" O LEU K 71 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR K 76 " --> pdb=" O SER K 72 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN K 113 " --> pdb=" O GLY K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 133 Proline residue: K 119 - end of helix Processing helix chain 'K' and resid 145 through 164 removed outlier: 3.774A pdb=" N ILE K 149 " --> pdb=" O ASP K 145 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU K 150 " --> pdb=" O VAL K 146 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ASP K 154 " --> pdb=" O GLU K 150 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ASP K 155 " --> pdb=" O SER K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 214 Processing helix chain 'K' and resid 214 through 223 Processing helix chain 'L' and resid 3 through 104 removed outlier: 3.686A pdb=" N LYS L 70 " --> pdb=" O GLY L 66 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ASP L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASP L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 75 removed outlier: 4.240A pdb=" N GLN M 55 " --> pdb=" O ASP M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 85 Processing helix chain 'M' and resid 118 through 122 removed outlier: 3.849A pdb=" N ARG M 121 " --> pdb=" O ASN M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 172 removed outlier: 4.419A pdb=" N GLN M 130 " --> pdb=" O GLY M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 172 through 224 Proline residue: M 179 - end of helix removed outlier: 4.135A pdb=" N SER M 190 " --> pdb=" O ALA M 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 24 Processing helix chain 'N' and resid 46 through 59 Processing helix chain 'N' and resid 73 through 78 Processing helix chain 'N' and resid 79 through 84 removed outlier: 3.931A pdb=" N PHE N 84 " --> pdb=" O ARG N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 116 removed outlier: 3.525A pdb=" N PHE N 116 " --> pdb=" O VAL N 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 36 Processing helix chain 'O' and resid 57 through 90 Processing helix chain 'O' and resid 90 through 95 Processing helix chain 'O' and resid 96 through 100 removed outlier: 3.945A pdb=" N LEU O 100 " --> pdb=" O TYR O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 112 Processing helix chain 'O' and resid 126 through 165 removed outlier: 3.736A pdb=" N LYS O 165 " --> pdb=" O ALA O 161 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 212 removed outlier: 3.778A pdb=" N GLU O 211 " --> pdb=" O GLU O 207 " (cutoff:3.500A) Processing helix chain 'O' and resid 213 through 217 Processing helix chain 'O' and resid 239 through 241 No H-bonds generated for 'chain 'O' and resid 239 through 241' Processing helix chain 'O' and resid 242 through 252 Processing helix chain 'O' and resid 263 through 316 removed outlier: 3.861A pdb=" N HIS O 274 " --> pdb=" O LEU O 270 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP O 275 " --> pdb=" O LYS O 271 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG O 290 " --> pdb=" O VAL O 286 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL O 297 " --> pdb=" O LYS O 293 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE O 300 " --> pdb=" O TYR O 296 " (cutoff:3.500A) Processing helix chain 'O' and resid 336 through 347 Processing helix chain 'P' and resid 6 through 10 removed outlier: 4.014A pdb=" N SER P 10 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 23 removed outlier: 4.553A pdb=" N ARG P 17 " --> pdb=" O PHE P 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 27 through 33 removed outlier: 3.513A pdb=" N ARG P 32 " --> pdb=" O ASP P 28 " (cutoff:3.500A) Processing helix chain 'P' and resid 37 through 48 Processing helix chain 'P' and resid 76 through 87 removed outlier: 3.564A pdb=" N ILE P 81 " --> pdb=" O LEU P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 106 Processing helix chain 'P' and resid 109 through 119 removed outlier: 4.109A pdb=" N PHE P 117 " --> pdb=" O THR P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 120 through 122 No H-bonds generated for 'chain 'P' and resid 120 through 122' Processing helix chain 'P' and resid 123 through 132 Processing helix chain 'P' and resid 135 through 152 removed outlier: 3.808A pdb=" N LEU P 140 " --> pdb=" O PHE P 136 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE P 141 " --> pdb=" O GLN P 137 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN P 145 " --> pdb=" O ILE P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 166 Processing helix chain 'P' and resid 167 through 176 Processing helix chain 'P' and resid 179 through 194 removed outlier: 4.302A pdb=" N VAL P 185 " --> pdb=" O ASP P 181 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU P 189 " --> pdb=" O VAL P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 196 No H-bonds generated for 'chain 'P' and resid 195 through 196' Processing helix chain 'P' and resid 197 through 198 No H-bonds generated for 'chain 'P' and resid 197 through 198' Processing helix chain 'P' and resid 199 through 206 Processing helix chain 'P' and resid 207 through 209 No H-bonds generated for 'chain 'P' and resid 207 through 209' Processing helix chain 'P' and resid 210 through 221 removed outlier: 3.512A pdb=" N ALA P 221 " --> pdb=" O ILE P 217 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 255 Processing helix chain 'P' and resid 256 through 267 removed outlier: 3.773A pdb=" N GLU P 262 " --> pdb=" O VAL P 258 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR P 267 " --> pdb=" O LEU P 263 " (cutoff:3.500A) Processing helix chain 'P' and resid 267 through 281 removed outlier: 4.363A pdb=" N LEU P 275 " --> pdb=" O PHE P 271 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS P 276 " --> pdb=" O LEU P 272 " (cutoff:3.500A) Processing helix chain 'P' and resid 283 through 298 Processing helix chain 'P' and resid 307 through 315 Processing helix chain 'P' and resid 318 through 328 Processing helix chain 'P' and resid 332 through 350 Processing helix chain 'P' and resid 350 through 355 removed outlier: 4.172A pdb=" N THR P 354 " --> pdb=" O TYR P 350 " (cutoff:3.500A) Processing helix chain 'P' and resid 355 through 365 Processing helix chain 'P' and resid 371 through 374 Processing helix chain 'P' and resid 375 through 380 Processing helix chain 'P' and resid 382 through 408 removed outlier: 4.000A pdb=" N GLU P 386 " --> pdb=" O ASP P 382 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP P 390 " --> pdb=" O GLU P 386 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ASN P 391 " --> pdb=" O PHE P 387 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE P 394 " --> pdb=" O ASP P 390 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE P 395 " --> pdb=" O ASN P 391 " (cutoff:3.500A) Processing helix chain 'P' and resid 413 through 434 Processing helix chain 'P' and resid 436 through 444 removed outlier: 4.167A pdb=" N VAL P 440 " --> pdb=" O GLU P 436 " (cutoff:3.500A) Processing helix chain 'P' and resid 445 through 454 removed outlier: 3.676A pdb=" N MET P 451 " --> pdb=" O LYS P 447 " (cutoff:3.500A) Processing helix chain 'P' and resid 458 through 477 Processing helix chain 'a' and resid 25 through 36 Processing helix chain 'a' and resid 55 through 79 Processing helix chain 'a' and resid 85 through 96 removed outlier: 3.776A pdb=" N ASP a 89 " --> pdb=" O GLU a 85 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS a 90 " --> pdb=" O GLY a 86 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU a 92 " --> pdb=" O THR a 88 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER a 95 " --> pdb=" O TYR a 91 " (cutoff:3.500A) Processing helix chain 'a' and resid 105 through 144 removed outlier: 3.742A pdb=" N GLN a 140 " --> pdb=" O ASN a 136 " (cutoff:3.500A) Processing helix chain 'a' and resid 192 through 194 No H-bonds generated for 'chain 'a' and resid 192 through 194' Processing helix chain 'a' and resid 195 through 207 removed outlier: 3.728A pdb=" N LEU a 207 " --> pdb=" O LEU a 203 " (cutoff:3.500A) Processing helix chain 'a' and resid 242 through 256 Processing helix chain 'a' and resid 266 through 325 removed outlier: 3.727A pdb=" N ASP a 283 " --> pdb=" O LYS a 279 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS a 304 " --> pdb=" O TYR a 300 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU a 305 " --> pdb=" O ALA a 301 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP a 307 " --> pdb=" O ALA a 303 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER a 308 " --> pdb=" O LYS a 304 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN a 311 " --> pdb=" O ASP a 307 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG a 315 " --> pdb=" O GLN a 311 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU a 316 " --> pdb=" O ASP a 312 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS a 317 " --> pdb=" O VAL a 313 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA a 318 " --> pdb=" O THR a 314 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS a 325 " --> pdb=" O GLU a 321 " (cutoff:3.500A) Processing helix chain 'a' and resid 345 through 361 Processing helix chain 'a' and resid 387 through 398 removed outlier: 4.291A pdb=" N TYR a 397 " --> pdb=" O ILE a 393 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY a 398 " --> pdb=" O CYS a 394 " (cutoff:3.500A) Processing helix chain 'a' and resid 407 through 424 removed outlier: 4.301A pdb=" N VAL a 413 " --> pdb=" O LEU a 409 " (cutoff:3.500A) Proline residue: a 416 - end of helix Processing helix chain 'a' and resid 425 through 442 removed outlier: 3.508A pdb=" N GLY a 429 " --> pdb=" O ASP a 425 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU a 439 " --> pdb=" O ALA a 435 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN a 442 " --> pdb=" O SER a 438 " (cutoff:3.500A) Processing helix chain 'a' and resid 442 through 448 removed outlier: 4.129A pdb=" N LYS a 448 " --> pdb=" O LYS a 444 " (cutoff:3.500A) Processing helix chain 'a' and resid 455 through 460 removed outlier: 3.506A pdb=" N THR a 460 " --> pdb=" O MET a 457 " (cutoff:3.500A) Processing helix chain 'a' and resid 461 through 480 Processing helix chain 'a' and resid 519 through 523 Processing helix chain 'a' and resid 527 through 562 removed outlier: 3.681A pdb=" N PHE a 554 " --> pdb=" O TYR a 550 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER a 555 " --> pdb=" O SER a 551 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU a 556 " --> pdb=" O TYR a 552 " (cutoff:3.500A) Processing helix chain 'a' and resid 565 through 596 removed outlier: 4.979A pdb=" N ILE a 573 " --> pdb=" O ILE a 569 " (cutoff:3.500A) Proline residue: a 574 - end of helix removed outlier: 4.614A pdb=" N TYR a 585 " --> pdb=" O GLY a 581 " (cutoff:3.500A) Processing helix chain 'a' and resid 597 through 602 Processing helix chain 'a' and resid 610 through 616 Processing helix chain 'a' and resid 629 through 651 removed outlier: 3.994A pdb=" N GLN a 634 " --> pdb=" O GLN a 630 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N VAL a 635 " --> pdb=" O ALA a 631 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N PHE a 636 " --> pdb=" O LYS a 632 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU a 637 " --> pdb=" O VAL a 633 " (cutoff:3.500A) Proline residue: a 646 - end of helix Processing helix chain 'a' and resid 710 through 733 removed outlier: 3.638A pdb=" N ILE a 717 " --> pdb=" O ILE a 713 " (cutoff:3.500A) Processing helix chain 'a' and resid 733 through 755 removed outlier: 4.560A pdb=" N TRP a 737 " --> pdb=" O TYR a 733 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE a 755 " --> pdb=" O TRP a 751 " (cutoff:3.500A) Processing helix chain 'a' and resid 763 through 803 Processing helix chain 'a' and resid 805 through 810 removed outlier: 4.027A pdb=" N PHE a 809 " --> pdb=" O SER a 805 