Starting phenix.real_space_refine on Sat Sep 28 10:27:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxd_13698/09_2024/7pxd_13698_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxd_13698/09_2024/7pxd_13698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxd_13698/09_2024/7pxd_13698.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxd_13698/09_2024/7pxd_13698.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxd_13698/09_2024/7pxd_13698_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxd_13698/09_2024/7pxd_13698_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 179 5.16 5 C 43207 2.51 5 N 12113 2.21 5 O 13377 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 169 residue(s): 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 68900 Number of models: 1 Model: "" Number of chains: 42 Chain: "0" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "1" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "2" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "4" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "6" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "8" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "A" Number of atoms: 3692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3692 Classifications: {'peptide': 471} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain breaks: 4 Chain: "B" Number of atoms: 3761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3761 Classifications: {'peptide': 481} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 458} Chain breaks: 2 Chain: "C" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3685 Classifications: {'peptide': 471} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 448} Chain breaks: 3 Chain: "D" Number of atoms: 3584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3584 Classifications: {'peptide': 457} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 433} Chain breaks: 4 Chain: "E" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3775 Classifications: {'peptide': 483} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 460} Chain breaks: 2 Chain: "F" Number of atoms: 3773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3773 Classifications: {'peptide': 483} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 460} Chain breaks: 2 Chain: "G" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 112 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1650 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 7, 'TRANS': 206} Chain breaks: 1 Chain: "J" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1668 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Chain: "L" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "P" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "R" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1650 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 7, 'TRANS': 206} Chain breaks: 1 Chain: "U" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1715 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 226} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1715 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 226} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1650 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 7, 'TRANS': 206} Chain breaks: 1 Chain: "Y" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Z" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "a" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "f" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 32.68, per 1000 atoms: 0.47 Number of scatterers: 68900 At special positions: 0 Unit cell: (140.53, 153.972, 282.282, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 179 16.00 P 18 15.00 Mg 6 11.99 O 13377 8.00 N 12113 7.00 C 43207 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: 13.16 Conformation dependent library (CDL) restraints added in 7.2 seconds 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16466 Finding SS restraints... Secondary structure from input PDB file: 316 helices and 88 sheets defined 45.3% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.46 Creating SS restraints... Processing helix chain '0' and resid 8 through 26 removed outlier: 3.538A pdb=" N ALA 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) Processing helix chain '0' and resid 67 through 89 Processing helix chain '0' and resid 90 through 94 Processing helix chain '0' and resid 95 through 114 Processing helix chain '0' and resid 159 through 171 removed outlier: 4.612A pdb=" N ILE 0 163 " --> pdb=" O THR 0 159 " (cutoff:3.500A) Processing helix chain '0' and resid 176 through 190 Processing helix chain '0' and resid 226 through 234 removed outlier: 3.531A pdb=" N LEU 0 230 " --> pdb=" O THR 0 226 " (cutoff:3.500A) Processing helix chain '2' and resid 9 through 27 Processing helix chain '2' and resid 67 through 89 removed outlier: 4.228A pdb=" N ASN 2 73 " --> pdb=" O ASN 2 69 " (cutoff:3.500A) Processing helix chain '2' and resid 90 through 94 Processing helix chain '2' and resid 95 through 114 Processing helix chain '2' and resid 159 through 171 removed outlier: 4.604A pdb=" N ILE 2 163 " --> pdb=" O THR 2 159 " (cutoff:3.500A) Processing helix chain '2' and resid 176 through 190 Processing helix chain '2' and resid 226 through 234 removed outlier: 3.567A pdb=" N LEU 2 230 " --> pdb=" O THR 2 226 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 26 Processing helix chain '4' and resid 67 through 89 Processing helix chain '4' and resid 90 through 94 Processing helix chain '4' and resid 95 through 114 Processing helix chain '4' and resid 159 through 171 removed outlier: 4.601A pdb=" N ILE 4 163 " --> pdb=" O THR 4 159 " (cutoff:3.500A) Processing helix chain '4' and resid 176 through 190 Processing helix chain '4' and resid 226 through 234 removed outlier: 3.560A pdb=" N LEU 4 230 " --> pdb=" O THR 4 226 " (cutoff:3.500A) Processing helix chain '6' and resid 9 through 26 Processing helix chain '6' and resid 67 through 89 Processing helix chain '6' and resid 90 through 94 Processing helix chain '6' and resid 95 through 114 Processing helix chain '6' and resid 159 through 171 removed outlier: 4.618A pdb=" N ILE 6 163 " --> pdb=" O THR 6 159 " (cutoff:3.500A) Processing helix chain '6' and resid 176 through 190 Processing helix chain '6' and resid 226 through 234 removed outlier: 3.608A pdb=" N LEU 6 230 " --> pdb=" O THR 6 226 " (cutoff:3.500A) Processing helix chain '8' and resid 9 through 26 Processing helix chain '8' and resid 67 through 89 Processing helix chain '8' and resid 90 through 94 Processing helix chain '8' and resid 95 through 114 Processing helix chain '8' and resid 159 through 171 removed outlier: 4.634A pdb=" N ILE 8 163 " --> pdb=" O THR 8 159 " (cutoff:3.500A) Processing helix chain '8' and resid 176 through 190 Processing helix chain '8' and resid 226 through 234 removed outlier: 3.553A pdb=" N LEU 8 230 " --> pdb=" O THR 8 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'A' and resid 258 through 274 removed outlier: 4.456A pdb=" N LEU A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 274 through 282 removed outlier: 3.657A pdb=" N TYR A 278 " --> pdb=" O HIS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 318 Processing helix chain 'A' and resid 335 through 338 removed outlier: 3.578A pdb=" N LEU A 338 " --> pdb=" O PRO A 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 335 through 338' Processing helix chain 'A' and resid 344 through 363 removed outlier: 3.890A pdb=" N ILE A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 404 removed outlier: 4.511A pdb=" N VAL A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 460 through 466 removed outlier: 3.961A pdb=" N GLU A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 487 Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 511 through 514 Processing helix chain 'A' and resid 515 through 537 Processing helix chain 'A' and resid 543 through 558 removed outlier: 3.871A pdb=" N LEU A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 565 removed outlier: 4.452A pdb=" N THR A 564 " --> pdb=" O LEU A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 578 Processing helix chain 'B' and resid 236 through 240 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 259 through 274 Proline residue: B 271 - end of helix Processing helix chain 'B' and resid 274 through 282 Processing helix chain 'B' and resid 298 through 318 Processing helix chain 'B' and resid 334 through 338 removed outlier: 4.088A pdb=" N LEU B 337 " --> pdb=" O GLY B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 360 Processing helix chain 'B' and resid 388 through 402 removed outlier: 4.533A pdb=" N VAL B 392 " --> pdb=" O VAL B 388 " (cutoff:3.500A) Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 441 through 453 Processing helix chain 'B' and resid 460 through 467 removed outlier: 3.567A pdb=" N PHE B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 487 Processing helix chain 'B' and resid 511 through 514 removed outlier: 3.751A pdb=" N ASN B 514 " --> pdb=" O LYS B 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 511 through 514' Processing helix chain 'B' and resid 515 through 538 Processing helix chain 'B' and resid 543 through 559 removed outlier: 3.560A pdb=" N LEU B 547 " --> pdb=" O ARG B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 578 Processing helix chain 'C' and resid 236 through 242 removed outlier: 3.960A pdb=" N ASP C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 274 removed outlier: 3.634A pdb=" N ALA C 267 " --> pdb=" O GLN C 263 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU C 270 " --> pdb=" O ASP C 266 " (cutoff:3.500A) Proline residue: C 271 - end of helix removed outlier: 3.551A pdb=" N HIS C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 282 removed outlier: 3.542A pdb=" N TYR C 278 " --> pdb=" O HIS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 314 Processing helix chain 'C' and resid 343 through 361 Processing helix chain 'C' and resid 388 through 401 Proline residue: C 394 - end of helix Processing helix chain 'C' and resid 441 through 453 Processing helix chain 'C' and resid 460 through 467 Processing helix chain 'C' and resid 470 through 487 Processing helix chain 'C' and resid 490 through 492 No H-bonds generated for 'chain 'C' and resid 490 through 492' Processing helix chain 'C' and resid 511 through 514 removed outlier: 3.860A pdb=" N ASN C 514 " --> pdb=" O LYS C 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 511 through 514' Processing helix chain 'C' and resid 515 through 538 Processing helix chain 'C' and resid 543 through 554 removed outlier: 3.810A pdb=" N LEU C 547 " --> pdb=" O ARG C 543 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 578 removed outlier: 3.698A pdb=" N TRP C 570 " --> pdb=" O ASN C 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 257 through 268 Processing helix chain 'D' and resid 268 through 274 removed outlier: 4.203A pdb=" N PHE D 272 " --> pdb=" O VAL D 268 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 273 " --> pdb=" O GLU D 269 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS D 274 " --> pdb=" O LEU D 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 268 through 274' Processing helix chain 'D' and resid 274 through 281 Processing helix chain 'D' and resid 300 through 315 removed outlier: 3.508A pdb=" N LYS D 304 " --> pdb=" O THR D 300 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 338 removed outlier: 3.627A pdb=" N LEU D 338 " --> pdb=" O GLY D 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 334 through 338' Processing helix chain 'D' and resid 339 through 342 removed outlier: 4.040A pdb=" N VAL D 342 " --> pdb=" O ASN D 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 339 through 342' Processing helix chain 'D' and resid 343 through 362 removed outlier: 3.657A pdb=" N ARG D 347 " --> pdb=" O GLY D 343 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU D 362 " --> pdb=" O GLU D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 376 Processing helix chain 'D' and resid 392 through 403 Processing helix chain 'D' and resid 422 through 427 removed outlier: 3.700A pdb=" N LEU D 426 " --> pdb=" O ASP D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 453 Processing helix chain 'D' and resid 460 through 466 removed outlier: 3.964A pdb=" N GLU D 466 " --> pdb=" O ASP D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 487 Processing helix chain 'D' and resid 490 through 494 removed outlier: 3.662A pdb=" N ARG D 494 " --> pdb=" O ASP D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 538 removed outlier: 3.558A pdb=" N GLU D 536 " --> pdb=" O LYS D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 559 Processing helix chain 'D' and resid 569 through 578 removed outlier: 3.818A pdb=" N ILE D 573 " --> pdb=" O ASP D 569 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 574 " --> pdb=" O TRP D 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 135 Processing helix chain 'E' and resid 236 through 243 removed outlier: 3.766A pdb=" N ASP E 240 " --> pdb=" O ALA E 236 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU E 243 " --> pdb=" O GLU E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 254 Processing helix chain 'E' and resid 258 through 274 removed outlier: 4.298A pdb=" N LEU E 270 " --> pdb=" O ASP E 266 " (cutoff:3.500A) Proline residue: E 271 - end of helix Processing helix chain 'E' and resid 274 through 282 removed outlier: 3.608A pdb=" N TYR E 278 " --> pdb=" O HIS E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 318 removed outlier: 3.669A pdb=" N ALA E 307 " --> pdb=" O ALA E 303 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN E 308 " --> pdb=" O LYS E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 327 removed outlier: 3.557A pdb=" N ALA E 325 " --> pdb=" O ASP E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 338 removed outlier: 4.117A pdb=" N LEU E 337 " --> pdb=" O GLY E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 360 removed outlier: 3.792A pdb=" N ARG E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS E 359 " --> pdb=" O ARG E 355 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA E 360 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 376 removed outlier: 3.559A pdb=" N ILE E 376 " --> pdb=" O MET E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 401 removed outlier: 3.948A pdb=" N THR E 391 " --> pdb=" O ASP E 387 " (cutoff:3.500A) Proline residue: E 394 - end of helix Processing helix chain 'E' and resid 441 through 453 Processing helix chain 'E' and resid 460 through 467 removed outlier: 4.260A pdb=" N GLU E 466 " --> pdb=" O ASP E 462 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE E 467 " --> pdb=" O ASP E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 487 Processing helix chain 'E' and resid 490 through 492 No H-bonds generated for 'chain 'E' and resid 490 through 492' Processing helix chain 'E' and resid 515 through 538 Processing helix chain 'E' and resid 543 through 558 removed outlier: 3.911A pdb=" N LEU E 547 " --> pdb=" O ARG E 543 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 578 removed outlier: 3.978A pdb=" N ILE E 573 " --> pdb=" O ASP E 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 193 Processing helix chain 'F' and resid 250 through 254 Processing helix chain 'F' and resid 257 through 274 removed outlier: 4.438A pdb=" N LEU F 270 " --> pdb=" O ASP F 266 " (cutoff:3.500A) Proline residue: F 271 - end of helix Processing helix chain 'F' and resid 274 through 282 removed outlier: 3.933A pdb=" N TYR F 278 " --> pdb=" O HIS F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 316 Processing helix chain 'F' and resid 323 through 328 removed outlier: 3.559A pdb=" N TYR F 328 " --> pdb=" O GLU F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 338 Processing helix chain 'F' and resid 344 through 360 Processing helix chain 'F' and resid 388 through 400 Proline residue: F 394 - end of helix Processing helix chain 'F' and resid 417 through 421 Processing helix chain 'F' and resid 422 through 426 removed outlier: 3.605A pdb=" N ILE F 425 " --> pdb=" O ASP F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 453 Processing helix chain 'F' and resid 460 through 466 removed outlier: 4.332A pdb=" N GLU F 466 " --> pdb=" O ASP F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 487 Processing helix chain 'F' and resid 490 through 492 No H-bonds generated for 'chain 'F' and resid 490 through 492' Processing helix chain 'F' and resid 511 through 514 Processing helix chain 'F' and resid 515 through 538 Processing helix chain 'F' and resid 543 through 558 removed outlier: 3.650A pdb=" N LEU F 547 " --> pdb=" O ARG F 543 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL F 552 " --> pdb=" O LEU F 548 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 578 Processing helix chain 'H' and resid 348 through 371 Processing helix chain 'H' and resid 375 through 390 removed outlier: 3.520A pdb=" N ASN H 390 " --> pdb=" O MET H 386 " (cutoff:3.500A) Processing helix chain 'H' and resid 390 through 396 Processing helix chain 'H' and resid 413 through 416 Processing helix chain 'H' and resid 442 through 454 removed outlier: 4.062A pdb=" N LYS H 452 " --> pdb=" O SER H 448 " (cutoff:3.500A) Processing helix chain 'H' and resid 455 through 457 No H-bonds generated for 'chain 'H' and resid 455 through 457' Processing helix chain 'H' and resid 459 through 478 Processing helix chain 'H' and resid 506 through 522 removed outlier: 3.908A pdb=" N ILE H 510 " --> pdb=" O PRO H 506 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 26 Processing helix chain 'I' and resid 67 through 89 Processing helix chain 'I' and resid 90 through 94 Processing helix chain 'I' and resid 95 through 114 Processing helix chain 'I' and resid 160 through 171 Processing helix chain 'I' and resid 176 through 190 Processing helix chain 'I' and resid 204 through 206 No H-bonds generated for 'chain 'I' and resid 204 through 206' Processing helix chain 'I' and resid 226 through 234 Processing helix chain 'J' and resid 348 through 371 Processing helix chain 'J' and resid 375 through 390 removed outlier: 3.591A pdb=" N ASN J 390 " --> pdb=" O MET J 386 " (cutoff:3.500A) Processing helix chain 'J' and resid 390 through 396 removed outlier: 3.597A pdb=" N GLN J 396 " --> pdb=" O ALA J 392 " (cutoff:3.500A) Processing helix chain 'J' and resid 413 through 416 removed outlier: 3.508A pdb=" N SER J 416 " --> pdb=" O ASP J 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 413 through 416' Processing helix chain 'J' and resid 442 through 454 removed outlier: 3.718A pdb=" N LYS J 452 " --> pdb=" O SER J 448 " (cutoff:3.500A) Processing helix chain 'J' and resid 455 through 457 No H-bonds generated for 'chain 'J' and resid 455 through 457' Processing helix chain 'J' and resid 459 through 478 Processing helix chain 'J' and resid 506 through 522 removed outlier: 3.706A pdb=" N ILE J 510 " --> pdb=" O PRO J 506 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 26 Processing helix chain 'K' and resid 67 through 89 Processing helix chain 'K' and resid 90 through 94 Processing helix chain 'K' and resid 95 through 114 Processing helix chain 'K' and resid 159 through 171 removed outlier: 4.632A pdb=" N ILE K 163 " --> pdb=" O THR K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 190 Processing helix chain 'K' and resid 204 through 206 No H-bonds generated for 'chain 'K' and resid 204 through 206' Processing helix chain 'K' and resid 226 through 233 removed outlier: 3.513A pdb=" N LEU K 230 " --> pdb=" O THR K 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 348 through 371 Processing helix chain 'L' and resid 375 through 390 Processing helix chain 'L' and resid 390 through 396 Processing helix chain 'L' and resid 413 through 416 Processing helix chain 'L' and resid 442 through 454 removed outlier: 3.702A pdb=" N LYS L 452 " --> pdb=" O SER L 448 " (cutoff:3.500A) Processing helix chain 'L' and resid 455 through 457 No H-bonds generated for 'chain 'L' and resid 455 through 457' Processing helix chain 'L' and resid 459 through 478 Processing helix chain 'L' and resid 506 through 522 removed outlier: 3.697A pdb=" N ILE L 510 " --> pdb=" O PRO L 506 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 371 Processing helix chain 'M' and resid 375 through 390 Processing helix chain 'M' and resid 390 through 396 Processing helix chain 'M' and resid 413 through 416 Processing helix chain 'M' and resid 442 through 454 removed outlier: 4.009A pdb=" N LYS M 452 " --> pdb=" O SER M 448 " (cutoff:3.500A) Processing helix chain 'M' and resid 455 through 457 No H-bonds generated for 'chain 'M' and resid 455 through 457' Processing helix chain 'M' and resid 459 through 478 Processing helix chain 'M' and resid 506 through 522 removed outlier: 3.874A pdb=" N ILE M 510 " --> pdb=" O PRO M 506 " (cutoff:3.500A) Processing helix chain 'N' and resid 348 through 371 Processing helix chain 'N' and resid 375 through 390 Processing helix chain 'N' and resid 390 through 396 Processing helix chain 'N' and resid 413 through 416 Processing helix chain 'N' and resid 442 through 454 removed outlier: 4.094A pdb=" N LYS N 452 " --> pdb=" O SER N 448 " (cutoff:3.500A) Processing helix chain 'N' and resid 455 through 457 No H-bonds generated for 'chain 'N' and resid 455 through 457' Processing helix chain 'N' and resid 459 through 478 Processing helix chain 'N' and resid 506 through 522 removed outlier: 3.821A pdb=" N ILE N 510 " --> pdb=" O PRO N 506 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 26 removed outlier: 3.643A pdb=" N ARG O 14 " --> pdb=" O GLU O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 89 Processing helix chain 'O' and resid 90 through 94 Processing helix chain 'O' and resid 95 through 114 Processing helix chain 'O' and resid 160 through 171 Processing helix chain 'O' and resid 176 through 190 removed outlier: 3.540A pdb=" N ALA O 190 " --> pdb=" O ALA O 186 " (cutoff:3.500A) Processing helix chain 'O' and resid 226 through 234 removed outlier: 3.504A pdb=" N LEU O 230 " --> pdb=" O THR O 226 " (cutoff:3.500A) Processing helix chain 'P' and resid 348 through 371 Processing helix chain 'P' and resid 375 through 390 removed outlier: 3.587A pdb=" N ASN P 390 " --> pdb=" O MET P 386 " (cutoff:3.500A) Processing helix chain 'P' and resid 390 through 395 Processing helix chain 'P' and resid 413 through 416 removed outlier: 3.514A pdb=" N SER P 416 " --> pdb=" O ASP P 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 413 through 416' Processing helix chain 'P' and resid 442 through 454 removed outlier: 3.785A pdb=" N LYS P 452 " --> pdb=" O SER P 448 " (cutoff:3.500A) Processing helix chain 'P' and resid 455 through 457 No H-bonds generated for 'chain 'P' and resid 455 through 457' Processing helix chain 'P' and resid 459 through 478 Processing helix chain 'P' and resid 506 through 523 removed outlier: 3.695A pdb=" N ILE P 510 " --> pdb=" O PRO P 506 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY P 523 " --> pdb=" O GLU P 519 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 27 removed outlier: 3.692A pdb=" N ALA Q 27 " --> pdb=" O GLY Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 89 Processing helix chain 'Q' and resid 90 through 94 Processing helix chain 'Q' and resid 95 through 114 Processing helix chain 'Q' and resid 160 through 171 Processing helix chain 'Q' and resid 176 through 190 removed outlier: 3.568A pdb=" N ALA Q 190 " --> pdb=" O ALA Q 186 " (cutoff:3.500A) Processing helix chain 'Q' and resid 204 through 206 No H-bonds generated for 'chain 'Q' and resid 204 through 206' Processing helix chain 'Q' and resid 226 through 234 removed outlier: 3.539A pdb=" N LEU Q 230 " --> pdb=" O THR Q 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 348 through 371 Processing helix chain 'R' and resid 375 through 390 Processing helix chain 'R' and resid 390 through 396 Processing helix chain 'R' and resid 413 through 416 Processing helix chain 'R' and resid 442 through 454 removed outlier: 3.718A pdb=" N LYS R 452 " --> pdb=" O SER R 448 " (cutoff:3.500A) Processing helix chain 'R' and resid 455 through 457 No H-bonds generated for 'chain 'R' and resid 455 through 457' Processing helix chain 'R' and resid 459 through 478 Processing helix chain 'R' and resid 506 through 522 removed outlier: 3.757A pdb=" N ILE R 510 " --> pdb=" O PRO R 506 " (cutoff:3.500A) Processing helix chain 'S' and resid 348 through 371 Processing helix chain 'S' and resid 375 through 390 Processing helix chain 'S' and resid 390 through 396 Processing helix chain 'S' and resid 413 through 416 Processing helix chain 'S' and resid 442 through 454 removed outlier: 4.024A pdb=" N LYS S 452 " --> pdb=" O SER S 448 " (cutoff:3.500A) Processing helix chain 'S' and resid 455 through 457 No H-bonds generated for 'chain 'S' and resid 455 through 457' Processing helix chain 'S' and resid 459 through 478 Processing helix chain 'S' and resid 506 through 522 removed outlier: 3.835A pdb=" N ILE S 510 " --> pdb=" O PRO S 506 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 26 Processing helix chain 'T' and resid 67 through 89 Processing helix chain 'T' and resid 90 through 94 Processing helix chain 'T' and resid 95 through 114 Processing helix chain 'T' and resid 160 through 171 Processing helix chain 'T' and resid 176 through 190 Processing helix chain 'T' and resid 204 through 206 No H-bonds generated for 'chain 'T' and resid 204 through 206' Processing helix chain 'T' and resid 226 through 233 removed outlier: 3.614A pdb=" N LEU T 233 " --> pdb=" O ALA T 229 " (cutoff:3.500A) Processing helix chain 'U' and resid 348 through 371 Processing helix chain 'U' and resid 375 through 390 Processing helix chain 'U' and resid 390 through 396 removed outlier: 3.660A pdb=" N GLN U 396 " --> pdb=" O ALA U 392 " (cutoff:3.500A) Processing helix chain 'U' and resid 413 through 416 Processing helix chain 'U' and resid 442 through 454 removed outlier: 3.764A pdb=" N LYS U 452 " --> pdb=" O SER U 448 " (cutoff:3.500A) Processing helix chain 'U' and resid 455 through 457 No H-bonds generated for 'chain 'U' and resid 455 through 457' Processing helix chain 'U' and resid 459 through 478 Processing helix chain 'U' and resid 506 through 528 removed outlier: 3.728A pdb=" N ILE U 510 " --> pdb=" O PRO U 506 " (cutoff:3.500A) Processing helix chain 'V' and resid 348 through 371 Processing helix chain 'V' and resid 375 through 390 Processing helix chain 'V' and resid 390 through 396 Processing helix chain 'V' and resid 413 through 416 Processing helix chain 'V' and resid 442 through 454 removed outlier: 4.082A pdb=" N LYS V 452 " --> pdb=" O SER V 448 " (cutoff:3.500A) Processing helix chain 'V' and resid 455 through 457 No H-bonds generated for 'chain 'V' and resid 455 through 457' Processing helix chain 'V' and resid 459 through 478 Processing helix chain 'V' and resid 506 through 523 removed outlier: 3.864A pdb=" N ILE V 510 " --> pdb=" O PRO V 506 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY V 523 " --> pdb=" O GLU V 519 " (cutoff:3.500A) Processing helix chain 'W' and resid 348 through 371 Processing helix chain 'W' and resid 375 through 390 removed outlier: 3.522A pdb=" N ASN W 390 " --> pdb=" O MET W 386 " (cutoff:3.500A) Processing helix chain 'W' and resid 390 through 396 Processing helix chain 'W' and resid 413 through 416 Processing helix chain 'W' and resid 442 through 454 removed outlier: 4.097A pdb=" N LYS W 452 " --> pdb=" O SER W 448 " (cutoff:3.500A) Processing helix chain 'W' and resid 455 through 457 No H-bonds generated for 'chain 'W' and resid 455 through 457' Processing helix chain 'W' and resid 459 through 478 Processing helix chain 'W' and resid 506 through 528 removed outlier: 3.953A pdb=" N ILE W 510 " --> pdb=" O PRO W 506 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 26 removed outlier: 3.544A pdb=" N ARG X 14 " --> pdb=" O GLU X 10 " (cutoff:3.500A) Processing helix chain 'X' and resid 67 through 89 Processing helix chain 'X' and resid 90 through 94 Processing helix chain 'X' and resid 95 through 114 Processing helix chain 'X' and resid 160 through 171 Processing helix chain 'X' and resid 176 through 190 Processing helix chain 'X' and resid 227 through 233 removed outlier: 3.564A pdb=" N LEU X 233 " --> pdb=" O ALA X 229 " (cutoff:3.500A) Processing helix chain 'Y' and resid 348 through 371 Processing helix chain 'Y' and resid 375 through 390 Processing helix chain 'Y' and resid 390 through 396 Processing helix chain 'Y' and resid 413 through 416 Processing helix chain 'Y' and resid 442 through 454 removed outlier: 3.722A pdb=" N LYS Y 452 " --> pdb=" O SER Y 448 " (cutoff:3.500A) Processing helix chain 'Y' and resid 455 through 457 No H-bonds generated for 'chain 'Y' and resid 455 through 457' Processing helix chain 'Y' and resid 459 through 478 Processing helix chain 'Y' and resid 506 through 523 removed outlier: 3.708A pdb=" N ILE Y 510 " --> pdb=" O PRO Y 506 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY Y 523 " --> pdb=" O GLU Y 519 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 26 removed outlier: 4.151A pdb=" N MET Z 13 " --> pdb=" O PRO Z 9 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG Z 14 " --> pdb=" O GLU Z 10 " (cutoff:3.500A) Processing helix chain 'Z' and resid 67 through 89 Processing helix chain 'Z' and resid 90 through 94 Processing helix chain 'Z' and resid 95 through 114 Processing helix chain 'Z' and resid 160 through 171 Processing helix chain 'Z' and resid 176 through 190 removed outlier: 3.536A pdb=" N ALA Z 190 " --> pdb=" O ALA Z 186 " (cutoff:3.500A) Processing helix chain 'Z' and resid 204 through 206 No H-bonds generated for 'chain 'Z' and resid 204 through 206' Processing helix chain 'Z' and resid 226 through 233 Processing helix chain 'a' and resid 348 through 371 Processing helix chain 'a' and resid 375 through 389 Processing helix chain 'a' and resid 390 through 396 Processing helix chain 'a' and resid 413 through 416 removed outlier: 3.503A pdb=" N SER a 416 " --> pdb=" O ASP a 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 413 through 416' Processing helix chain 'a' and resid 442 through 454 removed outlier: 3.716A pdb=" N LYS a 452 " --> pdb=" O SER a 448 " (cutoff:3.500A) Processing helix chain 'a' and resid 455 through 457 No H-bonds generated for 'chain 'a' and resid 455 through 457' Processing helix chain 'a' and resid 459 through 478 Processing helix chain 'a' and resid 506 through 523 removed outlier: 3.751A pdb=" N ILE a 510 " --> pdb=" O PRO a 506 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY a 523 " --> pdb=" O GLU a 519 " (cutoff:3.500A) Processing helix chain 'b' and resid 348 through 371 Processing helix chain 'b' and resid 375 through 390 Processing helix chain 'b' and resid 390 through 396 Processing helix chain 'b' and resid 413 through 416 Processing helix chain 'b' and resid 442 through 454 removed outlier: 4.078A pdb=" N LYS b 452 " --> pdb=" O SER b 448 " (cutoff:3.500A) Processing helix chain 'b' and resid 455 through 457 No H-bonds generated for 'chain 'b' and resid 455 through 457' Processing helix chain 'b' and resid 459 through 478 Processing helix chain 'b' and resid 506 through 522 removed outlier: 3.854A pdb=" N ILE b 510 " --> pdb=" O PRO b 506 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 26 removed outlier: 3.662A pdb=" N ARG d 16 " --> pdb=" O ALA d 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 89 Processing helix chain 'd' and resid 90 through 94 Processing helix chain 'd' and resid 95 through 114 Processing helix chain 'd' and resid 159 through 171 removed outlier: 4.631A pdb=" N ILE d 163 " --> pdb=" O THR d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 190 Processing helix chain 'd' and resid 226 through 234 removed outlier: 3.551A pdb=" N LEU d 230 " --> pdb=" O THR d 226 " (cutoff:3.500A) Processing helix chain 'f' and resid 9 through 26 Processing helix chain 'f' and resid 67 through 89 Processing helix chain 'f' and resid 90 through 94 Processing helix chain 'f' and resid 95 through 114 removed outlier: 3.687A pdb=" N PHE f 111 " --> pdb=" O LEU f 107 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR f 112 " --> pdb=" O GLY f 108 " (cutoff:3.500A) Processing helix chain 'f' and resid 159 through 171 removed outlier: 3.961A pdb=" N ILE f 163 " --> pdb=" O THR f 159 " (cutoff:3.500A) Processing helix chain 'f' and resid 176 through 190 Processing helix chain 'f' and resid 226 through 234 removed outlier: 3.536A pdb=" N LEU f 230 " --> pdb=" O THR f 226 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '0' and resid 153 through 156 Processing sheet with id=AA2, first strand: chain '0' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL 0 60 " --> pdb=" O LEU 0 56 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU 0 138 " --> pdb=" O GLU 0 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 153 through 156 Processing sheet with id=AA4, first strand: chain '2' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL 2 60 " --> pdb=" O LEU 2 56 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU 2 138 " --> pdb=" O GLU 2 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '4' and resid 153 through 156 Processing sheet with id=AA6, first strand: chain '4' and resid 53 through 57 removed outlier: 6.490A pdb=" N VAL 4 60 " --> pdb=" O LEU 4 56 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU 4 138 " --> pdb=" O GLU 4 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '6' and resid 153 through 156 Processing sheet with id=AA8, first strand: chain '6' and resid 53 through 57 removed outlier: 6.466A pdb=" N VAL 6 60 " --> pdb=" O LEU 6 56 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU 6 138 " --> pdb=" O GLU 6 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '8' and resid 153 through 156 Processing sheet with id=AB1, first strand: chain '8' and resid 53 through 57 removed outlier: 6.462A pdb=" N VAL 8 60 " --> pdb=" O LEU 8 56 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU 8 138 " --> pdb=" O GLU 8 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 120 through 125 removed outlier: 7.256A pdb=" N THR A 112 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N THR A 107 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP A 114 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A 151 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 159 through 167 removed outlier: 6.873A pdb=" N LEU A 175 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE A 167 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ARG A 173 " --> pdb=" O ILE A 167 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 184 through 188 current: chain 'A' and resid 228 through 232 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 228 through 232 current: chain 'B' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 183 through 188 current: chain 'B' and resid 228 through 232 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 228 through 232 current: chain 'C' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 183 through 188 current: chain 'C' and resid 228 through 233 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 228 through 233 current: chain 'D' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 183 through 188 current: chain 'D' and resid 228 through 233 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 228 through 233 current: chain 'E' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 183 through 188 current: chain 'E' and resid 228 through 232 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 228 through 232 current: chain 'F' and resid 173 through 176 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 184 through 188 current: chain 'F' and resid 228 through 233 Processing sheet with id=AB4, first strand: chain 'A' and resid 329 through 333 removed outlier: 6.519A pdb=" N VAL A 366 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE A 412 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL A 368 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ALA A 414 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE A 370 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLY A 288 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE A 435 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU A 290 " --> pdb=" O ILE A 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 506 through 509 removed outlier: 6.199A pdb=" N GLU A 506 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLU A 497 " --> pdb=" O GLU A 506 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N MET A 508 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N PHE A 495 " --> pdb=" O THR A 586 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N THR A 586 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLU A 497 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE A 584 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR A 499 " --> pdb=" O VAL A 582 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 99 through 107 removed outlier: 6.641A pdb=" N ASP B 114 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N THR B 107 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N THR B 112 " --> pdb=" O THR B 107 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 120 through 125 current: chain 'B' and resid 151 through 152 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 151 through 152 current: chain 'E' and resid 112 through 117 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 120 through 125 current: chain 'E' and resid 151 through 153 Processing sheet with id=AB7, first strand: chain 'B' and resid 329 through 332 Processing sheet with id=AB8, first strand: chain 'B' and resid 505 through 509 Processing sheet with id=AB9, first strand: chain 'C' and resid 120 through 125 removed outlier: 7.232A pdb=" N THR C 112 " --> pdb=" O THR C 107 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N THR C 107 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASP C 114 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU C 151 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 328 through 332 removed outlier: 6.827A pdb=" N TYR C 328 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N PHE C 369 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU C 330 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL C 289 " --> pdb=" O GLY C 413 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N SER C 415 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU C 291 " --> pdb=" O SER C 415 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 507 through 509 removed outlier: 3.989A pdb=" N TYR C 583 " --> pdb=" O THR C 499 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 120 through 125 removed outlier: 7.513A pdb=" N THR D 112 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N THR D 107 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASP D 114 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU D 151 " --> pdb=" O ARG D 142 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 328 through 333 removed outlier: 3.566A pdb=" N ILE D 367 " --> pdb=" O TYR D 328 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL D 366 " --> pdb=" O ILE D 410 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ILE D 412 " --> pdb=" O VAL D 366 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N VAL D 368 " --> pdb=" O ILE D 412 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ALA D 414 " --> pdb=" O VAL D 368 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE D 370 " --> pdb=" O ALA D 414 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER D 415 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY D 288 " --> pdb=" O VAL D 433 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE D 435 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU D 290 " --> pdb=" O ILE D 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 496 through 499 Processing sheet with id=AC6, first strand: chain 'E' and resid 329 through 331 removed outlier: 6.565A pdb=" N LEU E 330 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL E 366 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE E 412 " --> pdb=" O VAL E 366 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL E 368 " --> pdb=" O ILE E 412 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ALA E 414 " --> pdb=" O VAL E 368 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE E 370 " --> pdb=" O ALA E 414 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL E 289 " --> pdb=" O GLY E 413 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N SER E 415 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU E 291 " --> pdb=" O SER E 415 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL E 433 " --> pdb=" O GLY E 288 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 494 through 498 removed outlier: 6.790A pdb=" N MET E 508 " --> pdb=" O PHE E 495 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU E 497 " --> pdb=" O GLU E 506 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLU E 506 " --> pdb=" O GLU E 497 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 120 through 125 removed outlier: 7.558A pdb=" N THR F 112 " --> pdb=" O THR F 107 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N THR F 107 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP F 114 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU F 151 " --> pdb=" O ARG F 142 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 330 through 333 removed outlier: 6.910A pdb=" N LEU F 330 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ASP F 371 " --> pdb=" O LEU F 330 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE F 332 " --> pdb=" O ASP F 371 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU F 290 " --> pdb=" O ILE F 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 505 through 509 Processing sheet with id=AD2, first strand: chain 'H' and resid 436 through 439 Processing sheet with id=AD3, first strand: chain 'H' and resid 320 through 322 removed outlier: 6.421A pdb=" N SER H 320 " --> pdb=" O SER H 327 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 334 through 338 removed outlier: 6.644A pdb=" N THR H 341 " --> pdb=" O THR H 337 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE H 423 " --> pdb=" O PRO H 402 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 153 through 156 Processing sheet with id=AD6, first strand: chain 'I' and resid 53 through 57 removed outlier: 6.557A pdb=" N VAL I 60 " --> pdb=" O LEU I 56 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU I 138 " --> pdb=" O GLU I 150 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 436 through 440 Processing sheet with id=AD8, first strand: chain 'J' and resid 320 through 322 removed outlier: 6.490A pdb=" N SER J 320 " --> pdb=" O SER J 327 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET J 325 " --> pdb=" O GLN J 322 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 334 through 338 removed outlier: 6.345A pdb=" N VAL J 334 " --> pdb=" O ILE J 345 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE J 345 " --> pdb=" O VAL J 334 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ILE J 336 " --> pdb=" O THR J 343 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR J 343 " --> pdb=" O ILE J 336 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP J 338 " --> pdb=" O THR J 341 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE J 423 " --> pdb=" O PRO J 402 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 153 through 156 Processing sheet with id=AE2, first strand: chain 'K' and resid 53 through 57 removed outlier: 6.599A pdb=" N VAL K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU K 138 " --> pdb=" O GLU K 150 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 436 through 440 Processing sheet with id=AE4, first strand: chain 'L' and resid 320 through 322 removed outlier: 6.473A pdb=" N SER L 320 " --> pdb=" O SER L 327 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET L 325 " --> pdb=" O GLN L 322 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 334 through 338 removed outlier: 6.508A pdb=" N THR L 341 " --> pdb=" O THR L 337 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE L 423 " --> pdb=" O PRO L 402 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 436 through 440 Processing sheet with id=AE7, first strand: chain 'M' and resid 320 through 322 removed outlier: 6.385A pdb=" N SER M 320 " --> pdb=" O SER M 327 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 334 through 338 removed outlier: 6.648A pdb=" N THR M 341 " --> pdb=" O THR M 337 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE M 423 " --> pdb=" O PRO M 402 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 436 through 439 Processing sheet with id=AF1, first strand: chain 'N' and resid 320 through 322 removed outlier: 6.439A pdb=" N SER N 320 " --> pdb=" O SER N 327 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 334 through 338 removed outlier: 6.535A pdb=" N THR N 341 " --> pdb=" O THR N 337 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE N 423 " --> pdb=" O PRO N 402 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 153 through 156 Processing sheet with id=AF4, first strand: chain 'O' and resid 53 through 57 removed outlier: 6.573A pdb=" N VAL O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU O 138 " --> pdb=" O GLU O 150 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P' and resid 436 through 440 Processing sheet with id=AF6, first strand: chain 'P' and resid 320 through 322 removed outlier: 6.434A pdb=" N SER P 320 " --> pdb=" O SER P 327 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET P 325 " --> pdb=" O GLN P 322 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'P' and resid 334 through 338 removed outlier: 6.480A pdb=" N THR P 341 " --> pdb=" O THR P 337 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE P 423 " --> pdb=" O PRO P 402 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Q' and resid 153 through 156 Processing sheet with id=AF9, first strand: chain 'Q' and resid 53 through 57 removed outlier: 6.604A pdb=" N VAL Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU Q 138 " --> pdb=" O GLU Q 150 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'R' and resid 436 through 440 Processing sheet with id=AG2, first strand: chain 'R' and resid 320 through 322 removed outlier: 6.527A pdb=" N SER R 320 " --> pdb=" O SER R 327 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET R 325 " --> pdb=" O GLN R 322 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'R' and resid 334 through 338 removed outlier: 6.483A pdb=" N THR R 341 " --> pdb=" O THR R 337 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE R 423 " --> pdb=" O PRO R 402 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'S' and resid 436 through 439 Processing sheet with id=AG5, first strand: chain 'S' and resid 320 through 322 removed outlier: 6.384A pdb=" N SER S 320 " --> pdb=" O SER S 327 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'S' and resid 334 through 338 removed outlier: 6.496A pdb=" N THR S 341 " --> pdb=" O THR S 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE S 423 " --> pdb=" O PRO S 402 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'T' and resid 153 through 156 Processing sheet with id=AG8, first strand: chain 'T' and resid 53 through 57 removed outlier: 6.557A pdb=" N VAL T 60 " --> pdb=" O LEU T 56 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU T 138 " --> pdb=" O GLU T 150 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'U' and resid 436 through 440 Processing sheet with id=AH1, first strand: chain 'U' and resid 320 through 322 removed outlier: 6.517A pdb=" N SER U 320 " --> pdb=" O SER U 327 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET U 325 " --> pdb=" O GLN U 322 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'U' and resid 334 through 338 removed outlier: 6.496A pdb=" N THR U 341 " --> pdb=" O THR U 337 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE U 423 " --> pdb=" O PRO U 402 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE U 420 " --> pdb=" O GLU U 432 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'V' and resid 436 through 439 Processing sheet with id=AH4, first strand: chain 'V' and resid 320 through 322 removed outlier: 6.375A pdb=" N SER V 320 " --> pdb=" O SER V 327 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'V' and resid 334 through 338 removed outlier: 6.543A pdb=" N THR V 341 " --> pdb=" O THR V 337 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE V 423 " --> pdb=" O PRO V 402 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'W' and resid 436 through 439 Processing sheet with id=AH7, first strand: chain 'W' and resid 320 through 322 removed outlier: 6.414A pdb=" N SER W 320 " --> pdb=" O SER W 327 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'W' and resid 334 through 338 removed outlier: 6.646A pdb=" N THR W 341 " --> pdb=" O THR W 337 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE W 423 " --> pdb=" O PRO W 402 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'X' and resid 153 through 156 Processing sheet with id=AI1, first strand: chain 'X' and resid 53 through 57 removed outlier: 6.604A pdb=" N VAL X 60 " --> pdb=" O LEU X 56 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU X 138 " --> pdb=" O GLU X 150 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Y' and resid 436 through 440 Processing sheet with id=AI3, first strand: chain 'Y' and resid 320 through 322 removed outlier: 6.640A pdb=" N SER Y 320 " --> pdb=" O SER Y 327 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET Y 325 " --> pdb=" O GLN Y 322 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Y' and resid 334 through 338 removed outlier: 6.369A pdb=" N VAL Y 334 " --> pdb=" O ILE Y 345 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE Y 345 " --> pdb=" O VAL Y 334 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ILE Y 336 " --> pdb=" O THR Y 343 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR Y 343 " --> pdb=" O ILE Y 336 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP Y 338 " --> pdb=" O THR Y 341 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE Y 423 " --> pdb=" O PRO Y 402 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Z' and resid 153 through 156 Processing sheet with id=AI6, first strand: chain 'Z' and resid 53 through 57 removed outlier: 6.596A pdb=" N VAL Z 60 " --> pdb=" O LEU Z 56 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU Z 138 " --> pdb=" O GLU Z 150 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'a' and resid 436 through 440 Processing sheet with id=AI8, first strand: chain 'a' and resid 320 through 322 removed outlier: 6.396A pdb=" N GLN a 322 " --> pdb=" O ILE a 326 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE a 326 " --> pdb=" O GLN a 322 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'a' and resid 334 through 338 removed outlier: 6.397A pdb=" N VAL a 334 " --> pdb=" O ILE a 345 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE a 345 " --> pdb=" O VAL a 334 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE a 336 " --> pdb=" O THR a 343 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR a 343 " --> pdb=" O ILE a 336 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP a 338 " --> pdb=" O THR a 341 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE a 423 " --> pdb=" O PRO a 402 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'b' and resid 436 through 440 Processing sheet with id=AJ2, first strand: chain 'b' and resid 320 through 322 removed outlier: 6.392A pdb=" N SER b 320 " --> pdb=" O SER b 327 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'b' and resid 334 through 338 removed outlier: 6.630A pdb=" N THR b 341 " --> pdb=" O THR b 337 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE b 423 " --> pdb=" O PRO b 402 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'd' and resid 153 through 156 Processing sheet with id=AJ5, first strand: chain 'd' and resid 53 through 57 removed outlier: 6.492A pdb=" N VAL d 60 " --> pdb=" O LEU d 56 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU d 138 " --> pdb=" O GLU d 150 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'f' and resid 153 through 156 Processing sheet with id=AJ7, first strand: chain 'f' and resid 53 through 57 removed outlier: 6.493A pdb=" N VAL f 60 " --> pdb=" O LEU f 56 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU f 138 " --> pdb=" O GLU f 150 " (cutoff:3.500A) 3916 hydrogen bonds defined for protein. 