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 245 Processing helix chain 'b' and resid 250 through 255 Processing helix chain 'c' and resid 17 through 40 Processing helix chain 'c' and resid 46 through 54 Processing helix chain 'c' and resid 55 through 93 removed outlier: 3.844A pdb=" N TRP c 59 " --> pdb=" O SER c 55 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL c 68 " --> pdb=" O ILE c 64 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER c 85 " --> pdb=" O ILE c 81 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG c 92 " --> pdb=" O GLY c 88 " (cutoff:3.500A) Processing helix chain 'c' and resid 95 through 123 removed outlier: 4.638A pdb=" N LYS c 99 " --> pdb=" O ARG c 95 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE c 102 " --> pdb=" O THR c 98 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N SER c 103 " --> pdb=" O LYS c 99 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE c 104 " --> pdb=" O ASN c 100 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL c 110 " --> pdb=" O PHE c 106 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA c 111 " --> pdb=" O CYS c 107 " (cutoff:3.500A) Processing helix chain 'c' and resid 135 through 177 Processing helix chain 'c' and resid 177 through 208 removed outlier: 3.617A pdb=" N PHE c 181 " --> pdb=" O ASP c 177 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL c 182 " --> pdb=" O SER c 178 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL c 186 " --> pdb=" O VAL c 182 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE c 187 " --> pdb=" O LYS c 183 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU c 188 " --> pdb=" O ILE c 184 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU c 194 " --> pdb=" O PHE c 190 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY c 195 " --> pdb=" O GLY c 191 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS c 208 " --> pdb=" O LEU c 204 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 9 removed outlier: 3.938A pdb=" N ASP d 9 " --> pdb=" O PHE d 6 " (cutoff:3.500A) Processing helix chain 'd' and resid 10 through 23 Processing helix chain 'd' and resid 26 through 35 Processing helix chain 'd' and resid 38 through 48 removed outlier: 4.024A pdb=" N SER d 48 " --> pdb=" O LEU d 44 " (cutoff:3.500A) Processing helix chain 'd' and resid 51 through 56 removed outlier: 4.639A pdb=" N LEU d 55 " --> pdb=" O GLY d 52 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 86 Processing helix chain 'd' and resid 89 through 112 removed outlier: 3.830A pdb=" N GLY d 101 " --> pdb=" O TYR d 97 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR d 102 " --> pdb=" O ILE d 98 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR d 112 " --> pdb=" O ALA d 108 " (cutoff:3.500A) Processing helix chain 'd' and resid 120 through 127 Processing helix chain 'd' and resid 128 through 132 removed outlier: 3.619A pdb=" N GLY d 131 " --> pdb=" O HIS d 128 " (cutoff:3.500A) Processing helix chain 'd' and resid 135 through 141 Processing helix chain 'd' and resid 144 through 153 Processing helix chain 'd' and resid 158 through 166 Processing helix chain 'd' and resid 179 through 200 Processing helix chain 'd' and resid 203 through 227 removed outlier: 4.208A pdb=" N THR d 210 " --> pdb=" O GLU d 206 " (cutoff:3.500A) Processing helix chain 'd' and resid 234 through 242 Processing helix chain 'd' and resid 252 through 259 Processing helix chain 'd' and resid 261 through 270 Processing helix chain 'd' and resid 271 through 276 removed outlier: 6.585A pdb=" N GLU d 274 " --> pdb=" O ASN d 271 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR d 275 " --> pdb=" O VAL d 272 " (cutoff:3.500A) Processing helix chain 'd' and resid 283 through 302 removed outlier: 3.660A pdb=" N HIS d 287 " --> pdb=" O ASN d 283 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN d 302 " --> pdb=" O ASP d 298 " (cutoff:3.500A) Processing helix chain 'd' and resid 306 through 332 removed outlier: 4.413A pdb=" N TRP d 310 " --> pdb=" O ILE d 306 " (cutoff:3.500A) Processing helix chain 'd' and resid 334 through 341 removed outlier: 3.559A pdb=" N ARG d 337 " --> pdb=" O GLN d 334 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASN d 339 " --> pdb=" O GLU d 336 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN d 340 " --> pdb=" O ARG d 337 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR d 341 " --> pdb=" O ILE d 338 " (cutoff:3.500A) Processing helix chain 'e' and resid 6 through 24 Processing helix chain 'e' and resid 29 through 54 removed outlier: 3.967A pdb=" N TRP e 33 " --> pdb=" O ASN e 29 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE e 38 " --> pdb=" O ARG e 34 " (cutoff:3.500A) Processing helix chain 'f' and resid 12 through 33 removed outlier: 3.833A pdb=" N LEU f 16 " --> pdb=" O CYS f 12 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU f 24 " --> pdb=" O GLY f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 47 through 70 removed outlier: 3.607A pdb=" N THR f 54 " --> pdb=" O ALA f 50 " (cutoff:3.500A) Processing helix chain 'f' and resid 71 through 73 No H-bonds generated for 'chain 'f' and resid 71 through 73' Processing helix chain 'g' and resid 8 through 44 removed outlier: 4.227A pdb=" N PHE g 12 " --> pdb=" O TYR g 8 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY g 13 " --> pdb=" O ALA g 9 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE g 21 " --> pdb=" O CYS g 17 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR g 24 " --> pdb=" O ALA g 20 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL g 44 " --> pdb=" O CYS g 40 " (cutoff:3.500A) Processing helix chain 'g' and resid 46 through 48 No H-bonds generated for 'chain 'g' and resid 46 through 48' Processing helix chain 'g' and resid 49 through 54 removed outlier: 3.562A pdb=" N ILE g 54 " --> pdb=" O LEU g 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 54 through 76 Processing helix chain 'g' and resid 83 through 122 removed outlier: 3.891A pdb=" N GLN g 121 " --> pdb=" O ARG g 117 " (cutoff:3.500A) Processing helix chain 'g' and resid 124 through 155 removed outlier: 3.894A pdb=" N GLY g 128 " --> pdb=" O ARG g 124 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY g 140 " --> pdb=" O ALA g 136 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY g 143 " --> pdb=" O LEU g 139 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR g 155 " --> pdb=" O ASN g 151 " (cutoff:3.500A) Processing helix chain 'h' and resid 8 through 43 removed outlier: 3.857A pdb=" N PHE h 12 " --> pdb=" O TYR h 8 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE h 21 " --> pdb=" O CYS h 17 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR h 24 " --> pdb=" O ALA h 20 " (cutoff:3.500A) Processing helix chain 'h' and resid 46 through 53 removed outlier: 4.651A pdb=" N PHE h 51 " --> pdb=" O ASP h 48 " (cutoff:3.500A) Processing helix chain 'h' and resid 54 through 78 removed outlier: 3.557A pdb=" N TYR h 76 " --> pdb=" O VAL h 72 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER h 77 " --> pdb=" O LEU h 73 " (cutoff:3.500A) Processing helix chain 'h' and resid 83 through 120 Processing helix chain 'h' and resid 124 through 154 removed outlier: 4.376A pdb=" N GLY h 128 " --> pdb=" O ARG h 124 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU h 139 " --> pdb=" O PHE h 135 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY h 140 " --> pdb=" O ALA h 136 " (cutoff:3.500A) Processing helix chain 'i' and resid 8 through 44 removed outlier: 4.215A pdb=" N PHE i 12 " --> pdb=" O TYR i 8 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY i 13 " --> pdb=" O ALA i 9 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE i 21 " --> pdb=" O CYS i 17 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR i 24 " --> pdb=" O ALA i 20 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL i 44 " --> pdb=" O CYS i 40 " (cutoff:3.500A) Processing helix chain 'i' and resid 46 through 53 removed outlier: 4.640A pdb=" N PHE i 51 " --> pdb=" O ASP i 48 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS i 52 " --> pdb=" O LEU i 49 " (cutoff:3.500A) Processing helix chain 'i' and resid 54 through 76 Processing helix chain 'i' and resid 83 through 120 removed outlier: 3.597A pdb=" N SER i 120 " --> pdb=" O VAL i 116 " (cutoff:3.500A) Processing helix chain 'i' and resid 121 through 123 No H-bonds generated for 'chain 'i' and resid 121 through 123' Processing helix chain 'i' and resid 124 through 154 removed outlier: 4.599A pdb=" N GLY i 128 " --> pdb=" O ARG i 124 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU i 139 " --> pdb=" O PHE i 135 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY i 140 " --> pdb=" O ALA i 136 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 44 removed outlier: 4.399A pdb=" N PHE j 12 " --> pdb=" O TYR j 8 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY j 13 " --> pdb=" O ALA j 9 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE j 21 " --> pdb=" O CYS j 17 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR j 24 " --> pdb=" O ALA j 20 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL j 44 " --> pdb=" O CYS j 40 " (cutoff:3.500A) Processing helix chain 'j' and resid 46 through 48 No H-bonds generated for 'chain 'j' and resid 46 through 48' Processing helix chain 'j' and resid 49 through 54 Processing helix chain 'j' and resid 54 through 78 removed outlier: 3.503A pdb=" N ILE j 58 " --> pdb=" O ILE j 54 " (cutoff:3.500A) Processing helix chain 'j' and resid 83 through 120 Processing helix chain 'j' and resid 124 through 154 removed outlier: 4.529A pdb=" N GLY j 128 " --> pdb=" O ARG j 124 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LEU j 139 " --> pdb=" O PHE j 135 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY j 140 " --> pdb=" O ALA j 136 " (cutoff:3.500A) Processing helix chain 'k' and resid 9 through 44 removed outlier: 4.175A pdb=" N GLY k 13 " --> pdb=" O ALA k 9 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE k 21 " --> pdb=" O CYS k 17 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR k 24 " --> pdb=" O ALA k 20 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 52 removed outlier: 4.228A pdb=" N PHE k 51 " --> pdb=" O ASP k 48 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 77 removed outlier: 3.534A pdb=" N TYR k 76 " --> pdb=" O VAL k 72 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER k 77 " --> pdb=" O LEU k 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 83 through 122 removed outlier: 3.853A pdb=" N SER k 120 " --> pdb=" O VAL k 116 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLN k 121 " --> pdb=" O ARG k 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 125 through 156 removed outlier: 4.755A pdb=" N LEU k 139 " --> pdb=" O PHE k 135 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLY k 140 " --> pdb=" O ALA k 136 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR k 155 " --> pdb=" O ASN k 151 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLN k 156 " --> pdb=" O SER k 152 " (cutoff:3.500A) Processing helix chain 'l' and resid 8 through 44 removed outlier: 4.268A pdb=" N PHE l 12 " --> pdb=" O TYR l 8 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY l 13 " --> pdb=" O ALA l 9 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE l 21 " --> pdb=" O CYS l 17 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL l 44 " --> pdb=" O CYS l 40 " (cutoff:3.500A) Processing helix chain 'l' and resid 49 through 54 Processing helix chain 'l' and resid 54 through 77 removed outlier: 3.716A pdb=" N ILE l 58 " --> pdb=" O ILE l 54 " (cutoff:3.500A) Processing helix chain 'l' and resid 83 through 122 removed outlier: 4.085A pdb=" N GLN l 121 " --> pdb=" O ARG l 117 " (cutoff:3.500A) Processing helix chain 'l' and resid 124 through 155 removed outlier: 4.226A pdb=" N GLY l 128 " --> pdb=" O ARG l 124 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU l 139 " --> pdb=" O PHE l 135 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY l 140 " --> pdb=" O ALA l 136 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG l 153 " --> pdb=" O LEU l 149 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR l 155 " --> pdb=" O ASN l 151 " (cutoff:3.500A) Processing helix chain 'm' and resid 8 through 46 removed outlier: 4.421A pdb=" N PHE m 12 " --> pdb=" O TYR m 8 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY m 13 " --> pdb=" O ALA m 9 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE m 21 " --> pdb=" O CYS m 17 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR m 24 " --> pdb=" O ALA m 20 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU m 45 " --> pdb=" O ALA m 41 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 54 Processing helix chain 'm' and resid 54 through 76 removed outlier: 4.065A pdb=" N ILE m 63 " --> pdb=" O MET m 59 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA m 64 " --> pdb=" O ALA m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 83 through 122 removed outlier: 3.906A pdb=" N GLN m 121 " --> pdb=" O ARG m 117 " (cutoff:3.500A) Processing helix chain 'm' and resid 125 through 153 removed outlier: 3.702A pdb=" N GLY m 140 " --> pdb=" O ALA m 136 " (cutoff:3.500A) Processing helix chain 'm' and resid 154 through 156 No H-bonds generated for 'chain 'm' and resid 154 through 156' Processing helix chain 'n' and resid 9 through 43 removed outlier: 3.887A pdb=" N GLY n 13 " --> pdb=" O ALA n 9 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE n 21 " --> pdb=" O CYS n 17 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR n 24 " --> pdb=" O ALA n 20 " (cutoff:3.500A) Processing helix chain 'n' and resid 49 through 54 Processing helix chain 'n' and resid 54 through 78 removed outlier: 3.505A pdb=" N ILE n 58 " --> pdb=" O ILE n 54 " (cutoff:3.500A) Processing helix chain 'n' and resid 83 through 122 removed outlier: 3.556A pdb=" N GLN n 121 " --> pdb=" O ARG n 117 " (cutoff:3.500A) Processing helix chain 'n' and resid 124 through 154 removed outlier: 4.288A pdb=" N GLY n 128 " --> pdb=" O ARG n 124 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY n 140 " --> pdb=" O ALA n 136 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 50 removed outlier: 3.758A pdb=" N PHE o 18 " --> pdb=" O TYR o 14 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR o 50 " --> pdb=" O ALA o 46 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 60 Processing helix chain 'o' and resid 60 through 83 removed outlier: 3.581A pdb=" N VAL o 64 " --> pdb=" O LEU o 60 " (cutoff:3.500A) Processing helix chain 'o' and resid 91 through 128 removed outlier: 3.673A pdb=" N MET o 128 " --> pdb=" O VAL o 124 " (cutoff:3.500A) Processing helix chain 'o' and resid 130 through 132 No H-bonds generated for 'chain 'o' and resid 130 through 132' Processing helix chain 'o' and resid 133 through 164 removed outlier: 4.376A pdb=" N LEU o 147 " --> pdb=" O PHE o 143 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY o 148 " --> pdb=" O SER o 144 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY o 151 " --> pdb=" O LEU o 147 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 31 removed outlier: 3.965A pdb=" N ILE A 36 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL A 30 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 34 through 38 current: chain 'A' and resid 56 through 64 removed outlier: 6.328A pdb=" N THR A 69 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE A 63 " --> pdb=" O LYS A 67 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYS A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 67 through 72 current: chain 'B' and resid 38 through 41 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 41 current: chain 'B' and resid 62 through 71 removed outlier: 6.358A pdb=" N ILE B 76 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE B 70 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ARG B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 74 through 79 current: chain 'C' and resid 34 through 38 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 34 through 38 current: chain 'C' and resid 56 through 63 removed outlier: 6.376A pdb=" N THR C 69 " --> pdb=" O ILE C 61 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 72 current: chain 'D' and resid 38 through 41 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 38 through 41 current: chain 'D' and resid 62 through 71 removed outlier: 6.501A pdb=" N ILE D 76 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE D 70 " --> pdb=" O ARG D 74 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 74 through 79 current: chain 'E' and resid 34 through 38 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 34 through 38 current: chain 'E' and resid 56 through 64 removed outlier: 6.137A pdb=" N VAL E 60 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN E 71 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG E 62 " --> pdb=" O THR E 69 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 67 through 72 current: chain 'F' and resid 38 through 41 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 38 through 41 current: chain 'F' and resid 62 through 71 removed outlier: 5.306A pdb=" N VAL F 67 " --> pdb=" O GLN F 78 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN F 78 " --> pdb=" O VAL F 67 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 74 through 79 current: chain 'G' and resid 171 through 174 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 171 through 174 current: chain 'G' and resid 197 through 200 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 197 through 200 current: chain 'I' and resid 171 through 174 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 171 through 174 current: chain 'I' and resid 197 through 202 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 197 through 202 current: chain 'K' and resid 171 through 174 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 171 through 174 current: chain 'K' and resid 197 through 202 Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 96 Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 105 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 104 through 105 current: chain 'A' and resid 315 through 321 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 321 current: chain 'A' and resid 407 through 416 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 407 through 416 current: chain 'A' and resid 460 through 461 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 173 removed outlier: 3.940A pdb=" N GLY A 159 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 152 removed outlier: 6.695A pdb=" N GLU A 199 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE A 185 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE A 197 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 377 removed outlier: 6.353A pdb=" N PHE A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 102 through 104 Processing sheet with id=AA9, first strand: chain 'B' and resid 112 through 113 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 112 through 113 current: chain 'B' and resid 238 through 241 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 238 through 241 current: chain 'B' and resid 328 through 336 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 164 through 165 removed outlier: 4.541A pdb=" N ILE B 164 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 93 through 96 Processing sheet with id=AB3, first strand: chain 'C' and resid 104 through 105 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 104 through 105 current: chain 'C' and resid 315 through 321 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 321 current: chain 'C' and resid 407 through 416 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 407 through 416 current: chain 'C' and resid 460 through 461 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 170 through 173 removed outlier: 3.771A pdb=" N GLY C 159 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLN C 140 " --> pdb=" O PHE C 162 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 151 through 152 removed outlier: 6.585A pdb=" N GLU C 199 " --> pdb=" O THR C 183 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AB7, first strand: chain 'C' and resid 375 through 377 removed outlier: 6.156A pdb=" N PHE C 380 " --> pdb=" O ALA C 376 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 101 through 104 removed outlier: 3.642A pdb=" N ASP D 130 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 112 through 114 removed outlier: 6.845A pdb=" N ILE D 210 " --> pdb=" O SER D 239 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N PHE D 241 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE D 212 " --> pdb=" O PHE D 241 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASN D 243 " --> pdb=" O PHE D 212 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA D 214 " --> pdb=" O ASN D 243 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N SER D 209 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE D 277 " --> pdb=" O SER D 209 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL D 211 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N THR D 279 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA D 213 " --> pdb=" O THR D 279 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL D 274 " --> pdb=" O THR D 330 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE D 332 " --> pdb=" O VAL D 274 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR D 276 " --> pdb=" O ILE D 332 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE D 334 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU D 278 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N THR D 336 " --> pdb=" O LEU D 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 144 through 145 removed outlier: 4.070A pdb=" N ARG D 321 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 150 through 151 removed outlier: 4.599A pdb=" N ILE D 164 " --> pdb=" O ILE D 151 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 93 through 96 Processing sheet with id=AC4, first strand: chain 'E' and resid 104 through 105 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 104 through 105 current: chain 'E' and resid 315 through 320 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 320 current: chain 'E' and resid 407 through 416 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 407 through 416 current: chain 'E' and resid 460 through 461 No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 170 through 173 removed outlier: 3.881A pdb=" N GLY E 159 " --> pdb=" O ILE E 172 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 151 through 152 removed outlier: 6.561A pdb=" N GLU E 199 " --> pdb=" O THR E 183 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 301 through 302 Processing sheet with id=AC8, first strand: chain 'E' and resid 375 through 377 removed outlier: 6.387A pdb=" N PHE E 380 " --> pdb=" O ALA E 376 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 101 through 104 removed outlier: 3.577A pdb=" N ASP F 130 " --> pdb=" O VAL F 104 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 112 through 114 removed outlier: 6.290A pdb=" N PHE F 113 " --> pdb=" O LEU F 242 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU F 244 " --> pdb=" O PHE F 113 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET F 215 " --> pdb=" O THR F 279 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL F 274 " --> pdb=" O THR F 330 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ILE F 332 " --> pdb=" O VAL F 274 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR F 276 " --> pdb=" O ILE F 332 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE F 334 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU F 278 " --> pdb=" O ILE F 334 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N THR F 336 " --> pdb=" O LEU F 278 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.276A pdb=" N ARG F 321 " --> pdb=" O ILE F 145 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 151 through 152 Processing sheet with id=AD4, first strand: chain 'M' and resid 92 through 95 Processing sheet with id=AD5, first strand: chain 'M' and resid 99 through 101 Processing sheet with id=AD6, first strand: chain 'N' and resid 28 through 29 Processing sheet with id=AD7, first strand: chain 'O' and resid 45 through 46 removed outlier: 3.744A pdb=" N SER O 46 " --> pdb=" O ILE O 329 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 196 through 197 removed outlier: 3.686A pdb=" N ALA O 197 " --> pdb=" O PHE O 234 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE O 234 " --> pdb=" O ALA O 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'a' and resid 335 through 342 removed outlier: 3.583A pdb=" N GLY a 339 " --> pdb=" O VAL a 17 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL a 17 " --> pdb=" O GLY a 339 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE a 367 " --> pdb=" O TYR a 20 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'a' and resid 187 through 191 Processing sheet with id=AE2, first strand: chain 'a' and resid 222 through 224 removed outlier: 3.543A pdb=" N LYS a 231 " --> pdb=" O VAL a 222 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU a 229 " --> pdb=" O ASP a 224 " (cutoff:3.500A) 3970 hydrogen bonds defined for protein. 