11214 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: 41.31 Time building geometry restraints manager: 15.87 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: 19764 1.33 - 1.46: 13417 1.46 - 1.58: 36418 1.58 - 1.70: 32 1.70 - 1.83: 326 Bond restraints: 69957 Sorted by residual: bond pdb=" C4 ATP E 701 " pdb=" C5 ATP E 701 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.88e+01 bond pdb=" C4 ATP C 701 " pdb=" C5 ATP C 701 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.72e+01 bond pdb=" CA TYR Z 89 " pdb=" C TYR Z 89 " ideal model delta sigma weight residual 1.517 1.466 0.051 6.30e-03 2.52e+04 6.68e+01 bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.66e+01 bond pdb=" C4 ATP B 701 " pdb=" C5 ATP B 701 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.59e+01 ... (remaining 69952 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.25: 94309 4.25 - 8.50: 360 8.50 - 12.75: 15 12.75 - 17.00: 1 17.00 - 21.25: 9 Bond angle restraints: 94694 Sorted by residual: angle pdb=" PB ATP D 701 " pdb=" O3B ATP D 701 " pdb=" PG ATP D 701 " ideal model delta sigma weight residual 139.87 118.62 21.25 1.00e+00 1.00e+00 4.51e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 118.03 18.80 1.00e+00 1.00e+00 3.53e+02 angle pdb=" PA ATP B 701 " pdb=" O3A ATP B 701 " pdb=" PB ATP B 701 " ideal model delta sigma weight residual 136.83 118.22 18.61 1.00e+00 1.00e+00 3.46e+02 angle pdb=" PA ATP C 701 " pdb=" O3A ATP C 701 " pdb=" PB ATP C 701 " ideal model delta sigma weight residual 136.83 118.38 18.45 1.00e+00 1.00e+00 3.40e+02 angle pdb=" PA ATP E 701 " pdb=" O3A ATP E 701 " pdb=" PB ATP E 701 " ideal model delta sigma weight residual 136.83 118.77 18.06 1.00e+00 1.00e+00 3.26e+02 ... (remaining 94689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.26: 39011 18.26 - 36.52: 2589 36.52 - 54.78: 603 54.78 - 73.04: 156 73.04 - 91.30: 98 Dihedral angle restraints: 42457 sinusoidal: 16692 harmonic: 25765 Sorted by residual: dihedral pdb=" CA ARG D 439 " pdb=" C ARG D 439 " pdb=" N PRO D 440 " pdb=" CA PRO D 440 " ideal model delta harmonic sigma weight residual -180.00 -153.38 -26.62 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA VAL D 242 " pdb=" C VAL D 242 " pdb=" N LEU D 243 " pdb=" CA LEU D 243 " ideal model delta harmonic sigma weight residual 180.00 156.85 23.15 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA LYS D 340 " pdb=" C LYS D 340 " pdb=" N PHE D 341 " pdb=" CA PHE D 341 " ideal model delta harmonic sigma weight residual 180.00 -158.00 -22.00 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 42454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 9064 0.069 - 0.138: 1557 0.138 - 0.208: 119 0.208 - 0.277: 17 0.277 - 0.346: 2 Chirality restraints: 10759 Sorted by residual: chirality pdb=" CA ASP B 504 " pdb=" N ASP B 504 " pdb=" C ASP B 504 " pdb=" CB ASP B 504 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA ARG 0 26 " pdb=" N ARG 0 26 " pdb=" C ARG 0 26 " pdb=" CB ARG 0 26 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA TYR 8 103 " pdb=" N TYR 8 103 " pdb=" C TYR 8 103 " pdb=" CB TYR 8 103 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 10756 not shown) Planarity restraints: 12440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 566 " 0.053 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO E 567 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO E 567 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 567 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU W 401 " 0.050 5.00e-02 4.00e+02 7.58e-02 9.19e+00 pdb=" N PRO W 402 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO W 402 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO W 402 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU M 401 " -0.045 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO M 402 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO M 402 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO M 402 " -0.036 5.00e-02 4.00e+02 ... (remaining 12437 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 607 2.63 - 3.20: 62672 3.20 - 3.77: 105530 3.77 - 4.33: 149819 4.33 - 4.90: 241807 Nonbonded interactions: 560435 Sorted by model distance: nonbonded pdb=" O1B ATP A 701 " pdb="MG MG A 702 " model vdw 2.068 2.170 nonbonded pdb=" O1B ATP E 701 " pdb="MG MG E 702 " model vdw 2.076 2.170 nonbonded pdb=" O1B ATP C 701 " pdb="MG MG C 702 " model vdw 2.077 2.170 nonbonded pdb=" O1B ATP B 701 " pdb="MG MG B 702 " model vdw 2.079 2.170 nonbonded pdb=" O1B ATP D 701 " pdb="MG MG D 702 " model vdw 2.097 2.170 ... (remaining 560430 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 '0' and (resid 8 through 190 or resid 204 through 234)) selection = (chain '2' and (resid 8 through 190 or resid 204 through 234)) selection = (chain '4' and (resid 8 through 190 or resid 204 through 234)) selection = (chain '6' and (resid 8 through 190 or resid 204 through 234)) selection = (chain '8' and (resid 8 through 190 or resid 204 through 234)) selection = chain 'I' selection = (chain 'K' and (resid 8 through 190 or resid 204 through 234)) selection = (chain 'O' and (resid 8 through 190 or resid 204 through 234)) selection = (chain 'Q' and (resid 8 through 190 or resid 204 through 234)) selection = chain 'T' selection = chain 'X' selection = (chain 'Z' and (resid 8 through 190 or resid 204 through 234)) selection = (chain 'd' and (resid 8 through 190 or resid 204 through 234)) selection = (chain 'f' and (resid 8 through 190 or resid 204 through 234)) } ncs_group { reference = (chain 'A' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587 or resid 605 through 609 or resid 701 through 702)) selection = (chain 'B' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587 or resid 605 through 609 or resid 701 through 702)) selection = (chain 'C' and (resid 97 through 377 or resid 390 through 587 or resid 605 throu \ gh 609 or resid 701 through 702)) selection = chain 'D' selection = (chain 'E' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587 or resid 605 through 609 or resid 701 through 702)) selection = (chain 'F' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587 or resid 605 through 609 or resid 701 through 702)) } ncs_group { reference = chain 'H' selection = (chain 'J' and resid 301 through 522) selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = (chain 'P' and resid 301 through 522) selection = chain 'R' selection = chain 'S' selection = (chain 'U' and resid 301 through 522) selection = (chain 'V' and resid 301 through 522) selection = (chain 'W' and resid 301 through 522) selection = (chain 'Y' and resid 301 through 522) selection = (chain 'a' and resid 301 through 522) selection = (chain 'b' and resid 301 through 522) } 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: 2.310 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: 0.110 Extract box with map and model: 2.040 Check model and map are aligned: 0.430 Set scattering table: 0.490 Process input model: 140.940 Find NCS groups from input model: 3.530 Set up NCS constraints: 0.360 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: 0.030 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 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 : 0.006 0.101 69957 Z= 0.415 Angle : 0.929 21.248 94694 Z= 0.595 Chirality : 0.051 0.346 10759 Planarity : 0.005 0.081 12440 Dihedral : 14.198 91.299 25991 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.97 % Favored : 95.92 % Rotamer: Outliers : 3.29 % Allowed : 4.67 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -1.07 (0.08), residues: 8881 helix: -0.60 (0.08), residues: 3515 sheet: -0.44 (0.11), residues: 2027 loop : -0.74 (0.11), residues: 3339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 187 HIS 0.007 0.001 HIS V 365 PHE 0.034 0.003 PHE K 71 TYR 0.022 0.002 TYR 6 130 ARG 0.008 0.001 ARG d 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1850 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1618 time to evaluate : 5.787 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: 0 29 SER cc_start: 0.7095 (m) cc_final: 0.6676 (p) REVERT: 0 44 GLU cc_start: 0.5889 (tt0) cc_final: 0.5619 (tm-30) REVERT: 0 54 SER cc_start: 0.7318 (t) cc_final: 0.6921 (m) REVERT: 0 101 ASN cc_start: 0.6627 (t0) cc_final: 0.6398 (m-40) REVERT: 0 233 LEU cc_start: 0.7090 (mp) cc_final: 0.6773 (mm) REVERT: 2 28 LYS cc_start: 0.6990 (mmtt) cc_final: 0.6745 (mmtt) REVERT: 2 130 TYR cc_start: 0.7587 (t80) cc_final: 0.7375 (t80) REVERT: 4 21 ARG cc_start: 0.6079 (ttp80) cc_final: 0.5844 (ttp80) REVERT: 4 44 GLU cc_start: 0.6927 (tt0) cc_final: 0.6405 (pt0) REVERT: 4 97 ARG cc_start: 0.6093 (ttt-90) cc_final: 0.5844 (ttm-80) REVERT: 4 101 ASN cc_start: 0.6767 (t0) cc_final: 0.6334 (m-40) REVERT: 4 163 ILE cc_start: 0.6454 (mt) cc_final: 0.6126 (mt) REVERT: 4 171 TYR cc_start: 0.6329 (t80) cc_final: 0.5839 (t80) REVERT: 6 13 MET cc_start: 0.5839 (mtt) cc_final: 0.5613 (mmp) REVERT: 6 44 GLU cc_start: 0.7339 (tt0) cc_final: 0.6588 (tm-30) REVERT: 6 67 LYS cc_start: 0.7182 (tttm) cc_final: 0.6928 (ttmt) REVERT: 6 97 ARG cc_start: 0.5948 (ttt-90) cc_final: 0.5621 (ttt-90) REVERT: 6 101 ASN cc_start: 0.6823 (t0) cc_final: 0.6506 (m-40) REVERT: 6 113 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6094 (tt0) REVERT: 6 182 ARG cc_start: 0.4883 (OUTLIER) cc_final: 0.4631 (mtm-85) REVERT: 6 233 LEU cc_start: 0.7609 (mp) cc_final: 0.7111 (mt) REVERT: 6 234 LEU cc_start: 0.5533 (OUTLIER) cc_final: 0.4950 (pt) REVERT: 8 44 GLU cc_start: 0.6973 (tt0) cc_final: 0.6771 (tp30) REVERT: 8 69 ASN cc_start: 0.7099 (OUTLIER) cc_final: 0.6653 (p0) REVERT: 8 73 ASN cc_start: 0.6529 (OUTLIER) cc_final: 0.5916 (m-40) REVERT: 8 74 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7212 (mt) REVERT: 8 97 ARG cc_start: 0.6946 (ttt-90) cc_final: 0.6586 (ttt90) REVERT: 8 110 ILE cc_start: 0.7599 (mt) cc_final: 0.6286 (mt) REVERT: 8 118 TYR cc_start: 0.7737 (m-10) cc_final: 0.6953 (m-10) REVERT: 8 156 MET cc_start: 0.7519 (mtm) cc_final: 0.7131 (mtm) REVERT: 8 163 ILE cc_start: 0.6951 (mt) cc_final: 0.6335 (mt) REVERT: 8 169 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6757 (mp0) REVERT: 8 209 GLU cc_start: 0.7683 (tt0) cc_final: 0.7447 (mt-10) REVERT: A 160 GLU cc_start: 0.7466 (tp30) cc_final: 0.6839 (tp30) REVERT: B 314 MET cc_start: 0.8268 (mmm) cc_final: 0.7745 (mmt) REVERT: B 395 GLN cc_start: 0.7793 (tp40) cc_final: 0.5857 (tp40) REVERT: B 426 LEU cc_start: 0.8899 (mp) cc_final: 0.8555 (mp) REVERT: C 332 ILE cc_start: 0.8895 (mp) cc_final: 0.8560 (mm) REVERT: D 164 LEU cc_start: 0.6867 (tp) cc_final: 0.6523 (tp) REVERT: D 314 MET cc_start: 0.5950 (ptt) cc_final: 0.5405 (tpt) REVERT: D 406 LEU cc_start: 0.7098 (mt) cc_final: 0.6702 (mt) REVERT: D 446 GLN cc_start: 0.8917 (mt0) cc_final: 0.8664 (tm-30) REVERT: D 474 CYS cc_start: 0.7648 (t) cc_final: 0.7133 (p) REVERT: D 520 GLN cc_start: 0.8240 (mm110) cc_final: 0.7680 (mm110) REVERT: E 124 LEU cc_start: 0.7720 (mp) cc_final: 0.7515 (mp) REVERT: E 520 GLN cc_start: 0.8266 (tt0) cc_final: 0.8014 (tt0) REVERT: F 314 MET cc_start: 0.5929 (mmt) cc_final: 0.5507 (mmp) REVERT: F 529 ASN cc_start: 0.8654 (m-40) cc_final: 0.8325 (t0) REVERT: G 1 MET cc_start: 0.6043 (pmm) cc_final: 0.5531 (mtp) REVERT: H 325 MET cc_start: 0.7834 (mtm) cc_final: 0.7604 (mtt) REVERT: H 363 LEU cc_start: 0.5859 (OUTLIER) cc_final: 0.5630 (mp) REVERT: H 388 ARG cc_start: 0.6199 (tpt-90) cc_final: 0.5999 (ttm170) REVERT: H 519 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7122 (tp30) REVERT: I 17 SER cc_start: 0.5856 (m) cc_final: 0.5648 (t) REVERT: I 18 GLU cc_start: 0.6658 (mm-30) cc_final: 0.6311 (tp30) REVERT: I 85 ARG cc_start: 0.7246 (mmt90) cc_final: 0.6820 (tpp80) REVERT: I 105 GLN cc_start: 0.7369 (tt0) cc_final: 0.7002 (tm-30) REVERT: I 121 GLU cc_start: 0.6663 (tt0) cc_final: 0.6439 (tp30) REVERT: I 140 ARG cc_start: 0.7127 (ttp-110) cc_final: 0.6561 (ttm110) REVERT: I 153 PHE cc_start: 0.5306 (p90) cc_final: 0.4865 (p90) REVERT: I 209 GLU cc_start: 0.5050 (tt0) cc_final: 0.4363 (tt0) REVERT: I 233 LEU cc_start: 0.5967 (mm) cc_final: 0.5407 (tp) REVERT: J 325 MET cc_start: 0.7929 (mtm) cc_final: 0.7508 (ttp) REVERT: J 354 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6587 (mt-10) REVERT: J 361 VAL cc_start: 0.7553 (OUTLIER) cc_final: 0.7173 (t) REVERT: J 364 GLU cc_start: 0.7200 (tt0) cc_final: 0.6983 (pt0) REVERT: J 431 ILE cc_start: 0.7959 (mt) cc_final: 0.7670 (mp) REVERT: J 433 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6696 (mp0) REVERT: J 507 GLU cc_start: 0.7306 (tt0) cc_final: 0.7058 (tp30) REVERT: K 13 MET cc_start: 0.5988 (tpt) cc_final: 0.5696 (mmt) REVERT: K 18 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6086 (mm-30) REVERT: K 26 ARG cc_start: 0.6478 (OUTLIER) cc_final: 0.6104 (ptt90) REVERT: K 89 TYR cc_start: 0.7626 (m-80) cc_final: 0.7274 (m-80) REVERT: K 112 THR cc_start: 0.7524 (m) cc_final: 0.7223 (p) REVERT: K 116 LYS cc_start: 0.6694 (ttpp) cc_final: 0.6320 (ttpt) REVERT: K 119 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6677 (mp0) REVERT: K 130 TYR cc_start: 0.7520 (t80) cc_final: 0.7317 (t80) REVERT: K 146 SER cc_start: 0.7503 (m) cc_final: 0.6961 (p) REVERT: K 209 GLU cc_start: 0.5686 (tt0) cc_final: 0.5395 (tt0) REVERT: K 216 ASN cc_start: 0.7414 (t0) cc_final: 0.6612 (m-40) REVERT: L 325 MET cc_start: 0.7870 (mtm) cc_final: 0.6938 (ttm) REVERT: L 332 ARG cc_start: 0.7488 (mtt-85) cc_final: 0.6493 (mtt180) REVERT: L 361 VAL cc_start: 0.7695 (OUTLIER) cc_final: 0.7280 (t) REVERT: L 364 GLU cc_start: 0.7788 (tt0) cc_final: 0.7282 (pt0) REVERT: L 388 ARG cc_start: 0.6175 (tpt-90) cc_final: 0.5786 (ttm-80) REVERT: M 307 LYS cc_start: 0.7732 (mtpt) cc_final: 0.7446 (mtmm) REVERT: M 325 MET cc_start: 0.7835 (mtm) cc_final: 0.7408 (ttt) REVERT: M 370 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6726 (mm-30) REVERT: M 390 ASN cc_start: 0.7497 (t0) cc_final: 0.7182 (t0) REVERT: M 395 MET cc_start: 0.7260 (mtm) cc_final: 0.7002 (mtt) REVERT: M 432 GLU cc_start: 0.6753 (tp30) cc_final: 0.6340 (mm-30) REVERT: N 325 MET cc_start: 0.7599 (mtm) cc_final: 0.7286 (ttp) REVERT: N 364 GLU cc_start: 0.7805 (tt0) cc_final: 0.7508 (pt0) REVERT: N 432 GLU cc_start: 0.6550 (tp30) cc_final: 0.5893 (mm-30) REVERT: N 434 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6390 (pm20) REVERT: N 461 ASP cc_start: 0.5942 (t70) cc_final: 0.5523 (t0) REVERT: N 509 ARG cc_start: 0.5600 (OUTLIER) cc_final: 0.5221 (tpt-90) REVERT: N 519 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6813 (mm-30) REVERT: O 19 LEU cc_start: 0.6432 (tt) cc_final: 0.6208 (mt) REVERT: O 26 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6664 (ppt170) REVERT: O 33 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6619 (pp) REVERT: O 74 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6546 (mt) REVERT: O 101 ASN cc_start: 0.6948 (t0) cc_final: 0.6648 (m-40) REVERT: O 116 LYS cc_start: 0.7019 (ttpp) cc_final: 0.6640 (mttt) REVERT: O 137 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7109 (mt-10) REVERT: O 143 TYR cc_start: 0.5210 (p90) cc_final: 0.4803 (p90) REVERT: O 155 VAL cc_start: 0.7112 (t) cc_final: 0.6891 (p) REVERT: O 156 MET cc_start: 0.6344 (mtm) cc_final: 0.6098 (mtm) REVERT: O 174 ASN cc_start: 0.6787 (t0) cc_final: 0.6490 (t0) REVERT: O 178 THR cc_start: 0.5778 (m) cc_final: 0.5571 (p) REVERT: O 181 LEU cc_start: 0.5733 (tp) cc_final: 0.5515 (tt) REVERT: O 228 SER cc_start: 0.4914 (p) cc_final: 0.4551 (p) REVERT: P 325 MET cc_start: 0.7816 (mtm) cc_final: 0.7138 (ttp) REVERT: P 361 VAL cc_start: 0.8089 (OUTLIER) cc_final: 0.7811 (t) REVERT: P 364 GLU cc_start: 0.7556 (tt0) cc_final: 0.7282 (pt0) REVERT: P 388 ARG cc_start: 0.5866 (tpt-90) cc_final: 0.5391 (ttm110) REVERT: P 509 ARG cc_start: 0.6558 (ttp80) cc_final: 0.6079 (tpt90) REVERT: P 519 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7037 (tp30) REVERT: Q 10 GLU cc_start: 0.4363 (OUTLIER) cc_final: 0.4122 (mp0) REVERT: Q 44 GLU cc_start: 0.6286 (tt0) cc_final: 0.6045 (mt-10) REVERT: Q 105 GLN cc_start: 0.7166 (mt0) cc_final: 0.6861 (tm-30) REVERT: Q 135 ARG cc_start: 0.6891 (ttm110) cc_final: 0.6579 (ttm110) REVERT: Q 146 SER cc_start: 0.6794 (m) cc_final: 0.6495 (p) REVERT: Q 155 VAL cc_start: 0.6339 (t) cc_final: 0.5800 (m) REVERT: Q 156 MET cc_start: 0.6218 (mtm) cc_final: 0.5840 (mtm) REVERT: Q 159 THR cc_start: 0.3872 (p) cc_final: 0.2968 (m) REVERT: Q 169 GLU cc_start: 0.5905 (OUTLIER) cc_final: 0.5700 (tp30) REVERT: Q 234 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6089 (tp) REVERT: R 322 GLN cc_start: 0.8008 (mt0) cc_final: 0.7757 (mt0) REVERT: R 325 MET cc_start: 0.7385 (mtm) cc_final: 0.6437 (mmt) REVERT: R 330 ASP cc_start: 0.7474 (p0) cc_final: 0.7235 (p0) REVERT: R 354 GLU cc_start: 0.7520 (tt0) cc_final: 0.7106 (tp30) REVERT: R 507 GLU cc_start: 0.7435 (tt0) cc_final: 0.6433 (tp30) REVERT: S 322 GLN cc_start: 0.7225 (mt0) cc_final: 0.6993 (mt0) REVERT: S 324 ASN cc_start: 0.6996 (m-40) cc_final: 0.6705 (m-40) REVERT: S 325 MET cc_start: 0.7305 (mtm) cc_final: 0.6464 (mmt) REVERT: S 345 ILE cc_start: 0.7106 (OUTLIER) cc_final: 0.6813 (mt) REVERT: S 370 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6883 (mm-30) REVERT: S 432 GLU cc_start: 0.6764 (tp30) cc_final: 0.6477 (mm-30) REVERT: S 519 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7345 (tm-30) REVERT: T 49 SER cc_start: 0.7213 (m) cc_final: 0.6857 (m) REVERT: T 97 ARG cc_start: 0.5538 (ttp80) cc_final: 0.4966 (ttt180) REVERT: T 106 THR cc_start: 0.6752 (m) cc_final: 0.6393 (t) REVERT: T 111 PHE cc_start: 0.6814 (t80) cc_final: 0.6468 (t80) REVERT: T 112 THR cc_start: 0.7136 (m) cc_final: 0.6574 (p) REVERT: T 119 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7430 (mp0) REVERT: T 121 GLU cc_start: 0.7042 (tt0) cc_final: 0.6500 (tp30) REVERT: T 134 LYS cc_start: 0.7212 (ttpt) cc_final: 0.6825 (ttpt) REVERT: T 174 ASN cc_start: 0.7219 (m-40) cc_final: 0.6538 (m110) REVERT: T 178 THR cc_start: 0.5840 (m) cc_final: 0.5617 (p) REVERT: T 228 SER cc_start: 0.6261 (p) cc_final: 0.5918 (t) REVERT: U 314 MET cc_start: 0.8496 (ttm) cc_final: 0.7949 (ttm) REVERT: U 330 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6923 (p0) REVERT: U 447 LYS cc_start: 0.6613 (mtmt) cc_final: 0.6332 (mtmt) REVERT: V 390 ASN cc_start: 0.7092 (t0) cc_final: 0.6648 (t0) REVERT: V 432 GLU cc_start: 0.5850 (mm-30) cc_final: 0.5312 (mm-30) REVERT: V 509 ARG cc_start: 0.6172 (OUTLIER) cc_final: 0.5617 (ttt180) REVERT: V 519 GLU cc_start: 0.7422 (tt0) cc_final: 0.7092 (tp30) REVERT: W 307 LYS cc_start: 0.7496 (mtpt) cc_final: 0.7144 (mtpt) REVERT: W 354 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6584 (tt0) REVERT: W 364 GLU cc_start: 0.7348 (tt0) cc_final: 0.7011 (pt0) REVERT: W 509 ARG cc_start: 0.6483 (tpt170) cc_final: 0.6050 (ttp-170) REVERT: W 519 GLU cc_start: 0.6485 (mt-10) cc_final: 0.6107 (mm-30) REVERT: W 522 SER cc_start: 0.5773 (t) cc_final: 0.5555 (m) REVERT: X 24 ILE cc_start: 0.6347 (mt) cc_final: 0.6140 (mt) REVERT: X 69 ASN cc_start: 0.6914 (OUTLIER) cc_final: 0.6528 (p0) REVERT: X 101 ASN cc_start: 0.6573 (t0) cc_final: 0.6296 (m-40) REVERT: X 111 PHE cc_start: 0.6473 (t80) cc_final: 0.6265 (t80) REVERT: X 119 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7579 (mp0) REVERT: X 130 TYR cc_start: 0.7257 (t80) cc_final: 0.6239 (t80) REVERT: X 135 ARG cc_start: 0.7231 (ttm110) cc_final: 0.6903 (mmp80) REVERT: X 156 MET cc_start: 0.4841 (mtm) cc_final: 0.4571 (mtm) REVERT: X 163 ILE cc_start: 0.6538 (mt) cc_final: 0.6200 (mt) REVERT: X 216 ASN cc_start: 0.7490 (t0) cc_final: 0.6990 (t0) REVERT: X 233 LEU cc_start: 0.6735 (mp) cc_final: 0.6332 (mm) REVERT: Y 314 MET cc_start: 0.8247 (ttm) cc_final: 0.7939 (ttm) REVERT: Y 325 MET cc_start: 0.7760 (mtm) cc_final: 0.6863 (ttm) REVERT: Y 430 ASN cc_start: 0.7711 (t0) cc_final: 0.6969 (t0) REVERT: Y 432 GLU cc_start: 0.6355 (tp30) cc_final: 0.5894 (mm-30) REVERT: Y 450 MET cc_start: 0.6867 (mtm) cc_final: 0.6631 (mtm) REVERT: Y 509 ARG cc_start: 0.7237 (tpt170) cc_final: 0.6157 (ttt180) REVERT: Z 28 LYS cc_start: 0.7476 (mmtt) cc_final: 0.7213 (mmtp) REVERT: Z 33 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6377 (pt) REVERT: Z 52 LYS cc_start: 0.7462 (mtpt) cc_final: 0.6885 (mttm) REVERT: Z 98 GLN cc_start: 0.6091 (mt0) cc_final: 0.5844 (mt0) REVERT: Z 101 ASN cc_start: 0.7428 (t0) cc_final: 0.7065 (m-40) REVERT: Z 121 GLU cc_start: 0.7534 (tt0) cc_final: 0.7281 (tt0) REVERT: Z 138 LEU cc_start: 0.7837 (mt) cc_final: 0.7617 (mp) REVERT: Z 178 THR cc_start: 0.5281 (m) cc_final: 0.5065 (p) REVERT: Z 209 GLU cc_start: 0.5530 (tt0) cc_final: 0.4822 (tt0) REVERT: Z 216 ASN cc_start: 0.8141 (t0) cc_final: 0.7462 (m-40) REVERT: a 325 MET cc_start: 0.7623 (mtm) cc_final: 0.6955 (ttp) REVERT: a 345 ILE cc_start: 0.6765 (OUTLIER) cc_final: 0.6525 (mt) REVERT: a 354 GLU cc_start: 0.7148 (tt0) cc_final: 0.6816 (mt-10) REVERT: a 432 GLU cc_start: 0.6937 (tp30) cc_final: 0.6700 (tp30) REVERT: b 354 GLU cc_start: 0.7019 (tt0) cc_final: 0.6551 (mm-30) REVERT: b 355 PHE cc_start: 0.7118 (m-10) cc_final: 0.6746 (m-80) REVERT: b 390 ASN cc_start: 0.7212 (t0) cc_final: 0.6882 (t0) REVERT: b 432 GLU cc_start: 0.6695 (tp30) cc_final: 0.6442 (mm-30) REVERT: b 461 ASP cc_start: 0.5951 (t70) cc_final: 0.5747 (t0) REVERT: b 519 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6426 (mm-30) REVERT: d 19 LEU cc_start: 0.8166 (tt) cc_final: 0.7633 (tp) REVERT: d 97 ARG cc_start: 0.6062 (ttt-90) cc_final: 0.5820 (ttt180) REVERT: d 101 ASN cc_start: 0.7256 (t0) cc_final: 0.6705 (m110) REVERT: d 110 ILE cc_start: 0.8189 (mt) cc_final: 0.7940 (mm) REVERT: d 118 TYR cc_start: 0.7512 (m-10) cc_final: 0.7102 (m-10) REVERT: d 146 SER cc_start: 0.7735 (m) cc_final: 0.7287 (t) REVERT: d 179 ASP cc_start: 0.7044 (m-30) cc_final: 0.6624 (t0) REVERT: d 234 LEU cc_start: 0.6172 (OUTLIER) cc_final: 0.5857 (pt) REVERT: f 15 GLU cc_start: 0.7825 (tt0) cc_final: 0.7476 (tp30) REVERT: f 26 ARG cc_start: 0.6920 (ttt180) cc_final: 0.6498 (ttp80) REVERT: f 44 GLU cc_start: 0.7019 (tt0) cc_final: 0.6508 (tm-30) REVERT: f 69 ASN cc_start: 0.7178 (OUTLIER) cc_final: 0.6566 (m-40) REVERT: f 101 ASN cc_start: 0.6682 (t0) cc_final: 0.6279 (m-40) REVERT: f 146 SER cc_start: 0.7306 (p) cc_final: 0.6796 (p) REVERT: f 163 ILE cc_start: 0.6400 (mt) cc_final: 0.5941 (mm) REVERT: f 165 ASN cc_start: 0.5712 (m-40) cc_final: 0.5459 (m110) REVERT: f 234 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6759 (pt) outliers start: 232 outliers final: 42 residues processed: 1791 average time/residue: 0.7110 time to fit residues: 2097.3086 Evaluate side-chains 990 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 920 time to evaluate : 5.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 205 VAL Chi-restraints excluded: chain 0 residue 234 LEU Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 205 VAL Chi-restraints excluded: chain 4 residue 234 LEU Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 205 VAL Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 69 ASN Chi-restraints excluded: chain 8 residue 73 ASN Chi-restraints excluded: chain 8 residue 74 LEU Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 234 LEU Chi-restraints excluded: chain B residue 505 LYS Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 354 GLU Chi-restraints excluded: chain J residue 361 VAL Chi-restraints excluded: chain J residue 486 LEU Chi-restraints excluded: chain K residue 26 ARG Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 345 ILE Chi-restraints excluded: chain L residue 361 VAL Chi-restraints excluded: chain L residue 441 SER Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain M residue 503 VAL Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 509 ARG Chi-restraints excluded: chain O residue 26 ARG Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 123 CYS Chi-restraints excluded: chain P residue 361 VAL Chi-restraints excluded: chain P residue 444 LEU Chi-restraints excluded: chain Q residue 10 GLU Chi-restraints excluded: chain Q residue 123 CYS Chi-restraints excluded: chain Q residue 169 GLU Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 361 VAL Chi-restraints excluded: chain R residue 363 LEU Chi-restraints excluded: chain S residue 345 ILE Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain U residue 330 ASP Chi-restraints excluded: chain U residue 345 ILE Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 345 ILE Chi-restraints excluded: chain W residue 354 GLU Chi-restraints excluded: chain W residue 363 LEU Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain Y residue 345 ILE Chi-restraints excluded: chain Y residue 361 VAL Chi-restraints excluded: chain Y residue 444 LEU Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 123 CYS Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain a residue 345 ILE Chi-restraints excluded: chain d residue 74 LEU Chi-restraints excluded: chain d residue 144 ASP Chi-restraints excluded: chain d residue 205 VAL Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 69 ASN Chi-restraints excluded: chain f residue 234 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 749 optimal weight: 8.9990 chunk 673 optimal weight: 2.9990 chunk 373 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 454 optimal weight: 9.9990 chunk 359 optimal weight: 5.9990 chunk 696 optimal weight: 1.9990 chunk 269 optimal weight: 6.9990 chunk 423 optimal weight: 5.9990 chunk 518 optimal weight: 0.9990 chunk 806 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 114 GLN 6 114 GLN 6 231 GLN 8 69 ASN 8 80 GLN 8 98 GLN 8 114 GLN 8 165 ASN 8 231 GLN A 529 ASN B 139 GLN B 460 HIS B 502 ASN B 566 ASN C 172 HIS C 446 GLN ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 558 ASN ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 GLN D 416 ASN E 408 ASN E 529 ASN F 323 HIS F 339 ASN F 348 HIS F 395 GLN F 607 GLN G 5 GLN H 456 GLN I 45 ASN I 98 GLN I 114 GLN I 129 HIS J 456 GLN K 80 GLN K 114 GLN L 322 GLN L 396 GLN L 456 GLN M 381 ASN M 456 GLN N 456 GLN O 51 GLN O 80 GLN O 114 GLN P 456 GLN Q 11 GLN ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 456 GLN S 456 GLN T 69 ASN T 80 GLN T 174 ASN U 322 GLN U 456 GLN V 322 GLN V 415 GLN V 456 GLN W 456 GLN X 69 ASN X 73 ASN X 80 GLN X 114 GLN Y 456 GLN Z 114 GLN a 456 GLN b 322 GLN b 456 GLN d 11 GLN d 69 ASN d 114 GLN f 45 ASN f 69 ASN ** f 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 69957 Z= 0.289 Angle : 0.655 10.378 94694 Z= 0.346 Chirality : 0.046 0.262 10759 Planarity : 0.006 0.115 12440 Dihedral : 6.848 108.069 10316 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.59 % Favored : 97.40 % Rotamer: Outliers : 2.53 % Allowed : 10.08 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: 0.75 (0.09), residues: 8881 helix: 1.50 (0.08), residues: 3557 sheet: 0.29 (0.11), residues: 1999 loop : -0.36 (0.11), residues: 3325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 187 HIS 0.016 0.002 HIS F 546 PHE 0.037 0.003 PHE 0 71 TYR 0.025 0.002 TYR L 359 ARG 0.009 0.001 ARG 4 182 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1142 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 964 time to evaluate : 5.844 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: 0 28 LYS cc_start: 0.7264 (mmtt) cc_final: 0.6920 (mmtm) REVERT: 0 114 GLN cc_start: 0.5939 (mp10) cc_final: 0.5461 (mp10) REVERT: 0 143 TYR cc_start: 0.6265 (p90) cc_final: 0.5935 (p90) REVERT: 2 135 ARG cc_start: 0.7764 (tpp80) cc_final: 0.6848 (ttm-80) REVERT: 2 234 LEU cc_start: 0.6622 (OUTLIER) cc_final: 0.6281 (pt) REVERT: 4 45 ASN cc_start: 0.7530 (t0) cc_final: 0.6726 (t0) REVERT: 4 101 ASN cc_start: 0.6464 (t0) cc_final: 0.6097 (m-40) REVERT: 6 21 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6581 (ttp-170) REVERT: 6 44 GLU cc_start: 0.7222 (tt0) cc_final: 0.6693 (tm-30) REVERT: 6 51 GLN cc_start: 0.6779 (mm-40) cc_final: 0.6561 (mm-40) REVERT: 6 97 ARG cc_start: 0.6293 (ttt-90) cc_final: 0.6007 (ttt-90) REVERT: 6 101 ASN cc_start: 0.6996 (t0) cc_final: 0.6771 (m-40) REVERT: 6 113 GLU cc_start: 0.6867 (mm-30) cc_final: 0.6305 (tt0) REVERT: 6 118 TYR cc_start: 0.8256 (m-10) cc_final: 0.8015 (m-80) REVERT: 6 171 TYR cc_start: 0.5947 (t80) cc_final: 0.5706 (t80) REVERT: 6 182 ARG cc_start: 0.4936 (OUTLIER) cc_final: 0.4587 (mtm-85) REVERT: 6 233 LEU cc_start: 0.7454 (mp) cc_final: 0.7027 (mt) REVERT: 6 234 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.5594 (pt) REVERT: 8 73 ASN cc_start: 0.6796 (OUTLIER) cc_final: 0.6517 (m-40) REVERT: 8 80 GLN cc_start: 0.7506 (tp40) cc_final: 0.7119 (tp40) REVERT: 8 179 ASP cc_start: 0.7127 (m-30) cc_final: 0.6912 (t0) REVERT: A 160 GLU cc_start: 0.7521 (tp30) cc_final: 0.6930 (tp30) REVERT: B 137 LYS cc_start: 0.7070 (ttmt) cc_final: 0.6352 (tptt) REVERT: B 546 HIS cc_start: 0.8083 (m170) cc_final: 0.7869 (m170) REVERT: C 260 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7688 (mm110) REVERT: C 332 ILE cc_start: 0.8850 (mp) cc_final: 0.8573 (mm) REVERT: C 420 MET cc_start: 0.6811 (mtp) cc_final: 0.6524 (mtm) REVERT: D 122 MET cc_start: 0.7871 (mpp) cc_final: 0.7582 (mpp) REVERT: D 164 LEU cc_start: 0.6933 (tp) cc_final: 0.6520 (tp) REVERT: D 314 MET cc_start: 0.5971 (ptt) cc_final: 0.5126 (tpt) REVERT: D 486 MET cc_start: 0.8040 (tpp) cc_final: 0.7812 (tpp) REVERT: E 379 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.7994 (p) REVERT: E 520 GLN cc_start: 0.8507 (tt0) cc_final: 0.8253 (tt0) REVERT: F 122 MET cc_start: 0.6825 (mmm) cc_final: 0.6474 (mmm) REVERT: F 529 ASN cc_start: 0.8583 (m-40) cc_final: 0.8301 (t0) REVERT: G 1 MET cc_start: 0.6067 (pmm) cc_final: 0.5716 (mtp) REVERT: H 325 MET cc_start: 0.7887 (mtm) cc_final: 0.7609 (mtt) REVERT: H 388 ARG cc_start: 0.6867 (tpt-90) cc_final: 0.6371 (ttp-170) REVERT: H 396 GLN cc_start: 0.6780 (tm-30) cc_final: 0.6492 (tp40) REVERT: H 519 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7206 (tp30) REVERT: I 18 GLU cc_start: 0.6653 (mm-30) cc_final: 0.6305 (tp30) REVERT: I 73 ASN cc_start: 0.6709 (t0) cc_final: 0.6440 (t0) REVERT: I 105 GLN cc_start: 0.7358 (tt0) cc_final: 0.6897 (tm-30) REVERT: I 111 PHE cc_start: 0.7183 (t80) cc_final: 0.6653 (t80) REVERT: I 121 GLU cc_start: 0.6635 (tt0) cc_final: 0.6158 (mm-30) REVERT: I 140 ARG cc_start: 0.6975 (ttp-110) cc_final: 0.6774 (ttp80) REVERT: I 233 LEU cc_start: 0.6360 (mm) cc_final: 0.5846 (tp) REVERT: J 325 MET cc_start: 0.7781 (mtm) cc_final: 0.7467 (ttm) REVERT: J 343 THR cc_start: 0.8069 (m) cc_final: 0.7845 (t) REVERT: J 364 GLU cc_start: 0.7209 (tt0) cc_final: 0.6994 (pt0) REVERT: J 507 GLU cc_start: 0.7289 (tt0) cc_final: 0.6940 (tp30) REVERT: J 509 ARG cc_start: 0.6531 (tpt90) cc_final: 0.5998 (ttt180) REVERT: K 18 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6915 (mm-30) REVERT: K 26 ARG cc_start: 0.6398 (ttm110) cc_final: 0.6005 (ppt170) REVERT: K 52 LYS cc_start: 0.7545 (mtpt) cc_final: 0.7199 (mtpt) REVERT: K 112 THR cc_start: 0.7315 (m) cc_final: 0.6933 (p) REVERT: K 116 LYS cc_start: 0.6570 (ttpp) cc_final: 0.6261 (ttpp) REVERT: K 146 SER cc_start: 0.6826 (m) cc_final: 0.6554 (m) REVERT: K 150 GLU cc_start: 0.7495 (mm-30) cc_final: 0.6870 (mm-30) REVERT: K 216 ASN cc_start: 0.7237 (t0) cc_final: 0.6518 (m-40) REVERT: L 325 MET cc_start: 0.7887 (mtm) cc_final: 0.7180 (ttp) REVERT: L 332 ARG cc_start: 0.7413 (mtt-85) cc_final: 0.6411 (mtt180) REVERT: L 364 GLU cc_start: 0.7814 (tt0) cc_final: 0.7167 (pt0) REVERT: L 401 LEU cc_start: 0.7485 (mt) cc_final: 0.7168 (tp) REVERT: M 307 LYS cc_start: 0.7960 (mtpt) cc_final: 0.7675 (mtmm) REVERT: M 325 MET cc_start: 0.7638 (mtm) cc_final: 0.7307 (ttt) REVERT: N 325 MET cc_start: 0.7433 (mtm) cc_final: 0.7163 (ttp) REVERT: N 354 GLU cc_start: 0.6715 (mt-10) cc_final: 0.6272 (mm-30) REVERT: N 364 GLU cc_start: 0.7517 (tt0) cc_final: 0.7169 (pt0) REVERT: N 432 GLU cc_start: 0.6844 (tp30) cc_final: 0.6240 (mm-30) REVERT: N 433 GLU cc_start: 0.7862 (tp30) cc_final: 0.7492 (mt-10) REVERT: N 434 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7526 (pm20) REVERT: N 461 ASP cc_start: 0.6038 (t70) cc_final: 0.5677 (t0) REVERT: N 509 ARG cc_start: 0.5686 (OUTLIER) cc_final: 0.5164 (ttt-90) REVERT: N 512 GLU cc_start: 0.6800 (tm-30) cc_final: 0.6541 (mt-10) REVERT: O 26 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6507 (ppt170) REVERT: O 116 LYS cc_start: 0.7151 (ttpp) cc_final: 0.6797 (mttt) REVERT: O 143 TYR cc_start: 0.5430 (p90) cc_final: 0.4887 (p90) REVERT: O 146 SER cc_start: 0.6858 (m) cc_final: 0.6591 (t) REVERT: O 174 ASN cc_start: 0.7106 (t0) cc_final: 0.6882 (t0) REVERT: O 214 ASP cc_start: 0.7030 (t0) cc_final: 0.6732 (t0) REVERT: O 226 THR cc_start: 0.5689 (t) cc_final: 0.5340 (m) REVERT: P 325 MET cc_start: 0.7770 (mtm) cc_final: 0.7123 (ttp) REVERT: P 388 ARG cc_start: 0.6694 (tpt-90) cc_final: 0.6075 (ttm110) REVERT: Q 113 GLU cc_start: 0.7282 (tp30) cc_final: 0.6603 (tt0) REVERT: Q 135 ARG cc_start: 0.7243 (ttm110) cc_final: 0.6971 (ttm110) REVERT: Q 146 SER cc_start: 0.6964 (m) cc_final: 0.6566 (p) REVERT: Q 156 MET cc_start: 0.5898 (mtm) cc_final: 0.5563 (mtm) REVERT: Q 228 SER cc_start: 0.6808 (p) cc_final: 0.6555 (p) REVERT: Q 234 LEU cc_start: 0.6449 (OUTLIER) cc_final: 0.6038 (tp) REVERT: R 325 MET cc_start: 0.7318 (mtm) cc_final: 0.6609 (ttp) REVERT: R 357 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6284 (mtp85) REVERT: R 430 ASN cc_start: 0.8098 (t0) cc_final: 0.7803 (t0) REVERT: S 395 MET cc_start: 0.6794 (mmm) cc_final: 0.6391 (mtp) REVERT: S 512 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.6124 (mm-30) REVERT: S 519 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7006 (mm-30) REVERT: T 52 LYS cc_start: 0.7236 (mtpt) cc_final: 0.6824 (mtmm) REVERT: T 113 GLU cc_start: 0.7017 (tp30) cc_final: 0.6732 (tm-30) REVERT: T 121 GLU cc_start: 0.7235 (tt0) cc_final: 0.6702 (mm-30) REVERT: T 134 LYS cc_start: 0.7247 (ttpt) cc_final: 0.7017 (ttpt) REVERT: T 156 MET cc_start: 0.5807 (mtm) cc_final: 0.5549 (mtm) REVERT: T 173 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6581 (tm-30) REVERT: T 174 ASN cc_start: 0.6881 (m110) cc_final: 0.6452 (m-40) REVERT: T 214 ASP cc_start: 0.6120 (t0) cc_final: 0.5712 (t0) REVERT: T 216 ASN cc_start: 0.7552 (t0) cc_final: 0.6791 (m110) REVERT: U 314 MET cc_start: 0.8264 (ttm) cc_final: 0.7693 (ttm) REVERT: U 433 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6791 (tm-30) REVERT: V 325 MET cc_start: 0.7168 (ttp) cc_final: 0.6049 (mmt) REVERT: V 509 ARG cc_start: 0.6194 (OUTLIER) cc_final: 0.5768 (ttt180) REVERT: V 519 GLU cc_start: 0.7308 (tt0) cc_final: 0.6829 (mt-10) REVERT: W 364 GLU cc_start: 0.7155 (tt0) cc_final: 0.6635 (pt0) REVERT: W 509 ARG cc_start: 0.6231 (tpt170) cc_final: 0.5647 (ttt-90) REVERT: W 522 SER cc_start: 0.5751 (t) cc_final: 0.5462 (m) REVERT: X 52 LYS cc_start: 0.7253 (mtpt) cc_final: 0.6738 (mtmm) REVERT: X 101 ASN cc_start: 0.6408 (t0) cc_final: 0.6175 (m-40) REVERT: X 119 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7759 (mp0) REVERT: X 130 TYR cc_start: 0.7309 (t80) cc_final: 0.5984 (t80) REVERT: X 135 ARG cc_start: 0.7011 (ttm110) cc_final: 0.6760 (mmp-170) REVERT: X 179 ASP cc_start: 0.6701 (m-30) cc_final: 0.6059 (t0) REVERT: X 216 ASN cc_start: 0.7655 (t0) cc_final: 0.7070 (t0) REVERT: Y 325 MET cc_start: 0.7769 (mtm) cc_final: 0.6844 (ttm) REVERT: Z 28 LYS cc_start: 0.7572 (mmtt) cc_final: 0.7273 (mmtm) REVERT: Z 52 LYS cc_start: 0.7562 (mtpt) cc_final: 0.6973 (mttm) REVERT: Z 113 GLU cc_start: 0.6979 (mm-30) cc_final: 0.6457 (tm-30) REVERT: Z 121 GLU cc_start: 0.7457 (tt0) cc_final: 0.7179 (tt0) REVERT: Z 152 HIS cc_start: 0.7324 (m-70) cc_final: 0.6945 (m-70) REVERT: Z 216 ASN cc_start: 0.8443 (t0) cc_final: 0.7904 (m-40) REVERT: a 325 MET cc_start: 0.7379 (mtm) cc_final: 0.6789 (ttm) REVERT: a 351 VAL cc_start: 0.7561 (p) cc_final: 0.7110 (m) REVERT: a 354 GLU cc_start: 0.6936 (tt0) cc_final: 0.6668 (pt0) REVERT: a 401 LEU cc_start: 0.7038 (mt) cc_final: 0.6709 (mp) REVERT: d 97 ARG cc_start: 0.6269 (ttt-90) cc_final: 0.6036 (ttt180) REVERT: d 101 ASN cc_start: 0.7255 (t0) cc_final: 0.6722 (m110) REVERT: d 169 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7256 (mp0) REVERT: d 179 ASP cc_start: 0.7327 (m-30) cc_final: 0.7058 (t0) REVERT: d 189 ARG cc_start: 0.5584 (ttm-80) cc_final: 0.5178 (mtm-85) REVERT: d 234 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6544 (pt) REVERT: f 15 GLU cc_start: 0.7569 (tt0) cc_final: 0.7264 (tp30) REVERT: f 26 ARG cc_start: 0.6828 (ttt180) cc_final: 0.6470 (ttp80) REVERT: f 44 GLU cc_start: 0.7028 (tt0) cc_final: 0.6473 (tm-30) REVERT: f 69 ASN cc_start: 0.7175 (p0) cc_final: 0.6344 (m-40) REVERT: f 101 ASN cc_start: 0.6967 (t0) cc_final: 0.6422 (m-40) REVERT: f 112 THR cc_start: 0.7957 (OUTLIER) cc_final: 0.7491 (p) REVERT: f 146 SER cc_start: 0.7639 (p) cc_final: 0.7406 (p) REVERT: f 165 ASN cc_start: 0.5675 (m-40) cc_final: 0.5450 (m110) outliers start: 178 outliers final: 86 residues processed: 1076 average time/residue: 0.6759 time to fit residues: 1225.2033 Evaluate side-chains 893 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 792 time to evaluate : 5.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 2 residue 133 THR Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 170 SER Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 4 residue 234 LEU Chi-restraints excluded: chain 6 residue 21 ARG Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 205 VAL Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 73 ASN Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 147 ILE Chi-restraints excluded: chain 8 residue 185 VAL Chi-restraints excluded: chain 8 residue 226 THR Chi-restraints excluded: chain 8 residue 234 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 607 GLN Chi-restraints excluded: chain F residue 474 CYS Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain L residue 345 ILE Chi-restraints excluded: chain L residue 363 LEU Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 509 ARG Chi-restraints excluded: chain O residue 26 ARG Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 444 LEU Chi-restraints excluded: chain Q residue 10 GLU Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 357 ARG Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain S residue 345 ILE Chi-restraints excluded: chain S residue 386 MET Chi-restraints excluded: chain S residue 409 ILE Chi-restraints excluded: chain S residue 512 GLU Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain T residue 173 GLU Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 345 ILE Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 412 SER Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 331 VAL Chi-restraints excluded: chain W residue 345 ILE Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain X residue 147 ILE Chi-restraints excluded: chain Y residue 307 LYS Chi-restraints excluded: chain Y residue 345 ILE Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 444 LEU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain a residue 396 GLN Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain d residue 74 LEU Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 144 ASP Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Chi-restraints excluded: chain f residue 233 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 448 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 chunk 671 optimal weight: 2.9990 chunk 549 optimal weight: 0.9990 chunk 222 optimal weight: 7.9990 chunk 807 optimal weight: 3.9990 chunk 872 optimal weight: 1.9990 chunk 719 optimal weight: 1.9990 chunk 801 optimal weight: 10.0000 chunk 275 optimal weight: 40.0000 chunk 648 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 69 ASN 6 98 GLN 8 73 ASN B 395 GLN C 263 GLN ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 GLN E 539 GLN ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN ** M 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 11 GLN Q 114 GLN T 80 GLN U 322 GLN X 80 GLN Y 390 ASN Z 69 ASN Z 98 GLN b 322 GLN f 114 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 69957 Z= 0.240 Angle : 0.570 10.425 94694 Z= 0.301 Chirality : 0.044 0.193 10759 Planarity : 0.005 0.108 12440 Dihedral : 6.188 89.288 10248 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.97 % Favored : 97.02 % Rotamer: Outliers : 2.68 % Allowed : 11.70 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: 1.25 (0.09), residues: 8881 helix: 2.05 (0.08), residues: 3576 sheet: 0.50 (0.11), residues: 2010 loop : -0.27 (0.11), residues: 3295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 187 HIS 0.007 0.001 HIS F 348 PHE 0.033 0.002 PHE 6 71 TYR 0.016 0.002 TYR Z 171 ARG 0.009 0.001 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 844 time to evaluate : 5.899 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: 0 143 TYR cc_start: 0.6287 (p90) cc_final: 0.6010 (p90) REVERT: 2 135 ARG cc_start: 0.7913 (tpp80) cc_final: 0.7038 (ttm-80) REVERT: 2 234 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6431 (pt) REVERT: 4 45 ASN cc_start: 0.7617 (t0) cc_final: 0.7116 (t0) REVERT: 4 214 ASP cc_start: 0.6354 (t0) cc_final: 0.6121 (t0) REVERT: 6 13 MET cc_start: 0.4061 (ttt) cc_final: 0.3548 (ttm) REVERT: 6 44 GLU cc_start: 0.7307 (tt0) cc_final: 0.6793 (tm-30) REVERT: 6 51 GLN cc_start: 0.6814 (mm-40) cc_final: 0.6526 (mm-40) REVERT: 6 97 ARG cc_start: 0.6208 (ttt-90) cc_final: 0.5846 (ttt-90) REVERT: 6 101 ASN cc_start: 0.6998 (t0) cc_final: 0.6733 (m-40) REVERT: 6 113 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6457 (tt0) REVERT: 6 118 TYR cc_start: 0.8354 (m-10) cc_final: 0.7932 (m-80) REVERT: 6 182 ARG cc_start: 0.5471 (OUTLIER) cc_final: 0.4951 (mtm-85) REVERT: 6 233 LEU cc_start: 0.7434 (mp) cc_final: 0.7020 (mt) REVERT: 6 234 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5529 (pt) REVERT: 8 52 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.7093 (mtpt) REVERT: 8 73 ASN cc_start: 0.7182 (OUTLIER) cc_final: 0.6971 (m-40) REVERT: 8 80 GLN cc_start: 0.7391 (tp40) cc_final: 0.7131 (tp40) REVERT: 8 101 ASN cc_start: 0.7473 (t0) cc_final: 0.7126 (m-40) REVERT: 8 205 VAL cc_start: 0.7490 (OUTLIER) cc_final: 0.7122 (p) REVERT: 8 209 GLU cc_start: 0.7667 (tt0) cc_final: 0.7262 (mt-10) REVERT: A 122 MET cc_start: 0.8843 (mmm) cc_final: 0.8476 (mmm) REVERT: A 243 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7364 (pp) REVERT: B 122 MET cc_start: 0.7781 (mpp) cc_final: 0.7464 (mpp) REVERT: B 137 LYS cc_start: 0.6915 (ttmt) cc_final: 0.6446 (tptt) REVERT: D 122 MET cc_start: 0.7892 (mpp) cc_final: 0.7414 (mpp) REVERT: D 164 LEU cc_start: 0.6977 (tp) cc_final: 0.6607 (tp) REVERT: D 314 MET cc_start: 0.6286 (ptt) cc_final: 0.5246 (tpt) REVERT: D 518 MET cc_start: 0.8516 (tmm) cc_final: 0.8185 (ttp) REVERT: E 124 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7140 (tp) REVERT: E 379 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7956 (p) REVERT: E 520 GLN cc_start: 0.8414 (tt0) cc_final: 0.8103 (tt0) REVERT: F 187 TRP cc_start: 0.7052 (m100) cc_final: 0.6804 (m100) REVERT: F 314 MET cc_start: 0.6133 (mmt) cc_final: 0.5778 (mmp) REVERT: F 373 MET cc_start: 0.8123 (mmm) cc_final: 0.7820 (mmm) REVERT: F 420 MET cc_start: 0.7990 (tpp) cc_final: 0.7670 (tpt) REVERT: F 529 ASN cc_start: 0.8638 (m-40) cc_final: 0.8270 (t0) REVERT: F 544 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8548 (tp) REVERT: G 1 MET cc_start: 0.6043 (pmm) cc_final: 0.5693 (mtp) REVERT: H 325 MET cc_start: 0.7949 (mtm) cc_final: 0.7631 (mtt) REVERT: H 396 GLN cc_start: 0.6977 (tm-30) cc_final: 0.6702 (tp40) REVERT: H 519 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7222 (mm-30) REVERT: I 73 ASN cc_start: 0.6701 (t0) cc_final: 0.6447 (t0) REVERT: I 105 GLN cc_start: 0.7206 (tt0) cc_final: 0.6731 (tm-30) REVERT: I 121 GLU cc_start: 0.6542 (tt0) cc_final: 0.6212 (mm-30) REVERT: I 140 ARG cc_start: 0.7085 (ttp-110) cc_final: 0.6641 (ttp-170) REVERT: I 182 ARG cc_start: 0.5728 (OUTLIER) cc_final: 0.5433 (mpt-90) REVERT: I 214 ASP cc_start: 0.6445 (t0) cc_final: 0.6085 (t0) REVERT: I 233 LEU cc_start: 0.6837 (mm) cc_final: 0.6632 (mm) REVERT: J 325 MET cc_start: 0.7937 (mtm) cc_final: 0.7442 (ttm) REVERT: J 364 GLU cc_start: 0.7069 (tt0) cc_final: 0.6833 (pt0) REVERT: J 434 GLU cc_start: 0.7874 (tp30) cc_final: 0.7586 (tt0) REVERT: J 507 GLU cc_start: 0.7281 (tt0) cc_final: 0.6877 (tp30) REVERT: J 509 ARG cc_start: 0.6312 (tpt90) cc_final: 0.5883 (ttt180) REVERT: K 13 MET cc_start: 0.5900 (mmt) cc_final: 0.4742 (ttp) REVERT: K 18 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6497 (mm-30) REVERT: K 26 ARG cc_start: 0.6562 (ttm110) cc_final: 0.6215 (ppt170) REVERT: K 112 THR cc_start: 0.7210 (m) cc_final: 0.6977 (p) REVERT: K 146 SER cc_start: 0.6933 (m) cc_final: 0.6460 (p) REVERT: K 150 GLU cc_start: 0.7376 (mm-30) cc_final: 0.6838 (mm-30) REVERT: K 216 ASN cc_start: 0.7369 (t0) cc_final: 0.6594 (m-40) REVERT: L 325 MET cc_start: 0.7951 (mtm) cc_final: 0.7220 (ttm) REVERT: L 332 ARG cc_start: 0.7408 (mtt-85) cc_final: 0.6444 (mtt180) REVERT: L 388 ARG cc_start: 0.6410 (tpt-90) cc_final: 0.6155 (tpt-90) REVERT: L 401 LEU cc_start: 0.7633 (mt) cc_final: 0.7306 (tp) REVERT: M 307 LYS cc_start: 0.7920 (mtpt) cc_final: 0.7638 (mtmm) REVERT: M 325 MET cc_start: 0.7833 (mtm) cc_final: 0.7478 (ttt) REVERT: N 325 MET cc_start: 0.7477 (mtm) cc_final: 0.7157 (ttp) REVERT: N 364 GLU cc_start: 0.7879 (tt0) cc_final: 0.7339 (pt0) REVERT: N 399 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7440 (tt) REVERT: N 432 GLU cc_start: 0.6884 (tp30) cc_final: 0.6441 (mm-30) REVERT: N 433 GLU cc_start: 0.7827 (tp30) cc_final: 0.7494 (mt-10) REVERT: N 434 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7317 (pm20) REVERT: N 461 ASP cc_start: 0.5863 (t70) cc_final: 0.5525 (t0) REVERT: N 509 ARG cc_start: 0.5805 (OUTLIER) cc_final: 0.5278 (ttt-90) REVERT: N 512 GLU cc_start: 0.6600 (tm-30) cc_final: 0.6326 (mt-10) REVERT: O 26 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.6462 (ppt170) REVERT: O 99 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7490 (mt) REVERT: O 146 SER cc_start: 0.6881 (m) cc_final: 0.6555 (t) REVERT: O 214 ASP cc_start: 0.7000 (t0) cc_final: 0.6690 (t0) REVERT: O 226 THR cc_start: 0.5985 (t) cc_final: 0.5633 (m) REVERT: P 325 MET cc_start: 0.7913 (mtm) cc_final: 0.7255 (ttp) REVERT: P 388 ARG cc_start: 0.7142 (tpt-90) cc_final: 0.6562 (ttm110) REVERT: P 432 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6199 (mp0) REVERT: P 519 GLU cc_start: 0.7522 (tp30) cc_final: 0.7171 (tm-30) REVERT: Q 24 ILE cc_start: 0.6298 (mt) cc_final: 0.6081 (mt) REVERT: Q 49 SER cc_start: 0.7275 (m) cc_final: 0.6855 (p) REVERT: Q 113 GLU cc_start: 0.7545 (tp30) cc_final: 0.7069 (tt0) REVERT: Q 135 ARG cc_start: 0.7127 (ttm110) cc_final: 0.6893 (ttm110) REVERT: Q 140 ARG cc_start: 0.7046 (ttp-110) cc_final: 0.6809 (ttm-80) REVERT: Q 146 SER cc_start: 0.7067 (m) cc_final: 0.6608 (p) REVERT: Q 156 MET cc_start: 0.5804 (mtm) cc_final: 0.5465 (mtm) REVERT: Q 228 SER cc_start: 0.6849 (p) cc_final: 0.6641 (p) REVERT: Q 234 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.5857 (tp) REVERT: R 325 MET cc_start: 0.7410 (mtm) cc_final: 0.6760 (ttp) REVERT: S 512 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6688 (mm-30) REVERT: S 519 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7180 (tm-30) REVERT: T 52 LYS cc_start: 0.7396 (mtpt) cc_final: 0.6873 (mtmm) REVERT: T 113 GLU cc_start: 0.7287 (tp30) cc_final: 0.6923 (tm-30) REVERT: T 121 GLU cc_start: 0.7034 (tt0) cc_final: 0.6310 (mm-30) REVERT: T 134 LYS cc_start: 0.7121 (ttpt) cc_final: 0.6846 (ttpt) REVERT: T 170 SER cc_start: 0.5017 (p) cc_final: 0.4269 (t) REVERT: T 216 ASN cc_start: 0.7531 (t0) cc_final: 0.6926 (m110) REVERT: U 314 MET cc_start: 0.8231 (ttm) cc_final: 0.7734 (ttm) REVERT: U 433 GLU cc_start: 0.7248 (tm-30) cc_final: 0.6904 (mm-30) REVERT: U 509 ARG cc_start: 0.6590 (tpt170) cc_final: 0.6318 (ttp80) REVERT: V 325 MET cc_start: 0.7577 (ttp) cc_final: 0.6410 (mmt) REVERT: V 432 GLU cc_start: 0.6260 (mm-30) cc_final: 0.6007 (mm-30) REVERT: V 509 ARG cc_start: 0.6304 (OUTLIER) cc_final: 0.5685 (ttt180) REVERT: V 519 GLU cc_start: 0.7223 (tt0) cc_final: 0.6851 (mt-10) REVERT: W 345 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7465 (mm) REVERT: W 364 GLU cc_start: 0.7115 (tt0) cc_final: 0.6618 (pt0) REVERT: W 522 SER cc_start: 0.5943 (t) cc_final: 0.5611 (m) REVERT: X 26 ARG cc_start: 0.7577 (ptm-80) cc_final: 0.7204 (mtm110) REVERT: X 52 LYS cc_start: 0.7439 (mtpt) cc_final: 0.6988 (mtmm) REVERT: X 101 ASN cc_start: 0.6469 (t0) cc_final: 0.6251 (m-40) REVERT: X 111 PHE cc_start: 0.6203 (t80) cc_final: 0.5930 (t80) REVERT: X 130 TYR cc_start: 0.7350 (t80) cc_final: 0.5913 (t80) REVERT: X 179 ASP cc_start: 0.6718 (m-30) cc_final: 0.6020 (t0) REVERT: X 216 ASN cc_start: 0.7603 (t0) cc_final: 0.6970 (t0) REVERT: Y 325 MET cc_start: 0.7827 (mtm) cc_final: 0.6856 (ttt) REVERT: Y 399 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7311 (tp) REVERT: Y 519 GLU cc_start: 0.7184 (tt0) cc_final: 0.6503 (tp30) REVERT: Z 31 VAL cc_start: 0.7703 (m) cc_final: 0.7447 (p) REVERT: Z 52 LYS cc_start: 0.7532 (mtpt) cc_final: 0.7126 (mttp) REVERT: Z 113 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6426 (tm-30) REVERT: Z 156 MET cc_start: 0.6910 (mtm) cc_final: 0.6651 (mtm) REVERT: Z 216 ASN cc_start: 0.8505 (t0) cc_final: 0.8052 (m-40) REVERT: a 325 MET cc_start: 0.7579 (mtm) cc_final: 0.6869 (ttm) REVERT: b 339 ASP cc_start: 0.8077 (t0) cc_final: 0.7668 (m-30) REVERT: d 101 ASN cc_start: 0.7228 (t0) cc_final: 0.6837 (m-40) REVERT: d 179 ASP cc_start: 0.7464 (m-30) cc_final: 0.7038 (t0) REVERT: d 189 ARG cc_start: 0.5600 (ttm-80) cc_final: 0.5282 (mtm-85) REVERT: d 234 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6773 (pt) REVERT: f 15 GLU cc_start: 0.7715 (tt0) cc_final: 0.7334 (tp30) REVERT: f 26 ARG cc_start: 0.6373 (ttt180) cc_final: 0.6094 (ttp80) REVERT: f 52 LYS cc_start: 0.6636 (OUTLIER) cc_final: 0.6246 (mtpt) REVERT: f 69 ASN cc_start: 0.7044 (p0) cc_final: 0.6362 (m-40) REVERT: f 97 ARG cc_start: 0.6552 (ttp-170) cc_final: 0.5875 (ttm170) REVERT: f 101 ASN cc_start: 0.6705 (t0) cc_final: 0.6228 (m-40) REVERT: f 112 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7668 (p) REVERT: f 165 ASN cc_start: 0.5674 (m-40) cc_final: 0.5470 (m110) REVERT: f 209 GLU cc_start: 0.6996 (tt0) cc_final: 0.6478 (mt-10) outliers start: 189 outliers final: 105 residues processed: 971 average time/residue: 0.7314 time to fit residues: 1215.5901 Evaluate side-chains 875 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 746 time to evaluate : 5.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 51 GLN Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 0 residue 225 ILE Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 216 ASN Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 133 THR Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 52 LYS Chi-restraints excluded: chain 8 residue 73 ASN Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 147 ILE Chi-restraints excluded: chain 8 residue 205 VAL Chi-restraints excluded: chain 8 residue 226 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 474 CYS Chi-restraints excluded: chain F residue 544 ILE Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 123 CYS Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 182 ARG Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain L residue 345 ILE Chi-restraints excluded: chain L residue 363 LEU Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain L residue 434 GLU Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 509 ARG Chi-restraints excluded: chain O residue 26 ARG Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain P residue 444 LEU Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 210 VAL Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain S residue 409 ILE Chi-restraints excluded: chain S residue 512 GLU Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 345 ILE Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain U residue 441 SER Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 399 LEU Chi-restraints excluded: chain V residue 412 SER Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 345 ILE Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain X residue 210 VAL Chi-restraints excluded: chain Y residue 307 LYS Chi-restraints excluded: chain Y residue 345 ILE Chi-restraints excluded: chain Y residue 399 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 444 LEU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain a residue 409 ILE Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 144 ASP Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 52 LYS Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 147 ILE Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Chi-restraints excluded: chain f residue 233 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 798 optimal weight: 7.9990 chunk 607 optimal weight: 0.2980 chunk 419 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 385 optimal weight: 0.9980 chunk 542 optimal weight: 0.9980 chunk 810 optimal weight: 2.9990 chunk 858 optimal weight: 5.9990 chunk 423 optimal weight: 0.8980 chunk 768 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 69 ASN B 546 HIS ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 529 ASN E 172 HIS E 408 ASN E 514 ASN ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN K 129 HIS Q 73 ASN T 80 GLN U 322 GLN V 322 GLN X 80 GLN Z 129 HIS f 80 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 69957 Z= 0.167 Angle : 0.516 11.871 94694 Z= 0.273 Chirality : 0.042 0.189 10759 Planarity : 0.004 0.046 12440 Dihedral : 5.880 89.879 10234 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.53 % Allowed : 12.90 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: 1.57 (0.09), residues: 8881 helix: 2.42 (0.08), residues: 3584 sheet: 0.60 (0.11), residues: 2019 loop : -0.19 (0.11), residues: 3278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 187 HIS 0.008 0.001 HIS F 348 PHE 0.033 0.002 PHE 0 71 TYR 0.015 0.001 TYR D 452 ARG 0.016 0.000 ARG O 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 790 time to evaluate : 5.843 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: 0 143 TYR cc_start: 0.6313 (p90) cc_final: 0.6033 (p90) REVERT: 2 110 ILE cc_start: 0.8030 (mt) cc_final: 0.7705 (tp) REVERT: 2 135 ARG cc_start: 0.7902 (tpp80) cc_final: 0.7089 (ttm-80) REVERT: 2 205 VAL cc_start: 0.6043 (m) cc_final: 0.5706 (p) REVERT: 2 234 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6502 (pt) REVERT: 4 45 ASN cc_start: 0.7514 (t0) cc_final: 0.7043 (t0) REVERT: 4 51 GLN cc_start: 0.6880 (mm-40) cc_final: 0.6067 (mm-40) REVERT: 6 44 GLU cc_start: 0.7297 (tt0) cc_final: 0.6752 (tm-30) REVERT: 6 51 GLN cc_start: 0.6794 (mm-40) cc_final: 0.6552 (mm-40) REVERT: 6 97 ARG cc_start: 0.6315 (ttt-90) cc_final: 0.5850 (ttt-90) REVERT: 6 101 ASN cc_start: 0.6938 (t0) cc_final: 0.6667 (m-40) REVERT: 6 113 GLU cc_start: 0.6871 (mm-30) cc_final: 0.6480 (tt0) REVERT: 6 182 ARG cc_start: 0.5557 (OUTLIER) cc_final: 0.4911 (mtm-85) REVERT: 6 209 GLU cc_start: 0.7431 (tt0) cc_final: 0.6985 (tt0) REVERT: 6 233 LEU cc_start: 0.7504 (mp) cc_final: 0.7068 (mt) REVERT: 6 234 LEU cc_start: 0.6211 (OUTLIER) cc_final: 0.5601 (pt) REVERT: 8 52 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.7111 (mtpt) REVERT: 8 73 ASN cc_start: 0.7131 (OUTLIER) cc_final: 0.6525 (m-40) REVERT: 8 80 GLN cc_start: 0.7310 (tp40) cc_final: 0.7097 (tp40) REVERT: 8 101 ASN cc_start: 0.7393 (t0) cc_final: 0.7053 (m-40) REVERT: A 122 MET cc_start: 0.8786 (mmm) cc_final: 0.8319 (mmm) REVERT: A 243 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7367 (pp) REVERT: A 395 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.8082 (tt0) REVERT: B 137 LYS cc_start: 0.7149 (ttmt) cc_final: 0.6426 (tptt) REVERT: D 122 MET cc_start: 0.7969 (mpp) cc_final: 0.7494 (mpp) REVERT: D 164 LEU cc_start: 0.6926 (tp) cc_final: 0.6561 (tp) REVERT: D 268 VAL cc_start: 0.6722 (t) cc_final: 0.6390 (p) REVERT: D 314 MET cc_start: 0.6312 (ptt) cc_final: 0.5103 (tpt) REVERT: D 480 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7866 (tp30) REVERT: D 518 MET cc_start: 0.8643 (tmm) cc_final: 0.8411 (ttp) REVERT: E 124 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7221 (tp) REVERT: E 379 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7921 (p) REVERT: E 520 GLN cc_start: 0.8447 (tt0) cc_final: 0.8229 (tt0) REVERT: F 187 TRP cc_start: 0.6963 (m100) cc_final: 0.6740 (m100) REVERT: F 314 MET cc_start: 0.6166 (mmt) cc_final: 0.5801 (mmp) REVERT: F 420 MET cc_start: 0.8002 (tpp) cc_final: 0.7570 (tpt) REVERT: F 529 ASN cc_start: 0.8521 (m-40) cc_final: 0.8245 (t0) REVERT: G 1 MET cc_start: 0.6161 (pmm) cc_final: 0.5732 (mtp) REVERT: H 325 MET cc_start: 0.8001 (mtm) cc_final: 0.7753 (mtt) REVERT: H 386 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7688 (ttp) REVERT: H 396 GLN cc_start: 0.7039 (tm-30) cc_final: 0.6698 (tp40) REVERT: H 519 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7304 (mm-30) REVERT: I 18 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7289 (tm-30) REVERT: I 73 ASN cc_start: 0.6602 (t0) cc_final: 0.6338 (t0) REVERT: I 105 GLN cc_start: 0.7155 (tt0) cc_final: 0.6721 (tm-30) REVERT: I 111 PHE cc_start: 0.7452 (t80) cc_final: 0.7132 (t80) REVERT: I 121 GLU cc_start: 0.6501 (tt0) cc_final: 0.6224 (mm-30) REVERT: I 140 ARG cc_start: 0.7192 (ttp-110) cc_final: 0.6738 (ttp80) REVERT: I 156 MET cc_start: 0.6158 (mtm) cc_final: 0.5900 (mtm) REVERT: I 182 ARG cc_start: 0.5877 (OUTLIER) cc_final: 0.5567 (mpt-90) REVERT: J 325 MET cc_start: 0.7862 (mtm) cc_final: 0.7359 (ttm) REVERT: J 364 GLU cc_start: 0.6633 (tt0) cc_final: 0.6283 (pt0) REVERT: J 509 ARG cc_start: 0.6259 (tpt90) cc_final: 0.5943 (ttt180) REVERT: K 13 MET cc_start: 0.5912 (mmt) cc_final: 0.4559 (ttp) REVERT: K 14 ARG cc_start: 0.5059 (tpm170) cc_final: 0.4742 (tpm170) REVERT: K 18 GLU cc_start: 0.6694 (mm-30) cc_final: 0.6391 (mm-30) REVERT: K 26 ARG cc_start: 0.6712 (ttm110) cc_final: 0.6383 (ppt170) REVERT: K 101 ASN cc_start: 0.6646 (t0) cc_final: 0.6207 (m-40) REVERT: K 112 THR cc_start: 0.7066 (m) cc_final: 0.6782 (p) REVERT: K 146 SER cc_start: 0.6924 (m) cc_final: 0.6459 (p) REVERT: K 150 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6795 (mm-30) REVERT: K 216 ASN cc_start: 0.7370 (t0) cc_final: 0.6585 (m-40) REVERT: L 325 MET cc_start: 0.7919 (mtm) cc_final: 0.7170 (ttm) REVERT: L 332 ARG cc_start: 0.7344 (mtt-85) cc_final: 0.6422 (mtt180) REVERT: L 401 LEU cc_start: 0.7624 (mt) cc_final: 0.7313 (tp) REVERT: M 307 LYS cc_start: 0.7793 (mtpt) cc_final: 0.7431 (mtmm) REVERT: M 325 MET cc_start: 0.7829 (mtm) cc_final: 0.7485 (ttt) REVERT: M 424 ASP cc_start: 0.6627 (p0) cc_final: 0.6315 (p0) REVERT: N 325 MET cc_start: 0.7440 (mtm) cc_final: 0.7191 (mtp) REVERT: N 364 GLU cc_start: 0.7717 (tt0) cc_final: 0.7133 (pt0) REVERT: N 432 GLU cc_start: 0.6918 (tp30) cc_final: 0.6475 (mm-30) REVERT: N 434 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7429 (pm20) REVERT: N 461 ASP cc_start: 0.5912 (t70) cc_final: 0.5668 (t0) REVERT: N 509 ARG cc_start: 0.5870 (OUTLIER) cc_final: 0.5343 (tpt-90) REVERT: N 512 GLU cc_start: 0.6487 (tm-30) cc_final: 0.6269 (mt-10) REVERT: O 26 ARG cc_start: 0.7147 (ttm110) cc_final: 0.6728 (ppt170) REVERT: O 44 GLU cc_start: 0.4594 (OUTLIER) cc_final: 0.3358 (tm-30) REVERT: O 146 SER cc_start: 0.6827 (m) cc_final: 0.6506 (t) REVERT: O 151 PRO cc_start: 0.7912 (Cg_endo) cc_final: 0.7670 (Cg_exo) REVERT: O 226 THR cc_start: 0.5940 (t) cc_final: 0.5553 (m) REVERT: P 325 MET cc_start: 0.7728 (mtm) cc_final: 0.7103 (ttp) REVERT: P 388 ARG cc_start: 0.7079 (tpt-90) cc_final: 0.6443 (ttm110) REVERT: P 432 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6255 (mp0) REVERT: Q 49 SER cc_start: 0.7288 (m) cc_final: 0.6870 (p) REVERT: Q 113 GLU cc_start: 0.7524 (tp30) cc_final: 0.7046 (tm-30) REVERT: Q 146 SER cc_start: 0.7033 (m) cc_final: 0.6611 (p) REVERT: Q 156 MET cc_start: 0.6067 (mtm) cc_final: 0.5659 (mtm) REVERT: Q 234 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6171 (tp) REVERT: R 325 MET cc_start: 0.7426 (mtm) cc_final: 0.6789 (ttp) REVERT: S 512 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6650 (mm-30) REVERT: S 519 GLU cc_start: 0.7436 (mt-10) cc_final: 0.6949 (mm-30) REVERT: T 52 LYS cc_start: 0.7298 (mtpt) cc_final: 0.6797 (mtmm) REVERT: T 72 ASP cc_start: 0.7784 (t70) cc_final: 0.7518 (t70) REVERT: T 113 GLU cc_start: 0.7223 (tp30) cc_final: 0.6920 (tm-30) REVERT: T 121 GLU cc_start: 0.7051 (tt0) cc_final: 0.6392 (mm-30) REVERT: T 134 LYS cc_start: 0.7133 (ttpt) cc_final: 0.6837 (ttpt) REVERT: T 170 SER cc_start: 0.4959 (p) cc_final: 0.4225 (t) REVERT: T 216 ASN cc_start: 0.7564 (t0) cc_final: 0.7145 (m110) REVERT: U 314 MET cc_start: 0.8197 (ttm) cc_final: 0.7703 (ttm) REVERT: U 401 LEU cc_start: 0.7663 (mt) cc_final: 0.7362 (mt) REVERT: U 509 ARG cc_start: 0.6224 (tpt170) cc_final: 0.5976 (ttp80) REVERT: V 325 MET cc_start: 0.7649 (ttp) cc_final: 0.6418 (mmt) REVERT: V 509 ARG cc_start: 0.6193 (OUTLIER) cc_final: 0.5630 (ttt180) REVERT: V 519 GLU cc_start: 0.7162 (tt0) cc_final: 0.6805 (mt-10) REVERT: W 364 GLU cc_start: 0.7039 (tt0) cc_final: 0.6512 (pt0) REVERT: W 522 SER cc_start: 0.5905 (t) cc_final: 0.5586 (m) REVERT: X 26 ARG cc_start: 0.7601 (ptm-80) cc_final: 0.7301 (mtm110) REVERT: X 52 LYS cc_start: 0.7444 (mtpt) cc_final: 0.6959 (mtmm) REVERT: X 105 GLN cc_start: 0.7131 (tt0) cc_final: 0.6251 (mm-40) REVERT: X 111 PHE cc_start: 0.6360 (t80) cc_final: 0.6113 (t80) REVERT: X 130 TYR cc_start: 0.7493 (t80) cc_final: 0.6031 (t80) REVERT: X 179 ASP cc_start: 0.6777 (m-30) cc_final: 0.6092 (t0) REVERT: X 216 ASN cc_start: 0.7557 (t0) cc_final: 0.6926 (t0) REVERT: Y 325 MET cc_start: 0.7790 (mtm) cc_final: 0.6950 (ttt) REVERT: Y 399 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7239 (tp) REVERT: Y 432 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6625 (mm-30) REVERT: Y 509 ARG cc_start: 0.7162 (tpt90) cc_final: 0.6462 (ttp80) REVERT: Z 52 LYS cc_start: 0.7602 (mtpt) cc_final: 0.7269 (mttp) REVERT: Z 113 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6569 (tm-30) REVERT: Z 116 LYS cc_start: 0.7363 (ptmm) cc_final: 0.6854 (ptmm) REVERT: Z 144 ASP cc_start: 0.4879 (p0) cc_final: 0.4562 (p0) REVERT: Z 156 MET cc_start: 0.6866 (mtm) cc_final: 0.6663 (mtm) REVERT: Z 216 ASN cc_start: 0.8474 (t0) cc_final: 0.7996 (m-40) REVERT: a 325 MET cc_start: 0.7602 (mtm) cc_final: 0.6902 (ttm) REVERT: b 339 ASP cc_start: 0.8019 (t0) cc_final: 0.7626 (m-30) REVERT: d 101 ASN cc_start: 0.7261 (t0) cc_final: 0.6826 (m-40) REVERT: d 179 ASP cc_start: 0.7641 (m-30) cc_final: 0.7246 (t0) REVERT: d 189 ARG cc_start: 0.5602 (ttm-80) cc_final: 0.5215 (mtm-85) REVERT: d 234 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6682 (pt) REVERT: f 15 GLU cc_start: 0.7801 (tt0) cc_final: 0.7424 (tp30) REVERT: f 26 ARG cc_start: 0.6422 (ttt180) cc_final: 0.6124 (ttp80) REVERT: f 73 ASN cc_start: 0.7076 (t0) cc_final: 0.6866 (t0) REVERT: f 97 ARG cc_start: 0.6549 (ttp-170) cc_final: 0.5874 (ttm170) REVERT: f 101 ASN cc_start: 0.6738 (t0) cc_final: 0.6203 (m-40) REVERT: f 112 THR cc_start: 0.8031 (OUTLIER) cc_final: 0.7704 (p) REVERT: f 209 GLU cc_start: 0.6960 (tt0) cc_final: 0.6608 (tt0) outliers start: 178 outliers final: 103 residues processed: 909 average time/residue: 0.6805 time to fit residues: 1047.8767 Evaluate side-chains 860 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 735 time to evaluate : 5.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 51 GLN Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 0 residue 225 ILE Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 69 ASN Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 73 ASN Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 216 ASN Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 133 THR Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 52 LYS Chi-restraints excluded: chain 8 residue 73 ASN Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 147 ILE Chi-restraints excluded: chain 8 residue 226 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 474 CYS Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 182 ARG Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 519 GLU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain L residue 322 GLN Chi-restraints excluded: chain L residue 337 THR Chi-restraints excluded: chain L residue 363 LEU Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain L residue 441 SER Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 509 ARG Chi-restraints excluded: chain O residue 44 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain P residue 396 GLN Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain P residue 444 LEU Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 409 ILE Chi-restraints excluded: chain S residue 512 GLU Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain T residue 225 ILE Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 441 SER Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 399 LEU Chi-restraints excluded: chain V residue 412 SER Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 307 LYS Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 363 LEU Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain Y residue 307 LYS Chi-restraints excluded: chain Y residue 345 ILE Chi-restraints excluded: chain Y residue 399 LEU Chi-restraints excluded: chain Y residue 444 LEU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain a residue 396 GLN Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 147 ILE Chi-restraints excluded: chain f residue 228 SER Chi-restraints excluded: chain f residue 233 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 714 optimal weight: 2.9990 chunk 487 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 639 optimal weight: 0.7980 chunk 354 optimal weight: 7.9990 chunk 732 optimal weight: 4.9990 chunk 593 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 438 optimal weight: 4.9990 chunk 770 optimal weight: 1.9990 chunk 216 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 69 ASN B 502 ASN B 546 HIS ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 HIS ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 HIS F 416 ASN G 5 GLN M 437 GLN O 174 ASN U 322 GLN V 322 GLN f 80 GLN f 129 HIS f 165 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 69957 Z= 0.274 Angle : 0.567 8.611 94694 Z= 0.299 Chirality : 0.044 0.189 10759 Planarity : 0.004 0.051 12440 Dihedral : 5.825 87.048 10218 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.92 % Allowed : 13.16 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: 1.49 (0.09), residues: 8881 helix: 2.34 (0.08), residues: 3586 sheet: 0.63 (0.12), residues: 1972 loop : -0.26 (0.11), residues: 3323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 187 HIS 0.009 0.001 HIS F 348 PHE 0.039 0.003 PHE 2 71 TYR 0.017 0.002 TYR I 143 ARG 0.010 0.001 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 770 time to evaluate : 5.776 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: 0 143 TYR cc_start: 0.6290 (p90) cc_final: 0.6014 (p90) REVERT: 2 110 ILE cc_start: 0.8087 (mt) cc_final: 0.7717 (tp) REVERT: 2 114 GLN cc_start: 0.6573 (tt0) cc_final: 0.6295 (tt0) REVERT: 2 135 ARG cc_start: 0.8001 (tpp80) cc_final: 0.7296 (ttm-80) REVERT: 2 205 VAL cc_start: 0.6067 (m) cc_final: 0.5794 (p) REVERT: 2 234 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.6561 (pt) REVERT: 4 45 ASN cc_start: 0.7535 (t0) cc_final: 0.7126 (t0) REVERT: 4 51 GLN cc_start: 0.6720 (mm-40) cc_final: 0.5823 (mm-40) REVERT: 4 149 ASP cc_start: 0.7985 (t0) cc_final: 0.7701 (m-30) REVERT: 6 44 GLU cc_start: 0.7307 (tt0) cc_final: 0.6736 (tm-30) REVERT: 6 97 ARG cc_start: 0.6386 (ttt-90) cc_final: 0.6072 (ttt-90) REVERT: 6 101 ASN cc_start: 0.6952 (t0) cc_final: 0.6703 (m-40) REVERT: 6 113 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6450 (tt0) REVERT: 6 168 LYS cc_start: 0.7160 (mttt) cc_final: 0.6925 (mttt) REVERT: 6 182 ARG cc_start: 0.5638 (OUTLIER) cc_final: 0.4958 (mtm-85) REVERT: 6 233 LEU cc_start: 0.7594 (mp) cc_final: 0.7131 (mt) REVERT: 6 234 LEU cc_start: 0.6273 (OUTLIER) cc_final: 0.5660 (pt) REVERT: 8 52 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.6917 (mtpp) REVERT: 8 73 ASN cc_start: 0.7238 (OUTLIER) cc_final: 0.6599 (m-40) REVERT: 8 101 ASN cc_start: 0.7507 (t0) cc_final: 0.7181 (m-40) REVERT: 8 174 ASN cc_start: 0.7818 (m110) cc_final: 0.7557 (m110) REVERT: A 122 MET cc_start: 0.8846 (mmm) cc_final: 0.8415 (mmm) REVERT: A 243 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7402 (pp) REVERT: A 396 LEU cc_start: 0.8284 (mm) cc_final: 0.7885 (tt) REVERT: B 122 MET cc_start: 0.7770 (mpp) cc_final: 0.7413 (mpp) REVERT: B 137 LYS cc_start: 0.7149 (ttmt) cc_final: 0.6374 (tptt) REVERT: C 420 MET cc_start: 0.7070 (mtm) cc_final: 0.6819 (mtm) REVERT: D 122 MET cc_start: 0.8019 (mpp) cc_final: 0.7558 (mpp) REVERT: D 164 LEU cc_start: 0.6964 (tp) cc_final: 0.6592 (tp) REVERT: D 268 VAL cc_start: 0.6745 (t) cc_final: 0.6411 (p) REVERT: D 314 MET cc_start: 0.6346 (ptt) cc_final: 0.5097 (tpt) REVERT: D 480 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7913 (tp30) REVERT: E 124 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7183 (tp) REVERT: E 323 HIS cc_start: 0.6357 (p-80) cc_final: 0.6091 (p-80) REVERT: E 379 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7915 (p) REVERT: E 520 GLN cc_start: 0.8502 (tt0) cc_final: 0.8292 (tt0) REVERT: F 314 MET cc_start: 0.6249 (mmt) cc_final: 0.5917 (mmp) REVERT: F 323 HIS cc_start: 0.6244 (m90) cc_final: 0.6002 (m90) REVERT: F 529 ASN cc_start: 0.8532 (m-40) cc_final: 0.8274 (t0) REVERT: G 1 MET cc_start: 0.6023 (pmm) cc_final: 0.5748 (mtp) REVERT: H 325 MET cc_start: 0.8087 (mtm) cc_final: 0.7831 (mtt) REVERT: H 386 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7709 (mtp) REVERT: H 388 ARG cc_start: 0.7486 (tpp-160) cc_final: 0.6395 (ttp-110) REVERT: H 396 GLN cc_start: 0.7190 (tm-30) cc_final: 0.6873 (tp40) REVERT: H 519 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7228 (mm-30) REVERT: I 73 ASN cc_start: 0.6778 (t0) cc_final: 0.6561 (t0) REVERT: I 105 GLN cc_start: 0.7219 (tt0) cc_final: 0.6756 (tm-30) REVERT: I 111 PHE cc_start: 0.7503 (t80) cc_final: 0.7174 (t80) REVERT: I 121 GLU cc_start: 0.6555 (tt0) cc_final: 0.6200 (mm-30) REVERT: I 140 ARG cc_start: 0.7358 (ttp-110) cc_final: 0.6986 (ttp80) REVERT: I 182 ARG cc_start: 0.6032 (OUTLIER) cc_final: 0.5761 (mpt-90) REVERT: J 325 MET cc_start: 0.8014 (mtm) cc_final: 0.7459 (ttm) REVERT: J 364 GLU cc_start: 0.6739 (tt0) cc_final: 0.6410 (pt0) REVERT: J 509 ARG cc_start: 0.6349 (tpt90) cc_final: 0.5914 (ttt180) REVERT: K 13 MET cc_start: 0.6097 (mmt) cc_final: 0.4587 (ttp) REVERT: K 14 ARG cc_start: 0.4798 (tpm170) cc_final: 0.4466 (tpm170) REVERT: K 18 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6305 (mm-30) REVERT: K 26 ARG cc_start: 0.6787 (ttm110) cc_final: 