11616 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: 22.63 Time building geometry restraints manager: 13.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11488 1.33 - 1.45: 13290 1.45 - 1.57: 33488 1.57 - 1.69: 3 1.69 - 1.82: 377 Bond restraints: 58646 Sorted by residual: bond pdb=" CG1 ILE m 22 " pdb=" CD1 ILE m 22 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.30e+00 bond pdb=" CG1 ILE E 333 " pdb=" CD1 ILE E 333 " ideal model delta sigma weight residual 1.513 1.437 0.076 3.90e-02 6.57e+02 3.82e+00 bond pdb=" CG GLN a 68 " pdb=" CD GLN a 68 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.57e+00 bond pdb=" CG1 ILE i 132 " pdb=" CD1 ILE i 132 " ideal model delta sigma weight residual 1.513 1.441 0.072 3.90e-02 6.57e+02 3.42e+00 bond pdb=" CG1 ILE n 89 " pdb=" CD1 ILE n 89 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.91e+00 ... (remaining 58641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 78615 2.17 - 4.35: 1175 4.35 - 6.52: 175 6.52 - 8.70: 34 8.70 - 10.87: 2 Bond angle restraints: 80001 Sorted by residual: angle pdb=" C ILE A 27 " pdb=" N TYR A 28 " pdb=" CA TYR A 28 " ideal model delta sigma weight residual 122.16 129.69 -7.53 1.32e+00 5.74e-01 3.25e+01 angle pdb=" C THR O 30 " pdb=" CA THR O 30 " pdb=" CB THR O 30 " ideal model delta sigma weight residual 117.23 109.66 7.57 1.36e+00 5.41e-01 3.10e+01 angle pdb=" C THR B 392 " pdb=" CA THR B 392 " pdb=" CB THR B 392 " ideal model delta sigma weight residual 117.23 110.29 6.94 1.36e+00 5.41e-01 2.61e+01 angle pdb=" C THR d 197 " pdb=" N GLU d 198 " pdb=" CA GLU d 198 " ideal model delta sigma weight residual 121.80 110.93 10.87 2.16e+00 2.14e-01 2.53e+01 angle pdb=" N ARG d 297 " pdb=" CA ARG d 297 " pdb=" C ARG d 297 " ideal model delta sigma weight residual 111.28 106.56 4.72 1.09e+00 8.42e-01 1.88e+01 ... (remaining 79996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 34447 35.74 - 71.49: 359 71.49 - 107.23: 46 107.23 - 142.98: 0 142.98 - 178.72: 1 Dihedral angle restraints: 34853 sinusoidal: 11196 harmonic: 23657 Sorted by residual: dihedral pdb=" O2A ADP E 701 " pdb=" O3A ADP E 701 " pdb=" PA ADP E 701 " pdb=" PB ADP E 701 " ideal model delta sinusoidal sigma weight residual 300.00 121.28 178.72 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" CA MET B 472 " pdb=" C MET B 472 " pdb=" N LEU B 473 " pdb=" CA LEU B 473 " ideal model delta harmonic sigma weight residual 180.00 153.27 26.73 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA ILE F 353 " pdb=" C ILE F 353 " pdb=" N THR F 354 " pdb=" CA THR F 354 " ideal model delta harmonic sigma weight residual 180.00 -154.17 -25.83 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 34850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 7489 0.052 - 0.104: 1774 0.104 - 0.156: 279 0.156 - 0.208: 18 0.208 - 0.261: 7 Chirality restraints: 9567 Sorted by residual: chirality pdb=" CA TRP c 147 " pdb=" N TRP c 147 " pdb=" C TRP c 147 " pdb=" CB TRP c 147 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB ILE E 104 " pdb=" CA ILE E 104 " pdb=" CG1 ILE E 104 " pdb=" CG2 ILE E 104 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA MET i 59 " pdb=" N MET i 59 " pdb=" C MET i 59 " pdb=" CB MET i 59 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 9564 not shown) Planarity restraints: 10420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP a 594 " 0.039 2.00e-02 2.50e+03 3.36e-02 2.83e+01 pdb=" CG TRP a 594 " -0.091 2.00e-02 2.50e+03 pdb=" CD1 TRP a 594 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP a 594 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP a 594 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP a 594 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP a 594 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 594 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 594 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP a 594 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP a 737 " 0.042 2.00e-02 2.50e+03 3.24e-02 2.63e+01 pdb=" CG TRP a 737 " -0.087 2.00e-02 2.50e+03 pdb=" CD1 TRP a 737 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP a 737 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP a 737 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP a 737 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP a 737 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 737 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 737 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP a 737 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR d 249 " -0.056 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PRO d 250 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO d 250 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO d 250 " -0.042 5.00e-02 4.00e+02 ... (remaining 10417 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 5862 2.74 - 3.28: 64333 3.28 - 3.82: 103533 3.82 - 4.36: 116091 4.36 - 4.90: 198556 Nonbonded interactions: 488375 Sorted by model distance: nonbonded pdb=" O ILE d 111 " pdb=" OG1 THR d 114 " model vdw 2.199 3.040 nonbonded pdb=" ND2 ASN c 61 " pdb=" O PHE g 88 " model vdw 2.201 3.120 nonbonded pdb=" OG1 THR a 488 " pdb=" NE2 HIS f 35 " model vdw 2.203 3.120 nonbonded pdb=" O LEU B 425 " pdb=" NZ LYS B 430 " model vdw 2.205 3.120 nonbonded pdb=" O THR B 350 " pdb=" OG1 THR B 354 " model vdw 2.207 3.040 ... (remaining 488370 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 261 or (resid 262 through 270 and (name N or na \ me CA or name C or name O or name CB )) or resid 271 through 273 or (resid 274 t \ hrough 277 and (name N or name CA or name C or name O or name CB )) or resid 278 \ through 615 or (resid 616 and (name N or name CA or name C or name O or name CB \ or name OXT)))) selection = (chain 'C' and (resid 24 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 or (resid 31 and (name N or name CA or nam \ e C or name O or name CB )) or resid 32 through 237 or (resid 238 and (name N or \ name CA or name C or name O or name CB )) or resid 239 through 284 or (resid 28 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 286 through \ 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or re \ sid 310 through 354 or (resid 355 through 356 and (name N or name CA or name C o \ r name O or name CB )) or resid 357 through 421 or (resid 422 and (name N or nam \ e CA or name C or name O or name CB )) or resid 423 through 589 or (resid 590 an \ d (name N or name CA or name C or name O or name CB )) or resid 591 through 592 \ or (resid 593 through 595 and (name N or name CA or name C or name O or name CB \ )) or resid 596 through 616)) selection = (chain 'E' and (resid 24 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 or (resid 31 and (name N or name CA or nam \ e C or name O or name CB )) or resid 32 through 237 or (resid 238 and (name N or \ name CA or name C or name O or name CB )) or resid 239 through 261 or (resid 26 \ 2 through 270 and (name N or name CA or name C or name O or name CB )) or resid \ 271 through 273 or (resid 274 through 277 and (name N or name CA or name C or na \ me O or name CB )) or resid 278 through 284 or (resid 285 and (name N or name CA \ or name C or name O or name CB )) or resid 286 through 308 or (resid 309 and (n \ ame N or name CA or name C or name O or name CB )) or resid 310 through 354 or ( \ resid 355 through 356 and (name N or name CA or name C or name O or name CB )) o \ r resid 357 through 421 or (resid 422 and (name N or name CA or name C or name O \ or name CB )) or resid 423 through 589 or (resid 590 and (name N or name CA or \ name C or name O or name CB )) or resid 591 through 592 or (resid 593 through 59 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 596 through \ 615 or (resid 616 and (name N or name CA or name C or name O or name CB or name \ OXT)))) } ncs_group { reference = (chain 'B' and (resid 14 through 104 or (resid 105 through 106 and (name N or na \ me CA or name C or name O or name CB )) or resid 107 through 487)) selection = (chain 'D' and (resid 14 through 41 or (resid 42 through 43 and (name N or name \ CA or name C or name O or name CB )) or resid 44 through 72 or (resid 73 and (na \ me N or name CA or name C or name O or name CB )) or resid 74 through 105 or (re \ sid 106 and (name N or name CA or name C or name O or name CB )) or resid 107 th \ rough 481 or (resid 482 and (name N or name CA or name C or name O or name CB )) \ or resid 483 through 487)) selection = (chain 'F' and ((resid 14 through 15 and (name N or name CA or name C or name O \ or name CB )) or resid 16 through 41 or (resid 42 through 43 and (name N or name \ CA or name C or name O or name CB )) or resid 44 through 72 or (resid 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 through 104 or (r \ esid 105 through 106 and (name N or name CA or name C or name O or name CB )) or \ resid 107 through 194 or (resid 195 and (name N or name CA or name C or name O \ or name CB )) or resid 196 through 204 or (resid 205 and (name N or name CA or n \ ame C or name O or name CB )) or resid 206 through 481 or (resid 482 and (name N \ or name CA or name C or name O or name CB )) or resid 483 through 487)) } ncs_group { reference = (chain 'G' and (resid 9 through 91 or (resid 92 through 97 and (name N or name C \ A or name C or name O or name CB )) or (resid 98 through 118 and (name N or name \ CA or name C or name O or name CB )) or resid 119 or (resid 120 and (name N or \ name CA or name C or name O or name CB )) or resid 121 through 125 or (resid 126 \ and (name N or name CA or name C or name O or name CB )) or resid 127 through 1 \ 39 or (resid 140 through 141 and (name N or name CA or name C or name O or name \ CB )) or resid 142 or (resid 143 and (name N or name CA or name C or name O or n \ ame CB )) or resid 144 or (resid 145 through 152 and (name N or name CA or name \ C or name O or name CB )) or resid 153 through 156 or (resid 157 through 159 and \ (name N or name CA or name C or name O or name CB )) or resid 160 through 164 o \ r (resid 165 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 66 through 168 or (resid 169 through 177 and (name N or name CA or name C or nam \ e O or name CB )) or resid 178 or (resid 179 through 185 and (name N or name CA \ or name C or name O or name CB )) or resid 186 through 187 or (resid 188 through \ 205 and (name N or name CA or name C or name O or name CB )) or resid 206 or (r \ esid 207 through 215 and (name N or name CA or name C or name O or name CB )) or \ resid 216 through 217 or (resid 218 and (name N or name CA or name C or name O \ or name CB )) or resid 219 or (resid 220 through 222 and (name N or name CA or n \ ame C or name O or name CB )) or resid 223 through 228)) selection = (chain 'I' and (resid 9 through 84 or (resid 85 through 97 and (name N or name C \ A or name C or name O or name CB )) or (resid 98 through 108 and (name N or name \ CA or name C or name O or name CB )) or (resid 109 through 118 and (name N or n \ ame CA or name C or name O or name CB )) or resid 119 or (resid 120 and (name N \ or name CA or name C or name O or name CB )) or resid 121 through 125 or (resid \ 126 and (name N or name CA or name C or name O or name CB )) or resid 127 throug \ h 139 or (resid 140 through 141 and (name N or name CA or name C or name O or na \ me CB )) or resid 142 through 147 or (resid 148 through 152 and (name N or name \ CA or name C or name O or name CB )) or resid 153 through 155 or (resid 156 thro \ ugh 159 and (name N or name CA or name C or name O or name CB )) or resid 160 th \ rough 162 or (resid 163 through 165 and (name N or name CA or name C or name O o \ r name CB )) or resid 166 through 168 or (resid 169 through 177 and (name N or n \ ame CA or name C or name O or name CB )) or resid 178 through 180 or (resid 181 \ through 185 and (name N or name CA or name C or name O or name CB )) or (resid 1 \ 86 through 205 and (name N or name CA or name C or name O or name CB )) or resid \ 206 or (resid 207 through 215 and (name N or name CA or name C or name O or nam \ e CB )) or resid 216 through 217 or (resid 218 and (name N or name CA or name C \ or name O or name CB )) or resid 219 or (resid 220 through 222 and (name N or na \ me CA or name C or name O or name CB )) or resid 223 through 228)) selection = (chain 'K' and (resid 9 through 99 or (resid 100 through 108 and (name N or name \ CA or name C or name O or name CB )) or (resid 109 through 118 and (name N or n \ ame CA or name C or name O or name CB )) or resid 119 through 144 or (resid 145 \ through 152 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 3 through 171 or (resid 172 through 177 and (name N or name CA or name C or name \ O or name CB )) or resid 178 through 196 or (resid 197 through 205 and (name N \ or name CA or name C or name O or name CB )) or resid 206 through 221 or (resid \ 222 and (name N or name CA or name C or name O or name CB )) or resid 223 throug \ h 228)) } ncs_group { reference = (chain 'H' and resid 2 through 112) selection = (chain 'J' and ((resid 2 through 62 and (name N or name CA or name C or name O o \ r name CB )) or (resid 63 through 104 and (name N or name CA or name C or name O \ or name CB )) or resid 105 through 112)) selection = (chain 'L' and (resid 2 through 109 or (resid 110 through 112 and (name N or nam \ e CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'g' and (resid 1 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 79 or (resid 80 through 83 and (nam \ e N or name CA or name C or name O or name CB )) or resid 84 through 85 or (resi \ d 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throug \ h 129 or (resid 130 through 131 and (name N or name CA or name C or name O or na \ me CB )) or resid 132 through 159)) selection = (chain 'h' and (resid 1 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 79 or (resid 80 through 83 and (nam \ e N or name CA or name C or name O or name CB )) or resid 84 through 85 or (resi \ d 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throug \ h 129 or (resid 130 through 131 and (name N or name CA or name C or name O or na \ me CB )) or resid 132 through 140 or (resid 141 and (name N or name CA or name C \ or name O or name CB )) or resid 142 through 152 or (resid 153 through 154 and \ (name N or name CA or name C or name O or name CB )) or resid 155 through 159)) selection = (chain 'i' and (resid 1 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 79 or (resid 80 through 83 and (nam \ e N or name CA or name C or name O or name CB )) or resid 84 through 85 or (resi \ d 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throug \ h 129 or (resid 130 through 131 and (name N or name CA or name C or name O or na \ me CB )) or resid 132 through 140 or (resid 141 and (name N or name CA or name C \ or name O or name CB )) or resid 142 through 152 or (resid 153 through 154 and \ (name N or name CA or name C or name O or name CB )) or resid 155 through 159)) selection = (chain 'j' and (resid 1 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 79 or (resid 80 through 83 and (nam \ e N or name CA or name C or name O or name CB )) or resid 84 through 85 or (resi \ d 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throug \ h 129 or (resid 130 through 131 and (name N or name CA or name C or name O or na \ me CB )) or resid 132 through 140 or (resid 141 and (name N or name CA or name C \ or name O or name CB )) or resid 142 through 152 or (resid 153 through 154 and \ (name N or name CA or name C or name O or name CB )) or resid 155 through 159)) selection = (chain 'k' and (resid 1 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 81 or (resid 82 through 83 and (nam \ e N or name CA or name C or name O or name CB )) or resid 84 through 85 or (resi \ d 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throug \ h 129 or (resid 130 through 131 and (name N or name CA or name C or name O or na \ me CB )) or resid 132 through 140 or (resid 141 and (name N or name CA or name C \ or name O or name CB )) or resid 142 through 152 or (resid 153 through 154 and \ (name N or name CA or name C or name O or name CB )) or resid 155 through 159)) selection = (chain 'l' and (resid 1 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 79 or (resid 80 through 83 and (nam \ e N or name CA or name C or name O or name CB )) or resid 84 through 129 or (res \ id 130 through 131 and (name N or name CA or name C or name O or name CB )) or r \ esid 132 through 140 or (resid 141 and (name N or name CA or name C or name O or \ name CB )) or resid 142 through 152 or (resid 153 through 154 and (name N or na \ me CA or name C or name O or name CB )) or resid 155 through 159)) selection = (chain 'm' and (resid 1 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 79 or (resid 80 through 83 and (nam \ e N or name CA or name C or name O or name CB )) or resid 84 through 85 or (resi \ d 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throug \ h 129 or (resid 130 through 131 and (name N or name CA or name C or name O or na \ me CB )) or resid 132 through 140 or (resid 141 and (name N or name CA or name C \ or name O or name CB )) or resid 142 through 152 or (resid 153 through 154 and \ (name N or name CA or name C or name O or name CB )) or resid 155 through 159)) selection = (chain 'n' and (resid 1 through 79 or (resid 80 through 83 and (name N or name C \ A or name C or name O or name CB )) or resid 84 through 85 or (resid 86 and (nam \ e N or name CA or name C or name O or name CB )) or resid 87 through 140 or (res \ id 141 and (name N or name CA or name C or name O or name CB )) or resid 142 thr \ ough 152 or (resid 153 through 154 and (name N or name CA or name C or name O or \ name CB )) or resid 155 through 159)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 1.830 Check model and map are aligned: 0.340 Set scattering table: 0.430 Process input model: 101.730 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.280 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: 0.020 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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 : 0.004 0.090 58646 Z= 0.265 Angle : 0.661 10.873 80001 Z= 0.356 Chirality : 0.045 0.261 9567 Planarity : 0.005 0.087 10420 Dihedral : 12.966 178.719 19647 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.34 % Favored : 96.64 % Rotamer: Outliers : 0.08 % Allowed : 0.41 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.09), residues: 8154 helix: 1.74 (0.07), residues: 4700 sheet: -1.23 (0.20), residues: 625 loop : -0.29 (0.12), residues: 2829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.002 TRP a 594 HIS 0.009 0.001 HIS o 98 PHE 0.040 0.002 PHE o 96 TYR 0.043 0.002 TYR k 142 ARG 0.014 0.001 ARG o 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1790 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1786 time to evaluate : 5.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8443 (p0) cc_final: 0.8210 (p0) REVERT: A 123 TYR cc_start: 0.8230 (m-80) cc_final: 0.7301 (m-80) REVERT: A 276 ASP cc_start: 0.8333 (m-30) cc_final: 0.8117 (m-30) REVERT: A 487 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7782 (pt0) REVERT: A 523 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7691 (mm-30) REVERT: B 69 GLU cc_start: 0.7318 (tp30) cc_final: 0.6899 (tp30) REVERT: B 182 GLU cc_start: 0.7722 (mp0) cc_final: 0.6957 (mp0) REVERT: B 412 ASP cc_start: 0.7786 (m-30) cc_final: 0.7044 (m-30) REVERT: B 434 GLU cc_start: 0.8048 (pp20) cc_final: 0.7553 (pp20) REVERT: B 441 LYS cc_start: 0.8270 (mtmm) cc_final: 0.8046 (mtmm) REVERT: B 456 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7588 (mt-10) REVERT: B 472 MET cc_start: 0.5247 (mtm) cc_final: 0.4913 (mtm) REVERT: C 108 ILE cc_start: 0.9049 (mm) cc_final: 0.8737 (mm) REVERT: C 118 GLU cc_start: 0.7726 (tp30) cc_final: 0.7304 (tp30) REVERT: C 192 THR cc_start: 0.8441 (p) cc_final: 0.8211 (p) REVERT: C 285 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6977 (mm-30) REVERT: C 292 GLU cc_start: 0.8038 (tp30) cc_final: 0.6898 (tp30) REVERT: C 360 TRP cc_start: 0.8710 (t60) cc_final: 0.8352 (t60) REVERT: C 442 ASP cc_start: 0.7576 (t0) cc_final: 0.7239 (t0) REVERT: C 444 LYS cc_start: 0.8342 (mttp) cc_final: 0.8020 (mttp) REVERT: C 504 LYS cc_start: 0.8877 (mttt) cc_final: 0.8639 (mmtp) REVERT: C 540 ILE cc_start: 0.8834 (tp) cc_final: 0.8598 (tt) REVERT: D 51 GLU cc_start: 0.7890 (tt0) cc_final: 0.7645 (tt0) REVERT: D 74 ARG cc_start: 0.7766 (ttm110) cc_final: 0.7134 (ttm110) REVERT: D 146 TYR cc_start: 0.8463 (t80) cc_final: 0.8169 (t80) REVERT: D 477 SER cc_start: 0.8824 (p) cc_final: 0.8593 (p) REVERT: E 124 ILE cc_start: 0.9131 (mm) cc_final: 0.8927 (mm) REVERT: E 129 ASP cc_start: 0.7526 (p0) cc_final: 0.7325 (p0) REVERT: E 362 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7585 (mt-10) REVERT: E 373 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7968 (mt-10) REVERT: E 425 ASP cc_start: 0.8558 (t70) cc_final: 0.8166 (t0) REVERT: E 500 GLN cc_start: 0.7823 (pp30) cc_final: 0.7484 (pp30) REVERT: E 522 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7702 (mtmt) REVERT: F 18 GLN cc_start: 0.6198 (mp10) cc_final: 0.5960 (mp10) REVERT: F 42 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7031 (mm-30) REVERT: F 98 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7698 (mt-10) REVERT: F 150 MET cc_start: 0.8079 (ttt) cc_final: 0.7788 (ttt) REVERT: F 220 GLU cc_start: 0.7792 (tp30) cc_final: 0.7163 (tp30) REVERT: F 297 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7175 (mt-10) REVERT: F 326 ASN cc_start: 0.8372 (m110) cc_final: 0.7895 (m110) REVERT: F 363 GLN cc_start: 0.7979 (mp10) cc_final: 0.7434 (mp10) REVERT: F 389 GLU cc_start: 0.8084 (tp30) cc_final: 0.7811 (tp30) REVERT: F 412 ASP cc_start: 0.7479 (m-30) cc_final: 0.6981 (m-30) REVERT: F 482 ASP cc_start: 0.7854 (m-30) cc_final: 0.7579 (m-30) REVERT: G 140 LYS cc_start: 0.7975 (tttp) cc_final: 0.7759 (tttm) REVERT: J 46 TYR cc_start: 0.8073 (t80) cc_final: 0.7822 (t80) REVERT: K 197 ILE cc_start: 0.8994 (mt) cc_final: 0.8771 (mt) REVERT: M 40 THR cc_start: 0.7878 (t) cc_final: 0.7621 (t) REVERT: M 42 ARG cc_start: 0.7980 (mmm-85) cc_final: 0.7757 (tpt-90) REVERT: M 55 GLN cc_start: 0.8666 (mp10) cc_final: 0.8440 (mp10) REVERT: M 182 GLU cc_start: 0.7741 (tp30) cc_final: 0.7509 (tp30) REVERT: a 31 TYR cc_start: 0.8228 (t80) cc_final: 0.7968 (t80) REVERT: a 41 PHE cc_start: 0.8247 (m-80) cc_final: 0.7795 (m-80) REVERT: a 53 ARG cc_start: 0.6312 (mpt180) cc_final: 0.5794 (mmt180) REVERT: a 57 ASN cc_start: 0.8705 (p0) cc_final: 0.8453 (p0) REVERT: a 60 ARG cc_start: 0.8871 (ptt90) cc_final: 0.8450 (ptt90) REVERT: a 285 TYR cc_start: 0.9079 (m-80) cc_final: 0.8859 (m-80) REVERT: a 312 ASP cc_start: 0.7258 (m-30) cc_final: 0.6954 (m-30) REVERT: a 344 ASP cc_start: 0.7709 (p0) cc_final: 0.7286 (p0) REVERT: a 437 LEU cc_start: 0.9062 (mt) cc_final: 0.8747 (mt) REVERT: a 465 ILE cc_start: 0.8602 (mt) cc_final: 0.8322 (mm) REVERT: a 529 LEU cc_start: 0.8639 (pt) cc_final: 0.7953 (pt) REVERT: a 536 LYS cc_start: 0.9186 (ptmt) cc_final: 0.8947 (ptmt) REVERT: a 737 TRP cc_start: 0.7778 (t60) cc_final: 0.7487 (t60) REVERT: a 753 MET cc_start: 0.7206 (ptm) cc_final: 0.6885 (tmm) REVERT: a 759 PHE cc_start: 0.7674 (t80) cc_final: 0.7272 (t80) REVERT: a 773 LEU cc_start: 0.8566 (tp) cc_final: 0.8128 (tp) REVERT: a 774 PHE cc_start: 0.8355 (t80) cc_final: 0.7465 (t80) REVERT: a 776 MET cc_start: 0.8345 (tpp) cc_final: 0.7824 (tpp) REVERT: a 791 THR cc_start: 0.9013 (p) cc_final: 0.8809 (p) REVERT: a 796 HIS cc_start: 0.7908 (m-70) cc_final: 0.7650 (m-70) REVERT: b 235 PHE cc_start: 0.7925 (t80) cc_final: 0.7603 (t80) REVERT: c 27 ILE cc_start: 0.9029 (tp) cc_final: 0.8789 (tp) REVERT: c 37 LEU cc_start: 0.9107 (tp) cc_final: 0.8869 (tp) REVERT: c 58 MET cc_start: 0.8223 (tmm) cc_final: 0.7753 (tmm) REVERT: c 102 ILE cc_start: 0.9278 (tp) cc_final: 0.9050 (tp) REVERT: c 105 ILE cc_start: 0.9244 (mm) cc_final: 0.8994 (mm) REVERT: c 147 TRP cc_start: 0.6559 (m-10) cc_final: 0.5925 (m-10) REVERT: c 158 ILE cc_start: 0.8958 (tp) cc_final: 0.8699 (tp) REVERT: c 197 LEU cc_start: 0.8960 (mt) cc_final: 0.8723 (mp) REVERT: d 6 PHE cc_start: 0.8635 (t80) cc_final: 0.8286 (t80) REVERT: d 79 GLU cc_start: 0.7145 (tp30) cc_final: 0.6800 (tp30) REVERT: d 125 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8425 (tm-30) REVERT: d 186 LYS cc_start: 0.9220 (ttpp) cc_final: 0.8869 (tttp) REVERT: d 189 LEU cc_start: 0.9395 (tp) cc_final: 0.8998 (tp) REVERT: d 215 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7998 (tm-30) REVERT: d 234 ASP cc_start: 0.7866 (t70) cc_final: 0.7658 (t0) REVERT: d 236 ASP cc_start: 0.8350 (p0) cc_final: 0.7711 (p0) REVERT: d 266 ARG cc_start: 0.8164 (mtm110) cc_final: 0.7821 (mtm110) REVERT: d 317 GLU cc_start: 0.6925 (tm-30) cc_final: 0.6675 (tm-30) REVERT: d 344 VAL cc_start: 0.8381 (p) cc_final: 0.8180 (p) REVERT: e 11 PHE cc_start: 0.8427 (t80) cc_final: 0.8061 (t80) REVERT: e 47 MET cc_start: 0.8492 (tmm) cc_final: 0.8290 (tmm) REVERT: e 53 LEU cc_start: 0.8787 (tp) cc_final: 0.8496 (tp) REVERT: f 30 LEU cc_start: 0.9041 (tp) cc_final: 0.8822 (tp) REVERT: g 43 CYS cc_start: 0.7568 (t) cc_final: 0.7365 (t) REVERT: g 68 LEU cc_start: 0.8826 (tp) cc_final: 0.8470 (tp) REVERT: h 65 ILE cc_start: 0.9124 (mm) cc_final: 0.8846 (mm) REVERT: h 77 SER cc_start: 0.8691 (p) cc_final: 0.8444 (p) REVERT: h 106 PHE cc_start: 0.6988 (m-10) cc_final: 0.6623 (m-10) REVERT: h 126 PHE cc_start: 0.8303 (t80) cc_final: 0.8101 (t80) REVERT: h 150 LEU cc_start: 0.8881 (mt) cc_final: 0.8528 (mt) REVERT: h 156 GLN cc_start: 0.8215 (tp-100) cc_final: 0.7359 (tp-100) REVERT: i 17 CYS cc_start: 0.8230 (t) cc_final: 0.8019 (t) REVERT: i 26 LEU cc_start: 0.8707 (mm) cc_final: 0.8408 (mm) REVERT: i 129 MET cc_start: 0.7767 (tmm) cc_final: 0.7534 (tmm) REVERT: j 21 ILE cc_start: 0.8674 (tp) cc_final: 0.8419 (tp) REVERT: j 30 TYR cc_start: 0.7853 (t80) cc_final: 0.7631 (t80) REVERT: j 39 ILE cc_start: 0.8814 (mm) cc_final: 0.8367 (mm) REVERT: j 52 LYS cc_start: 0.8337 (tptt) cc_final: 0.8026 (tppt) REVERT: j 73 LEU cc_start: 0.7948 (tp) cc_final: 0.7458 (tp) REVERT: j 117 ARG cc_start: 0.7996 (tpp80) cc_final: 0.7547 (mmm-85) REVERT: k 11 PHE cc_start: 0.8409 (t80) cc_final: 0.7901 (t80) REVERT: k 39 ILE cc_start: 0.8305 (mm) cc_final: 0.7688 (mt) REVERT: k 49 LEU cc_start: 0.8721 (tp) cc_final: 0.8448 (tp) REVERT: k 73 LEU cc_start: 0.8514 (tp) cc_final: 0.8153 (tp) REVERT: k 82 GLN cc_start: 0.6263 (pp30) cc_final: 0.5747 (pt0) REVERT: k 88 PHE cc_start: 0.7918 (m-80) cc_final: 0.7587 (m-80) REVERT: k 130 ILE cc_start: 0.8636 (mm) cc_final: 0.8292 (mm) REVERT: k 134 ILE cc_start: 0.9066 (mp) cc_final: 0.8858 (mp) REVERT: k 151 ASN cc_start: 0.7767 (t0) cc_final: 0.7346 (t0) REVERT: k 157 ASP cc_start: 0.8026 (p0) cc_final: 0.7825 (p0) REVERT: l 53 ASN cc_start: 0.7575 (m-40) cc_final: 0.7308 (m-40) REVERT: l 88 PHE cc_start: 0.7552 (m-80) cc_final: 0.7297 (m-80) REVERT: l 95 LEU cc_start: 0.8852 (mm) cc_final: 0.8517 (mm) REVERT: l 141 LEU cc_start: 0.8399 (tt) cc_final: 0.8183 (tt) REVERT: l 144 LEU cc_start: 0.8932 (tp) cc_final: 0.8432 (tp) REVERT: l 148 LEU cc_start: 0.8480 (mt) cc_final: 0.8227 (mt) REVERT: l 151 ASN cc_start: 0.8326 (t0) cc_final: 0.8078 (t0) REVERT: m 39 ILE cc_start: 0.8266 (mm) cc_final: 0.7434 (mm) REVERT: m 40 CYS cc_start: 0.8819 (m) cc_final: 0.8521 (m) REVERT: m 43 CYS cc_start: 0.7497 (m) cc_final: 0.7288 (m) REVERT: m 121 GLN cc_start: 0.7933 (mp10) cc_final: 0.7541 (mp10) REVERT: m 129 MET cc_start: 0.7529 (tmm) cc_final: 0.7189 (tmm) REVERT: m 156 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7750 (tm-30) REVERT: n 15 ILE cc_start: 0.8442 (mm) cc_final: 0.8222 (mm) REVERT: n 21 ILE cc_start: 0.8857 (tp) cc_final: 0.8593 (tp) REVERT: n 22 ILE cc_start: 0.8919 (mt) cc_final: 0.8701 (mt) REVERT: n 46 ARG cc_start: 0.8192 (ttp80) cc_final: 0.7867 (ttp80) REVERT: n 58 ILE cc_start: 0.9151 (mm) cc_final: 0.8944 (mm) REVERT: n 133 LEU cc_start: 0.9269 (mm) cc_final: 0.9048 (mt) REVERT: o 64 VAL cc_start: 0.8738 (t) cc_final: 0.8528 (t) REVERT: o 74 LEU cc_start: 0.8792 (tp) cc_final: 0.8309 (tp) REVERT: o 85 SER cc_start: 0.8854 (p) cc_final: 0.8165 (m) REVERT: o 152 MET cc_start: 0.7405 (tmm) cc_final: 0.6935 (tmm) outliers start: 4 outliers final: 0 residues processed: 1787 average time/residue: 0.5687 time to fit residues: 1680.0473 Evaluate side-chains 1595 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1595 time to evaluate : 5.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 681 optimal weight: 7.9990 chunk 611 optimal weight: 0.7980 chunk 339 optimal weight: 0.8980 chunk 208 optimal weight: 0.9990 chunk 412 optimal weight: 8.9990 chunk 326 optimal weight: 10.0000 chunk 632 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 384 optimal weight: 0.0050 chunk 470 optimal weight: 5.9990 chunk 732 optimal weight: 0.9980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 267 GLN B 78 GLN B 122 ASN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN D 135 ASN D 232 ASN ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 ASN K 122 GLN a 68 GLN a 134 GLN ** a 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 374 ASN ** a 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 132 ASN ** c 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 10 ASN d 29 GLN d 106 ASN ** d 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 209 GLN ** d 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 121 GLN ** g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 151 ASN m 90 GLN ** m 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 90 GLN ** o 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 58646 Z= 0.206 Angle : 0.629 11.465 80001 Z= 0.325 Chirality : 0.044 0.256 9567 Planarity : 0.005 0.082 10420 Dihedral : 4.941 170.114 8735 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.03 % Favored : 96.96 % Rotamer: Outliers : 1.77 % Allowed : 12.09 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.09), residues: 8154 helix: 1.78 (0.07), residues: 4756 sheet: -1.34 (0.19), residues: 648 loop : -0.32 (0.12), residues: 2750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP a 594 HIS 0.006 0.001 HIS a 796 PHE 0.034 0.002 PHE o 96 TYR 0.051 0.002 TYR g 66 ARG 0.009 0.001 ARG a 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1829 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1739 time to evaluate : 5.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8436 (p0) cc_final: 0.8207 (p0) REVERT: A 150 ASP cc_start: 0.8560 (m-30) cc_final: 0.8061 (m-30) REVERT: A 201 GLU cc_start: 0.7341 (tm-30) cc_final: 0.7003 (tm-30) REVERT: A 523 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7656 (mm-30) REVERT: A 541 TRP cc_start: 0.8611 (p-90) cc_final: 0.8384 (p-90) REVERT: B 69 GLU cc_start: 0.7444 (tp30) cc_final: 0.6947 (tp30) REVERT: B 78 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8121 (tt0) REVERT: B 87 ASP cc_start: 0.8860 (p0) cc_final: 0.8567 (p0) REVERT: B 257 ARG cc_start: 0.7949 (mtt90) cc_final: 0.7601 (mmt-90) REVERT: B 295 ARG cc_start: 0.8302 (ttp-170) cc_final: 0.8092 (ttp-170) REVERT: B 296 GLU cc_start: 0.7722 (mp0) cc_final: 0.7495 (mp0) REVERT: B 402 GLN cc_start: 0.8074 (tp-100) cc_final: 0.7872 (tp-100) REVERT: B 412 ASP cc_start: 0.7815 (m-30) cc_final: 0.7076 (m-30) REVERT: B 441 LYS cc_start: 0.8403 (mtmm) cc_final: 0.8118 (mtmm) REVERT: B 456 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7566 (mt-10) REVERT: C 40 MET cc_start: 0.8294 (mmm) cc_final: 0.7694 (mmm) REVERT: C 118 GLU cc_start: 0.7716 (tp30) cc_final: 0.7288 (tp30) REVERT: C 192 THR cc_start: 0.8918 (p) cc_final: 0.8392 (p) REVERT: C 285 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6919 (mm-30) REVERT: C 292 GLU cc_start: 0.7822 (tp30) cc_final: 0.7087 (tp30) REVERT: C 330 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7320 (tm-30) REVERT: C 352 MET cc_start: 0.8647 (ttp) cc_final: 0.8406 (ttp) REVERT: C 360 TRP cc_start: 0.8760 (t60) cc_final: 0.8427 (t60) REVERT: C 442 ASP cc_start: 0.7601 (t0) cc_final: 0.7252 (t70) REVERT: C 472 ASP cc_start: 0.7937 (m-30) cc_final: 0.7731 (m-30) REVERT: C 504 LYS cc_start: 0.8813 (mttt) cc_final: 0.8612 (mmtp) REVERT: C 540 ILE cc_start: 0.8855 (tp) cc_final: 0.8576 (tt) REVERT: C 601 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7969 (mm-30) REVERT: C 608 GLN cc_start: 0.8431 (tp40) cc_final: 0.8041 (tp-100) REVERT: D 51 GLU cc_start: 0.8012 (tt0) cc_final: 0.7685 (tt0) REVERT: D 74 ARG cc_start: 0.7972 (ttm110) cc_final: 0.7413 (ttm110) REVERT: D 223 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7534 (mtt90) REVERT: D 477 SER cc_start: 0.9006 (p) cc_final: 0.8699 (p) REVERT: E 124 ILE cc_start: 0.9132 (mm) cc_final: 0.8920 (mm) REVERT: E 362 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7579 (mt-10) REVERT: E 425 ASP cc_start: 0.8532 (t70) cc_final: 0.8163 (t70) REVERT: E 500 GLN cc_start: 0.7747 (pp30) cc_final: 0.7463 (pp30) REVERT: E 522 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7707 (mtmt) REVERT: F 42 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7362 (mm-30) REVERT: F 98 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7644 (mt-10) REVERT: F 106 GLU cc_start: 0.8176 (mp0) cc_final: 0.6942 (mp0) REVERT: F 150 MET cc_start: 0.8333 (ttt) cc_final: 0.8074 (ttt) REVERT: F 220 GLU cc_start: 0.7723 (tp30) cc_final: 0.7064 (tp30) REVERT: F 311 ASP cc_start: 0.7428 (t0) cc_final: 0.7154 (t0) REVERT: F 326 ASN cc_start: 0.8371 (m110) cc_final: 0.7903 (m110) REVERT: F 363 GLN cc_start: 0.7953 (mp10) cc_final: 0.7210 (mp10) REVERT: F 389 GLU cc_start: 0.8161 (tp30) cc_final: 0.7755 (tp30) REVERT: F 412 ASP cc_start: 0.7568 (m-30) cc_final: 0.7030 (m-30) REVERT: F 428 GLU cc_start: 0.7308 (tp30) cc_final: 0.7042 (tp30) REVERT: F 479 LYS cc_start: 0.8549 (mtpt) cc_final: 0.8334 (mtmt) REVERT: F 482 ASP cc_start: 0.7921 (m-30) cc_final: 