0.6351 (ppt170) REVERT: K 101 ASN cc_start: 0.6683 (t0) cc_final: 0.6235 (m-40) REVERT: K 112 THR cc_start: 0.7048 (m) cc_final: 0.6796 (p) REVERT: K 146 SER cc_start: 0.6933 (m) cc_final: 0.6500 (p) REVERT: K 150 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6662 (mm-30) REVERT: K 214 ASP cc_start: 0.6439 (t0) cc_final: 0.6132 (t0) REVERT: K 216 ASN cc_start: 0.7380 (t0) cc_final: 0.6527 (m-40) REVERT: L 325 MET cc_start: 0.7948 (mtm) cc_final: 0.7224 (ttm) REVERT: L 332 ARG cc_start: 0.7264 (mtt-85) cc_final: 0.6421 (mtt180) REVERT: L 401 LEU cc_start: 0.7574 (mt) cc_final: 0.7277 (tp) REVERT: M 307 LYS cc_start: 0.7823 (mtpt) cc_final: 0.7511 (mtmm) REVERT: M 325 MET cc_start: 0.7871 (mtm) cc_final: 0.7428 (ttm) REVERT: N 325 MET cc_start: 0.7499 (mtm) cc_final: 0.7227 (mtp) REVERT: N 364 GLU cc_start: 0.7927 (tt0) cc_final: 0.7303 (pt0) REVERT: N 399 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7551 (tt) REVERT: N 432 GLU cc_start: 0.7070 (tp30) cc_final: 0.6765 (mm-30) REVERT: N 461 ASP cc_start: 0.5774 (t70) cc_final: 0.5514 (t0) REVERT: N 509 ARG cc_start: 0.5942 (OUTLIER) cc_final: 0.5429 (tpt-90) REVERT: N 512 GLU cc_start: 0.6524 (tm-30) cc_final: 0.6235 (mt-10) REVERT: O 26 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6691 (ppt170) REVERT: O 44 GLU cc_start: 0.4564 (OUTLIER) cc_final: 0.3341 (tm-30) REVERT: O 113 GLU cc_start: 0.7238 (tt0) cc_final: 0.6954 (tm-30) REVERT: O 146 SER cc_start: 0.6874 (m) cc_final: 0.6552 (t) REVERT: O 151 PRO cc_start: 0.7875 (Cg_endo) cc_final: 0.7610 (Cg_exo) REVERT: O 168 LYS cc_start: 0.6571 (ttpt) cc_final: 0.6369 (ttmt) REVERT: O 214 ASP cc_start: 0.7087 (t0) cc_final: 0.6727 (t0) REVERT: O 226 THR cc_start: 0.6029 (t) cc_final: 0.5633 (m) REVERT: P 325 MET cc_start: 0.7653 (mtm) cc_final: 0.7071 (ttp) REVERT: P 345 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7493 (mm) REVERT: P 388 ARG cc_start: 0.7261 (tpt-90) cc_final: 0.6613 (ttm110) REVERT: P 432 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6473 (mp0) REVERT: Q 49 SER cc_start: 0.7462 (m) cc_final: 0.7106 (p) REVERT: Q 113 GLU cc_start: 0.7625 (tp30) cc_final: 0.7068 (tm-30) REVERT: Q 146 SER cc_start: 0.6917 (m) cc_final: 0.6562 (p) REVERT: Q 156 MET cc_start: 0.5714 (mtm) cc_final: 0.5290 (mtm) REVERT: R 325 MET cc_start: 0.7352 (mtm) cc_final: 0.6762 (ttp) REVERT: S 512 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6708 (mm-30) REVERT: S 519 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6986 (tm-30) REVERT: T 29 SER cc_start: 0.6213 (m) cc_final: 0.5782 (p) REVERT: T 52 LYS cc_start: 0.7315 (mtpt) cc_final: 0.6818 (mtmm) REVERT: T 72 ASP cc_start: 0.7548 (t70) cc_final: 0.7320 (t70) REVERT: T 113 GLU cc_start: 0.7349 (tp30) cc_final: 0.7059 (tm-30) REVERT: T 121 GLU cc_start: 0.7078 (tt0) cc_final: 0.6327 (mm-30) REVERT: T 170 SER cc_start: 0.5252 (p) cc_final: 0.4965 (m) REVERT: T 214 ASP cc_start: 0.6141 (t0) cc_final: 0.5825 (t0) REVERT: T 216 ASN cc_start: 0.7636 (t0) cc_final: 0.7234 (m110) REVERT: U 314 MET cc_start: 0.8164 (ttm) cc_final: 0.7755 (ttm) REVERT: U 337 THR cc_start: 0.7716 (p) cc_final: 0.7513 (p) REVERT: U 509 ARG cc_start: 0.6361 (tpt170) cc_final: 0.6100 (ttp80) REVERT: V 325 MET cc_start: 0.7700 (ttp) cc_final: 0.6505 (mmt) REVERT: V 401 LEU cc_start: 0.7218 (tp) cc_final: 0.6905 (mt) REVERT: V 509 ARG cc_start: 0.6341 (OUTLIER) cc_final: 0.5590 (ttt180) REVERT: V 519 GLU cc_start: 0.7253 (tt0) cc_final: 0.6908 (mt-10) REVERT: W 345 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7554 (mp) REVERT: W 364 GLU cc_start: 0.7108 (tt0) cc_final: 0.6563 (pt0) REVERT: W 522 SER cc_start: 0.6106 (t) cc_final: 0.5730 (m) REVERT: X 26 ARG cc_start: 0.7602 (ptm-80) cc_final: 0.7314 (mtm110) REVERT: X 52 LYS cc_start: 0.7599 (mtpt) cc_final: 0.7172 (mtmm) REVERT: X 105 GLN cc_start: 0.7175 (tt0) cc_final: 0.6280 (mm-40) REVERT: X 111 PHE cc_start: 0.6383 (t80) cc_final: 0.6180 (t80) REVERT: X 130 TYR cc_start: 0.7478 (t80) cc_final: 0.6009 (t80) REVERT: X 179 ASP cc_start: 0.6599 (m-30) cc_final: 0.5988 (t0) REVERT: X 205 VAL cc_start: 0.6445 (m) cc_final: 0.5890 (t) REVERT: X 216 ASN cc_start: 0.7537 (t0) cc_final: 0.6947 (t0) REVERT: Y 325 MET cc_start: 0.7747 (mtm) cc_final: 0.6959 (ttt) REVERT: Y 399 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7297 (tp) REVERT: Y 432 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6811 (mm-30) REVERT: Y 509 ARG cc_start: 0.7170 (tpt90) cc_final: 0.6471 (ttp80) REVERT: Z 113 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6545 (tm-30) REVERT: Z 144 ASP cc_start: 0.4802 (p0) cc_final: 0.4552 (p0) REVERT: Z 156 MET cc_start: 0.6966 (mtm) cc_final: 0.6732 (mtm) REVERT: Z 216 ASN cc_start: 0.8439 (t0) cc_final: 0.8040 (m-40) REVERT: a 325 MET cc_start: 0.7578 (mtm) cc_final: 0.6853 (ttm) REVERT: b 339 ASP cc_start: 0.8021 (t0) cc_final: 0.7634 (m-30) REVERT: b 433 GLU cc_start: 0.7591 (mm-30) cc_final: 0.6909 (mp0) REVERT: d 51 GLN cc_start: 0.6897 (mt0) cc_final: 0.6626 (mt0) REVERT: d 101 ASN cc_start: 0.7294 (t0) cc_final: 0.6848 (m-40) REVERT: d 179 ASP cc_start: 0.7725 (m-30) cc_final: 0.7331 (t0) REVERT: d 189 ARG cc_start: 0.5546 (ttm-80) cc_final: 0.5203 (mtm-85) REVERT: d 234 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6682 (pt) REVERT: f 15 GLU cc_start: 0.7768 (tt0) cc_final: 0.7383 (tp30) REVERT: f 26 ARG cc_start: 0.6364 (ttt180) cc_final: 0.6070 (ttp80) REVERT: f 52 LYS cc_start: 0.6579 (OUTLIER) cc_final: 0.6122 (mtpt) REVERT: f 69 ASN cc_start: 0.6961 (p0) cc_final: 0.6282 (m-40) REVERT: f 73 ASN cc_start: 0.7083 (t0) cc_final: 0.6864 (t0) REVERT: f 97 ARG cc_start: 0.6612 (ttp-170) cc_final: 0.5880 (ttm170) REVERT: f 101 ASN cc_start: 0.6728 (t0) cc_final: 0.6298 (m-40) REVERT: f 112 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7790 (p) outliers start: 206 outliers final: 130 residues processed: 910 average time/residue: 0.6794 time to fit residues: 1047.8922 Evaluate side-chains 887 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 733 time to evaluate : 6.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 51 GLN Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 0 residue 225 ILE Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 216 ASN Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 133 THR Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 52 LYS Chi-restraints excluded: chain 8 residue 73 ASN Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 147 ILE Chi-restraints excluded: chain 8 residue 185 VAL Chi-restraints excluded: chain 8 residue 226 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 474 CYS Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 182 ARG Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain L residue 337 THR Chi-restraints excluded: chain L residue 363 LEU Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain L residue 441 SER Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain M residue 345 ILE Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 450 MET Chi-restraints excluded: chain N residue 509 ARG Chi-restraints excluded: chain O residue 26 ARG Chi-restraints excluded: chain O residue 44 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain P residue 345 ILE Chi-restraints excluded: chain P residue 396 GLN Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain P residue 444 LEU Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 228 SER Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 409 ILE Chi-restraints excluded: chain S residue 512 GLU Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain T residue 225 ILE Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 320 SER Chi-restraints excluded: chain U residue 441 SER Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 399 LEU Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 345 ILE Chi-restraints excluded: chain W residue 363 LEU Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain X residue 210 VAL Chi-restraints excluded: chain Y residue 307 LYS Chi-restraints excluded: chain Y residue 320 SER Chi-restraints excluded: chain Y residue 345 ILE Chi-restraints excluded: chain Y residue 399 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 441 SER Chi-restraints excluded: chain Y residue 444 LEU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain a residue 396 GLN Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain a residue 409 ILE Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 52 LYS Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 147 ILE Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Chi-restraints excluded: chain f residue 233 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 288 optimal weight: 5.9990 chunk 772 optimal weight: 0.0370 chunk 169 optimal weight: 5.9990 chunk 503 optimal weight: 0.8980 chunk 211 optimal weight: 20.0000 chunk 859 optimal weight: 7.9990 chunk 713 optimal weight: 0.6980 chunk 397 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 284 optimal weight: 8.9990 chunk 451 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 546 HIS ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 HIS ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 HIS G 5 GLN I 152 HIS O 101 ASN O 174 ASN U 322 GLN f 80 GLN f 165 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 69957 Z= 0.140 Angle : 0.500 8.415 94694 Z= 0.264 Chirality : 0.042 0.173 10759 Planarity : 0.004 0.061 12440 Dihedral : 5.577 86.874 10216 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.24 % Allowed : 14.08 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: 1.76 (0.09), residues: 8881 helix: 2.64 (0.08), residues: 3586 sheet: 0.71 (0.12), residues: 1978 loop : -0.17 (0.11), residues: 3317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 187 HIS 0.009 0.001 HIS F 348 PHE 0.031 0.002 PHE 6 71 TYR 0.018 0.001 TYR I 143 ARG 0.010 0.000 ARG O 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 795 time to evaluate : 5.866 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: 0 156 MET cc_start: 0.7408 (mtm) cc_final: 0.6957 (mtm) REVERT: 2 110 ILE cc_start: 0.8133 (mt) cc_final: 0.7748 (tp) REVERT: 2 114 GLN cc_start: 0.6521 (tt0) cc_final: 0.6217 (tt0) REVERT: 2 135 ARG cc_start: 0.7995 (tpp80) cc_final: 0.7283 (ttm-80) REVERT: 2 205 VAL cc_start: 0.5844 (m) cc_final: 0.5506 (p) REVERT: 2 234 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6702 (pt) REVERT: 4 45 ASN cc_start: 0.7489 (t0) cc_final: 0.7096 (t0) REVERT: 4 51 GLN cc_start: 0.6775 (mm-40) cc_final: 0.5830 (mm-40) REVERT: 4 99 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6940 (mm) REVERT: 4 149 ASP cc_start: 0.8009 (t0) cc_final: 0.7729 (m-30) REVERT: 4 225 ILE cc_start: 0.8408 (mt) cc_final: 0.7968 (mm) REVERT: 6 44 GLU cc_start: 0.7546 (tt0) cc_final: 0.6927 (tm-30) REVERT: 6 97 ARG cc_start: 0.6333 (ttt-90) cc_final: 0.5946 (ttt-90) REVERT: 6 101 ASN cc_start: 0.6972 (t0) cc_final: 0.6737 (m-40) REVERT: 6 113 GLU cc_start: 0.6822 (mm-30) cc_final: 0.6392 (tt0) REVERT: 6 182 ARG cc_start: 0.5670 (OUTLIER) cc_final: 0.5035 (mtm-85) REVERT: 6 233 LEU cc_start: 0.7634 (mp) cc_final: 0.7164 (mt) REVERT: 6 234 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.5610 (pt) REVERT: 8 73 ASN cc_start: 0.7346 (m110) cc_final: 0.6999 (m110) REVERT: 8 101 ASN cc_start: 0.7385 (t0) cc_final: 0.7066 (m-40) REVERT: A 122 MET cc_start: 0.8820 (mmm) cc_final: 0.8510 (mmm) REVERT: A 243 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7218 (pp) REVERT: A 396 LEU cc_start: 0.8231 (mm) cc_final: 0.7893 (tt) REVERT: B 137 LYS cc_start: 0.7134 (ttmt) cc_final: 0.6294 (tptt) REVERT: B 395 GLN cc_start: 0.7598 (tp40) cc_final: 0.7286 (tp40) REVERT: C 420 MET cc_start: 0.6885 (mtm) cc_final: 0.6619 (mtm) REVERT: D 122 MET cc_start: 0.8085 (mpp) cc_final: 0.7673 (mpp) REVERT: D 164 LEU cc_start: 0.6889 (tp) cc_final: 0.6510 (tp) REVERT: D 268 VAL cc_start: 0.6712 (t) cc_final: 0.6383 (p) REVERT: D 314 MET cc_start: 0.6221 (ptt) cc_final: 0.5179 (tpt) REVERT: D 480 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7841 (tm-30) REVERT: E 124 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7209 (tp) REVERT: E 379 THR cc_start: 0.8215 (OUTLIER) cc_final: 0.7919 (p) REVERT: E 520 GLN cc_start: 0.8418 (tt0) cc_final: 0.8176 (tt0) REVERT: F 323 HIS cc_start: 0.6349 (m90) cc_final: 0.6047 (m90) REVERT: F 420 MET cc_start: 0.7966 (tpp) cc_final: 0.7585 (tpt) REVERT: F 529 ASN cc_start: 0.8508 (m-40) cc_final: 0.8265 (t0) REVERT: G 1 MET cc_start: 0.6043 (pmm) cc_final: 0.5788 (mtp) REVERT: H 325 MET cc_start: 0.8017 (mtm) cc_final: 0.7772 (mtt) REVERT: H 396 GLN cc_start: 0.7218 (tm-30) cc_final: 0.6916 (tp40) REVERT: H 519 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7182 (mm-30) REVERT: I 73 ASN cc_start: 0.6609 (t0) cc_final: 0.6308 (t0) REVERT: I 105 GLN cc_start: 0.7333 (tt0) cc_final: 0.6915 (tm-30) REVERT: I 121 GLU cc_start: 0.6603 (tt0) cc_final: 0.6297 (mm-30) REVERT: I 140 ARG cc_start: 0.7225 (ttp-110) cc_final: 0.6466 (ttp-170) REVERT: I 182 ARG cc_start: 0.6084 (OUTLIER) cc_final: 0.5803 (mpt-90) REVERT: J 325 MET cc_start: 0.7921 (mtm) cc_final: 0.7330 (ttm) REVERT: J 364 GLU cc_start: 0.6545 (tt0) cc_final: 0.6301 (mt-10) REVERT: J 509 ARG cc_start: 0.6213 (tpt90) cc_final: 0.5999 (ttt180) REVERT: K 13 MET cc_start: 0.6062 (mmt) cc_final: 0.4601 (ttp) REVERT: K 14 ARG cc_start: 0.4950 (tpm170) cc_final: 0.4606 (tpm170) REVERT: K 26 ARG cc_start: 0.6781 (ttm110) cc_final: 0.6286 (ppt170) REVERT: K 101 ASN cc_start: 0.6606 (t0) cc_final: 0.6238 (m-40) REVERT: K 112 THR cc_start: 0.6907 (m) cc_final: 0.6686 (p) REVERT: K 146 SER cc_start: 0.6958 (m) cc_final: 0.6512 (p) REVERT: K 150 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6451 (mm-30) REVERT: K 216 ASN cc_start: 0.7392 (t0) cc_final: 0.6623 (m-40) REVERT: L 325 MET cc_start: 0.7950 (mtm) cc_final: 0.7207 (ttp) REVERT: L 332 ARG cc_start: 0.7170 (mtt-85) cc_final: 0.6386 (mtt180) REVERT: L 401 LEU cc_start: 0.7598 (mt) cc_final: 0.7304 (tp) REVERT: M 307 LYS cc_start: 0.7760 (mtpt) cc_final: 0.7414 (mtmm) REVERT: M 325 MET cc_start: 0.7808 (mtm) cc_final: 0.7425 (ttm) REVERT: M 401 LEU cc_start: 0.7873 (mt) cc_final: 0.7568 (mt) REVERT: M 424 ASP cc_start: 0.7247 (p0) cc_final: 0.6969 (p0) REVERT: N 325 MET cc_start: 0.7502 (mtm) cc_final: 0.7224 (mtp) REVERT: N 364 GLU cc_start: 0.7724 (tt0) cc_final: 0.7117 (pt0) REVERT: N 399 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7251 (tt) REVERT: N 509 ARG cc_start: 0.5658 (OUTLIER) cc_final: 0.5128 (ttt-90) REVERT: N 512 GLU cc_start: 0.6457 (tm-30) cc_final: 0.6168 (mt-10) REVERT: O 26 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6783 (ppt170) REVERT: O 44 GLU cc_start: 0.4689 (OUTLIER) cc_final: 0.3433 (tm-30) REVERT: O 146 SER cc_start: 0.6823 (m) cc_final: 0.6511 (t) REVERT: O 151 PRO cc_start: 0.7823 (Cg_endo) cc_final: 0.7549 (Cg_exo) REVERT: O 226 THR cc_start: 0.5973 (t) cc_final: 0.5566 (m) REVERT: P 325 MET cc_start: 0.7636 (mtm) cc_final: 0.7058 (ttp) REVERT: P 345 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7511 (mm) REVERT: P 388 ARG cc_start: 0.7247 (tpt-90) cc_final: 0.6572 (ttm110) REVERT: P 432 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6484 (mp0) REVERT: Q 49 SER cc_start: 0.7440 (m) cc_final: 0.7111 (p) REVERT: Q 70 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7073 (mt-10) REVERT: Q 113 GLU cc_start: 0.7614 (tp30) cc_final: 0.7088 (tm-30) REVERT: Q 146 SER cc_start: 0.7069 (m) cc_final: 0.6637 (p) REVERT: Q 156 MET cc_start: 0.6059 (mtm) cc_final: 0.5753 (mtm) REVERT: R 325 MET cc_start: 0.7333 (mtm) cc_final: 0.6778 (ttp) REVERT: R 430 ASN cc_start: 0.8177 (t0) cc_final: 0.7505 (m-40) REVERT: S 396 GLN cc_start: 0.6777 (tt0) cc_final: 0.6520 (tp40) REVERT: S 512 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6614 (mm-30) REVERT: S 519 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6989 (tm-30) REVERT: T 29 SER cc_start: 0.5900 (m) cc_final: 0.5507 (p) REVERT: T 52 LYS cc_start: 0.7178 (mtpt) cc_final: 0.6644 (mtmm) REVERT: T 80 GLN cc_start: 0.6838 (tp-100) cc_final: 0.6501 (tp-100) REVERT: T 105 GLN cc_start: 0.6910 (tt0) cc_final: 0.6607 (tp40) REVERT: T 113 GLU cc_start: 0.7294 (tp30) cc_final: 0.6948 (tm-30) REVERT: T 121 GLU cc_start: 0.6960 (tt0) cc_final: 0.6410 (tp30) REVERT: T 214 ASP cc_start: 0.6087 (t0) cc_final: 0.5764 (t0) REVERT: T 216 ASN cc_start: 0.7632 (t0) cc_final: 0.7214 (m110) REVERT: U 314 MET cc_start: 0.8168 (ttm) cc_final: 0.7693 (ttm) REVERT: U 401 LEU cc_start: 0.7591 (mt) cc_final: 0.7105 (mt) REVERT: U 509 ARG cc_start: 0.6384 (tpt170) cc_final: 0.6179 (ttp80) REVERT: V 325 MET cc_start: 0.7587 (ttp) cc_final: 0.6500 (mmt) REVERT: V 509 ARG cc_start: 0.6199 (OUTLIER) cc_final: 0.5584 (ttt180) REVERT: V 519 GLU cc_start: 0.7064 (tt0) cc_final: 0.6655 (mm-30) REVERT: W 325 MET cc_start: 0.7737 (ttp) cc_final: 0.7367 (ttm) REVERT: W 345 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7382 (mp) REVERT: W 364 GLU cc_start: 0.7055 (tt0) cc_final: 0.6507 (pt0) REVERT: W 522 SER cc_start: 0.5897 (t) cc_final: 0.5559 (m) REVERT: X 26 ARG cc_start: 0.7559 (ptm-80) cc_final: 0.7310 (mtm110) REVERT: X 52 LYS cc_start: 0.7808 (mtpt) cc_final: 0.7450 (mtmm) REVERT: X 105 GLN cc_start: 0.7147 (tt0) cc_final: 0.6374 (mm-40) REVERT: X 111 PHE cc_start: 0.6276 (t80) cc_final: 0.6073 (t80) REVERT: X 130 TYR cc_start: 0.7501 (t80) cc_final: 0.6093 (t80) REVERT: X 179 ASP cc_start: 0.6605 (m-30) cc_final: 0.6205 (t0) REVERT: X 216 ASN cc_start: 0.7572 (t0) cc_final: 0.7043 (t0) REVERT: Y 325 MET cc_start: 0.7825 (mtm) cc_final: 0.7139 (ttm) REVERT: Y 399 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7278 (tp) REVERT: Y 509 ARG cc_start: 0.7142 (tpt90) cc_final: 0.6436 (ttp80) REVERT: Z 113 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6702 (tm-30) REVERT: Z 143 TYR cc_start: 0.5625 (p90) cc_final: 0.4819 (p90) REVERT: Z 144 ASP cc_start: 0.4757 (p0) cc_final: 0.4264 (p0) REVERT: Z 156 MET cc_start: 0.6875 (mtm) cc_final: 0.6675 (mtm) REVERT: Z 214 ASP cc_start: 0.6269 (t0) cc_final: 0.6013 (t0) REVERT: Z 216 ASN cc_start: 0.8413 (t0) cc_final: 0.8021 (m-40) REVERT: a 325 MET cc_start: 0.7587 (mtm) cc_final: 0.6930 (ttm) REVERT: b 339 ASP cc_start: 0.8033 (t0) cc_final: 0.7582 (m-30) REVERT: b 433 GLU cc_start: 0.7568 (mm-30) cc_final: 0.6914 (mp0) REVERT: d 51 GLN cc_start: 0.6959 (mt0) cc_final: 0.6700 (mt0) REVERT: d 101 ASN cc_start: 0.7268 (t0) cc_final: 0.6801 (m-40) REVERT: d 179 ASP cc_start: 0.7688 (m-30) cc_final: 0.7284 (t0) REVERT: d 189 ARG cc_start: 0.5640 (ttm-80) cc_final: 0.5319 (mtm-85) REVERT: d 234 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6780 (pt) REVERT: f 15 GLU cc_start: 0.7765 (tt0) cc_final: 0.7342 (tp30) REVERT: f 26 ARG cc_start: 0.6446 (ttt180) cc_final: 0.6115 (ttp80) REVERT: f 101 ASN cc_start: 0.6798 (t0) cc_final: 0.6374 (m-40) REVERT: f 112 THR cc_start: 0.8110 (OUTLIER) cc_final: 0.7775 (p) outliers start: 158 outliers final: 98 residues processed: 895 average time/residue: 0.6683 time to fit residues: 1015.3231 Evaluate side-chains 863 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 743 time to evaluate : 5.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 0 residue 225 ILE Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 73 ASN Chi-restraints excluded: chain 4 residue 99 LEU Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 216 ASN Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 133 THR Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 182 ARG Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 486 LEU Chi-restraints excluded: chain J residue 519 GLU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 123 CYS Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain L residue 337 THR Chi-restraints excluded: chain L residue 363 LEU Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain L residue 441 SER Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain M residue 339 ASP Chi-restraints excluded: chain M residue 345 ILE Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 509 ARG Chi-restraints excluded: chain O residue 26 ARG Chi-restraints excluded: chain O residue 44 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain P residue 345 ILE Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 386 MET Chi-restraints excluded: chain S residue 512 GLU Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain T residue 225 ILE Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 441 SER Chi-restraints excluded: chain V residue 399 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 307 LYS Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 345 ILE Chi-restraints excluded: chain W residue 363 LEU Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain Y residue 345 ILE Chi-restraints excluded: chain Y residue 399 LEU Chi-restraints excluded: chain Y residue 441 SER Chi-restraints excluded: chain Y residue 444 LEU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 147 ILE Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Chi-restraints excluded: chain f residue 233 LEU Chi-restraints excluded: chain f residue 234 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 828 optimal weight: 0.0770 chunk 96 optimal weight: 1.9990 chunk 489 optimal weight: 2.9990 chunk 627 optimal weight: 0.5980 chunk 486 optimal weight: 2.9990 chunk 723 optimal weight: 3.9990 chunk 479 optimal weight: 2.9990 chunk 855 optimal weight: 2.9990 chunk 535 optimal weight: 2.9990 chunk 521 optimal weight: 4.9990 chunk 395 optimal weight: 0.6980 overall best weight: 1.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 GLN B 546 HIS C 263 GLN ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 HIS E 172 HIS ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 HIS F 545 GLN G 5 GLN O 45 ASN Q 174 ASN U 322 GLN f 80 GLN f 105 GLN f 165 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 69957 Z= 0.188 Angle : 0.521 9.779 94694 Z= 0.274 Chirality : 0.042 0.193 10759 Planarity : 0.004 0.054 12440 Dihedral : 5.496 87.116 10210 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.63 % Allowed : 14.20 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: 1.78 (0.09), residues: 8881 helix: 2.68 (0.08), residues: 3585 sheet: 0.65 (0.12), residues: 2026 loop : -0.16 (0.11), residues: 3270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 187 HIS 0.008 0.001 HIS F 348 PHE 0.032 0.002 PHE 6 71 TYR 0.014 0.001 TYR 6 118 ARG 0.007 0.000 ARG X 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 759 time to evaluate : 5.769 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: 0 156 MET cc_start: 0.7491 (mtm) cc_final: 0.7174 (mtm) REVERT: 2 110 ILE cc_start: 0.8094 (mt) cc_final: 0.7770 (tp) REVERT: 2 135 ARG cc_start: 0.7955 (tpp80) cc_final: 0.7233 (ttm-80) REVERT: 2 205 VAL cc_start: 0.6233 (m) cc_final: 0.5906 (p) REVERT: 2 234 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6835 (pt) REVERT: 4 45 ASN cc_start: 0.7524 (t0) cc_final: 0.7151 (t0) REVERT: 4 51 GLN cc_start: 0.6868 (mm-40) cc_final: 0.5817 (mm-40) REVERT: 4 99 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6945 (mm) REVERT: 4 149 ASP cc_start: 0.7992 (t0) cc_final: 0.7690 (m-30) REVERT: 4 225 ILE cc_start: 0.8375 (mt) cc_final: 0.7929 (mm) REVERT: 6 44 GLU cc_start: 0.7753 (tt0) cc_final: 0.7074 (tm-30) REVERT: 6 97 ARG cc_start: 0.6338 (ttt-90) cc_final: 0.5948 (ttt-90) REVERT: 6 101 ASN cc_start: 0.6984 (t0) cc_final: 0.6748 (m-40) REVERT: 6 113 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6440 (tt0) REVERT: 6 118 TYR cc_start: 0.8289 (m-80) cc_final: 0.8073 (m-80) REVERT: 6 182 ARG cc_start: 0.5636 (OUTLIER) cc_final: 0.5005 (mtm-85) REVERT: 6 233 LEU cc_start: 0.7671 (mp) cc_final: 0.7173 (mt) REVERT: 6 234 LEU cc_start: 0.6102 (OUTLIER) cc_final: 0.5487 (pt) REVERT: 8 73 ASN cc_start: 0.7340 (m110) cc_final: 0.6670 (m-40) REVERT: 8 101 ASN cc_start: 0.7372 (t0) cc_final: 0.7116 (m-40) REVERT: 8 113 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7087 (mp0) REVERT: A 122 MET cc_start: 0.8704 (mmm) cc_final: 0.8459 (mmm) REVERT: A 243 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7235 (pp) REVERT: A 396 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7909 (tt) REVERT: D 122 MET cc_start: 0.8111 (mpp) cc_final: 0.7702 (mpp) REVERT: D 164 LEU cc_start: 0.6893 (tp) cc_final: 0.6520 (tp) REVERT: D 268 VAL cc_start: 0.6660 (t) cc_final: 0.6383 (p) REVERT: D 314 MET cc_start: 0.6222 (ptt) cc_final: 0.5165 (tpt) REVERT: D 480 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7909 (tm-30) REVERT: E 124 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7141 (tp) REVERT: E 379 THR cc_start: 0.8259 (OUTLIER) cc_final: 0.8056 (p) REVERT: E 520 GLN cc_start: 0.8433 (tt0) cc_final: 0.8198 (tt0) REVERT: F 314 MET cc_start: 0.6242 (mmt) cc_final: 0.5861 (mmp) REVERT: F 323 HIS cc_start: 0.6335 (m90) cc_final: 0.6051 (m90) REVERT: F 420 MET cc_start: 0.7979 (tpp) cc_final: 0.7606 (tpt) REVERT: F 529 ASN cc_start: 0.8528 (m-40) cc_final: 0.8265 (t0) REVERT: G 1 MET cc_start: 0.6045 (pmm) cc_final: 0.5767 (mtp) REVERT: H 325 MET cc_start: 0.8024 (mtm) cc_final: 0.7805 (mtt) REVERT: H 388 ARG cc_start: 0.7488 (tpp-160) cc_final: 0.6400 (ttp-110) REVERT: H 396 GLN cc_start: 0.7220 (tm-30) cc_final: 0.6904 (tp40) REVERT: H 519 GLU cc_start: 0.7571 (tt0) cc_final: 0.7200 (mm-30) REVERT: I 73 ASN cc_start: 0.6642 (t0) cc_final: 0.6305 (t0) REVERT: I 101 ASN cc_start: 0.6734 (t0) cc_final: 0.6224 (m-40) REVERT: I 105 GLN cc_start: 0.7408 (tt0) cc_final: 0.6905 (tm-30) REVERT: I 121 GLU cc_start: 0.6598 (tt0) cc_final: 0.6265 (mm-30) REVERT: I 140 ARG cc_start: 0.7064 (ttp-110) cc_final: 0.6704 (ttp80) REVERT: I 182 ARG cc_start: 0.6071 (OUTLIER) cc_final: 0.5842 (mpt-90) REVERT: J 325 MET cc_start: 0.7959 (mtm) cc_final: 0.7366 (ttm) REVERT: J 364 GLU cc_start: 0.6625 (tt0) cc_final: 0.6364 (mt-10) REVERT: J 509 ARG cc_start: 0.6239 (tpt90) cc_final: 0.6013 (ttt180) REVERT: K 13 MET cc_start: 0.6057 (mmt) cc_final: 0.4571 (ttp) REVERT: K 14 ARG cc_start: 0.5254 (tpm170) cc_final: 0.4828 (tpm170) REVERT: K 26 ARG cc_start: 0.6813 (ttm110) cc_final: 0.6236 (ttp80) REVERT: K 101 ASN cc_start: 0.6567 (t0) cc_final: 0.6205 (m-40) REVERT: K 146 SER cc_start: 0.6998 (m) cc_final: 0.6533 (p) REVERT: K 150 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6412 (mm-30) REVERT: K 216 ASN cc_start: 0.7387 (t0) cc_final: 0.6622 (m-40) REVERT: L 325 MET cc_start: 0.7952 (mtm) cc_final: 0.7248 (ttm) REVERT: L 332 ARG cc_start: 0.7119 (mtt-85) cc_final: 0.6433 (mtt180) REVERT: L 401 LEU cc_start: 0.7585 (mt) cc_final: 0.7295 (tp) REVERT: M 307 LYS cc_start: 0.7766 (mtpt) cc_final: 0.7462 (mtmm) REVERT: M 325 MET cc_start: 0.7895 (mtm) cc_final: 0.7387 (ttm) REVERT: M 401 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7595 (mt) REVERT: M 424 ASP cc_start: 0.7364 (p0) cc_final: 0.7114 (p0) REVERT: N 325 MET cc_start: 0.7502 (mtm) cc_final: 0.7216 (mtp) REVERT: N 364 GLU cc_start: 0.7852 (tt0) cc_final: 0.7188 (pt0) REVERT: N 399 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7550 (tt) REVERT: N 512 GLU cc_start: 0.6488 (tm-30) cc_final: 0.6167 (mt-10) REVERT: O 26 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6797 (ppt170) REVERT: O 44 GLU cc_start: 0.4718 (OUTLIER) cc_final: 0.3444 (tm-30) REVERT: O 113 GLU cc_start: 0.7217 (tt0) cc_final: 0.6945 (tm-30) REVERT: O 146 SER cc_start: 0.6790 (m) cc_final: 0.6510 (t) REVERT: O 151 PRO cc_start: 0.7859 (Cg_endo) cc_final: 0.7595 (Cg_exo) REVERT: O 226 THR cc_start: 0.5946 (t) cc_final: 0.5548 (m) REVERT: P 325 MET cc_start: 0.7676 (mtm) cc_final: 0.7087 (ttp) REVERT: P 345 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7534 (mm) REVERT: P 388 ARG cc_start: 0.7297 (tpt-90) cc_final: 0.6606 (ttm110) REVERT: P 432 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6500 (mp0) REVERT: Q 70 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7106 (mt-10) REVERT: Q 113 GLU cc_start: 0.7622 (tp30) cc_final: 0.7083 (tm-30) REVERT: Q 146 SER cc_start: 0.7019 (m) cc_final: 0.6578 (p) REVERT: R 325 MET cc_start: 0.7363 (mtm) cc_final: 0.6782 (ttp) REVERT: R 430 ASN cc_start: 0.8081 (t0) cc_final: 0.7460 (m-40) REVERT: S 386 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.7111 (mtm) REVERT: S 395 MET cc_start: 0.7454 (mmm) cc_final: 0.7087 (mtt) REVERT: S 396 GLN cc_start: 0.6776 (tt0) cc_final: 0.6547 (tp40) REVERT: S 512 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6641 (mm-30) REVERT: S 519 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6993 (tm-30) REVERT: T 52 LYS cc_start: 0.7009 (mtpt) cc_final: 0.6616 (mtmm) REVERT: T 105 GLN cc_start: 0.6781 (tt0) cc_final: 0.6556 (tp40) REVERT: T 113 GLU cc_start: 0.7274 (tp30) cc_final: 0.6938 (tm-30) REVERT: T 121 GLU cc_start: 0.6882 (tt0) cc_final: 0.6287 (tp30) REVERT: T 214 ASP cc_start: 0.6055 (t0) cc_final: 0.5751 (t0) REVERT: T 216 ASN cc_start: 0.7557 (t0) cc_final: 0.7201 (m110) REVERT: U 314 MET cc_start: 0.8160 (ttm) cc_final: 0.7677 (ttm) REVERT: U 401 LEU cc_start: 0.7507 (mt) cc_final: 0.6988 (mt) REVERT: U 509 ARG cc_start: 0.6748 (tpt170) cc_final: 0.6512 (ttp80) REVERT: V 325 MET cc_start: 0.7574 (ttp) cc_final: 0.6486 (mmt) REVERT: V 401 LEU cc_start: 0.7158 (tp) cc_final: 0.6810 (mt) REVERT: V 509 ARG cc_start: 0.6309 (OUTLIER) cc_final: 0.5646 (ttt180) REVERT: V 519 GLU cc_start: 0.7214 (tt0) cc_final: 0.6785 (mm-30) REVERT: W 364 GLU cc_start: 0.7094 (tt0) cc_final: 0.6522 (pt0) REVERT: W 522 SER cc_start: 0.5987 (t) cc_final: 0.5617 (m) REVERT: X 26 ARG cc_start: 0.7606 (ptm-80) cc_final: 0.7334 (mtm110) REVERT: X 52 LYS cc_start: 0.7563 (mtpt) cc_final: 0.7188 (mtmm) REVERT: X 105 GLN cc_start: 0.7148 (tt0) cc_final: 0.6370 (mm-40) REVERT: X 130 TYR cc_start: 0.7495 (t80) cc_final: 0.6077 (t80) REVERT: X 179 ASP cc_start: 0.6606 (m-30) cc_final: 0.6215 (t0) REVERT: X 216 ASN cc_start: 0.7602 (t0) cc_final: 0.7081 (t0) REVERT: Y 325 MET cc_start: 0.7786 (mtm) cc_final: 0.7209 (ttm) REVERT: Y 399 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7363 (tp) REVERT: Y 509 ARG cc_start: 0.7153 (tpt90) cc_final: 0.6426 (ttp80) REVERT: Z 113 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6804 (tm-30) REVERT: Z 143 TYR cc_start: 0.5600 (p90) cc_final: 0.4818 (p90) REVERT: Z 144 ASP cc_start: 0.4710 (p0) cc_final: 0.4256 (p0) REVERT: Z 156 MET cc_start: 0.6909 (mtm) cc_final: 0.6700 (mtm) REVERT: Z 214 ASP cc_start: 0.6294 (t0) cc_final: 0.6014 (t0) REVERT: Z 216 ASN cc_start: 0.8405 (t0) cc_final: 0.8023 (m-40) REVERT: a 325 MET cc_start: 0.7582 (mtm) cc_final: 0.6917 (ttm) REVERT: b 339 ASP cc_start: 0.8025 (t0) cc_final: 0.7569 (m-30) REVERT: b 433 GLU cc_start: 0.7559 (mm-30) cc_final: 0.6937 (mp0) REVERT: d 51 GLN cc_start: 0.7082 (mt0) cc_final: 0.6856 (mt0) REVERT: d 101 ASN cc_start: 0.7276 (t0) cc_final: 0.6791 (m-40) REVERT: d 179 ASP cc_start: 0.7686 (m-30) cc_final: 0.7319 (t0) REVERT: d 189 ARG cc_start: 0.5663 (ttm-80) cc_final: 0.5387 (mtm180) REVERT: d 234 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6978 (pt) REVERT: f 15 GLU cc_start: 0.7767 (tt0) cc_final: 0.7341 (tp30) REVERT: f 26 ARG cc_start: 0.6363 (ttt180) cc_final: 0.6141 (ttp80) REVERT: f 52 LYS cc_start: 0.6600 (OUTLIER) cc_final: 0.6154 (mtpt) REVERT: f 101 ASN cc_start: 0.6828 (t0) cc_final: 0.6404 (m-40) REVERT: f 112 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7795 (p) outliers start: 185 outliers final: 121 residues processed: 882 average time/residue: 0.7049 time to fit residues: 1055.4715 Evaluate side-chains 881 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 736 time to evaluate : 5.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 51 GLN Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 149 ASP Chi-restraints excluded: chain 0 residue 225 ILE Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 73 ASN Chi-restraints excluded: chain 4 residue 99 LEU Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 216 ASN Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 133 THR Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 434 GLU Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain I residue 182 ARG Chi-restraints excluded: chain J residue 486 LEU Chi-restraints excluded: chain K residue 123 CYS Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain L residue 337 THR Chi-restraints excluded: chain L residue 363 LEU Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain L residue 441 SER Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain M residue 345 ILE Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 509 ARG Chi-restraints excluded: chain O residue 26 ARG Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 44 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 178 THR Chi-restraints excluded: chain P residue 345 ILE Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 228 SER Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 386 MET Chi-restraints excluded: chain S residue 512 GLU Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain T residue 170 SER Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain T residue 225 ILE Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 320 SER Chi-restraints excluded: chain U residue 441 SER Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 338 ASP Chi-restraints excluded: chain V residue 399 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 307 LYS Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 363 LEU Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain Y residue 320 SER Chi-restraints excluded: chain Y residue 345 ILE Chi-restraints excluded: chain Y residue 399 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 441 SER Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain a residue 307 LYS Chi-restraints excluded: chain a residue 396 GLN Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 345 ILE Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 52 LYS Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 147 ILE Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Chi-restraints excluded: chain f residue 234 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 529 optimal weight: 3.9990 chunk 341 optimal weight: 5.9990 chunk 511 optimal weight: 4.9990 chunk 257 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 544 optimal weight: 2.9990 chunk 583 optimal weight: 1.9990 chunk 423 optimal weight: 0.0030 chunk 79 optimal weight: 5.9990 chunk 672 optimal weight: 2.9990 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 546 HIS ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 558 ASN E 172 HIS ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 HIS G 5 GLN O 105 GLN U 322 GLN Z 98 GLN f 80 GLN f 165 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 69957 Z= 0.231 Angle : 0.542 9.144 94694 Z= 0.286 Chirality : 0.043 0.183 10759 Planarity : 0.004 0.050 12440 Dihedral : 5.537 88.531 10204 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.48 % Allowed : 14.62 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: 1.68 (0.09), residues: 8881 helix: 2.55 (0.08), residues: 3600 sheet: 0.67 (0.12), residues: 2000 loop : -0.21 (0.11), residues: 3281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 570 HIS 0.008 0.001 HIS F 348 PHE 0.034 0.002 PHE 0 71 TYR 0.020 0.001 TYR A 449 ARG 0.013 0.000 ARG O 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 762 time to evaluate : 5.797 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: 2 135 ARG cc_start: 0.7972 (tpp80) cc_final: 0.7316 (mtm110) REVERT: 2 205 VAL cc_start: 0.5855 (m) cc_final: 0.5572 (p) REVERT: 2 234 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6879 (pt) REVERT: 4 45 ASN cc_start: 0.7487 (t0) cc_final: 0.7229 (t0) REVERT: 4 99 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.7016 (mm) REVERT: 4 149 ASP cc_start: 0.7967 (t0) cc_final: 0.7740 (m-30) REVERT: 4 214 ASP cc_start: 0.6338 (t0) cc_final: 0.5996 (t0) REVERT: 4 225 ILE cc_start: 0.8390 (mt) cc_final: 0.7937 (mm) REVERT: 6 44 GLU cc_start: 0.7747 (tt0) cc_final: 0.7040 (tm-30) REVERT: 6 97 ARG cc_start: 0.6345 (ttt-90) cc_final: 0.5903 (ttt-90) REVERT: 6 101 ASN cc_start: 0.7041 (t0) cc_final: 0.6794 (m-40) REVERT: 6 113 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6469 (tt0) REVERT: 6 182 ARG cc_start: 0.5636 (OUTLIER) cc_final: 0.5281 (mpt-90) REVERT: 6 233 LEU cc_start: 0.7658 (mp) cc_final: 0.7278 (mt) REVERT: 6 234 LEU cc_start: 0.6064 (OUTLIER) cc_final: 0.5480 (pt) REVERT: 8 73 ASN cc_start: 0.7303 (m110) cc_final: 0.6622 (m-40) REVERT: 8 101 ASN cc_start: 0.7398 (t0) cc_final: 0.7127 (m-40) REVERT: 8 113 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7014 (mp0) REVERT: 8 174 ASN cc_start: 0.7900 (m110) cc_final: 0.7617 (m110) REVERT: A 243 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7161 (pp) REVERT: A 260 GLN cc_start: 0.8819 (mp10) cc_final: 0.8570 (mp10) REVERT: A 396 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7911 (tt) REVERT: B 137 LYS cc_start: 0.7092 (ttmt) cc_final: 0.6086 (tptt) REVERT: C 457 LEU cc_start: 0.8535 (mt) cc_final: 0.7907 (pp) REVERT: D 122 MET cc_start: 0.8141 (mpp) cc_final: 0.7790 (mpp) REVERT: D 164 LEU cc_start: 0.6749 (tp) cc_final: 0.6431 (tp) REVERT: D 268 VAL cc_start: 0.6742 (t) cc_final: 0.6407 (p) REVERT: D 439 ARG cc_start: 0.3393 (OUTLIER) cc_final: 0.3073 (mtm110) REVERT: D 480 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7958 (tm-30) REVERT: E 124 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7396 (tp) REVERT: E 373 MET cc_start: 0.7025 (mmp) cc_final: 0.6629 (tpp) REVERT: E 520 GLN cc_start: 0.8453 (tt0) cc_final: 0.8226 (tt0) REVERT: F 314 MET cc_start: 0.6452 (mmt) cc_final: 0.6007 (mmp) REVERT: F 323 HIS cc_start: 0.6270 (m90) cc_final: 0.6030 (m90) REVERT: F 348 HIS cc_start: 0.7967 (OUTLIER) cc_final: 0.7694 (m90) REVERT: F 373 MET cc_start: 0.8075 (mmm) cc_final: 0.7769 (mmm) REVERT: F 420 MET cc_start: 0.8048 (tpp) cc_final: 0.7654 (tpt) REVERT: F 529 ASN cc_start: 0.8552 (m-40) cc_final: 0.8301 (t0) REVERT: G 1 MET cc_start: 0.6056 (pmm) cc_final: 0.5803 (mtp) REVERT: H 325 MET cc_start: 0.8081 (mtm) cc_final: 0.7866 (mtt) REVERT: H 396 GLN cc_start: 0.7194 (tm-30) cc_final: 0.6857 (tp40) REVERT: H 519 GLU cc_start: 0.7557 (tt0) cc_final: 0.7206 (mm-30) REVERT: I 73 ASN cc_start: 0.6683 (t0) cc_final: 0.6454 (t0) REVERT: I 101 ASN cc_start: 0.6700 (t0) cc_final: 0.6239 (m-40) REVERT: I 105 GLN cc_start: 0.7292 (tt0) cc_final: 0.6825 (tm-30) REVERT: I 111 PHE cc_start: 0.7721 (t80) cc_final: 0.7424 (t80) REVERT: I 121 GLU cc_start: 0.6629 (tt0) cc_final: 0.6283 (mm-30) REVERT: I 140 ARG cc_start: 0.7172 (ttp-110) cc_final: 0.6793 (ttp80) REVERT: I 182 ARG cc_start: 0.6137 (OUTLIER) cc_final: 0.5382 (mpt90) REVERT: I 233 LEU cc_start: 0.6799 (mm) cc_final: 0.6448 (mm) REVERT: J 325 MET cc_start: 0.7895 (mtm) cc_final: 0.7362 (ttm) REVERT: J 432 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: J 509 ARG cc_start: 0.6299 (tpt90) cc_final: 0.6008 (ttt180) REVERT: K 13 MET cc_start: 0.6056 (mmt) cc_final: 0.4492 (ttp) REVERT: K 14 ARG cc_start: 0.5232 (tpm170) cc_final: 0.4949 (tpm170) REVERT: K 26 ARG cc_start: 0.6923 (ttm110) cc_final: 0.6288 (ttp80) REVERT: K 101 ASN cc_start: 0.6599 (t0) cc_final: 0.6222 (m-40) REVERT: K 146 SER cc_start: 0.7072 (m) cc_final: 0.6595 (p) REVERT: K 150 GLU cc_start: 0.6958 (mm-30) cc_final: 0.6402 (mm-30) REVERT: K 214 ASP cc_start: 0.6422 (t0) cc_final: 0.6109 (t0) REVERT: K 216 ASN cc_start: 0.7372 (t0) cc_final: 0.6529 (m-40) REVERT: L 325 MET cc_start: 0.7927 (mtm) cc_final: 0.7176 (ttp) REVERT: L 332 ARG cc_start: 0.7185 (mtt-85) cc_final: 0.6286 (mtt180) REVERT: L 401 LEU cc_start: 0.7558 (mt) cc_final: 0.7271 (tp) REVERT: M 307 LYS cc_start: 0.7746 (mtpt) cc_final: 0.7414 (mtmm) REVERT: M 325 MET cc_start: 0.7887 (mtm) cc_final: 0.7378 (ttm) REVERT: M 401 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7666 (mt) REVERT: N 325 MET cc_start: 0.7510 (mtm) cc_final: 0.6837 (ttt) REVERT: N 364 GLU cc_start: 0.7907 (tt0) cc_final: 0.7259 (pt0) REVERT: N 399 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7561 (tt) REVERT: N 433 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8220 (mt-10) REVERT: N 509 ARG cc_start: 0.5912 (OUTLIER) cc_final: 0.5433 (ttt-90) REVERT: O 26 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6727 (ppt170) REVERT: O 44 GLU cc_start: 0.4649 (OUTLIER) cc_final: 0.3337 (tm-30) REVERT: O 135 ARG cc_start: 0.6561 (mtp85) cc_final: 0.6305 (mtm-85) REVERT: O 140 ARG cc_start: 0.6619 (ttp-110) cc_final: 0.6035 (ttp80) REVERT: O 146 SER cc_start: 0.6827 (m) cc_final: 0.6504 (t) REVERT: O 214 ASP cc_start: 0.7055 (t0) cc_final: 0.6705 (t0) REVERT: O 226 THR cc_start: 0.5997 (t) cc_final: 0.5590 (m) REVERT: P 325 MET cc_start: 0.7592 (mtm) cc_final: 0.7040 (ttp) REVERT: P 345 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7521 (mm) REVERT: P 432 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6573 (mp0) REVERT: Q 70 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7139 (mt-10) REVERT: Q 113 GLU cc_start: 0.7482 (tp30) cc_final: 0.6940 (tm-30) REVERT: Q 143 TYR cc_start: 0.4223 (p90) cc_final: 0.3978 (p90) REVERT: Q 146 SER cc_start: 0.6787 (m) cc_final: 0.6426 (p) REVERT: R 325 MET cc_start: 0.7386 (mtm) cc_final: 0.6692 (ttp) REVERT: R 430 ASN cc_start: 0.8072 (t0) cc_final: 0.7541 (m-40) REVERT: S 386 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7125 (mtm) REVERT: S 396 GLN cc_start: 0.6757 (tt0) cc_final: 0.6523 (tp40) REVERT: S 512 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6654 (mm-30) REVERT: S 519 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7002 (tm-30) REVERT: T 52 LYS cc_start: 0.6980 (mtpt) cc_final: 0.6488 (mtmm) REVERT: T 67 LYS cc_start: 0.7364 (tttm) cc_final: 0.7092 (tttt) REVERT: T 105 GLN cc_start: 0.6800 (tt0) cc_final: 0.6204 (tp40) REVERT: T 113 GLU cc_start: 0.7262 (tp30) cc_final: 0.7023 (mt-10) REVERT: T 121 GLU cc_start: 0.6929 (tt0) cc_final: 0.6218 (mm-30) REVERT: T 214 ASP cc_start: 0.6211 (t0) cc_final: 0.5915 (t0) REVERT: T 216 ASN cc_start: 0.7642 (t0) cc_final: 0.7320 (m110) REVERT: U 314 MET cc_start: 0.8144 (ttm) cc_final: 0.7710 (ttm) REVERT: U 401 LEU cc_start: 0.7389 (mt) cc_final: 0.6853 (mt) REVERT: U 509 ARG cc_start: 0.6711 (tpt170) cc_final: 0.6454 (ttp80) REVERT: V 325 MET cc_start: 0.7558 (ttp) cc_final: 0.6480 (mmt) REVERT: V 401 LEU cc_start: 0.7173 (tp) cc_final: 0.6875 (mt) REVERT: V 461 ASP cc_start: 0.7181 (p0) cc_final: 0.6649 (t0) REVERT: V 509 ARG cc_start: 0.6350 (OUTLIER) cc_final: 0.5702 (ttt180) REVERT: V 519 GLU cc_start: 0.7177 (tt0) cc_final: 0.6747 (mm-30) REVERT: W 364 GLU cc_start: 0.7104 (tt0) cc_final: 0.6528 (pt0) REVERT: W 522 SER cc_start: 0.6021 (t) cc_final: 0.5494 (m) REVERT: X 26 ARG cc_start: 0.7623 (ptm-80) cc_final: 0.7355 (mtm110) REVERT: X 52 LYS cc_start: 0.7676 (mtpt) cc_final: 0.7342 (mtmm) REVERT: X 105 GLN cc_start: 0.7131 (tt0) cc_final: 0.6351 (mm-40) REVERT: X 130 TYR cc_start: 0.7462 (t80) cc_final: 0.6013 (t80) REVERT: X 179 ASP cc_start: 0.6632 (m-30) cc_final: 0.6248 (t0) REVERT: X 216 ASN cc_start: 0.7594 (t0) cc_final: 0.7044 (t0) REVERT: Y 325 MET cc_start: 0.7815 (mtm) cc_final: 0.7266 (ttm) REVERT: Y 399 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7277 (tp) REVERT: Y 509 ARG cc_start: 0.7150 (tpt90) cc_final: 0.6448 (ttp80) REVERT: Z 113 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6684 (tm-30) REVERT: Z 143 TYR cc_start: 0.5626 (p90) cc_final: 0.4848 (p90) REVERT: Z 144 ASP cc_start: 0.4741 (p0) cc_final: 0.4277 (p0) REVERT: Z 152 HIS cc_start: 0.7118 (m-70) cc_final: 0.6599 (m-70) REVERT: Z 156 MET cc_start: 0.6996 (mtm) cc_final: 0.6791 (mtm) REVERT: Z 216 ASN cc_start: 0.8411 (t0) cc_final: 0.8016 (m-40) REVERT: a 325 MET cc_start: 0.7538 (mtm) cc_final: 0.6962 (ttm) REVERT: b 339 ASP cc_start: 0.8025 (t0) cc_final: 0.7631 (m-30) REVERT: b 433 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7182 (mp0) REVERT: d 51 GLN cc_start: 0.7090 (mt0) cc_final: 0.6864 (mt0) REVERT: d 101 ASN cc_start: 0.7285 (t0) cc_final: 0.6795 (m-40) REVERT: d 143 TYR cc_start: 0.5528 (p90) cc_final: 0.5076 (p90) REVERT: d 179 ASP cc_start: 0.7722 (m-30) cc_final: 0.7341 (t0) REVERT: d 189 ARG cc_start: 0.5782 (ttm-80) cc_final: 0.5504 (mtm180) REVERT: d 234 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6915 (pt) REVERT: f 15 GLU cc_start: 0.7728 (tt0) cc_final: 0.7280 (tp30) REVERT: f 26 ARG cc_start: 0.6322 (ttt180) cc_final: 0.6119 (ttp80) REVERT: f 69 ASN cc_start: 0.6857 (p0) cc_final: 0.6381 (m-40) REVERT: f 101 ASN cc_start: 0.6841 (t0) cc_final: 0.6395 (m-40) REVERT: f 112 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7849 (p) outliers start: 175 outliers final: 125 residues processed: 883 average time/residue: 0.6528 time to fit residues: 980.1152 Evaluate side-chains 888 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 737 time to evaluate : 5.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 51 GLN Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 225 ILE Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 73 ASN Chi-restraints excluded: chain 4 residue 99 LEU Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 216 ASN Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 133 THR Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 51 GLN Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 348 HIS Chi-restraints excluded: chain F residue 474 CYS Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain I residue 182 ARG Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 123 CYS Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain L residue 337 THR Chi-restraints excluded: chain L residue 363 LEU Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain L residue 441 SER Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain M residue 339 ASP Chi-restraints excluded: chain M residue 345 ILE Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 450 MET Chi-restraints excluded: chain N residue 509 ARG Chi-restraints excluded: chain O residue 26 ARG Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 44 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain O residue 178 THR Chi-restraints excluded: chain P residue 345 ILE Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 228 SER Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 476 ASP Chi-restraints excluded: chain S residue 386 MET Chi-restraints excluded: chain S residue 512 GLU Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain T residue 225 ILE Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 320 SER Chi-restraints excluded: chain U residue 325 MET Chi-restraints excluded: chain U residue 441 SER Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 338 ASP Chi-restraints excluded: chain V residue 399 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 363 LEU Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain Y residue 307 LYS Chi-restraints excluded: chain Y residue 320 SER Chi-restraints excluded: chain Y residue 345 ILE Chi-restraints excluded: chain Y residue 399 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 441 SER Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain a residue 396 GLN Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 345 ILE Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 133 THR Chi-restraints excluded: chain f residue 147 ILE Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Chi-restraints excluded: chain f residue 234 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 778 optimal weight: 4.9990 chunk 819 optimal weight: 3.9990 chunk 748 optimal weight: 0.1980 chunk 797 optimal weight: 9.9990 chunk 480 optimal weight: 0.6980 chunk 347 optimal weight: 10.0000 chunk 626 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 720 optimal weight: 2.9990 chunk 754 optimal weight: 5.9990 chunk 794 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 174 ASN 2 114 GLN B 546 HIS ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 HIS ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 HIS O 174 ASN U 322 GLN W 430 ASN f 80 GLN f 165 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 69957 Z= 0.272 Angle : 0.566 11.995 94694 Z= 0.298 Chirality : 0.044 0.188 10759 Planarity : 0.004 0.063 12440 Dihedral : 5.603 89.835 10204 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.46 % Allowed : 14.72 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: 1.58 (0.09), residues: 8881 helix: 2.47 (0.08), residues: 3597 sheet: 0.62 (0.12), residues: 2013 loop : -0.26 (0.11), residues: 3271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 570 HIS 0.030 0.001 HIS F 348 PHE 0.035 0.002 PHE 0 71 TYR 0.026 0.002 TYR I 143 ARG 0.011 0.001 ARG F 347 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 750 time to evaluate : 6.051 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: 0 156 MET cc_start: 0.7452 (mtm) cc_final: 0.6786 (mtt) REVERT: 2 44 GLU cc_start: 0.7648 (tt0) cc_final: 0.7371 (tm-30) REVERT: 2 135 ARG cc_start: 0.8049 (tpp80) cc_final: 0.7414 (mtm110) REVERT: 2 205 VAL cc_start: 0.5645 (m) cc_final: 0.5432 (p) REVERT: 2 234 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.7010 (pt) REVERT: 4 45 ASN cc_start: 0.7517 (t0) cc_final: 0.7290 (t0) REVERT: 4 99 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.7005 (mm) REVERT: 4 149 ASP cc_start: 0.8010 (t0) cc_final: 0.7795 (m-30) REVERT: 4 214 ASP cc_start: 0.6388 (t0) cc_final: 0.6024 (t0) REVERT: 4 225 ILE cc_start: 0.8383 (mt) cc_final: 0.7936 (mm) REVERT: 6 44 GLU cc_start: 0.7748 (tt0) cc_final: 0.7049 (tm-30) REVERT: 6 101 ASN cc_start: 0.7075 (t0) cc_final: 0.6824 (m-40) REVERT: 6 113 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6631 (tt0) REVERT: 6 182 ARG cc_start: 0.5688 (OUTLIER) cc_final: 0.5325 (mpt-90) REVERT: 6 233 LEU cc_start: 0.7617 (mp) cc_final: 0.7260 (mt) REVERT: 6 234 LEU cc_start: 0.6055 (OUTLIER) cc_final: 0.5463 (pt) REVERT: 8 101 ASN cc_start: 0.7300 (t0) cc_final: 0.7020 (m-40) REVERT: 8 113 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7165 (mp0) REVERT: 8 174 ASN cc_start: 0.7927 (m110) cc_final: 0.7638 (m110) REVERT: 8 205 VAL cc_start: 0.7374 (m) cc_final: 0.7070 (p) REVERT: A 243 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7183 (pp) REVERT: A 260 GLN cc_start: 0.8830 (mp10) cc_final: 0.8624 (mp10) REVERT: A 396 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7922 (tt) REVERT: B 122 MET cc_start: 0.7902 (mpp) cc_final: 0.7659 (mtt) REVERT: B 137 LYS cc_start: 0.7291 (ttmt) cc_final: 0.6657 (tptt) REVERT: C 457 LEU cc_start: 0.8566 (mt) cc_final: 0.7886 (pp) REVERT: D 122 MET cc_start: 0.8214 (mpp) cc_final: 0.7861 (mpp) REVERT: D 268 VAL cc_start: 0.6604 (t) cc_final: 0.6306 (p) REVERT: D 439 ARG cc_start: 0.3830 (OUTLIER) cc_final: 0.3470 (mtm110) REVERT: D 480 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7942 (tm-30) REVERT: E 124 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7495 (tp) REVERT: E 373 MET cc_start: 0.7021 (mmp) cc_final: 0.6644 (tpp) REVERT: E 520 GLN cc_start: 0.8471 (tt0) cc_final: 0.8255 (tt0) REVERT: F 314 MET cc_start: 0.6497 (mmt) cc_final: 0.6062 (mmp) REVERT: F 323 HIS cc_start: 0.6292 (m90) cc_final: 0.6065 (m90) REVERT: F 420 MET cc_start: 0.8052 (tpp) cc_final: 0.7655 (tpt) REVERT: F 520 GLN cc_start: 0.7733 (tt0) cc_final: 0.7236 (tt0) REVERT: F 529 ASN cc_start: 0.8582 (m-40) cc_final: 0.8300 (t0) REVERT: G 1 MET cc_start: 0.6064 (pmm) cc_final: 0.5819 (mtp) REVERT: H 325 MET cc_start: 0.8097 (mtm) cc_final: 0.7846 (mtt) REVERT: H 396 GLN cc_start: 0.7167 (tm-30) cc_final: 0.6835 (tp40) REVERT: H 519 GLU cc_start: 0.7556 (tt0) cc_final: 0.7211 (mm-30) REVERT: I 73 ASN cc_start: 0.6863 (t0) cc_final: 0.6623 (t0) REVERT: I 101 ASN cc_start: 0.6675 (t0) cc_final: 0.6257 (m-40) REVERT: I 105 GLN cc_start: 0.7195 (tt0) cc_final: 0.6733 (tm-30) REVERT: I 121 GLU cc_start: 0.6627 (tt0) cc_final: 0.6296 (mm-30) REVERT: I 140 ARG cc_start: 0.7161 (ttp-110) cc_final: 0.6510 (ttp-170) REVERT: I 182 ARG cc_start: 0.6058 (OUTLIER) cc_final: 0.5312 (mpt90) REVERT: I 233 LEU cc_start: 0.6916 (mm) cc_final: 0.6599 (mm) REVERT: J 325 MET cc_start: 0.8001 (mtm) cc_final: 0.7451 (ttm) REVERT: J 395 MET cc_start: 0.7807 (mmm) cc_final: 0.7587 (mmm) REVERT: J 432 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: J 509 ARG cc_start: 0.6338 (tpt90) cc_final: 0.5986 (ttt180) REVERT: K 14 ARG cc_start: 0.5244 (tpm170) cc_final: 0.4956 (tpm170) REVERT: K 26 ARG cc_start: 0.6929 (ttm110) cc_final: 0.6289 (ttp80) REVERT: K 146 SER cc_start: 0.7226 (m) cc_final: 0.6782 (p) REVERT: K 150 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6411 (mm-30) REVERT: K 214 ASP cc_start: 0.6359 (t0) cc_final: 0.6045 (t0) REVERT: K 216 ASN cc_start: 0.7341 (t0) cc_final: 0.6567 (m-40) REVERT: L 325 MET cc_start: 0.7932 (mtm) cc_final: 0.7215 (ttm) REVERT: L 332 ARG cc_start: 0.7306 (mtt-85) cc_final: 0.6345 (mtt180) REVERT: L 401 LEU cc_start: 0.7542 (mt) cc_final: 0.7261 (tp) REVERT: M 307 LYS cc_start: 0.7639 (mtpt) cc_final: 0.7176 (mtmm) REVERT: M 325 MET cc_start: 0.7899 (mtm) cc_final: 0.7387 (ttm) REVERT: M 401 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7652 (mt) REVERT: N 325 MET cc_start: 0.7518 (mtm) cc_final: 0.7254 (mtp) REVERT: N 364 GLU cc_start: 0.7937 (tt0) cc_final: 0.7269 (pt0) REVERT: N 399 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7509 (tt) REVERT: N 433 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8100 (mt-10) REVERT: O 26 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6736 (ppt170) REVERT: O 44 GLU cc_start: 0.4617 (OUTLIER) cc_final: 0.3275 (tm-30) REVERT: O 105 GLN cc_start: 0.6643 (tp40) cc_final: 0.6051 (tp40) REVERT: O 178 THR cc_start: 0.5796 (OUTLIER) cc_final: 0.5499 (t) REVERT: O 214 ASP cc_start: 0.6956 (t0) cc_final: 0.6630 (t0) REVERT: O 226 THR cc_start: 0.6099 (t) cc_final: 0.5727 (m) REVERT: P 325 MET cc_start: 0.7604 (mtm) cc_final: 0.7063 (ttp) REVERT: P 345 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7523 (mm) REVERT: P 432 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6383 (mp0) REVERT: Q 70 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7154 (mt-10) REVERT: Q 113 GLU cc_start: 0.7477 (tp30) cc_final: 0.6944 (tm-30) REVERT: Q 143 TYR cc_start: 0.4263 (p90) cc_final: 0.4008 (p90) REVERT: Q 146 SER cc_start: 0.6780 (m) cc_final: 0.6393 (p) REVERT: R 325 MET cc_start: 0.7357 (mtm) cc_final: 0.6688 (ttp) REVERT: R 430 ASN cc_start: 0.8035 (t0) cc_final: 0.7601 (m-40) REVERT: S 386 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.7119 (mtm) REVERT: S 395 MET cc_start: 0.7479 (mmm) cc_final: 0.7230 (mtt) REVERT: S 396 GLN cc_start: 0.6757 (tt0) cc_final: 0.6530 (tp40) REVERT: S 512 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6700 (mm-30) REVERT: S 519 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6980 (tm-30) REVERT: T 52 LYS cc_start: 0.7002 (mtpt) cc_final: 0.6530 (mtmm) REVERT: T 67 LYS cc_start: 0.7315 (tttm) cc_final: 0.7044 (tttt) REVERT: T 105 GLN cc_start: 0.6814 (tt0) cc_final: 0.6233 (tp40) REVERT: T 113 GLU cc_start: 0.7253 (tp30) cc_final: 0.7036 (mt-10) REVERT: T 121 GLU cc_start: 0.6909 (tt0) cc_final: 0.6207 (mm-30) REVERT: T 214 ASP cc_start: 0.6287 (t0) cc_final: 0.6007 (t0) REVERT: T 216 ASN cc_start: 0.7919 (t0) cc_final: 0.7340 (m110) REVERT: U 314 MET cc_start: 0.8151 (ttm) cc_final: 0.7740 (ttm) REVERT: U 401 LEU cc_start: 0.7409 (mt) cc_final: 0.6878 (mt) REVERT: U 509 ARG cc_start: 0.6702 (tpt170) cc_final: 0.6447 (ttp80) REVERT: V 325 MET cc_start: 0.7551 (ttp) cc_final: 0.6472 (mmt) REVERT: V 401 LEU cc_start: 0.7224 (tp) cc_final: 0.6908 (mt) REVERT: V 461 ASP cc_start: 0.7153 (p0) cc_final: 0.6674 (t0) REVERT: V 509 ARG cc_start: 0.6322 (OUTLIER) cc_final: 0.5648 (ttt180) REVERT: V 519 GLU cc_start: 0.7177 (tt0) cc_final: 0.6748 (mm-30) REVERT: W 364 GLU cc_start: 0.7119 (tt0) cc_final: 0.6542 (pt0) REVERT: W 522 SER cc_start: 0.6094 (t) cc_final: 0.5881 (p) REVERT: X 26 ARG cc_start: 0.7638 (ptm-80) cc_final: 0.7374 (mtm110) REVERT: X 52 LYS cc_start: 0.7674 (mtpt) cc_final: 0.7343 (mtmm) REVERT: X 105 GLN cc_start: 0.7116 (tt0) cc_final: 0.6355 (mm-40) REVERT: X 130 TYR cc_start: 0.7445 (t80) cc_final: 0.5993 (t80) REVERT: X 179 ASP cc_start: 0.6575 (m-30) cc_final: 0.6176 (t0) REVERT: X 216 ASN cc_start: 0.7560 (t0) cc_final: 0.7000 (t0) REVERT: Y 325 MET cc_start: 0.7746 (mtm) cc_final: 0.7281 (ttm) REVERT: Y 399 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7353 (tp) REVERT: Y 509 ARG cc_start: 0.7158 (tpt90) cc_final: 0.6452 (ttp80) REVERT: Z 113 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6674 (tm-30) REVERT: Z 143 TYR cc_start: 0.5390 (p90) cc_final: 0.4861 (p90) REVERT: Z 144 ASP cc_start: 0.4720 (p0) cc_final: 0.4295 (p0) REVERT: Z 152 HIS cc_start: 0.7242 (m-70) cc_final: 0.6581 (m-70) REVERT: Z 156 MET cc_start: 0.7027 (mtm) cc_final: 0.6806 (mtm) REVERT: Z 216 ASN cc_start: 0.8386 (t0) cc_final: 0.7997 (m-40) REVERT: a 325 MET cc_start: 0.7527 (mtm) cc_final: 0.6958 (ttm) REVERT: b 339 ASP cc_start: 0.7963 (t0) cc_final: 0.7584 (m-30) REVERT: b 433 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7185 (mp0) REVERT: d 51 GLN cc_start: 0.7089 (mt0) cc_final: 0.6863 (mt0) REVERT: d 101 ASN cc_start: 0.7200 (t0) cc_final: 0.6690 (m-40) REVERT: d 143 TYR cc_start: 0.5693 (p90) cc_final: 0.5263 (p90) REVERT: d 179 ASP cc_start: 0.7692 (m-30) cc_final: 0.7383 (t0) REVERT: d 189 ARG cc_start: 0.5723 (ttm-80) cc_final: 0.5425 (mtm-85) REVERT: d 234 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6963 (pt) REVERT: f 15 GLU cc_start: 0.7632 (tt0) cc_final: 0.7224 (tp30) REVERT: f 52 LYS cc_start: 0.6643 (OUTLIER) cc_final: 0.6199 (mtpt) REVERT: f 69 ASN cc_start: 0.6886 (p0) cc_final: 0.6419 (m-40) REVERT: f 101 ASN cc_start: 0.6845 (t0) cc_final: 0.6401 (m-40) REVERT: f 112 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7885 (p) outliers start: 173 outliers final: 127 residues processed: 870 average time/residue: 0.6618 time to fit residues: 980.0937 Evaluate side-chains 884 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 731 time to evaluate : 5.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 51 GLN Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 225 ILE Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 99 LEU Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 216 ASN Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 133 THR Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain I residue 182 ARG Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 123 CYS Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain L residue 337 THR Chi-restraints excluded: chain L residue 363 LEU Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain L residue 441 SER Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain M residue 339 ASP Chi-restraints excluded: chain M residue 345 ILE Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 450 MET Chi-restraints excluded: chain N residue 461 ASP Chi-restraints excluded: chain N residue 509 ARG Chi-restraints excluded: chain O residue 26 ARG Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 44 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 174 ASN Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain O residue 178 THR Chi-restraints excluded: chain P residue 345 ILE Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 228 SER Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 476 ASP Chi-restraints excluded: chain S residue 386 MET Chi-restraints excluded: chain S residue 512 GLU Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain T residue 170 SER Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 320 SER Chi-restraints excluded: chain U residue 325 MET Chi-restraints excluded: chain U residue 441 SER Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 338 ASP Chi-restraints excluded: chain V residue 399 LEU Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 363 LEU Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain Y residue 320 SER Chi-restraints excluded: chain Y residue 345 ILE Chi-restraints excluded: chain Y residue 399 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 441 SER Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 345 ILE Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 52 LYS Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 133 THR Chi-restraints excluded: chain f residue 147 ILE Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Chi-restraints excluded: chain f residue 234 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 523 optimal weight: 3.9990 chunk 843 optimal weight: 0.9990 chunk 514 optimal weight: 2.9990 chunk 400 optimal weight: 0.4980 chunk 586 optimal weight: 0.9980 chunk 884 optimal weight: 0.9980 chunk 814 optimal weight: 0.9980 chunk 704 optimal weight: 4.9990 chunk 73 optimal weight: 0.0040 chunk 544 optimal weight: 1.9990 chunk 431 optimal weight: 0.7980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 174 ASN 2 114 GLN B 172 HIS B 546 HIS ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 HIS E 408 ASN U 322 GLN f 80 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 69957 Z= 0.142 Angle : 0.508 11.340 94694 Z= 0.267 Chirality : 0.042 0.174 10759 Planarity : 0.004 0.046 12440 Dihedral : 5.412 88.806 10204 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.75 % Allowed : 15.55 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: 1.83 (0.09), residues: 8881 helix: 2.73 (0.08), residues: 3590 sheet: 0.73 (0.12), residues: 1982 loop : -0.17 (0.11), residues: 3309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 570 HIS 0.004 0.001 HIS C 460 PHE 0.041 0.002 PHE Z 111 TYR 0.023 0.001 TYR I 143 ARG 0.008 0.000 ARG X 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17762 Ramachandran restraints generated. 8881 Oldfield, 0 Emsley, 8881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 767 time to evaluate : 5.762 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: 0 156 MET cc_start: 0.7396 (mtm) cc_final: 0.6851 (mtt) REVERT: 2 44 GLU cc_start: 0.7566 (tt0) cc_final: 0.7296 (tm-30) REVERT: 2 135 ARG cc_start: 0.8014 (tpp80) cc_final: 0.7364 (mtm110) REVERT: 2 205 VAL cc_start: 0.5915 (m) cc_final: 0.5662 (p) REVERT: 2 234 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6971 (pt) REVERT: 4 45 ASN cc_start: 0.7476 (t0) cc_final: 0.7226 (t0) REVERT: 4 99 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.7025 (mm) REVERT: 4 149 ASP cc_start: 0.7995 (t0) cc_final: 0.7736 (m-30) REVERT: 4 156 MET cc_start: 0.6851 (mtm) cc_final: 0.6616 (mtp) REVERT: 4 214 ASP cc_start: 0.6361 (t0) cc_final: 0.5992 (t0) REVERT: 4 225 ILE cc_start: 0.8357 (mt) cc_final: 0.7924 (mm) REVERT: 6 44 GLU cc_start: 0.7753 (tt0) cc_final: 0.7031 (tm-30) REVERT: 6 51 GLN cc_start: 0.6707 (mm-40) cc_final: 0.6295 (mm-40) REVERT: 6 97 ARG cc_start: 0.6343 (ttt-90) cc_final: 0.5919 (ttt-90) REVERT: 6 101 ASN cc_start: 0.7067 (t0) cc_final: 0.6844 (m-40) REVERT: 6 113 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6653 (tt0) REVERT: 6 182 ARG cc_start: 0.5765 (OUTLIER) cc_final: 0.5457 (mpt-90) REVERT: 6 233 LEU cc_start: 0.7613 (mp) cc_final: 0.7258 (mt) REVERT: 6 234 LEU cc_start: 0.6099 (OUTLIER) cc_final: 0.5547 (pt) REVERT: 8 73 ASN cc_start: 0.7439 (m110) cc_final: 0.6754 (m-40) REVERT: 8 101 ASN cc_start: 0.7320 (t0) cc_final: 0.7072 (m-40) REVERT: 8 113 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7119 (mp0) REVERT: 8 174 ASN cc_start: 0.7881 (m110) cc_final: 0.7587 (m110) REVERT: 8 205 VAL cc_start: 0.7379 (m) cc_final: 0.7076 (p) REVERT: A 122 MET cc_start: 0.8805 (mmm) cc_final: 0.8507 (mmm) REVERT: A 155 PHE cc_start: 0.5029 (m-80) cc_final: 0.4751 (m-10) REVERT: A 243 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7116 (pp) REVERT: A 396 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7954 (tt) REVERT: B 137 LYS cc_start: 0.7194 (ttmt) cc_final: 0.6614 (tptt) REVERT: C 457 LEU cc_start: 0.8634 (mt) cc_final: 0.7912 (pp) REVERT: D 122 MET cc_start: 0.8117 (mpp) cc_final: 0.7807 (mpp) REVERT: D 268 VAL cc_start: 0.6558 (t) cc_final: 0.6266 (p) REVERT: D 439 ARG cc_start: 0.3361 (OUTLIER) cc_final: 0.3022 (mtm110) REVERT: D 480 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7949 (tm-30) REVERT: E 124 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7405 (tp) REVERT: E 373 MET cc_start: 0.7144 (mmp) cc_final: 0.6788 (tpp) REVERT: E 520 GLN cc_start: 0.8401 (tt0) cc_final: 0.8158 (tt0) REVERT: F 314 MET cc_start: 0.6430 (mmt) cc_final: 0.6030 (mmp) REVERT: F 373 MET cc_start: 0.8153 (mmm) cc_final: 0.7675 (mmm) REVERT: F 420 MET cc_start: 0.8010 (tpp) cc_final: 0.7597 (tpt) REVERT: F 520 GLN cc_start: 0.7685 (tt0) cc_final: 0.7406 (tt0) REVERT: F 529 ASN cc_start: 0.8534 (m-40) cc_final: 0.8250 (t0) REVERT: G 1 MET cc_start: 0.6012 (pmm) cc_final: 0.5729 (mtp) REVERT: H 396 GLN cc_start: 0.7218 (tm-30) cc_final: 0.6896 (tp40) REVERT: H 519 GLU cc_start: 0.7528 (tt0) cc_final: 0.7172 (mm-30) REVERT: I 73 ASN cc_start: 0.6487 (t0) cc_final: 0.6214 (t0) REVERT: I 101 ASN cc_start: 0.6647 (t0) cc_final: 0.6272 (m-40) REVERT: I 121 GLU cc_start: 0.6549 (tt0) cc_final: 0.6235 (mm-30) REVERT: I 140 ARG cc_start: 0.6968 (ttp-110) cc_final: 0.6663 (ttp80) REVERT: I 141 ILE cc_start: 0.7217 (mp) cc_final: 0.6973 (mt) REVERT: I 156 MET cc_start: 0.6190 (mtm) cc_final: 0.5819 (mtm) REVERT: I 182 ARG cc_start: 0.6104 (OUTLIER) cc_final: 0.5368 (mpt90) REVERT: I 233 LEU cc_start: 0.6779 (mm) cc_final: 0.6457 (mm) REVERT: J 325 MET cc_start: 0.7873 (mtm) cc_final: 0.7334 (ttm) REVERT: J 395 MET cc_start: 0.7827 (mmm) cc_final: 0.7606 (mmm) REVERT: J 432 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: K 13 MET cc_start: 0.6045 (mmt) cc_final: 0.4426 (ttp) REVERT: K 14 ARG cc_start: 0.5587 (tpm170) cc_final: 0.5380 (tpm170) REVERT: K 26 ARG cc_start: 0.6928 (ttm110) cc_final: 0.6280 (ttp80) REVERT: K 146 SER cc_start: 0.7454 (m) cc_final: 0.6975 (p) REVERT: K 216 ASN cc_start: 0.7368 (t0) cc_final: 0.6624 (m-40) REVERT: L 325 MET cc_start: 0.7918 (mtm) cc_final: 0.7191 (ttp) REVERT: L 332 ARG cc_start: 0.7211 (mtt-85) cc_final: 0.6341 (mtt180) REVERT: L 401 LEU cc_start: 0.7553 (mt) cc_final: 0.7264 (tp) REVERT: M 307 LYS cc_start: 0.7610 (mtpt) cc_final: 0.7267 (mtmm) REVERT: M 325 MET cc_start: 0.7808 (mtm) cc_final: 0.7376 (ttm) REVERT: M 401 LEU cc_start: 0.7902 (mt) cc_final: 0.7594 (mt) REVERT: M 424 ASP cc_start: 0.7599 (p0) cc_final: 0.7303 (p0) REVERT: N 325 MET cc_start: 0.7516 (mtm) cc_final: 0.6829 (ttt) REVERT: N 364 GLU cc_start: 0.7856 (tt0) cc_final: 0.7093 (pt0) REVERT: N 399 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7532 (tt) REVERT: N 433 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8117 (mt-10) REVERT: N 509 ARG cc_start: 0.5732 (OUTLIER) cc_final: 0.5313 (ttt-90) REVERT: O 26 ARG cc_start: 0.7411 (ttm110) cc_final: 0.6730 (ppt170) REVERT: O 44 GLU cc_start: 0.4655 (OUTLIER) cc_final: 0.3356 (tm-30) REVERT: O 105 GLN cc_start: 0.6890 (tp40) cc_final: 0.6291 (tp40) REVERT: O 146 SER cc_start: 0.6783 (m) cc_final: 0.6479 (t) REVERT: O 178 THR cc_start: 0.5769 (OUTLIER) cc_final: 0.5549 (t) REVERT: P 325 MET cc_start: 0.7642 (mtm) cc_final: 0.7039 (ttp) REVERT: P 345 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7529 (mm) REVERT: P 432 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6370 (mp0) REVERT: Q 70 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7080 (mt-10) REVERT: Q 113 GLU cc_start: 0.7299 (tp30) cc_final: 0.6765 (tm-30) REVERT: Q 143 TYR cc_start: 0.4143 (p90) cc_final: 0.3925 (p90) REVERT: Q 146 SER cc_start: 0.6910 (m) cc_final: 0.6483 (p) REVERT: Q 234 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6486 (tp) REVERT: R 325 MET cc_start: 0.7423 (mtm) cc_final: 0.6852 (ttp) REVERT: R 430 ASN cc_start: 0.8080 (t0) cc_final: 0.7577 (m-40) REVERT: S 396 GLN cc_start: 0.6772 (tt0) cc_final: 0.6552 (tp40) REVERT: S 512 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6623 (mm-30) REVERT: S 519 GLU cc_start: 0.7391 (mt-10) cc_final: 0.6993 (tm-30) REVERT: T 52 LYS cc_start: 0.6953 (mtpt) cc_final: 0.6495 (mtmm) REVERT: T 67 LYS cc_start: 0.7315 (tttm) cc_final: 0.7038 (tttt) REVERT: T 105 GLN cc_start: 0.6802 (tt0) cc_final: 0.6505 (tp40) REVERT: T 113 GLU cc_start: 0.7218 (tp30) cc_final: 0.6982 (mt-10) REVERT: T 121 GLU cc_start: 0.6806 (tt0) cc_final: 0.6164 (mm-30) REVERT: T 214 ASP cc_start: 0.6248 (t0) cc_final: 0.5976 (t0) REVERT: U 401 LEU cc_start: 0.7612 (mt) cc_final: 0.7135 (mt) REVERT: U 509 ARG cc_start: 0.6741 (tpt170) cc_final: 0.6496 (ttm170) REVERT: V 325 MET cc_start: 0.7573 (ttp) cc_final: 0.6493 (mmt) REVERT: V 401 LEU cc_start: 0.7226 (tp) cc_final: 0.6894 (mt) REVERT: V 461 ASP cc_start: 0.7219 (p0) cc_final: 0.6602 (t0) REVERT: V 509 ARG cc_start: 0.6223 (OUTLIER) cc_final: 0.5664 (ttt180) REVERT: V 519 GLU cc_start: 0.7034 (tt0) cc_final: 0.6617 (mm-30) REVERT: W 364 GLU cc_start: 0.7054 (tt0) cc_final: 0.6486 (pt0) REVERT: W 388 ARG cc_start: 0.6848 (ttt180) cc_final: 0.6116 (ttm110) REVERT: W 522 SER cc_start: 0.5995 (t) cc_final: 0.5485 (m) REVERT: X 52 LYS cc_start: 0.7862 (mtpt) cc_final: 0.7560 (mtmm) REVERT: X 80 GLN cc_start: 0.7338 (tp40) cc_final: 0.6780 (tp40) REVERT: X 105 GLN cc_start: 0.7092 (tt0) cc_final: 0.6337 (mm-40) REVERT: X 130 TYR cc_start: 0.7477 (t80) cc_final: 0.6040 (t80) REVERT: X 179 ASP cc_start: 0.6585 (m-30) cc_final: 0.6224 (t0) REVERT: X 216 ASN cc_start: 0.7651 (t0) cc_final: 0.7081 (t0) REVERT: Y 325 MET cc_start: 0.7840 (mtm) cc_final: 0.7280 (ttm) REVERT: Y 399 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7272 (tp) REVERT: Y 509 ARG cc_start: 0.7118 (tpt90) cc_final: 0.6413 (ttp80) REVERT: Z 113 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6786 (tm-30) REVERT: Z 143 TYR cc_start: 0.5849 (p90) cc_final: 0.5022 (p90) REVERT: Z 144 ASP cc_start: 0.4611 (p0) cc_final: 0.4072 (p0) REVERT: Z 152 HIS cc_start: 0.7221 (m-70) cc_final: 0.6564 (m-70) REVERT: Z 216 ASN cc_start: 0.8360 (t0) cc_final: 0.7982 (m-40) REVERT: a 325 MET cc_start: 0.7592 (mtm) cc_final: 0.7040 (ttm) REVERT: b 339 ASP cc_start: 0.8029 (t0) cc_final: 0.7591 (m-30) REVERT: b 433 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7191 (mp0) REVERT: d 101 ASN cc_start: 0.7260 (t0) cc_final: 0.6782 (m-40) REVERT: d 179 ASP cc_start: 0.7692 (m-30) cc_final: 0.7358 (t0) REVERT: d 189 ARG cc_start: 0.5734 (ttm-80) cc_final: 0.5474 (mtm-85) REVERT: d 234 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.7038 (pt) REVERT: f 15 GLU cc_start: 0.7760 (tt0) cc_final: 0.7290 (tp30) REVERT: f 52 LYS cc_start: 0.6583 (OUTLIER) cc_final: 0.6147 (mtpt) REVERT: f 101 ASN cc_start: 0.6831 (t0) cc_final: 0.6405 (m-40) REVERT: f 112 THR cc_start: 0.8102 (OUTLIER) cc_final: 0.7804 (p) outliers start: 123 outliers final: 85 residues processed: 852 average time/residue: 0.6641 time to fit residues: 964.1005 Evaluate side-chains 848 residues out of total 7058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 738 time to evaluate : 5.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 51 GLN Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 225 ILE Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 99 LEU Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 216 ASN Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 114 GLN Chi-restraints excluded: chain 6 residue 133 THR Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain I residue 182 ARG Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 123 CYS Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain L residue 337 THR Chi-restraints excluded: chain L residue 363 LEU Chi-restraints excluded: chain L residue 441 SER Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain M residue 339 ASP Chi-restraints excluded: chain M residue 345 ILE Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 509 ARG Chi-restraints excluded: chain O residue 44 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 178 THR Chi-restraints excluded: chain P residue 345 ILE Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 512 GLU Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 441 SER Chi-restraints excluded: chain V residue 399 LEU Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain Y residue 320 SER Chi-restraints excluded: chain Y residue 345 ILE Chi-restraints excluded: chain Y residue 399 LEU Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 345 ILE Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 52 LYS Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 133 THR Chi-restraints excluded: chain f residue 147 ILE Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 234 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 559 optimal weight: 9.9990 chunk 750 optimal weight: 0.0170 chunk 215 optimal weight: 6.9990 chunk 649 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 705 optimal weight: 0.0970 chunk 295 optimal weight: 30.0000 chunk 724 optimal weight: 0.0060 chunk 89 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 overall best weight: 0.3432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 174 ASN 2 114 GLN B 546 HIS ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 HIS E 172 HIS Q 174 ASN U 322 GLN Z 174 ASN d 80 GLN f 80 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.122252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.089105 restraints weight = 111071.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.087376 restraints weight = 234680.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.087841 restraints weight = 224348.385| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 69957 Z= 0.129 Angle : 0.495 10.614 94694 Z= 0.259 Chirality : 0.042 0.174 10759 Planarity : 0.003 0.046 12440 Dihedral : 5.230 88.133 10202 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.53 % Allowed : 15.91 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: 1.99 (0.09), residues: 8881 helix: 2.89 (0.08), residues: 3595 sheet: 0.76 (0.12), residues: 2027 loop : -0.07 (0.11), residues: 3259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 570 HIS 0.004 0.001 HIS C 460 PHE 0.030 0.001 PHE K 71 TYR 0.021 0.001 TYR I 143 ARG 0.008 0.000 ARG X 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16672.70 seconds wall clock time: 290 minutes 12.38 seconds (17412.38 seconds total)