0.7711 (m-30) REVERT: G 134 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8154 (mm-30) REVERT: G 198 GLU cc_start: 0.7743 (pm20) cc_final: 0.7449 (pm20) REVERT: G 200 ASN cc_start: 0.8977 (t0) cc_final: 0.8598 (t0) REVERT: J 46 TYR cc_start: 0.8097 (t80) cc_final: 0.7840 (t80) REVERT: K 122 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7838 (mp10) REVERT: K 197 ILE cc_start: 0.9166 (mt) cc_final: 0.8953 (mt) REVERT: M 34 ARG cc_start: 0.7838 (ptm160) cc_final: 0.7469 (mtp-110) REVERT: M 42 ARG cc_start: 0.7993 (mmm-85) cc_final: 0.7752 (tpt-90) REVERT: M 62 GLN cc_start: 0.6766 (pp30) cc_final: 0.6289 (pt0) REVERT: M 182 GLU cc_start: 0.7741 (tp30) cc_final: 0.7010 (tp30) REVERT: M 221 MET cc_start: 0.4041 (ppp) cc_final: 0.3651 (ppp) REVERT: a 31 TYR cc_start: 0.8294 (t80) cc_final: 0.7966 (t80) REVERT: a 41 PHE cc_start: 0.8122 (m-80) cc_final: 0.7698 (m-80) REVERT: a 60 ARG cc_start: 0.8872 (ptt90) cc_final: 0.8377 (ptt90) REVERT: a 68 GLN cc_start: 0.8359 (mm-40) cc_final: 0.7998 (mm110) REVERT: a 285 TYR cc_start: 0.9085 (m-80) cc_final: 0.8805 (m-80) REVERT: a 312 ASP cc_start: 0.7394 (m-30) cc_final: 0.7040 (m-30) REVERT: a 344 ASP cc_start: 0.7752 (p0) cc_final: 0.7298 (p0) REVERT: a 369 GLN cc_start: 0.7121 (tp-100) cc_final: 0.6900 (tp-100) REVERT: a 465 ILE cc_start: 0.8648 (mt) cc_final: 0.8374 (mm) REVERT: a 537 MET cc_start: 0.8275 (mmt) cc_final: 0.7754 (mmt) REVERT: a 737 TRP cc_start: 0.7728 (t60) cc_final: 0.7473 (t60) REVERT: a 753 MET cc_start: 0.6897 (ptm) cc_final: 0.6638 (tmm) REVERT: a 759 PHE cc_start: 0.7566 (t80) cc_final: 0.7058 (t80) REVERT: a 769 MET cc_start: 0.8282 (mtp) cc_final: 0.7622 (mtp) REVERT: a 773 LEU cc_start: 0.8488 (tp) cc_final: 0.7998 (tp) REVERT: a 774 PHE cc_start: 0.8114 (t80) cc_final: 0.7768 (t80) REVERT: a 776 MET cc_start: 0.8326 (tpp) cc_final: 0.7787 (tpp) REVERT: b 235 PHE cc_start: 0.7968 (t80) cc_final: 0.7622 (t80) REVERT: b 244 ILE cc_start: 0.9188 (tt) cc_final: 0.8977 (tt) REVERT: b 246 ASN cc_start: 0.8418 (m-40) cc_final: 0.8077 (t0) REVERT: c 21 LEU cc_start: 0.9448 (tt) cc_final: 0.9244 (tp) REVERT: c 27 ILE cc_start: 0.9049 (tp) cc_final: 0.8665 (tp) REVERT: c 58 MET cc_start: 0.8063 (tmm) cc_final: 0.7819 (tmm) REVERT: c 102 ILE cc_start: 0.9216 (tp) cc_final: 0.8941 (tp) REVERT: c 105 ILE cc_start: 0.9231 (mm) cc_final: 0.8993 (mm) REVERT: c 117 ILE cc_start: 0.8931 (tp) cc_final: 0.8648 (tp) REVERT: c 158 ILE cc_start: 0.8936 (tp) cc_final: 0.8621 (tp) REVERT: c 173 SER cc_start: 0.8913 (t) cc_final: 0.8695 (t) REVERT: c 183 LYS cc_start: 0.9063 (mtmm) cc_final: 0.8586 (mtmm) REVERT: d 10 ASN cc_start: 0.8506 (m-40) cc_final: 0.8084 (m-40) REVERT: d 79 GLU cc_start: 0.7341 (tp30) cc_final: 0.7011 (tp30) REVERT: d 93 LYS cc_start: 0.8821 (mmpt) cc_final: 0.8612 (mmpt) REVERT: d 125 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8485 (tm-30) REVERT: d 126 ARG cc_start: 0.7913 (ttt180) cc_final: 0.7690 (tmm-80) REVERT: d 266 ARG cc_start: 0.8400 (mtm110) cc_final: 0.8171 (mtm110) REVERT: d 313 MET cc_start: 0.7532 (tmm) cc_final: 0.7240 (tmm) REVERT: d 314 LYS cc_start: 0.9125 (mmmt) cc_final: 0.8029 (mmmt) REVERT: d 317 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6767 (tm-30) REVERT: e 47 MET cc_start: 0.8626 (tmm) cc_final: 0.8343 (tmm) REVERT: e 53 LEU cc_start: 0.8808 (tp) cc_final: 0.8501 (tp) REVERT: f 19 PHE cc_start: 0.8100 (m-80) cc_final: 0.7858 (m-80) REVERT: f 30 LEU cc_start: 0.9006 (tp) cc_final: 0.8762 (tp) REVERT: g 34 LYS cc_start: 0.8569 (mmmt) cc_final: 0.8346 (mmmt) REVERT: g 68 LEU cc_start: 0.8823 (tp) cc_final: 0.8465 (tp) REVERT: h 65 ILE cc_start: 0.9069 (mm) cc_final: 0.8814 (mm) REVERT: h 106 PHE cc_start: 0.7045 (m-10) cc_final: 0.6772 (m-10) REVERT: h 121 GLN cc_start: 0.7863 (mp10) cc_final: 0.7515 (mp10) REVERT: h 126 PHE cc_start: 0.8276 (t80) cc_final: 0.8074 (t80) REVERT: h 129 MET cc_start: 0.8139 (tmm) cc_final: 0.7881 (tmm) REVERT: h 156 GLN cc_start: 0.8312 (tp-100) cc_final: 0.8078 (tp-100) REVERT: i 17 CYS cc_start: 0.8175 (t) cc_final: 0.7968 (t) REVERT: i 26 LEU cc_start: 0.8558 (mm) cc_final: 0.8206 (mm) REVERT: i 49 LEU cc_start: 0.7141 (tp) cc_final: 0.6938 (tp) REVERT: i 66 TYR cc_start: 0.7801 (m-10) cc_final: 0.7206 (m-10) REVERT: i 144 LEU cc_start: 0.8892 (tp) cc_final: 0.8601 (tp) REVERT: j 21 ILE cc_start: 0.8650 (tp) cc_final: 0.8442 (tp) REVERT: j 34 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7896 (mmtt) REVERT: j 73 LEU cc_start: 0.8078 (tp) cc_final: 0.7692 (tp) REVERT: j 91 LEU cc_start: 0.8882 (tp) cc_final: 0.8509 (tt) REVERT: j 149 LEU cc_start: 0.8682 (tp) cc_final: 0.8315 (tt) REVERT: k 11 PHE cc_start: 0.8283 (t80) cc_final: 0.7993 (t80) REVERT: k 30 TYR cc_start: 0.8503 (t80) cc_final: 0.8286 (t80) REVERT: k 39 ILE cc_start: 0.8296 (mm) cc_final: 0.8067 (mm) REVERT: k 85 TYR cc_start: 0.8600 (t80) cc_final: 0.8366 (t80) REVERT: k 129 MET cc_start: 0.7045 (tmm) cc_final: 0.6807 (tmm) REVERT: k 130 ILE cc_start: 0.8699 (mm) cc_final: 0.8407 (mm) REVERT: k 138 VAL cc_start: 0.8928 (p) cc_final: 0.8594 (t) REVERT: k 157 ASP cc_start: 0.8044 (p0) cc_final: 0.7814 (p0) REVERT: l 88 PHE cc_start: 0.7541 (m-80) cc_final: 0.7228 (m-80) REVERT: l 95 LEU cc_start: 0.8790 (mm) cc_final: 0.8469 (mm) REVERT: l 141 LEU cc_start: 0.8350 (tt) cc_final: 0.8130 (tt) REVERT: l 144 LEU cc_start: 0.8858 (tp) cc_final: 0.8279 (tp) REVERT: l 148 LEU cc_start: 0.8486 (mt) cc_final: 0.8168 (mt) REVERT: m 39 ILE cc_start: 0.8265 (mm) cc_final: 0.7106 (mm) REVERT: m 40 CYS cc_start: 0.8844 (m) cc_final: 0.8567 (m) REVERT: m 43 CYS cc_start: 0.7608 (m) cc_final: 0.7284 (m) REVERT: m 80 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8185 (tm-30) REVERT: m 121 GLN cc_start: 0.7901 (mp10) cc_final: 0.7539 (mp10) REVERT: m 129 MET cc_start: 0.7476 (tmm) cc_final: 0.7030 (tmm) REVERT: m 156 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7897 (tm-30) REVERT: n 21 ILE cc_start: 0.8779 (tp) cc_final: 0.8576 (tp) REVERT: n 22 ILE cc_start: 0.8894 (mt) cc_final: 0.8645 (mt) REVERT: n 30 TYR cc_start: 0.7900 (t80) cc_final: 0.6472 (t80) REVERT: n 34 LYS cc_start: 0.9072 (mmmm) cc_final: 0.8174 (mmtt) REVERT: n 46 ARG cc_start: 0.8100 (ttp80) cc_final: 0.7896 (ttp80) REVERT: n 58 ILE cc_start: 0.9185 (mm) cc_final: 0.8943 (mm) REVERT: n 59 MET cc_start: 0.8502 (tpp) cc_final: 0.8200 (mmm) REVERT: n 117 ARG cc_start: 0.7903 (mmt180) cc_final: 0.7580 (mmt180) REVERT: o 74 LEU cc_start: 0.8639 (tp) cc_final: 0.8398 (tp) REVERT: o 85 SER cc_start: 0.8882 (p) cc_final: 0.8260 (m) REVERT: o 152 MET cc_start: 0.7302 (tmm) cc_final: 0.6938 (tmm) outliers start: 90 outliers final: 53 residues processed: 1754 average time/residue: 0.5942 time to fit residues: 1738.4807 Evaluate side-chains 1696 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1641 time to evaluate : 5.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain K residue 122 GLN Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain b residue 224 LEU Chi-restraints excluded: chain b residue 228 ILE Chi-restraints excluded: chain b residue 238 ILE Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 147 TRP Chi-restraints excluded: chain d residue 210 THR Chi-restraints excluded: chain d residue 295 LEU Chi-restraints excluded: chain d residue 306 ILE Chi-restraints excluded: chain g residue 15 ILE Chi-restraints excluded: chain g residue 65 ILE Chi-restraints excluded: chain g residue 95 LEU Chi-restraints excluded: chain g residue 113 ASP Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain g residue 149 LEU Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain h residue 130 ILE Chi-restraints excluded: chain i residue 45 LEU Chi-restraints excluded: chain i residue 99 LEU Chi-restraints excluded: chain i residue 130 ILE Chi-restraints excluded: chain i residue 134 ILE Chi-restraints excluded: chain j residue 138 VAL Chi-restraints excluded: chain k residue 65 ILE Chi-restraints excluded: chain k residue 95 LEU Chi-restraints excluded: chain l residue 91 LEU Chi-restraints excluded: chain l residue 106 PHE Chi-restraints excluded: chain l residue 113 ASP Chi-restraints excluded: chain m residue 62 ILE Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain n residue 62 ILE Chi-restraints excluded: chain n residue 63 ILE Chi-restraints excluded: chain n residue 78 LEU Chi-restraints excluded: chain n residue 138 VAL Chi-restraints excluded: chain n residue 144 LEU Chi-restraints excluded: chain o residue 36 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 407 optimal weight: 40.0000 chunk 227 optimal weight: 0.5980 chunk 609 optimal weight: 7.9990 chunk 499 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 chunk 734 optimal weight: 6.9990 chunk 793 optimal weight: 4.9990 chunk 653 optimal weight: 0.8980 chunk 728 optimal weight: 6.9990 chunk 250 optimal weight: 8.9990 chunk 588 optimal weight: 9.9990 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN B 122 ASN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN D 186 GLN D 402 GLN E 53 HIS E 170 HIS E 378 GLN ** E 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN E 608 GLN K 122 GLN ** a 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 756 GLN ** c 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 132 ASN d 29 GLN ** d 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 90 GLN ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 151 ASN ** k 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 53 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.120 58646 Z= 0.497 Angle : 0.706 10.747 80001 Z= 0.375 Chirality : 0.048 0.228 9567 Planarity : 0.005 0.077 10420 Dihedral : 5.184 175.983 8735 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.47 % Favored : 96.52 % Rotamer: Outliers : 3.30 % Allowed : 15.84 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.09), residues: 8154 helix: 1.61 (0.07), residues: 4744 sheet: -1.51 (0.19), residues: 652 loop : -0.49 (0.12), residues: 2758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP a 594 HIS 0.009 0.002 HIS o 98 PHE 0.040 0.002 PHE k 88 TYR 0.043 0.002 TYR c 22 ARG 0.010 0.001 ARG M 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1825 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1657 time to evaluate : 5.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7475 (OUTLIER) cc_final: 0.6937 (m-80) REVERT: A 38 GLU cc_start: 0.7960 (tt0) cc_final: 0.7325 (tt0) REVERT: A 201 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7378 (tm-30) REVERT: A 205 LYS cc_start: 0.8603 (tmtt) cc_final: 0.8337 (tmtt) REVERT: A 487 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7810 (pt0) REVERT: A 523 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7346 (mm-30) REVERT: A 541 TRP cc_start: 0.8710 (p-90) cc_final: 0.8345 (p-90) REVERT: B 69 GLU cc_start: 0.7551 (tp30) cc_final: 0.6908 (tp30) REVERT: B 87 ASP cc_start: 0.8844 (p0) cc_final: 0.8535 (p0) REVERT: B 182 GLU cc_start: 0.7810 (mp0) cc_final: 0.7289 (mp0) REVERT: B 290 GLU cc_start: 0.7918 (tt0) cc_final: 0.7601 (tt0) REVERT: B 412 ASP cc_start: 0.7759 (m-30) cc_final: 0.7092 (m-30) REVERT: B 441 LYS cc_start: 0.8382 (mtmm) cc_final: 0.8125 (mtmt) REVERT: B 472 MET cc_start: 0.5785 (mtm) cc_final: 0.5571 (mtm) REVERT: C 108 ILE cc_start: 0.9148 (mm) cc_final: 0.8867 (mm) REVERT: C 118 GLU cc_start: 0.7901 (tp30) cc_final: 0.7321 (tp30) REVERT: C 285 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6922 (mm-30) REVERT: C 290 MET cc_start: 0.8259 (mmm) cc_final: 0.8036 (mmm) REVERT: C 296 GLU cc_start: 0.7036 (mp0) cc_final: 0.6766 (mm-30) REVERT: C 352 MET cc_start: 0.8675 (ttp) cc_final: 0.8132 (tmm) REVERT: C 442 ASP cc_start: 0.7885 (t0) cc_final: 0.7539 (t0) REVERT: C 472 ASP cc_start: 0.8016 (m-30) cc_final: 0.7760 (m-30) REVERT: C 504 LYS cc_start: 0.8876 (mttt) cc_final: 0.8665 (mmtp) REVERT: C 540 ILE cc_start: 0.8874 (tp) cc_final: 0.8621 (tt) REVERT: C 608 GLN cc_start: 0.8468 (tp40) cc_final: 0.8083 (tp-100) REVERT: D 51 GLU cc_start: 0.8063 (tt0) cc_final: 0.7599 (tt0) REVERT: D 74 ARG cc_start: 0.8082 (ttm110) cc_final: 0.7845 (ttm110) REVERT: D 400 SER cc_start: 0.8199 (t) cc_final: 0.7903 (p) REVERT: D 477 SER cc_start: 0.8990 (p) cc_final: 0.8740 (p) REVERT: E 500 GLN cc_start: 0.7954 (pp30) cc_final: 0.7551 (pp30) REVERT: F 42 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7298 (mm-30) REVERT: F 98 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7713 (mt-10) REVERT: F 106 GLU cc_start: 0.8108 (mp0) cc_final: 0.7888 (mp0) REVERT: F 150 MET cc_start: 0.8303 (ttt) cc_final: 0.8085 (ttt) REVERT: F 311 ASP cc_start: 0.7486 (t0) cc_final: 0.7073 (t0) REVERT: F 326 ASN cc_start: 0.8463 (m110) cc_final: 0.7984 (m110) REVERT: F 363 GLN cc_start: 0.7943 (mp10) cc_final: 0.7173 (mp10) REVERT: F 389 GLU cc_start: 0.8196 (tp30) cc_final: 0.7776 (tp30) REVERT: F 412 ASP cc_start: 0.7588 (m-30) cc_final: 0.7068 (m-30) REVERT: F 482 ASP cc_start: 0.7999 (m-30) cc_final: 0.7769 (m-30) REVERT: G 136 LYS cc_start: 0.9037 (mtmm) cc_final: 0.8818 (mtmm) REVERT: I 105 GLU cc_start: 0.8314 (mp0) cc_final: 0.7902 (mp0) REVERT: J 46 TYR cc_start: 0.8105 (t80) cc_final: 0.7850 (t80) REVERT: K 122 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7149 (mp-120) REVERT: M 182 GLU cc_start: 0.7804 (tp30) cc_final: 0.7586 (tp30) REVERT: M 221 MET cc_start: 0.4219 (ppp) cc_final: 0.3767 (ppp) REVERT: a 8 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8657 (tt) REVERT: a 31 TYR cc_start: 0.8373 (t80) cc_final: 0.8084 (t80) REVERT: a 60 ARG cc_start: 0.8804 (ptt90) cc_final: 0.8368 (ptt90) REVERT: a 68 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8166 (mm110) REVERT: a 285 TYR cc_start: 0.9110 (m-80) cc_final: 0.8848 (m-80) REVERT: a 316 GLU cc_start: 0.7670 (mp0) cc_final: 0.7406 (mp0) REVERT: a 324 ASN cc_start: 0.8743 (t0) cc_final: 0.8525 (m-40) REVERT: a 344 ASP cc_start: 0.7827 (p0) cc_final: 0.7358 (p0) REVERT: a 369 GLN cc_start: 0.7152 (tp-100) cc_final: 0.6941 (tp-100) REVERT: a 425 ASP cc_start: 0.7666 (m-30) cc_final: 0.6873 (m-30) REVERT: a 537 MET cc_start: 0.8366 (mmt) cc_final: 0.7980 (mmm) REVERT: a 538 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7284 (mttt) REVERT: a 737 TRP cc_start: 0.7943 (t60) cc_final: 0.7715 (t60) REVERT: a 743 HIS cc_start: 0.7711 (t-170) cc_final: 0.7378 (t-170) REVERT: a 745 GLN cc_start: 0.8036 (tp40) cc_final: 0.7732 (tp40) REVERT: a 753 MET cc_start: 0.7343 (ptm) cc_final: 0.6933 (tmm) REVERT: a 759 PHE cc_start: 0.7709 (t80) cc_final: 0.7194 (t80) REVERT: a 769 MET cc_start: 0.8376 (mtp) cc_final: 0.7703 (mtp) REVERT: a 773 LEU cc_start: 0.8648 (tp) cc_final: 0.8249 (tp) REVERT: a 774 PHE cc_start: 0.8237 (t80) cc_final: 0.7785 (t80) REVERT: a 776 MET cc_start: 0.8386 (tpp) cc_final: 0.7851 (tpp) REVERT: a 778 PHE cc_start: 0.8848 (t80) cc_final: 0.8644 (t80) REVERT: a 787 LEU cc_start: 0.8753 (tt) cc_final: 0.8523 (tt) REVERT: a 796 HIS cc_start: 0.8453 (m-70) cc_final: 0.8238 (m-70) REVERT: b 235 PHE cc_start: 0.8147 (t80) cc_final: 0.7721 (t80) REVERT: b 246 ASN cc_start: 0.8561 (m-40) cc_final: 0.8214 (m-40) REVERT: c 27 ILE cc_start: 0.9008 (tp) cc_final: 0.8755 (tp) REVERT: c 58 MET cc_start: 0.8211 (tmm) cc_final: 0.7925 (tmm) REVERT: c 102 ILE cc_start: 0.9369 (tp) cc_final: 0.9161 (tp) REVERT: c 117 ILE cc_start: 0.9017 (tp) cc_final: 0.8690 (tp) REVERT: c 138 ASN cc_start: 0.8090 (t0) cc_final: 0.7862 (t0) REVERT: c 158 ILE cc_start: 0.8981 (tp) cc_final: 0.8692 (tp) REVERT: d 125 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8667 (tm-30) REVERT: d 126 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7796 (tmm-80) REVERT: d 215 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8054 (tm-30) REVERT: d 247 LYS cc_start: 0.7877 (ptmm) cc_final: 0.7597 (ptmm) REVERT: d 266 ARG cc_start: 0.8516 (mtm110) cc_final: 0.8296 (mtm110) REVERT: d 304 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.7929 (m-10) REVERT: d 313 MET cc_start: 0.7902 (tmm) cc_final: 0.7201 (tmm) REVERT: d 314 LYS cc_start: 0.9167 (mmmt) cc_final: 0.7801 (mmmt) REVERT: d 317 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7057 (tm-30) REVERT: e 24 MET cc_start: 0.7646 (ptt) cc_final: 0.7429 (ptt) REVERT: e 47 MET cc_start: 0.8682 (tmm) cc_final: 0.8478 (tmm) REVERT: e 53 LEU cc_start: 0.8900 (tp) cc_final: 0.8526 (tp) REVERT: f 30 LEU cc_start: 0.9056 (tp) cc_final: 0.8786 (tp) REVERT: g 66 TYR cc_start: 0.8268 (m-80) cc_final: 0.7926 (m-80) REVERT: g 68 LEU cc_start: 0.8908 (tp) cc_final: 0.8560 (tp) REVERT: h 52 LYS cc_start: 0.9101 (tmtt) cc_final: 0.8721 (tttm) REVERT: h 62 ILE cc_start: 0.8869 (tp) cc_final: 0.8546 (tp) REVERT: h 65 ILE cc_start: 0.9139 (mm) cc_final: 0.8803 (mm) REVERT: h 77 SER cc_start: 0.9052 (p) cc_final: 0.8850 (p) REVERT: h 106 PHE cc_start: 0.7204 (m-80) cc_final: 0.6946 (m-10) REVERT: h 121 GLN cc_start: 0.8140 (mp10) cc_final: 0.7703 (mp10) REVERT: h 151 ASN cc_start: 0.8262 (t0) cc_final: 0.7975 (m-40) REVERT: i 26 LEU cc_start: 0.8734 (mm) cc_final: 0.8354 (mm) REVERT: i 49 LEU cc_start: 0.7435 (tp) cc_final: 0.7081 (tp) REVERT: i 66 TYR cc_start: 0.8306 (m-10) cc_final: 0.7802 (m-80) REVERT: i 102 LEU cc_start: 0.8818 (tp) cc_final: 0.8395 (tt) REVERT: i 129 MET cc_start: 0.7922 (tmm) cc_final: 0.7659 (tmm) REVERT: i 144 LEU cc_start: 0.8993 (tp) cc_final: 0.8089 (tp) REVERT: j 73 LEU cc_start: 0.8174 (tp) cc_final: 0.7761 (tp) REVERT: j 91 LEU cc_start: 0.8995 (tp) cc_final: 0.8617 (tt) REVERT: j 121 GLN cc_start: 0.8090 (mp10) cc_final: 0.7859 (mp10) REVERT: j 151 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8348 (t0) REVERT: k 11 PHE cc_start: 0.8510 (t80) cc_final: 0.8045 (t80) REVERT: k 39 ILE cc_start: 0.8532 (mm) cc_final: 0.8294 (mm) REVERT: k 85 TYR cc_start: 0.8622 (t80) cc_final: 0.8417 (t80) REVERT: k 130 ILE cc_start: 0.8825 (mm) cc_final: 0.8356 (mm) REVERT: k 149 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8270 (tp) REVERT: k 157 ASP cc_start: 0.8215 (p0) cc_final: 0.7959 (p0) REVERT: l 48 ASP cc_start: 0.8655 (p0) cc_final: 0.8450 (p0) REVERT: l 69 VAL cc_start: 0.9236 (m) cc_final: 0.9010 (p) REVERT: l 88 PHE cc_start: 0.7856 (m-80) cc_final: 0.7509 (m-80) REVERT: l 95 LEU cc_start: 0.8865 (mm) cc_final: 0.8519 (mm) REVERT: l 141 LEU cc_start: 0.8499 (tt) cc_final: 0.8247 (tt) REVERT: l 144 LEU cc_start: 0.8811 (tp) cc_final: 0.8309 (tp) REVERT: l 148 LEU cc_start: 0.8557 (mt) cc_final: 0.8249 (mt) REVERT: m 40 CYS cc_start: 0.8984 (m) cc_final: 0.8711 (m) REVERT: m 43 CYS cc_start: 0.7882 (m) cc_final: 0.7644 (m) REVERT: m 52 LYS cc_start: 0.9060 (tptm) cc_final: 0.8396 (tptp) REVERT: m 90 GLN cc_start: 0.8643 (mt0) cc_final: 0.7903 (mt0) REVERT: m 121 GLN cc_start: 0.8104 (mp10) cc_final: 0.7657 (mp10) REVERT: m 129 MET cc_start: 0.7598 (tmm) cc_final: 0.7115 (tmm) REVERT: m 153 ARG cc_start: 0.8260 (ttm170) cc_final: 0.7992 (ttp-170) REVERT: m 156 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7870 (tm-30) REVERT: n 21 ILE cc_start: 0.8863 (tp) cc_final: 0.8630 (tp) REVERT: n 22 ILE cc_start: 0.9007 (mt) cc_final: 0.8748 (mt) REVERT: n 59 MET cc_start: 0.8580 (tpp) cc_final: 0.8365 (mmm) REVERT: n 117 ARG cc_start: 0.8008 (mmt180) cc_final: 0.7517 (mmt180) REVERT: n 133 LEU cc_start: 0.9178 (mt) cc_final: 0.8966 (mm) REVERT: n 134 ILE cc_start: 0.9093 (mm) cc_final: 0.8884 (mm) REVERT: o 152 MET cc_start: 0.7476 (tmm) cc_final: 0.7145 (tmm) outliers start: 168 outliers final: 122 residues processed: 1708 average time/residue: 0.5543 time to fit residues: 1575.6925 Evaluate side-chains 1726 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1596 time to evaluate : 5.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 497 GLN Chi-restraints excluded: chain C residue 546 MET Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain K residue 122 GLN Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain a residue 8 ILE Chi-restraints excluded: chain a residue 14 MET Chi-restraints excluded: chain a residue 19 PHE Chi-restraints excluded: chain a residue 441 LEU Chi-restraints excluded: chain a residue 449 MET Chi-restraints excluded: chain a residue 481 ASP Chi-restraints excluded: chain a residue 518 LEU Chi-restraints excluded: chain a residue 538 LYS Chi-restraints excluded: chain a residue 546 ILE Chi-restraints excluded: chain a residue 586 LEU Chi-restraints excluded: chain a residue 596 VAL Chi-restraints excluded: chain a residue 601 ASP Chi-restraints excluded: chain b residue 224 LEU Chi-restraints excluded: chain b residue 227 LEU Chi-restraints excluded: chain b residue 238 ILE Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 243 TRP Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain c residue 147 TRP Chi-restraints excluded: chain c residue 197 LEU Chi-restraints excluded: chain d residue 29 GLN Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 126 ARG Chi-restraints excluded: chain d residue 210 THR Chi-restraints excluded: chain d residue 295 LEU Chi-restraints excluded: chain d residue 301 THR Chi-restraints excluded: chain d residue 304 PHE Chi-restraints excluded: chain d residue 320 VAL Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 50 ILE Chi-restraints excluded: chain f residue 27 ILE Chi-restraints excluded: chain g residue 15 ILE Chi-restraints excluded: chain g residue 32 THR Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 65 ILE Chi-restraints excluded: chain g residue 73 LEU Chi-restraints excluded: chain g residue 95 LEU Chi-restraints excluded: chain g residue 113 ASP Chi-restraints excluded: chain g residue 120 SER Chi-restraints excluded: chain g residue 133 LEU Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 130 ILE Chi-restraints excluded: chain h residue 131 LEU Chi-restraints excluded: chain i residue 45 LEU Chi-restraints excluded: chain i residue 99 LEU Chi-restraints excluded: chain i residue 130 ILE Chi-restraints excluded: chain i residue 134 ILE Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 137 GLU Chi-restraints excluded: chain j residue 145 ILE Chi-restraints excluded: chain j residue 151 ASN Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 49 LEU Chi-restraints excluded: chain k residue 86 THR Chi-restraints excluded: chain k residue 95 LEU Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain k residue 149 LEU Chi-restraints excluded: chain k residue 155 THR Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 63 ILE Chi-restraints excluded: chain l residue 72 VAL Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 91 LEU Chi-restraints excluded: chain l residue 108 ILE Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 113 ASP Chi-restraints excluded: chain l residue 150 LEU Chi-restraints excluded: chain m residue 37 VAL Chi-restraints excluded: chain m residue 62 ILE Chi-restraints excluded: chain m residue 69 VAL Chi-restraints excluded: chain m residue 73 LEU Chi-restraints excluded: chain m residue 75 CYS Chi-restraints excluded: chain m residue 81 LYS Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 119 SER Chi-restraints excluded: chain m residue 145 ILE Chi-restraints excluded: chain n residue 53 ASN Chi-restraints excluded: chain n residue 63 ILE Chi-restraints excluded: chain n residue 138 VAL Chi-restraints excluded: chain n residue 155 THR Chi-restraints excluded: chain o residue 84 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 725 optimal weight: 0.9980 chunk 551 optimal weight: 0.9980 chunk 381 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 350 optimal weight: 10.0000 chunk 492 optimal weight: 9.9990 chunk 736 optimal weight: 3.9990 chunk 780 optimal weight: 6.9990 chunk 384 optimal weight: 0.0770 chunk 698 optimal weight: 0.9990 chunk 210 optimal weight: 0.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: